t forsythia Atcc Search Results


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    ATCC t forsythia atcc 43037
    Analysis of codon usage for <t>ATCC</t> 43037 (left panel) and BU063 (right panel). The continuous curves indicate the NC values to be expected for a given GC3s content in the absence of other factors shaping codon usage. Every dot represents a protein coding gene, dots not positioned near the curve therefore represent genes that display a considerable codon usage bias. GC3s: G + C content at synonymous positions, NC: effective number of codons used within the sequence of a gene
    T Forsythia Atcc 43037, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 702 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 702 article reviews
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    t forsythia atcc 43037 - by Bioz Stars, 2020-08
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    85
    ATCC t forsythia atcc 700198
    Analysis of codon usage for <t>ATCC</t> 43037 (left panel) and BU063 (right panel). The continuous curves indicate the NC values to be expected for a given GC3s content in the absence of other factors shaping codon usage. Every dot represents a protein coding gene, dots not positioned near the curve therefore represent genes that display a considerable codon usage bias. GC3s: G + C content at synonymous positions, NC: effective number of codons used within the sequence of a gene
    T Forsythia Atcc 700198, supplied by ATCC, used in various techniques. Bioz Stars score: 85/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    ATCC t forsythia atcc 43037 genome
    The percentage sequence coverage of modern and ancient known virulence factor genes; the T. forsythia 92A2 sequence was used as a reference, apart from leg when <t>ATCC</t> 43037 was used as a reference; and KLIKK protease genes when our in-home determined KLIKK protease locus was used as a reference [ 10 ]
    T Forsythia Atcc 43037 Genome, supplied by ATCC, used in various techniques. Bioz Stars score: 89/100, based on 76 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t forsythia atcc 43037 genome/product/ATCC
    Average 89 stars, based on 76 article reviews
    Price from $9.99 to $1999.99
    t forsythia atcc 43037 genome - by Bioz Stars, 2020-08
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    Image Search Results


    Analysis of codon usage for ATCC 43037 (left panel) and BU063 (right panel). The continuous curves indicate the NC values to be expected for a given GC3s content in the absence of other factors shaping codon usage. Every dot represents a protein coding gene, dots not positioned near the curve therefore represent genes that display a considerable codon usage bias. GC3s: G + C content at synonymous positions, NC: effective number of codons used within the sequence of a gene

    Journal: BMC Genomics

    Article Title: Comparative genome characterization of the periodontal pathogen Tannerella forsythia

    doi: 10.1186/s12864-020-6535-y

    Figure Lengend Snippet: Analysis of codon usage for ATCC 43037 (left panel) and BU063 (right panel). The continuous curves indicate the NC values to be expected for a given GC3s content in the absence of other factors shaping codon usage. Every dot represents a protein coding gene, dots not positioned near the curve therefore represent genes that display a considerable codon usage bias. GC3s: G + C content at synonymous positions, NC: effective number of codons used within the sequence of a gene

    Article Snippet: Mate-pairs of T. forsythia ATCC 43037 were deposited in the Sequence Read Archive under accession SRR9302598 (BioProject PRJNA548889, BioSample SAMN12058270).

    Techniques: Sequencing

    Multiple whole genome alignment of eight T. forsythia strains. Each coloured block represents a genomic region that aligned to a region in at least one other genome, plotted in the same colour, to which it was predicted to be homologous based on sequence similarity. Blocks above the centre line indicate forward orientation; blocks below the line indicate reverse orientation relative to strain 92A2. A histogram within each block shows the average similarity of a region to its counterparts in the other genomes. Red vertical lines indicate contig boundaries. Strain ATCC 43037 displayed two translocations compared to strain 92A2 with lengths of approximately 500 kbp (blue and yellow blocks at the right end of 92A2 and in the centre of ATCC) and 30 kbp (pink block at approx. 1.25 Mbp in 92A2 and at approx. 2.7 Mbp in ATCC), respectively. Previously described large-scale inversions in strain KS16 could be confirmed (reverted blocks in the left half of the alignment)

    Journal: BMC Genomics

    Article Title: Comparative genome characterization of the periodontal pathogen Tannerella forsythia

    doi: 10.1186/s12864-020-6535-y

    Figure Lengend Snippet: Multiple whole genome alignment of eight T. forsythia strains. Each coloured block represents a genomic region that aligned to a region in at least one other genome, plotted in the same colour, to which it was predicted to be homologous based on sequence similarity. Blocks above the centre line indicate forward orientation; blocks below the line indicate reverse orientation relative to strain 92A2. A histogram within each block shows the average similarity of a region to its counterparts in the other genomes. Red vertical lines indicate contig boundaries. Strain ATCC 43037 displayed two translocations compared to strain 92A2 with lengths of approximately 500 kbp (blue and yellow blocks at the right end of 92A2 and in the centre of ATCC) and 30 kbp (pink block at approx. 1.25 Mbp in 92A2 and at approx. 2.7 Mbp in ATCC), respectively. Previously described large-scale inversions in strain KS16 could be confirmed (reverted blocks in the left half of the alignment)

    Article Snippet: Mate-pairs of T. forsythia ATCC 43037 were deposited in the Sequence Read Archive under accession SRR9302598 (BioProject PRJNA548889, BioSample SAMN12058270).

    Techniques: Blocking Assay, Sequencing

    Whole genome alignment between the six frame amino acid translations of both Tannerella sp. BU063 and the scaffolded and ordered ATCC 43037 assembly. Whereas the amino acid alignment reflects similarity with respect to gene content, the order of genes is not preserved

    Journal: BMC Genomics

    Article Title: Comparative genome characterization of the periodontal pathogen Tannerella forsythia

    doi: 10.1186/s12864-020-6535-y

    Figure Lengend Snippet: Whole genome alignment between the six frame amino acid translations of both Tannerella sp. BU063 and the scaffolded and ordered ATCC 43037 assembly. Whereas the amino acid alignment reflects similarity with respect to gene content, the order of genes is not preserved

    Article Snippet: Mate-pairs of T. forsythia ATCC 43037 were deposited in the Sequence Read Archive under accession SRR9302598 (BioProject PRJNA548889, BioSample SAMN12058270).

    Techniques:

    Dual fluorescence in situ hybridization staining of Tannerella forsythia and Campylobacter rectus for biofilms harboring ATCC 43037 wild‐type (A), UB 4 wild‐type (B), and ATCC 43037 ∆tfs AB (C). Red/yellow: T. forsythia , cyan: C. rectus; green: non‐hybridized cells ( DNA staining YoPro‐1+Sytox). Scale bars 20 μm (A, B) and 15 μm (C)

    Journal: Molecular Oral Microbiology

    Article Title: Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms. Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms

    doi: 10.1111/omi.12182

    Figure Lengend Snippet: Dual fluorescence in situ hybridization staining of Tannerella forsythia and Campylobacter rectus for biofilms harboring ATCC 43037 wild‐type (A), UB 4 wild‐type (B), and ATCC 43037 ∆tfs AB (C). Red/yellow: T. forsythia , cyan: C. rectus; green: non‐hybridized cells ( DNA staining YoPro‐1+Sytox). Scale bars 20 μm (A, B) and 15 μm (C)

    Article Snippet: In contrast, deficiency in the O ‐glycan's terminal nonulosonic acid in a T. forsythia ATCC 43037 ΔpseC and a T. forsythia UB4 ΔlegC mutant, respectively, decreased biofilm formation on a mucin‐coated surface.

    Techniques: Fluorescence, In Situ Hybridization, Staining

    Fluorescence in situ hybridization staining of biofilms harboring Tannerella forsythia ATCC 43037 mutants (A) ∆pseC , (B) ∆wecC , and (C) ∆tfs AB . Red: T. forsythia , cyan: Porphyromonas gingivalis , green: non‐hybridized cells ( DNA staining YoPro‐1+Sytox). Scale bars 20 μm (A) and 10 μm (B, C)

    Journal: Molecular Oral Microbiology

    Article Title: Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms. Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms

    doi: 10.1111/omi.12182

    Figure Lengend Snippet: Fluorescence in situ hybridization staining of biofilms harboring Tannerella forsythia ATCC 43037 mutants (A) ∆pseC , (B) ∆wecC , and (C) ∆tfs AB . Red: T. forsythia , cyan: Porphyromonas gingivalis , green: non‐hybridized cells ( DNA staining YoPro‐1+Sytox). Scale bars 20 μm (A) and 10 μm (B, C)

    Article Snippet: In contrast, deficiency in the O ‐glycan's terminal nonulosonic acid in a T. forsythia ATCC 43037 ΔpseC and a T. forsythia UB4 ΔlegC mutant, respectively, decreased biofilm formation on a mucin‐coated surface.

    Techniques: Fluorescence, In Situ Hybridization, Staining

    Box plots showing cell numbers of all species determined by quantitative real‐time PCR for biofilms with Tannerella forsythia ATCC 43037 wild‐type or mutants (∆pseC , ∆wecC , ∆tfs AB , ∆pseC comp ) (A) and UB 4 wild‐type or mutants (∆legC , ∆legC comp ), respectively (B). Data derived from three independent experiments were plotted on a logarithmic scale. Asterisk (*) indicates significant differences ( P ≤.05) between the groups

    Journal: Molecular Oral Microbiology

    Article Title: Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms. Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms

    doi: 10.1111/omi.12182

    Figure Lengend Snippet: Box plots showing cell numbers of all species determined by quantitative real‐time PCR for biofilms with Tannerella forsythia ATCC 43037 wild‐type or mutants (∆pseC , ∆wecC , ∆tfs AB , ∆pseC comp ) (A) and UB 4 wild‐type or mutants (∆legC , ∆legC comp ), respectively (B). Data derived from three independent experiments were plotted on a logarithmic scale. Asterisk (*) indicates significant differences ( P ≤.05) between the groups

    Article Snippet: In contrast, deficiency in the O ‐glycan's terminal nonulosonic acid in a T. forsythia ATCC 43037 ΔpseC and a T. forsythia UB4 ΔlegC mutant, respectively, decreased biofilm formation on a mucin‐coated surface.

    Techniques: Real-time Polymerase Chain Reaction, Derivative Assay

    Comparison of 10‐species biofilms with two Tannerella forsythia wild‐type strains. (A) Whiskers boxplots (5th to 95th centile) show bacterial numbers determined by quantitative real‐time PCR from three independent experiments. Asterisk (*) indicates a statistically significant difference ( P ≤.05) between groups. The two groups represent biofilms with either T. forsythia ATCC 43037 wild‐type or T. forsythia UB 4 wild‐type. (B, C) Fluorescence in situ hybridization stainings of fixed biofilms showing the localization of ATCC 43037 wild‐type (B) and UB 4 wild‐type (C). Red/yellow: T. forsythia; cyan: Porphyromonas gingivalis , green: non‐hybridized cells ( DNA staining YoPro‐1+Sytox). Here a representative area for one disk each is shown with a top view in the left panel and a side view with the biofilm–disk interface directed towards the top view; scale bars 5 μm (B) and 10 μm (C)

    Journal: Molecular Oral Microbiology

    Article Title: Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms. Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms

    doi: 10.1111/omi.12182

    Figure Lengend Snippet: Comparison of 10‐species biofilms with two Tannerella forsythia wild‐type strains. (A) Whiskers boxplots (5th to 95th centile) show bacterial numbers determined by quantitative real‐time PCR from three independent experiments. Asterisk (*) indicates a statistically significant difference ( P ≤.05) between groups. The two groups represent biofilms with either T. forsythia ATCC 43037 wild‐type or T. forsythia UB 4 wild‐type. (B, C) Fluorescence in situ hybridization stainings of fixed biofilms showing the localization of ATCC 43037 wild‐type (B) and UB 4 wild‐type (C). Red/yellow: T. forsythia; cyan: Porphyromonas gingivalis , green: non‐hybridized cells ( DNA staining YoPro‐1+Sytox). Here a representative area for one disk each is shown with a top view in the left panel and a side view with the biofilm–disk interface directed towards the top view; scale bars 5 μm (B) and 10 μm (C)

    Article Snippet: In contrast, deficiency in the O ‐glycan's terminal nonulosonic acid in a T. forsythia ATCC 43037 ΔpseC and a T. forsythia UB4 ΔlegC mutant, respectively, decreased biofilm formation on a mucin‐coated surface.

    Techniques: Real-time Polymerase Chain Reaction, Fluorescence, In Situ Hybridization, Staining

    Monospecies biofilm formation of Tannerella forsythia wild‐type and mutant strains. (A) Biofilm formation of T. forsythia ATCC 43037 wild‐type compared with its mutants ATCC 43037 Δ pseC , Δ wecC , Δ tfs AB and the complemented mutant Δ pseC comp . (B) Biofilm formation of T. forsythia UB 4 wild‐type compared with its mutant UB 4 Δ legC and the complemented mutant Δ legC comp . Mean values ± SD of four independent experiments with three replicates, each, are shown. Asterisks (**) indicate significant differences between samples as determined by the unpaired Student's t ‐test ( P ≤.01)

    Journal: Molecular Oral Microbiology

    Article Title: Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms. Behavior of two Tannerella forsythia strains and their cell surface mutants in multispecies oral biofilms

    doi: 10.1111/omi.12182

    Figure Lengend Snippet: Monospecies biofilm formation of Tannerella forsythia wild‐type and mutant strains. (A) Biofilm formation of T. forsythia ATCC 43037 wild‐type compared with its mutants ATCC 43037 Δ pseC , Δ wecC , Δ tfs AB and the complemented mutant Δ pseC comp . (B) Biofilm formation of T. forsythia UB 4 wild‐type compared with its mutant UB 4 Δ legC and the complemented mutant Δ legC comp . Mean values ± SD of four independent experiments with three replicates, each, are shown. Asterisks (**) indicate significant differences between samples as determined by the unpaired Student's t ‐test ( P ≤.01)

    Article Snippet: In contrast, deficiency in the O ‐glycan's terminal nonulosonic acid in a T. forsythia ATCC 43037 ΔpseC and a T. forsythia UB4 ΔlegC mutant, respectively, decreased biofilm formation on a mucin‐coated surface.

    Techniques: Mutagenesis

    (A) Coomassie Brilliant Blue staining of crude cell extracts from T. forsythia ATCC 43037 wild-type and glycosyltransferase-deficient mutants after separation on a 7.5% SDS-PA gel. The S-layer glycoproteins (labeled TfsA and TfsB) are indicated and the downshifts resulting from glycan truncation can be seen in the mutants. S-layer glycoprotein bands were further processed for MS analyses. PageRuler Plus Prestained Protein Ladder (Thermo Fisher Scientific) was used as a protein molecular weight marker. (B) Western-blots probed with α-TfsA and α-TfsB antiserum for confirmation of the identity of S-layer glycoproteins. Glycoproteins from all glycosyltransferase-deficient mutants (Δ gtfSMILE ) experienced a downshift resulting from glycan truncation, whereas the reconstituted strains (denoted with +) regained wild-type migration, indicating the presence of the complete mature glycan, proving successful recombination. (C, i–vi) ESI-MS sum spectra of β-eliminated TfsB O -glycans from T. forsythia wild-type and mutants. The glycan structures of the signals corresponding to the largest mass (bold m / z values) are shown in SNFG representations ( Varki et al., 2015 ). O -Glycan signals detected for the respective mutants were assigned based on the m / z mass differences corresponding to the loss of individual sugar units and/or modifications.

    Journal: Frontiers in Microbiology

    Article Title: A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications

    doi: 10.3389/fmicb.2018.02008

    Figure Lengend Snippet: (A) Coomassie Brilliant Blue staining of crude cell extracts from T. forsythia ATCC 43037 wild-type and glycosyltransferase-deficient mutants after separation on a 7.5% SDS-PA gel. The S-layer glycoproteins (labeled TfsA and TfsB) are indicated and the downshifts resulting from glycan truncation can be seen in the mutants. S-layer glycoprotein bands were further processed for MS analyses. PageRuler Plus Prestained Protein Ladder (Thermo Fisher Scientific) was used as a protein molecular weight marker. (B) Western-blots probed with α-TfsA and α-TfsB antiserum for confirmation of the identity of S-layer glycoproteins. Glycoproteins from all glycosyltransferase-deficient mutants (Δ gtfSMILE ) experienced a downshift resulting from glycan truncation, whereas the reconstituted strains (denoted with +) regained wild-type migration, indicating the presence of the complete mature glycan, proving successful recombination. (C, i–vi) ESI-MS sum spectra of β-eliminated TfsB O -glycans from T. forsythia wild-type and mutants. The glycan structures of the signals corresponding to the largest mass (bold m / z values) are shown in SNFG representations ( Varki et al., 2015 ). O -Glycan signals detected for the respective mutants were assigned based on the m / z mass differences corresponding to the loss of individual sugar units and/or modifications.

    Article Snippet: In comparison to the T. forsythia ATCC 43037 wild-type, in which the glycosylated S-layer proteins TfsA and TfsB migrate on the SDS-PAGE gel at ∼230 kDa (calculated MW of the protein, 135 kDa) and ∼270 kDa (calculated MW of the protein, 152 kDa), respectively, each Gtf-deficient mutant experienced a downshift of these prominent T. forsythia glycoproteins ( Figure ).

    Techniques: Staining, Labeling, Mass Spectrometry, Molecular Weight, Marker, Western Blot, Migration

    Alignment of protein O- glycosylation gene clusters from different T. forsythia strains showing comparable sizes and gene organizations (drawn to scale). Genes showing sequence identity > 50% and sequence coverage > 50% between strains appear in the same color. The major difference in the analyzed strains are for genes synthesizing either CMP-Pse ( pseBCFHGI ; light green colors; strains ATCC 43037 and UB20) or CMP-Leg ( legBCHIGF, ptmE ; dark green colors; strains FDC 92A2, UB4, KS16, UB22). Genes encoding Gtfs ( gtfSMILE ; blue color), Mtfs ( mtfJOY ; yellow color) and carbohydrate modifying enzymes ( asnB, wecC, wecB ; gray color) show high sequence homology between analyzed strains. Genomes of all strains synthesizing CMP-Leg encode an additional putative Mtf gene ( mtfX ), which does not share sequence homology to other Mtfs located within the cluster. In strain UB22, mtfJ is not predicted and for strain 3313 only five out of seven genes needed for the synthesis of CMP-Leg are predicted confidently. Due to low homology, isolate Tannerella sp. HOT-286 (phylotype BU063) could not be aligned with the other T. forsythia strains; for that isolate, the genomic area between a wzx -like gene and the gtfE gene is shown for comparison. P, Pse transferase; L, Leg transferase; HP, hypothetical protein; the star symbol ( ∗ ) indicates a transposable element; genes written in bold letters were investigated in detail in course of this study.

    Journal: Frontiers in Microbiology

    Article Title: A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications

    doi: 10.3389/fmicb.2018.02008

    Figure Lengend Snippet: Alignment of protein O- glycosylation gene clusters from different T. forsythia strains showing comparable sizes and gene organizations (drawn to scale). Genes showing sequence identity > 50% and sequence coverage > 50% between strains appear in the same color. The major difference in the analyzed strains are for genes synthesizing either CMP-Pse ( pseBCFHGI ; light green colors; strains ATCC 43037 and UB20) or CMP-Leg ( legBCHIGF, ptmE ; dark green colors; strains FDC 92A2, UB4, KS16, UB22). Genes encoding Gtfs ( gtfSMILE ; blue color), Mtfs ( mtfJOY ; yellow color) and carbohydrate modifying enzymes ( asnB, wecC, wecB ; gray color) show high sequence homology between analyzed strains. Genomes of all strains synthesizing CMP-Leg encode an additional putative Mtf gene ( mtfX ), which does not share sequence homology to other Mtfs located within the cluster. In strain UB22, mtfJ is not predicted and for strain 3313 only five out of seven genes needed for the synthesis of CMP-Leg are predicted confidently. Due to low homology, isolate Tannerella sp. HOT-286 (phylotype BU063) could not be aligned with the other T. forsythia strains; for that isolate, the genomic area between a wzx -like gene and the gtfE gene is shown for comparison. P, Pse transferase; L, Leg transferase; HP, hypothetical protein; the star symbol ( ∗ ) indicates a transposable element; genes written in bold letters were investigated in detail in course of this study.

    Article Snippet: In comparison to the T. forsythia ATCC 43037 wild-type, in which the glycosylated S-layer proteins TfsA and TfsB migrate on the SDS-PAGE gel at ∼230 kDa (calculated MW of the protein, 135 kDa) and ∼270 kDa (calculated MW of the protein, 152 kDa), respectively, each Gtf-deficient mutant experienced a downshift of these prominent T. forsythia glycoproteins ( Figure ).

    Techniques: Sequencing

    ESI-MS sum spectra of β-eliminated TfsB O -glycans from T. forsythia ATCC 43037 methyltransferase knock-out mutants. The glycan structures of the signals corresponding to the largest mass (bold m / z values) are shown in SNFG representation ( Varki et al., 2015 ). Other O -glycan signals detected for the respective mutants were assigned based on the m / z mass differences corresponding to the loss of individual sugar units and/or modifications. The lack of methyl modifications is indicated by a red circle in the symbolic O -glycan structure representation.

    Journal: Frontiers in Microbiology

    Article Title: A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications

    doi: 10.3389/fmicb.2018.02008

    Figure Lengend Snippet: ESI-MS sum spectra of β-eliminated TfsB O -glycans from T. forsythia ATCC 43037 methyltransferase knock-out mutants. The glycan structures of the signals corresponding to the largest mass (bold m / z values) are shown in SNFG representation ( Varki et al., 2015 ). Other O -glycan signals detected for the respective mutants were assigned based on the m / z mass differences corresponding to the loss of individual sugar units and/or modifications. The lack of methyl modifications is indicated by a red circle in the symbolic O -glycan structure representation.

    Article Snippet: In comparison to the T. forsythia ATCC 43037 wild-type, in which the glycosylated S-layer proteins TfsA and TfsB migrate on the SDS-PAGE gel at ∼230 kDa (calculated MW of the protein, 135 kDa) and ∼270 kDa (calculated MW of the protein, 152 kDa), respectively, each Gtf-deficient mutant experienced a downshift of these prominent T. forsythia glycoproteins ( Figure ).

    Techniques: Mass Spectrometry, Knock-Out

    (A) Scheme of the T. forsythia ATCC 43037 S-layer O -glycan structure. Monosaccharide symbols are shown according to the Symbol Nomenclature for Glycans (SNFG) ( Varki et al., 2015 ). Please note that the position of the branching Fuc remained unclear ( Posch et al., 2011 ) until it was determined in the course of this study to be on the reducing-end Gal. (B) Scheme of the 27-kb protein O -glycosylation gene cluster of T. forsythia ATCC 43037. Wzx (black), flippase; pseBCFHGI (green), CMP-Pse biosynthesis genes; gtfSMILE (blue), Gtf genes; mtfJOY (yellow), Mtf genes; asnB (putative asparagine synthetase B), wecC (UDP- N -acetyl- D -mannosamine dehydrogenase) and wecB (UDP- N- acetylglucosamine 2-epimerase) (purple); hypothetical proteins, HP (gray). Genes are not drawn to scale.

    Journal: Frontiers in Microbiology

    Article Title: A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications

    doi: 10.3389/fmicb.2018.02008

    Figure Lengend Snippet: (A) Scheme of the T. forsythia ATCC 43037 S-layer O -glycan structure. Monosaccharide symbols are shown according to the Symbol Nomenclature for Glycans (SNFG) ( Varki et al., 2015 ). Please note that the position of the branching Fuc remained unclear ( Posch et al., 2011 ) until it was determined in the course of this study to be on the reducing-end Gal. (B) Scheme of the 27-kb protein O -glycosylation gene cluster of T. forsythia ATCC 43037. Wzx (black), flippase; pseBCFHGI (green), CMP-Pse biosynthesis genes; gtfSMILE (blue), Gtf genes; mtfJOY (yellow), Mtf genes; asnB (putative asparagine synthetase B), wecC (UDP- N -acetyl- D -mannosamine dehydrogenase) and wecB (UDP- N- acetylglucosamine 2-epimerase) (purple); hypothetical proteins, HP (gray). Genes are not drawn to scale.

    Article Snippet: In comparison to the T. forsythia ATCC 43037 wild-type, in which the glycosylated S-layer proteins TfsA and TfsB migrate on the SDS-PAGE gel at ∼230 kDa (calculated MW of the protein, 135 kDa) and ∼270 kDa (calculated MW of the protein, 152 kDa), respectively, each Gtf-deficient mutant experienced a downshift of these prominent T. forsythia glycoproteins ( Figure ).

    Techniques:

    Model for the biosynthesis of the species-specific portion of the T. forsythia ATCC 43037 O -glycan. Upon synthesis of the pentasaccharide core on an undP lipid carrier, the first carbohydrate residue of the species-specific glycan is a Fuc residue conferred by GtfE. The glycan is elongated with a Gal residue which is transferred by GtfL and methylated by MtfY. The assembly of the three sugar branch, consisting of a ManNAcA residue (transferred by GtfI), a ManNAcCONH 2 residue (GtfM), which is methylated by either MtfJ or MtfO, and a Pse5Am7Gra residue (transferred via GtfS), completes the synthesis of the decasaccharide.

    Journal: Frontiers in Microbiology

    Article Title: A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications

    doi: 10.3389/fmicb.2018.02008

    Figure Lengend Snippet: Model for the biosynthesis of the species-specific portion of the T. forsythia ATCC 43037 O -glycan. Upon synthesis of the pentasaccharide core on an undP lipid carrier, the first carbohydrate residue of the species-specific glycan is a Fuc residue conferred by GtfE. The glycan is elongated with a Gal residue which is transferred by GtfL and methylated by MtfY. The assembly of the three sugar branch, consisting of a ManNAcA residue (transferred by GtfI), a ManNAcCONH 2 residue (GtfM), which is methylated by either MtfJ or MtfO, and a Pse5Am7Gra residue (transferred via GtfS), completes the synthesis of the decasaccharide.

    Article Snippet: In comparison to the T. forsythia ATCC 43037 wild-type, in which the glycosylated S-layer proteins TfsA and TfsB migrate on the SDS-PAGE gel at ∼230 kDa (calculated MW of the protein, 135 kDa) and ∼270 kDa (calculated MW of the protein, 152 kDa), respectively, each Gtf-deficient mutant experienced a downshift of these prominent T. forsythia glycoproteins ( Figure ).

    Techniques: Methylation

    Deconvoluted ESI-IT-MS sum spectra of β-eliminated TfsB O -glycans from T. forsythia parent and mutant strains. ( A ) Comparison of the spectra from T. forsythia ATCC 43037 wild-type, Δ Tanf_01245 mutant, reconstituted mutant Δ Tanf_01245 + and cross-complemented mutant Δ Tanf_01245 + TFUB4_00887 . ( B ) Comparison of the spectra from T. forsythia UB4 wild-type, Δ TFUB4_00887 mutant, reconstituted mutant Δ TFUB4_00887 + and cross-complemented mutant Δ TFUB4_00887 + Tanf_01245 . Another glycan species with additional +16 Da at the position of the digitoxose was observed, indicative of the presence of a deoxyhexose instead of a dideoxyhexose in some forms of the glycan. The glycan structures of the highest mass peaks are shown as symbolic representations. Mass peaks from the subsequent fragmentation pattern were assigned according to the loss of carbohydrate units and modifications. Relative peak intensities of occurring peaks are given on the y axis. This figure is available in black and white in print and in color at Glycobiology online.

    Journal: Glycobiology

    Article Title: A pseudaminic acid or a legionaminic acid derivative transferase is strain-specifically implicated in the general protein O-glycosylation system of the periodontal pathogen Tannerella forsythia

    doi: 10.1093/glycob/cwx019

    Figure Lengend Snippet: Deconvoluted ESI-IT-MS sum spectra of β-eliminated TfsB O -glycans from T. forsythia parent and mutant strains. ( A ) Comparison of the spectra from T. forsythia ATCC 43037 wild-type, Δ Tanf_01245 mutant, reconstituted mutant Δ Tanf_01245 + and cross-complemented mutant Δ Tanf_01245 + TFUB4_00887 . ( B ) Comparison of the spectra from T. forsythia UB4 wild-type, Δ TFUB4_00887 mutant, reconstituted mutant Δ TFUB4_00887 + and cross-complemented mutant Δ TFUB4_00887 + Tanf_01245 . Another glycan species with additional +16 Da at the position of the digitoxose was observed, indicative of the presence of a deoxyhexose instead of a dideoxyhexose in some forms of the glycan. The glycan structures of the highest mass peaks are shown as symbolic representations. Mass peaks from the subsequent fragmentation pattern were assigned according to the loss of carbohydrate units and modifications. Relative peak intensities of occurring peaks are given on the y axis. This figure is available in black and white in print and in color at Glycobiology online.

    Article Snippet: Secondary structure predictions performed at http://bioinf.sce.carleton.ca/PCISS/start.php indicate for T. forsythia ATCC 43037 Tanf_01245 and T. forsythia UB4 TFUB4_00887, an α-helix content of 34.38% and 32.58%, a β-sheet content of 20.90% and 22.40%, respectively, and 45% turns, each.

    Techniques: Mass Spectrometry, Mutagenesis

    ESI-IT-MS analysis of cellular nucleotide sugar pools from T. forsythia strains. ( A ) CMP-activated Pse5Am7Gra ( m / z 683.3) was detected in the T. forsythia ATCC 43037 wild-type and in the Δ Tanf_01245 mutant, whereas this mass was absent in a Pse biosynthesis deficient strain (Δ pseC ) which served as a negative control. ( B ) In T. forsythia UB4 wild-type and in the Δ TFUB4_00887 mutant, a m / z 654.3 peak was identified, which was attributed to a CMP-activated Leg derivative (CMP-Leg*). This mass is consistent with having Ac and Gc modifications on Leg, based on calculation. Notably, this peak was absent in the Legbiosynthesis deficient strain (Δ legC ) which served as a negative control. Relative peak intensities are given on the y axis.

    Journal: Glycobiology

    Article Title: A pseudaminic acid or a legionaminic acid derivative transferase is strain-specifically implicated in the general protein O-glycosylation system of the periodontal pathogen Tannerella forsythia

    doi: 10.1093/glycob/cwx019

    Figure Lengend Snippet: ESI-IT-MS analysis of cellular nucleotide sugar pools from T. forsythia strains. ( A ) CMP-activated Pse5Am7Gra ( m / z 683.3) was detected in the T. forsythia ATCC 43037 wild-type and in the Δ Tanf_01245 mutant, whereas this mass was absent in a Pse biosynthesis deficient strain (Δ pseC ) which served as a negative control. ( B ) In T. forsythia UB4 wild-type and in the Δ TFUB4_00887 mutant, a m / z 654.3 peak was identified, which was attributed to a CMP-activated Leg derivative (CMP-Leg*). This mass is consistent with having Ac and Gc modifications on Leg, based on calculation. Notably, this peak was absent in the Legbiosynthesis deficient strain (Δ legC ) which served as a negative control. Relative peak intensities are given on the y axis.

    Article Snippet: Secondary structure predictions performed at http://bioinf.sce.carleton.ca/PCISS/start.php indicate for T. forsythia ATCC 43037 Tanf_01245 and T. forsythia UB4 TFUB4_00887, an α-helix content of 34.38% and 32.58%, a β-sheet content of 20.90% and 22.40%, respectively, and 45% turns, each.

    Techniques: Mass Spectrometry, Mutagenesis, Negative Control

    SDS-PAGE and Western immunoblot analyses of T. forsythia ATCC 43037 and T. forsythia UB4 wild-type and mutants. ( A ) CBB staining of crude cell extracts from T. forsythia ATCC 43037 wild-type, Δ Tanf_01245 mutant, reconstituted mutant Δ Tanf_01245 + and cross-complemented mutant Δ Tanf_01245 + TFUB4_00887 after separation on a 7.5% SDS-PA gel. The S-layer glycoproteins (labeled TfsA and TfsB) are indicated and the down-shift resulting from the loss of the Pse5Am7Gra residue can be observed in the deletion mutant and in the cross-complemented mutant, while in the reconstituted strain the bands are up-shifted again to wild-type level. The same migration profiles could be observed for T. forsythia UB4 wild-type, Δ TFUB4_00887 mutant, reconstituted mutant Δ TFUB4_00887 + and cross-complemented mutant Δ TFUB4_00887 + Tanf_01245 . PageRuler Plus Prestained Protein Ladder (Thermo Fisher Scientific) was used as a protein molecular weight marker. The S-layer glycoprotein bands were further processed for MS analyses. Western immunoblots probed with anti-TfsA antiserum ( B ) and anti-TfsB antiserum ( C ) confirmed the identity of the S-layer glycoproteins in all analyzed T. forsythia species. PageRuler Prestained Protein Ladder (Thermo Fisher Scientific) was used as a molecular weight marker.

    Journal: Glycobiology

    Article Title: A pseudaminic acid or a legionaminic acid derivative transferase is strain-specifically implicated in the general protein O-glycosylation system of the periodontal pathogen Tannerella forsythia

    doi: 10.1093/glycob/cwx019

    Figure Lengend Snippet: SDS-PAGE and Western immunoblot analyses of T. forsythia ATCC 43037 and T. forsythia UB4 wild-type and mutants. ( A ) CBB staining of crude cell extracts from T. forsythia ATCC 43037 wild-type, Δ Tanf_01245 mutant, reconstituted mutant Δ Tanf_01245 + and cross-complemented mutant Δ Tanf_01245 + TFUB4_00887 after separation on a 7.5% SDS-PA gel. The S-layer glycoproteins (labeled TfsA and TfsB) are indicated and the down-shift resulting from the loss of the Pse5Am7Gra residue can be observed in the deletion mutant and in the cross-complemented mutant, while in the reconstituted strain the bands are up-shifted again to wild-type level. The same migration profiles could be observed for T. forsythia UB4 wild-type, Δ TFUB4_00887 mutant, reconstituted mutant Δ TFUB4_00887 + and cross-complemented mutant Δ TFUB4_00887 + Tanf_01245 . PageRuler Plus Prestained Protein Ladder (Thermo Fisher Scientific) was used as a protein molecular weight marker. The S-layer glycoprotein bands were further processed for MS analyses. Western immunoblots probed with anti-TfsA antiserum ( B ) and anti-TfsB antiserum ( C ) confirmed the identity of the S-layer glycoproteins in all analyzed T. forsythia species. PageRuler Prestained Protein Ladder (Thermo Fisher Scientific) was used as a molecular weight marker.

    Article Snippet: Secondary structure predictions performed at http://bioinf.sce.carleton.ca/PCISS/start.php indicate for T. forsythia ATCC 43037 Tanf_01245 and T. forsythia UB4 TFUB4_00887, an α-helix content of 34.38% and 32.58%, a β-sheet content of 20.90% and 22.40%, respectively, and 45% turns, each.

    Techniques: SDS Page, Western Blot, Staining, Mutagenesis, Labeling, Migration, Molecular Weight, Marker, Mass Spectrometry

    Model for the biosynthesis of the species-specific portion of the T. forsythia ATCC 43037 O -glycan. Upon synthesis of the pentasaccharide core on an undP lipid carrier, the first carbohydrate residue of the species-specific glycan is a Fuc residue conferred by GtfE. The glycan is elongated with a Gal residue which is transferred by GtfL and methylated by MtfY. The assembly of the three sugar branch, consisting of a ManNAcA residue (transferred by GtfI), a ManNAcCONH 2 residue (GtfM), which is methylated by either MtfJ or MtfO, and a Pse5Am7Gra residue (transferred via GtfS), completes the synthesis of the decasaccharide.

    Journal: Frontiers in Microbiology

    Article Title: A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications

    doi: 10.3389/fmicb.2018.02008

    Figure Lengend Snippet: Model for the biosynthesis of the species-specific portion of the T. forsythia ATCC 43037 O -glycan. Upon synthesis of the pentasaccharide core on an undP lipid carrier, the first carbohydrate residue of the species-specific glycan is a Fuc residue conferred by GtfE. The glycan is elongated with a Gal residue which is transferred by GtfL and methylated by MtfY. The assembly of the three sugar branch, consisting of a ManNAcA residue (transferred by GtfI), a ManNAcCONH 2 residue (GtfM), which is methylated by either MtfJ or MtfO, and a Pse5Am7Gra residue (transferred via GtfS), completes the synthesis of the decasaccharide.

    Article Snippet: Using a gene deletion approach targeted at predicted glycosyltransferases (Gtfs) and methyltransferases encoded in this gene cluster, in combination with mass spectrometry of the protein-released O- glycans, we show that the gene cluster encodes the species-specific part of the T. forsythia ATCC 43037 decasaccharide and that this is assembled step-wise on a pentasaccharide core.

    Techniques: Methylation

    Gene arrangement of T. forsythia ATCC 43037 KLIKK proteases. (A) A GenBank (accession number: CP003191, http://www.ncbi.nlm.nih.gov/genbank ) deposited sequence, prior to re-sequencing. Arrows framed by a gray line—ORFs identified as pseudogenes; hatched and color arrows framed with a broken line - protease genes absent in the genome and with errors in the prediction of ORF N-termini, respectively. (B) Re-sequenced and corrected gene arrangement. Arrow boxes: black, genes; gray, pseudogenes; color filled, genes encoding proteases; and brown, genes encoding putative lipoproteins. Designations of the peptidase family (M, metallopeptidase; S, serine peptidase; and C, cysteine peptidase) of putative proteases are indicated below the arrows on (A) . Names of the proteases characterized with respect to expression by T. forsythia and proteolytic activity is shown in (B) . Red, metalloproteases; blue, serine proteases. HOMD: Human Oral Microbiome Taxon Description, Tannerella forsythia strain 92A2 (HOMD, http://www.homd.org ); BROP: Bioinformatics Resource for Oral Pathogens, Tannerella forsythia 92A2 (BROP, http://www.brop.org ). These sequence data have been submitted to the GenBank database under accession numbers KP715368 and KP715369.

    Journal: Frontiers in Microbiology

    Article Title: KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure

    doi: 10.3389/fmicb.2015.00312

    Figure Lengend Snippet: Gene arrangement of T. forsythia ATCC 43037 KLIKK proteases. (A) A GenBank (accession number: CP003191, http://www.ncbi.nlm.nih.gov/genbank ) deposited sequence, prior to re-sequencing. Arrows framed by a gray line—ORFs identified as pseudogenes; hatched and color arrows framed with a broken line - protease genes absent in the genome and with errors in the prediction of ORF N-termini, respectively. (B) Re-sequenced and corrected gene arrangement. Arrow boxes: black, genes; gray, pseudogenes; color filled, genes encoding proteases; and brown, genes encoding putative lipoproteins. Designations of the peptidase family (M, metallopeptidase; S, serine peptidase; and C, cysteine peptidase) of putative proteases are indicated below the arrows on (A) . Names of the proteases characterized with respect to expression by T. forsythia and proteolytic activity is shown in (B) . Red, metalloproteases; blue, serine proteases. HOMD: Human Oral Microbiome Taxon Description, Tannerella forsythia strain 92A2 (HOMD, http://www.homd.org ); BROP: Bioinformatics Resource for Oral Pathogens, Tannerella forsythia 92A2 (BROP, http://www.brop.org ). These sequence data have been submitted to the GenBank database under accession numbers KP715368 and KP715369.

    Article Snippet: Molecular cloning Genomic DNA was isolated from T. forsythia strain ATCC 43037 using the Genomic Mini System (A & A Biotechnology, Gdansk, Poland), according to the manufacturer's recommendations.

    Techniques: Sequencing, Expressing, Activity Assay

    Square S-layer lattice on a T. forsythia ATCC 43037 cell as visualized by freeze-etching and metal-shadowing.

    Journal: Interface Focus

    Article Title: Nonulosonic acids contribute to the pathogenicity of the oral bacterium Tannerella forsythia

    doi: 10.1098/rsfs.2018.0064

    Figure Lengend Snippet: Square S-layer lattice on a T. forsythia ATCC 43037 cell as visualized by freeze-etching and metal-shadowing.

    Article Snippet: By using T. forsythia ATCC 43037 wild-type cells in comparison to the S-layer-deficient ΔtfsAB mutant, Sakakibara et al. supported the evidence that the glycosylated S-layer of T. forsythia ATCC 43037 is involved in the adherence to and invasion of human epithelial cell-like gingival carcinoma cells (Ca9–22) and KB cells; this suggested that the T. forsythia S-layer plays an important role in the initiation stage of periodontal disease [ ].

    Techniques:

    Biosynthesis pathway of the T. forsythia ATCC 43037 O -glycan. Modified after [ 21 ]. (Online version in colour.)

    Journal: Interface Focus

    Article Title: Nonulosonic acids contribute to the pathogenicity of the oral bacterium Tannerella forsythia

    doi: 10.1098/rsfs.2018.0064

    Figure Lengend Snippet: Biosynthesis pathway of the T. forsythia ATCC 43037 O -glycan. Modified after [ 21 ]. (Online version in colour.)

    Article Snippet: By using T. forsythia ATCC 43037 wild-type cells in comparison to the S-layer-deficient ΔtfsAB mutant, Sakakibara et al. supported the evidence that the glycosylated S-layer of T. forsythia ATCC 43037 is involved in the adherence to and invasion of human epithelial cell-like gingival carcinoma cells (Ca9–22) and KB cells; this suggested that the T. forsythia S-layer plays an important role in the initiation stage of periodontal disease [ ].

    Techniques: Modification

    Fluorescence- in-situ -hybridization staining of fixed multispecies biofilms showing the localization of T. forsythia ATCC 43073 WT ( a ) and the NulO deficient mutant T. forsythia ATCC 43037 ΔpseC ( b ). Red: T. forsythia ; cyan: P. gingivalis ( a )/ T. denticola ( b ); green: non-hybridized cells (DNA staining YoPro-1 + Sytox). A representative area for one disc each is shown with a top view in the middle panel and side views with the biofilm–disc interface directed towards the top view. Scale bars, ( a ) 20 µm and ( b ) 15 µm. Both T. forsythia strains can be clearly detected in the form of microcolonies at the surface of the biofilm. Alteration of the surface glycosylation does not influence the bacteria's capability to grow in the multispecies consortium.

    Journal: Interface Focus

    Article Title: Nonulosonic acids contribute to the pathogenicity of the oral bacterium Tannerella forsythia

    doi: 10.1098/rsfs.2018.0064

    Figure Lengend Snippet: Fluorescence- in-situ -hybridization staining of fixed multispecies biofilms showing the localization of T. forsythia ATCC 43073 WT ( a ) and the NulO deficient mutant T. forsythia ATCC 43037 ΔpseC ( b ). Red: T. forsythia ; cyan: P. gingivalis ( a )/ T. denticola ( b ); green: non-hybridized cells (DNA staining YoPro-1 + Sytox). A representative area for one disc each is shown with a top view in the middle panel and side views with the biofilm–disc interface directed towards the top view. Scale bars, ( a ) 20 µm and ( b ) 15 µm. Both T. forsythia strains can be clearly detected in the form of microcolonies at the surface of the biofilm. Alteration of the surface glycosylation does not influence the bacteria's capability to grow in the multispecies consortium.

    Article Snippet: By using T. forsythia ATCC 43037 wild-type cells in comparison to the S-layer-deficient ΔtfsAB mutant, Sakakibara et al. supported the evidence that the glycosylated S-layer of T. forsythia ATCC 43037 is involved in the adherence to and invasion of human epithelial cell-like gingival carcinoma cells (Ca9–22) and KB cells; this suggested that the T. forsythia S-layer plays an important role in the initiation stage of periodontal disease [ ].

    Techniques: Fluorescence, In Situ Hybridization, Staining, Mutagenesis

    The percentage sequence coverage of modern and ancient known virulence factor genes; the T. forsythia 92A2 sequence was used as a reference, apart from leg when ATCC 43037 was used as a reference; and KLIKK protease genes when our in-home determined KLIKK protease locus was used as a reference [ 10 ]

    Journal: BMC Genomics

    Article Title: Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia

    doi: 10.1186/s12864-020-06810-9

    Figure Lengend Snippet: The percentage sequence coverage of modern and ancient known virulence factor genes; the T. forsythia 92A2 sequence was used as a reference, apart from leg when ATCC 43037 was used as a reference; and KLIKK protease genes when our in-home determined KLIKK protease locus was used as a reference [ 10 ]

    Article Snippet: Sequencing of the T. forsythia ATCC 43037 genome, apart from bspA (BFO_RS14480 ), revealed five more genes (BFO_RS14345 (bspB ), BFO_RS08355 , BFO_RS14330 , BFO_RS14330 , and BFO_RS14330 ) encoding putative BspA-like proteins.

    Techniques: Sequencing

    DNA sequence comparison of the  T. forsythia  reference genome to the ancient  T. forsythia  genomes and to publicly available modern  T. forsythia  genomes. The two outermost rings depict the forward and reverse coding strands of the reference genome. The next 13 rings moving towards the inner part of the figure display regions of sequence similarity detected by BLAST comparison between the DNA of the reference genome and the DNA of the 13 compared  T. forsythia  genomes. The following genome order reflects the order of the circles starting from the outer part of the figure and moving towards the inner part: PCA0332, PCA0198, UB20, PCA0088, KS16, UB4, UB22, NSLJ, G12, 3313, NSLK, ATCC 43037, and 9610. Genes associated with  T. forsythia  virulence are labeled in the plot

    Journal: BMC Genomics

    Article Title: Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia

    doi: 10.1186/s12864-020-06810-9

    Figure Lengend Snippet: DNA sequence comparison of the T. forsythia reference genome to the ancient T. forsythia genomes and to publicly available modern T. forsythia genomes. The two outermost rings depict the forward and reverse coding strands of the reference genome. The next 13 rings moving towards the inner part of the figure display regions of sequence similarity detected by BLAST comparison between the DNA of the reference genome and the DNA of the 13 compared T. forsythia genomes. The following genome order reflects the order of the circles starting from the outer part of the figure and moving towards the inner part: PCA0332, PCA0198, UB20, PCA0088, KS16, UB4, UB22, NSLJ, G12, 3313, NSLK, ATCC 43037, and 9610. Genes associated with T. forsythia virulence are labeled in the plot

    Article Snippet: Sequencing of the T. forsythia ATCC 43037 genome, apart from bspA (BFO_RS14480 ), revealed five more genes (BFO_RS14345 (bspB ), BFO_RS08355 , BFO_RS14330 , BFO_RS14330 , and BFO_RS14330 ) encoding putative BspA-like proteins.

    Techniques: Sequencing, Labeling