rhodospirillum rubrum atcc 11170  (ATCC)


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    ATCC rhodospirillum rubrum atcc 11170
    Rhodospirillum Rubrum Atcc 11170, 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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    rhodospirillum rubrum atcc 11170 rbcl  (ATCC)


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    ATCC rhodospirillum rubrum atcc 11170 rbcl
    Rhodospirillum Rubrum Atcc 11170 Rbcl, 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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    t rubrum dmst 30263  (ATCC)


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    ATCC t rubrum dmst 30263
    T Rubrum Dmst 30263, 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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    trichophyton rubrum atcc 28188  (ATCC)


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    ATCC trichophyton rubrum atcc 28188
    Accession numbers obtained for NCBI submissions.
    Trichophyton Rubrum Atcc 28188, 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 "Diagnostic ability of Peptidase S8 gene in the Arthrodermataceae causing dermatophytoses: A metadata analysis"

    Article Title: Diagnostic ability of Peptidase S8 gene in the Arthrodermataceae causing dermatophytoses: A metadata analysis

    Journal: PLOS ONE

    doi: 10.1371/journal.pone.0306829

    Accession numbers obtained for NCBI submissions.
    Figure Legend Snippet: Accession numbers obtained for NCBI submissions.

    Techniques Used:

    rhodospirillum rubrum  (ATCC)


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    ATCC rhodospirillum rubrum
    Rhodospirillum Rubrum, 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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    rubrum  (ATCC)


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    ATCC rubrum
    Accession numbers obtained for NCBI submissions.
    Rubrum, 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 "Diagnostic ability of Peptidase S8 gene in the Arthrodermataceae causing dermatophytoses: A metadata analysis"

    Article Title: Diagnostic ability of Peptidase S8 gene in the Arthrodermataceae causing dermatophytoses: A metadata analysis

    Journal: PLOS ONE

    doi: 10.1371/journal.pone.0306829

    Accession numbers obtained for NCBI submissions.
    Figure Legend Snippet: Accession numbers obtained for NCBI submissions.

    Techniques Used:

    trichophyton rubrum cbs 118892  (ATCC)


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    ATCC trichophyton rubrum cbs 118892
    List of Candidate Antifungal Resistance Genes Found after HMM Analysis Using the ResFungi HMM Database <xref ref-type= a " width="250" height="auto" />
    Trichophyton Rubrum Cbs 118892, 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 "ResFungi: A Novel Protein Database of Antifungal Drug Resistance Genes Using a Hidden Markov Model Profile"

    Article Title: ResFungi: A Novel Protein Database of Antifungal Drug Resistance Genes Using a Hidden Markov Model Profile

    Journal: ACS Omega

    doi: 10.1021/acsomega.4c02198

    List of Candidate Antifungal Resistance Genes Found after HMM Analysis Using the ResFungi HMM Database <xref ref-type= a " title="List of Candidate Antifungal Resistance Genes Found after HMM Analysis Using the ResFungi ... " property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: List of Candidate Antifungal Resistance Genes Found after HMM Analysis Using the ResFungi HMM Database a

    Techniques Used: Activity Assay, Variant Assay


    Structured Review

    Addgene inc r rubrum cbbm coding region
    (A) General workflow. A library of IDPs , , – was fused to <t>CbbM</t> ( R. <t>rubrum</t> Rubisco). Each fusion protein was individually tested in a condensation screen for phase-separation, no effect (i.e., homogenous dispersal), or aggregation. Condensates were further subjected to carboxylation activity and specificity tests. (B) Overview of the fusion protein library and condensation screen results. Full (or shortened) IDPs were fused to the C-terminus (IDP-C, IDP short -C), or the N and C terminus (IDP-N&C) of CbbM. Red indicates aggregation, grey indicates homogeneously dispersed protein, white indicates not-producible (CbbM-Laf1N&C, CbbM-Ddx4N&C, CbbM-EPYC1 CS ), or not tested (CbbM-Ddx4 short , CbbM-FXR1 short , CbbM-LEM2 short ), green indicates condensate formation at concentrations of 1-20 μM. CbbM-Laf1 short undergoes liquid-liquid phase separation when mixed with 1 μM GFP and shows aggregation at all other conditions tested. (C) Architecture and behaviour of different EPYC1-IDP variants from C. reinhardtii . Teal arrows indicate repeat domains, yellow helices show SSU-recognition domains. CR = full length IDP, Δα = SSU-recognition domain deletion variant, ΔFR = repetition domains deletion variant. Light microscopy pictures show homogeneously dispersed CbbM and CbbM-EPYC1 CR ΔFR, while CbbM-EPYC1 CR and CbbM-EPYC1 CR Δα form condensates in 50 mM Tris (pH 7.5 & 8.0), 1 mM MgCl 2 , 5 mM NaHCO 3 , 0.1 mg/mL CA, and 0.3 mM RuBP. (D) Fluorescence microscopy pictures from the resorufin-coupled activity assay (supplementary figure 6) inside and outside of condensates before and after 25 minutes. (E) Fluorescence formation inside and outside of condensates. (F) Ratio of initial fluorescence formation rates between condensate inside and outside. (G) Ratio of maximum fluorescence levels between condensate inside and outside. Error bars represent standard errors from eight replicates.
    R Rubrum Cbbm Coding Region, supplied by Addgene inc, 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 "Bottom-up reconstruction of minimal pyrenoids provides insights into the evolution and mechanisms of carbon concentration by EPYC1 proteins"

    Article Title: Bottom-up reconstruction of minimal pyrenoids provides insights into the evolution and mechanisms of carbon concentration by EPYC1 proteins

    Journal: bioRxiv

    doi: 10.1101/2024.06.28.601168

    (A) General workflow. A library of IDPs , , – was fused to CbbM ( R. rubrum Rubisco). Each fusion protein was individually tested in a condensation screen for phase-separation, no effect (i.e., homogenous dispersal), or aggregation. Condensates were further subjected to carboxylation activity and specificity tests. (B) Overview of the fusion protein library and condensation screen results. Full (or shortened) IDPs were fused to the C-terminus (IDP-C, IDP short -C), or the N and C terminus (IDP-N&C) of CbbM. Red indicates aggregation, grey indicates homogeneously dispersed protein, white indicates not-producible (CbbM-Laf1N&C, CbbM-Ddx4N&C, CbbM-EPYC1 CS ), or not tested (CbbM-Ddx4 short , CbbM-FXR1 short , CbbM-LEM2 short ), green indicates condensate formation at concentrations of 1-20 μM. CbbM-Laf1 short undergoes liquid-liquid phase separation when mixed with 1 μM GFP and shows aggregation at all other conditions tested. (C) Architecture and behaviour of different EPYC1-IDP variants from C. reinhardtii . Teal arrows indicate repeat domains, yellow helices show SSU-recognition domains. CR = full length IDP, Δα = SSU-recognition domain deletion variant, ΔFR = repetition domains deletion variant. Light microscopy pictures show homogeneously dispersed CbbM and CbbM-EPYC1 CR ΔFR, while CbbM-EPYC1 CR and CbbM-EPYC1 CR Δα form condensates in 50 mM Tris (pH 7.5 & 8.0), 1 mM MgCl 2 , 5 mM NaHCO 3 , 0.1 mg/mL CA, and 0.3 mM RuBP. (D) Fluorescence microscopy pictures from the resorufin-coupled activity assay (supplementary figure 6) inside and outside of condensates before and after 25 minutes. (E) Fluorescence formation inside and outside of condensates. (F) Ratio of initial fluorescence formation rates between condensate inside and outside. (G) Ratio of maximum fluorescence levels between condensate inside and outside. Error bars represent standard errors from eight replicates.
    Figure Legend Snippet: (A) General workflow. A library of IDPs , , – was fused to CbbM ( R. rubrum Rubisco). Each fusion protein was individually tested in a condensation screen for phase-separation, no effect (i.e., homogenous dispersal), or aggregation. Condensates were further subjected to carboxylation activity and specificity tests. (B) Overview of the fusion protein library and condensation screen results. Full (or shortened) IDPs were fused to the C-terminus (IDP-C, IDP short -C), or the N and C terminus (IDP-N&C) of CbbM. Red indicates aggregation, grey indicates homogeneously dispersed protein, white indicates not-producible (CbbM-Laf1N&C, CbbM-Ddx4N&C, CbbM-EPYC1 CS ), or not tested (CbbM-Ddx4 short , CbbM-FXR1 short , CbbM-LEM2 short ), green indicates condensate formation at concentrations of 1-20 μM. CbbM-Laf1 short undergoes liquid-liquid phase separation when mixed with 1 μM GFP and shows aggregation at all other conditions tested. (C) Architecture and behaviour of different EPYC1-IDP variants from C. reinhardtii . Teal arrows indicate repeat domains, yellow helices show SSU-recognition domains. CR = full length IDP, Δα = SSU-recognition domain deletion variant, ΔFR = repetition domains deletion variant. Light microscopy pictures show homogeneously dispersed CbbM and CbbM-EPYC1 CR ΔFR, while CbbM-EPYC1 CR and CbbM-EPYC1 CR Δα form condensates in 50 mM Tris (pH 7.5 & 8.0), 1 mM MgCl 2 , 5 mM NaHCO 3 , 0.1 mg/mL CA, and 0.3 mM RuBP. (D) Fluorescence microscopy pictures from the resorufin-coupled activity assay (supplementary figure 6) inside and outside of condensates before and after 25 minutes. (E) Fluorescence formation inside and outside of condensates. (F) Ratio of initial fluorescence formation rates between condensate inside and outside. (G) Ratio of maximum fluorescence levels between condensate inside and outside. Error bars represent standard errors from eight replicates.

    Techniques Used: Activity Assay, Variant Assay, Light Microscopy, Fluorescence, Microscopy

    rhodospirillum rubrum atcc  (ATCC)


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    ATCC rhodospirillum rubrum atcc
    Rhodospirillum Rubrum Atcc, 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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    Tianma Microelectronics Co plumbum rubrum huangdan
    Plumbum Rubrum Huangdan, supplied by Tianma Microelectronics Co, 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 rhodospirillum rubrum atcc 11170
    Rhodospirillum Rubrum Atcc 11170, 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 trichophyton rubrum atcc 28188
    Accession numbers obtained for NCBI submissions.
    Trichophyton Rubrum Atcc 28188, 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 rhodospirillum rubrum
    Accession numbers obtained for NCBI submissions.
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    rubrum  (ATCC)
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    ATCC trichophyton rubrum cbs 118892
    List of Candidate Antifungal Resistance Genes Found after HMM Analysis Using the ResFungi HMM Database <xref ref-type= a " width="250" height="auto" />
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    (A) General workflow. A library of IDPs , , – was fused to <t>CbbM</t> ( R. <t>rubrum</t> Rubisco). Each fusion protein was individually tested in a condensation screen for phase-separation, no effect (i.e., homogenous dispersal), or aggregation. Condensates were further subjected to carboxylation activity and specificity tests. (B) Overview of the fusion protein library and condensation screen results. Full (or shortened) IDPs were fused to the C-terminus (IDP-C, IDP short -C), or the N and C terminus (IDP-N&C) of CbbM. Red indicates aggregation, grey indicates homogeneously dispersed protein, white indicates not-producible (CbbM-Laf1N&C, CbbM-Ddx4N&C, CbbM-EPYC1 CS ), or not tested (CbbM-Ddx4 short , CbbM-FXR1 short , CbbM-LEM2 short ), green indicates condensate formation at concentrations of 1-20 μM. CbbM-Laf1 short undergoes liquid-liquid phase separation when mixed with 1 μM GFP and shows aggregation at all other conditions tested. (C) Architecture and behaviour of different EPYC1-IDP variants from C. reinhardtii . Teal arrows indicate repeat domains, yellow helices show SSU-recognition domains. CR = full length IDP, Δα = SSU-recognition domain deletion variant, ΔFR = repetition domains deletion variant. Light microscopy pictures show homogeneously dispersed CbbM and CbbM-EPYC1 CR ΔFR, while CbbM-EPYC1 CR and CbbM-EPYC1 CR Δα form condensates in 50 mM Tris (pH 7.5 & 8.0), 1 mM MgCl 2 , 5 mM NaHCO 3 , 0.1 mg/mL CA, and 0.3 mM RuBP. (D) Fluorescence microscopy pictures from the resorufin-coupled activity assay (supplementary figure 6) inside and outside of condensates before and after 25 minutes. (E) Fluorescence formation inside and outside of condensates. (F) Ratio of initial fluorescence formation rates between condensate inside and outside. (G) Ratio of maximum fluorescence levels between condensate inside and outside. Error bars represent standard errors from eight replicates.
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    (A) General workflow. A library of IDPs , , – was fused to <t>CbbM</t> ( R. <t>rubrum</t> Rubisco). Each fusion protein was individually tested in a condensation screen for phase-separation, no effect (i.e., homogenous dispersal), or aggregation. Condensates were further subjected to carboxylation activity and specificity tests. (B) Overview of the fusion protein library and condensation screen results. Full (or shortened) IDPs were fused to the C-terminus (IDP-C, IDP short -C), or the N and C terminus (IDP-N&C) of CbbM. Red indicates aggregation, grey indicates homogeneously dispersed protein, white indicates not-producible (CbbM-Laf1N&C, CbbM-Ddx4N&C, CbbM-EPYC1 CS ), or not tested (CbbM-Ddx4 short , CbbM-FXR1 short , CbbM-LEM2 short ), green indicates condensate formation at concentrations of 1-20 μM. CbbM-Laf1 short undergoes liquid-liquid phase separation when mixed with 1 μM GFP and shows aggregation at all other conditions tested. (C) Architecture and behaviour of different EPYC1-IDP variants from C. reinhardtii . Teal arrows indicate repeat domains, yellow helices show SSU-recognition domains. CR = full length IDP, Δα = SSU-recognition domain deletion variant, ΔFR = repetition domains deletion variant. Light microscopy pictures show homogeneously dispersed CbbM and CbbM-EPYC1 CR ΔFR, while CbbM-EPYC1 CR and CbbM-EPYC1 CR Δα form condensates in 50 mM Tris (pH 7.5 & 8.0), 1 mM MgCl 2 , 5 mM NaHCO 3 , 0.1 mg/mL CA, and 0.3 mM RuBP. (D) Fluorescence microscopy pictures from the resorufin-coupled activity assay (supplementary figure 6) inside and outside of condensates before and after 25 minutes. (E) Fluorescence formation inside and outside of condensates. (F) Ratio of initial fluorescence formation rates between condensate inside and outside. (G) Ratio of maximum fluorescence levels between condensate inside and outside. Error bars represent standard errors from eight replicates.
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    Tianma Microelectronics Co plumbum rubrum huangdan
    (A) General workflow. A library of IDPs , , – was fused to <t>CbbM</t> ( R. <t>rubrum</t> Rubisco). Each fusion protein was individually tested in a condensation screen for phase-separation, no effect (i.e., homogenous dispersal), or aggregation. Condensates were further subjected to carboxylation activity and specificity tests. (B) Overview of the fusion protein library and condensation screen results. Full (or shortened) IDPs were fused to the C-terminus (IDP-C, IDP short -C), or the N and C terminus (IDP-N&C) of CbbM. Red indicates aggregation, grey indicates homogeneously dispersed protein, white indicates not-producible (CbbM-Laf1N&C, CbbM-Ddx4N&C, CbbM-EPYC1 CS ), or not tested (CbbM-Ddx4 short , CbbM-FXR1 short , CbbM-LEM2 short ), green indicates condensate formation at concentrations of 1-20 μM. CbbM-Laf1 short undergoes liquid-liquid phase separation when mixed with 1 μM GFP and shows aggregation at all other conditions tested. (C) Architecture and behaviour of different EPYC1-IDP variants from C. reinhardtii . Teal arrows indicate repeat domains, yellow helices show SSU-recognition domains. CR = full length IDP, Δα = SSU-recognition domain deletion variant, ΔFR = repetition domains deletion variant. Light microscopy pictures show homogeneously dispersed CbbM and CbbM-EPYC1 CR ΔFR, while CbbM-EPYC1 CR and CbbM-EPYC1 CR Δα form condensates in 50 mM Tris (pH 7.5 & 8.0), 1 mM MgCl 2 , 5 mM NaHCO 3 , 0.1 mg/mL CA, and 0.3 mM RuBP. (D) Fluorescence microscopy pictures from the resorufin-coupled activity assay (supplementary figure 6) inside and outside of condensates before and after 25 minutes. (E) Fluorescence formation inside and outside of condensates. (F) Ratio of initial fluorescence formation rates between condensate inside and outside. (G) Ratio of maximum fluorescence levels between condensate inside and outside. Error bars represent standard errors from eight replicates.
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    Accession numbers obtained for NCBI submissions.

    Journal: PLOS ONE

    Article Title: Diagnostic ability of Peptidase S8 gene in the Arthrodermataceae causing dermatophytoses: A metadata analysis

    doi: 10.1371/journal.pone.0306829

    Figure Lengend Snippet: Accession numbers obtained for NCBI submissions.

    Article Snippet: Trichophyton interdigitale ATCC 9533, Trichophyton rubrum ATCC 28188, Trichophyton tonsurans ATCC 28942, and Microsporum canis ATCC 36299 (HiMedia India), anonymized clinical isolates from tinea corporis presentation, phenotypically identified (based on colony morphology, pigmentation, growth rate, and microscopic examination of hyphae, microconidia, macroconidia on lactophenol cotton blue mount preparation followed by hair perforation test and urease test) and genotypically based on sequencing of internal transcribed spacer region (data not provided) as T . mentagrophytes complex (n = 34), Epidermophyton floccosum (n = 1), Nannizzia gypsea (n = 3), saprophytes one each of Rhizopus stolonifer , Aspergillus flavus , and A . niger and nine Penicillium spp. isolated from the environment were included.

    Techniques:

    Accession numbers obtained for NCBI submissions.

    Journal: PLOS ONE

    Article Title: Diagnostic ability of Peptidase S8 gene in the Arthrodermataceae causing dermatophytoses: A metadata analysis

    doi: 10.1371/journal.pone.0306829

    Figure Lengend Snippet: Accession numbers obtained for NCBI submissions.

    Article Snippet: 2 , ATCC 28188 T . rubrum , MW149250.

    Techniques:

    List of Candidate Antifungal Resistance Genes Found after HMM Analysis Using the ResFungi HMM Database <xref ref-type= a " width="100%" height="100%">

    Journal: ACS Omega

    Article Title: ResFungi: A Novel Protein Database of Antifungal Drug Resistance Genes Using a Hidden Markov Model Profile

    doi: 10.1021/acsomega.4c02198

    Figure Lengend Snippet: List of Candidate Antifungal Resistance Genes Found after HMM Analysis Using the ResFungi HMM Database a

    Article Snippet: The following species had their genome and proteome data obtained from public databases: Candida albicans SC5314 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000182965.3/ ), Candida auris B8441 ( http://www.candidagenome.org/download/sequence/C_auris_B8441/current/ ), Cryptococcus neoformans var. grubii H99 ( https://fungi.ensembl.org/Cryptococcus_neoformans_var_grubii_h99_gca_000149245/Info/Index ), Aspergillus fumigatus Af293 ( https://www.ncbi.nlm.nih.gov/datasets/taxonomy/746128/ ), Aspergillus terreus NIH2624 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000149615.1/ ), Sporothrix brasiliensis 5110 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000820605.1/ ), Sporothrix schenckii ATCC 58251 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000474925.1/ ), Histoplasma capsulatum G186AR ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000150115.1/ ), Coccidioides immitis H538.4 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000149815.1/ ), Paracoccidioides brasiliensis Pb03 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000150475.2/ ), Trichophyton rubrum CBS 118892 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000151425.1/ ), Microsporum canis CBS 113480 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000151145.1/ ), Fusarium graminearum PH-1 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000240135.3/ ), Exophiala mesophila CBS 40295 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000836275.1/ ), and Fonsecaea multimorphosa CBS 102226 ( https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000836435.1/ ).

    Techniques: Activity Assay, Variant Assay

    (A) General workflow. A library of IDPs , , – was fused to CbbM ( R. rubrum Rubisco). Each fusion protein was individually tested in a condensation screen for phase-separation, no effect (i.e., homogenous dispersal), or aggregation. Condensates were further subjected to carboxylation activity and specificity tests. (B) Overview of the fusion protein library and condensation screen results. Full (or shortened) IDPs were fused to the C-terminus (IDP-C, IDP short -C), or the N and C terminus (IDP-N&C) of CbbM. Red indicates aggregation, grey indicates homogeneously dispersed protein, white indicates not-producible (CbbM-Laf1N&C, CbbM-Ddx4N&C, CbbM-EPYC1 CS ), or not tested (CbbM-Ddx4 short , CbbM-FXR1 short , CbbM-LEM2 short ), green indicates condensate formation at concentrations of 1-20 μM. CbbM-Laf1 short undergoes liquid-liquid phase separation when mixed with 1 μM GFP and shows aggregation at all other conditions tested. (C) Architecture and behaviour of different EPYC1-IDP variants from C. reinhardtii . Teal arrows indicate repeat domains, yellow helices show SSU-recognition domains. CR = full length IDP, Δα = SSU-recognition domain deletion variant, ΔFR = repetition domains deletion variant. Light microscopy pictures show homogeneously dispersed CbbM and CbbM-EPYC1 CR ΔFR, while CbbM-EPYC1 CR and CbbM-EPYC1 CR Δα form condensates in 50 mM Tris (pH 7.5 & 8.0), 1 mM MgCl 2 , 5 mM NaHCO 3 , 0.1 mg/mL CA, and 0.3 mM RuBP. (D) Fluorescence microscopy pictures from the resorufin-coupled activity assay (supplementary figure 6) inside and outside of condensates before and after 25 minutes. (E) Fluorescence formation inside and outside of condensates. (F) Ratio of initial fluorescence formation rates between condensate inside and outside. (G) Ratio of maximum fluorescence levels between condensate inside and outside. Error bars represent standard errors from eight replicates.

    Journal: bioRxiv

    Article Title: Bottom-up reconstruction of minimal pyrenoids provides insights into the evolution and mechanisms of carbon concentration by EPYC1 proteins

    doi: 10.1101/2024.06.28.601168

    Figure Lengend Snippet: (A) General workflow. A library of IDPs , , – was fused to CbbM ( R. rubrum Rubisco). Each fusion protein was individually tested in a condensation screen for phase-separation, no effect (i.e., homogenous dispersal), or aggregation. Condensates were further subjected to carboxylation activity and specificity tests. (B) Overview of the fusion protein library and condensation screen results. Full (or shortened) IDPs were fused to the C-terminus (IDP-C, IDP short -C), or the N and C terminus (IDP-N&C) of CbbM. Red indicates aggregation, grey indicates homogeneously dispersed protein, white indicates not-producible (CbbM-Laf1N&C, CbbM-Ddx4N&C, CbbM-EPYC1 CS ), or not tested (CbbM-Ddx4 short , CbbM-FXR1 short , CbbM-LEM2 short ), green indicates condensate formation at concentrations of 1-20 μM. CbbM-Laf1 short undergoes liquid-liquid phase separation when mixed with 1 μM GFP and shows aggregation at all other conditions tested. (C) Architecture and behaviour of different EPYC1-IDP variants from C. reinhardtii . Teal arrows indicate repeat domains, yellow helices show SSU-recognition domains. CR = full length IDP, Δα = SSU-recognition domain deletion variant, ΔFR = repetition domains deletion variant. Light microscopy pictures show homogeneously dispersed CbbM and CbbM-EPYC1 CR ΔFR, while CbbM-EPYC1 CR and CbbM-EPYC1 CR Δα form condensates in 50 mM Tris (pH 7.5 & 8.0), 1 mM MgCl 2 , 5 mM NaHCO 3 , 0.1 mg/mL CA, and 0.3 mM RuBP. (D) Fluorescence microscopy pictures from the resorufin-coupled activity assay (supplementary figure 6) inside and outside of condensates before and after 25 minutes. (E) Fluorescence formation inside and outside of condensates. (F) Ratio of initial fluorescence formation rates between condensate inside and outside. (G) Ratio of maximum fluorescence levels between condensate inside and outside. Error bars represent standard errors from eight replicates.

    Article Snippet: Constructs were cloned to the C-terminus or N & C-terminus of the R. Rubrum CbbM coding region in a His-bdSUMO plasmid acquired from Addgene using OneShot TM Top10 cells (Invitrogen).

    Techniques: Activity Assay, Variant Assay, Light Microscopy, Fluorescence, Microscopy