n punctiforme atcc 29133  (ATCC)


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    ATCC n punctiforme atcc 29133
    N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    n punctiforme atcc 29133  (ATCC)


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    ATCC n punctiforme atcc 29133
    N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    n punctiforme atcc 29133  (ATCC)


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    ATCC n punctiforme atcc 29133
    N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    n punctiforme atcc 29133  (ATCC)


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    ATCC n punctiforme atcc 29133
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Accelerating the discovery of alkyl halide-derived natural products using halide depletion"

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    Journal: Nature Chemistry

    doi: 10.1038/s41557-023-01390-z

    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    Figure Legend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Techniques Used: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.
    Figure Legend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Techniques Used: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.
    Figure Legend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Techniques Used: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.
    Figure Legend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Techniques Used: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection

    n punctiforme atcc 29133  (ATCC)


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    ATCC n punctiforme atcc 29133
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/n punctiforme atcc 29133/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    n punctiforme atcc 29133 - by Bioz Stars, 2024-06
    86/100 stars

    Images

    1) Product Images from "Accelerating the discovery of alkyl halide-derived natural products using halide depletion"

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    Journal: Nature Chemistry

    doi: 10.1038/s41557-023-01390-z

    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    Figure Legend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Techniques Used: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.
    Figure Legend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Techniques Used: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.
    Figure Legend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Techniques Used: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.
    Figure Legend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Techniques Used: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection

    n punctiforme atcc 29133  (ATCC)


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    Structured Review

    ATCC n punctiforme atcc 29133
    N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    type n punctiforme atcc 29133  (ATCC)


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    ATCC type n punctiforme atcc 29133
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    Type N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    type n punctiforme atcc 29133 - by Bioz Stars, 2024-06
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    1) Product Images from "Accelerating the discovery of alkyl halide-derived natural products using halide depletion"

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    Journal: Nature Chemistry

    doi: 10.1038/s41557-023-01390-z

    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    Figure Legend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Techniques Used: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.
    Figure Legend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Techniques Used: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.
    Figure Legend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Techniques Used: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.
    Figure Legend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Techniques Used: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection

    n punctiforme atcc 29133 genomic dna  (ATCC)


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    Structured Review

    ATCC n punctiforme atcc 29133 genomic dna
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    N Punctiforme Atcc 29133 Genomic Dna, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/n punctiforme atcc 29133 genomic dna/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    n punctiforme atcc 29133 genomic dna - by Bioz Stars, 2024-06
    86/100 stars

    Images

    1) Product Images from "Accelerating the discovery of alkyl halide-derived natural products using halide depletion"

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    Journal: Nature Chemistry

    doi: 10.1038/s41557-023-01390-z

    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    Figure Legend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Techniques Used: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.
    Figure Legend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Techniques Used: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.
    Figure Legend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Techniques Used: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.
    Figure Legend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Techniques Used: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection

    n punctiforme atcc 29133  (ATCC)


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    Structured Review

    ATCC n punctiforme atcc 29133
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/n punctiforme atcc 29133/product/ATCC
    Average 86 stars, based on 1 article reviews
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    n punctiforme atcc 29133 - by Bioz Stars, 2024-06
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    Images

    1) Product Images from "Accelerating the discovery of alkyl halide-derived natural products using halide depletion"

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    Journal: Nature Chemistry

    doi: 10.1038/s41557-023-01390-z

    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    Figure Legend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Techniques Used: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.
    Figure Legend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Techniques Used: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.
    Figure Legend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Techniques Used: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.
    Figure Legend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Techniques Used: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection

    n punctiforme atcc 29133 comparing cultures  (ATCC)


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    Structured Review

    ATCC n punctiforme atcc 29133 comparing cultures
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    N Punctiforme Atcc 29133 Comparing Cultures, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Accelerating the discovery of alkyl halide-derived natural products using halide depletion"

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    Journal: Nature Chemistry

    doi: 10.1038/s41557-023-01390-z

    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    Figure Legend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Techniques Used: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.
    Figure Legend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Techniques Used: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.
    Figure Legend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Techniques Used: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.
    Figure Legend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Techniques Used: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection

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    ATCC n punctiforme atcc 29133
    N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATCC type n punctiforme atcc 29133
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    Type N Punctiforme Atcc 29133, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATCC n punctiforme atcc 29133 genomic dna
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
    N Punctiforme Atcc 29133 Genomic Dna, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    ATCC n punctiforme atcc 29133 comparing cultures
    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme <t>ATCC</t> <t>29133</t> cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.
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    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Article Snippet: Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133.

    Techniques: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Article Snippet: Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133.

    Techniques: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Article Snippet: Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133.

    Techniques: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Article Snippet: Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133.

    Techniques: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection

    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Article Snippet: Regions of length ~1 kb upstream and downstream of the target locus were amplified from N. punctiforme ATCC 29133 genomic DNA.

    Techniques: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Article Snippet: Regions of length ~1 kb upstream and downstream of the target locus were amplified from N. punctiforme ATCC 29133 genomic DNA.

    Techniques: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Article Snippet: Regions of length ~1 kb upstream and downstream of the target locus were amplified from N. punctiforme ATCC 29133 genomic DNA.

    Techniques: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Article Snippet: Regions of length ~1 kb upstream and downstream of the target locus were amplified from N. punctiforme ATCC 29133 genomic DNA.

    Techniques: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection

    a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , The CylC- and CylK-encoding BGC ( ngl ) from N. punctiforme ATCC 29133. The ngl BGC represents 36,029 bp comprising the genes Npun_R3355 to Npun_F3373 (NPUN_RS17000 to NPUN_RS17085). Predicted functions are based on annotations from the Conserved Domain Database. KS, ketosynthase; KR, ketoreductase; AT, acyltransferase; DH, dehydrogenase; ER, enoylreductase; ACP, acyl carrier protein; KS*, ketosynthase with an inactivating point mutation in an active-site residue. Brackets indicate the genomic regions deleted to generate strains ∆ ngl and ∆ nglO . b , c , LC–MS analysis of N. punctiforme ATCC 29133 cultures grown with and without chloride: features detected using the same chromatographic separation used for cylindrocyclophanes ( b ) and additional features detected using a chromatographic separation optimized for lipids ( c ). Fold changes represent mean feature abundance in cultures grown without chloride relative to those grown with chloride (three independent biological replicates per condition), and P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. d , The metabolic network of features identified in b and c . Each circle represents a unique feature from the LC–MS data, with the circle area proportional to the m / z value ( z = 1 for all features). Colours represent the fold change of the feature. e , A list of measured m / z values ( z = 1 for all features, positive ionization) of the chlorinated metabolites and their assigned molecular formulae. f , Lipidomics comparison of extracts from ∆ ngl relative to wild-type N. punctiforme ATCC 29133. P values were determined by a two-tailed Student’s t -test. Purple diamonds represent the parent ion of features of interest. Purple circles represent features originating from alternative ion adducts or source fragment artefacts. Grey circles represent other features. g , Extracted ion chromatograms for 5 ( m / z = 555.3658 ± 5 ppm) and 7 ( m / z = 838.6533 ± 5 ppm) from the wild type compared to ∆ ngl and ∆ nglO . Each trace represents an independent biological replicate.

    Article Snippet: Supplementary Table 9: RNA-seq of N. punctiforme ATCC 29133 comparing cultures grown without chloride to those with chloride.

    Techniques: Mutagenesis, Residue, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test, Comparison

    a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , The proposed structures of nostochlorosides A and C–G ( 5 and 7 – 11 ) based on a detailed characterization of 5 and 7 . Carbons are numbered as referenced in the main text. b , Key NMR interactions used to establish bond connectivity. c , Identification of the sugar moiety. The scheme shows treatment of 5 to produce a permethylated sugar that was analysed by GC–MS. The traces represent extracted ion chromatography (EIC) results for the C 4 H 8 O 2 •+ fragment ( m / z = 88.0519 ± 5 ppm) for the permethylated product derived from 5 , the product derived from 5 co-injected with permethylated gulose, permethylated gulose and permethylated glucose. EICs are normalized to the peak height for their respective m / z ranges. Each sugar yields multiple peaks that originate from the α- and β-anomers of the pyranose and furanose forms. d , Identification of the position of the chlorine substituent. Left: interpretation of deuterium-labelling experiments in N. punctiforme ATCC 29133. Right: strain ∆ nglO was fed palmitic- d 2 acid as indicated. Black traces represent the mass spectrum of unlabelled 5 and coloured traces the experimentally observed mixture of unlabelled and labelled 5 . Red boxes mark the theoretical centroided mass spectrum for a mixture of unlabelled and labelled 5 as indicated. Traces are normalized to M + 0. The increase in intensity at M + 1 with palmitic-7-7- d 2 acid indicates replacement of a deuterium atom with chlorine.

    Article Snippet: Supplementary Table 9: RNA-seq of N. punctiforme ATCC 29133 comparing cultures grown without chloride to those with chloride.

    Techniques: Gas Chromatography-Mass Spectrometry, Ion Exchange Chromatography, Derivative Assay, Injection

    a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: a , Homology modeling of NglO. Five AlphaFold predictions (gray and blue) are shown super-imposed onto the solved CylK X-ray crystal structure (PDB ID 7RON, pink). The RTX domain in NglO is shown in blue, corresponding to the region truncated in NglO′. b , Comparison of features detected in the in vitro assay with extracts of wild-type ATCC 29133. Traces are scaled to the largest peak. Left, EICs of the dimer and trimer for the in vitro assay and the cell extracts. Arrows indicate the peak analyzed by MS/MS. Right, MS/MS spectra of the dimer and trimer of 5 . The structure shows the observed loss of the sugar moiety. c , Close-up view of the MS/MS spectra for the in vitro dimer and trimer showing the peak corresponding to the fragment C 28 H 55 O 9 . The structural interpretation of the fragmentation is shown for reference.

    Article Snippet: Supplementary Table 9: RNA-seq of N. punctiforme ATCC 29133 comparing cultures grown without chloride to those with chloride.

    Techniques: Comparison, In Vitro, Tandem Mass Spectroscopy

    For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Journal: Nature Chemistry

    Article Title: Accelerating the discovery of alkyl halide-derived natural products using halide depletion

    doi: 10.1038/s41557-023-01390-z

    Figure Lengend Snippet: For statistical analyses, error bars represent the standard error of three independent biological replicates. Significance markers represent the p -value from a two-tailed Student’s t-test: n.s., not significant ( p > 0.05); *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Black points represent individual measurements and bars represent the mean. a , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium (top) or on soft agar AA/4 medium (bottom). b , Quantitation of soft agar growth by colony area (left) or pixel intensity (right). Pixel intensity represents an indirect measurement of cell density. c , Representative cultures of N. punctiforme strains growing in liquid BG-11 medium without a fixed nitrogen source. d , LC–MS quantitation of glycolipids 5 – 11 from wild-type ATCC 29133 grown in liquid BG-11 with or without fixed nitrogen (nitrate). Injection volumes were normalized by chlorophyll absorbance of the sample measured at 665 nm.

    Article Snippet: Supplementary Table 9: RNA-seq of N. punctiforme ATCC 29133 comparing cultures grown without chloride to those with chloride.

    Techniques: Two Tailed Test, Quantitation Assay, Liquid Chromatography with Mass Spectroscopy, Injection