Journal: Scientific Reports

Article Title: Probiotics in human gut microbiota can degrade host glycosaminoglycans

doi: 10.1038/s41598-018-28886-w

Figure Lengend Snippet: List of bacteria used in this study and their preculture condition.

Article Snippet: Specific primers of the Bacteroides UGL gene were designed based on the nucleotide sequences of genes coding for five Bacteroides UGLs (Bache_1615 of B. helcogenes P 36–108, BT3348 of B. thetaiotaomicron VPI-5482, BXY_37650 of Bacteroides xylanisolvens XBIA, BF0331 of Bacteroides fragilis NCTC 9343 and BVU_0115 of B. vulgatus ATCC 8482) (Table ).

Techniques: Bacteria

Journal: Biomolecules

Article Title: A Combination of Structural, Genetic, Phenotypic and Enzymatic Analyses Reveals the Importance of a Predicted Fucosyltransferase to Protein O -Glycosylation in the Bacteroidetes

doi: 10.3390/biom11121795

Figure Lengend Snippet: ( A ) Cladogram of the FucT orthologs in diverse species of the Bacteroidetes phylum. The maximum likelihood tree with the highest log likelihood (−9554.64) is shown, with initial trees generated using the Neighbor-Join and BioNJ methods applied to a JTT matrix-based model of pairwise distances. The branch lengths of the tree indicate the number of substitutions per site (35 amino acid sequences comprising 359 positions). The tree was produced using MEGA X . ( B ) Amino acid sequence alignment of T. forsythia Tanf_01305 (KKY62509.1), B. fragilis BF4306 (CAH09973.1), and P. heparinus Phep_4048 (ACU06239.1) illustrates the sequence similarity for compared sequences. The conserved DXD-motif typical of glycosyltransferases is indicated within a black box, and predicted metal binding sites are written in boldface. Amino acids identical in all three proteins are indicated with *. The alignment was calculated with the software Clustal Omega ( www.ebi.ac.uk/Tools/msa/clustalo ; accessed on 1 July 2021).

Article Snippet: Two predicted FucT orthologs (BF4306, B. fragilis NCTC 9343 NC_003228: 5112881..5113649; Tanf_01305, T. forsythia ATCC 43037 NZ_JUET01000030: 51799..52566) were used to query this database using blastp, and the best hits from each genome to each query by bitscore were retained.

Techniques: Generated, Produced, Sequencing, Binding Assay, Software

Journal: Biomolecules

Article Title: A Combination of Structural, Genetic, Phenotypic and Enzymatic Analyses Reveals the Importance of a Predicted Fucosyltransferase to Protein O -Glycosylation in the Bacteroidetes

doi: 10.3390/biom11121795

Figure Lengend Snippet: Comparison of the O -linked glycan structures from B. fragilis wild-type (this study), B. fragilis Δ BF4306 (this study) , B. fragilis Δ gmd-fcl Δ fkp , T. forsythia wild-type , T. forsythia Δ Tanf_01305 , and T. forsythia Δ fcl (this study). The severe truncation of the glycans upon deletion of the fucT or the fcl gene is indicated in grey. Glycan structures are drawn according to the symbol nomenclature of glycans SNFG .

Article Snippet: Two predicted FucT orthologs (BF4306, B. fragilis NCTC 9343 NC_003228: 5112881..5113649; Tanf_01305, T. forsythia ATCC 43037 NZ_JUET01000030: 51799..52566) were used to query this database using blastp, and the best hits from each genome to each query by bitscore were retained.

Techniques: Comparison, Glycoproteomics

Journal: Biomolecules

Article Title: A Combination of Structural, Genetic, Phenotypic and Enzymatic Analyses Reveals the Importance of a Predicted Fucosyltransferase to Protein O -Glycosylation in the Bacteroidetes

doi: 10.3390/biom11121795

Figure Lengend Snippet: ( A ) Analysis of crude cell extracts from T. forsythia ATCC 43037 wild-type, the FucT-deficient mutant (Δ Tanf_01305 ) and cross-complemented strains ( ΔTanf_01305 + BF4306 ; ΔTanf_01305 + Phep_4048 ) after separation on 7.5% SDS-PAGE gels. Top panels—CBB staining of the S-layer glycoproteins (labeled TfsA and TfsB) showing the downshifts resulting from glycan truncation in the mutant. S-layer glycoprotein bands were further processed for MS analyses. Bottom panels—same samples processed for Western immunoblot analysis probed with a α-TfsA and α-TfsB antiserum, respectively. PageRuler Plus Prestained Protein Ladder (Thermo Fisher Scientific) was used as a protein molecular weight marker. ( B ) Western immunoblot analyses of crude cell extracts from B. fragilis wild-type, the FucT-deficient mutant (Δ BF4306 ) and cross-complemented strains (Δ BF4306 + Phep_4048 ; Δ BF4306 + Tanf_01305 ) probed with α-BF2494 antiserum. ( C ) ESI-MS sum spectra of β-eliminated TfsB O -glycans from T. forsythia wild-type, Δ Tanf_01305 and cross-complemented strains. The glycan structures of the signals corresponding to the largest mass (bold m / z values) are drawn according to the symbol nomenclature of glycans SNFG . O -glycan signals detected for the mutant and cross-complemented strains were assigned based on the m / z mass differences corresponding to the loss of individual sugar units and/or modifications. Peak intensities are shown on the y axis.

Article Snippet: Two predicted FucT orthologs (BF4306, B. fragilis NCTC 9343 NC_003228: 5112881..5113649; Tanf_01305, T. forsythia ATCC 43037 NZ_JUET01000030: 51799..52566) were used to query this database using blastp, and the best hits from each genome to each query by bitscore were retained.

Techniques: Mutagenesis, SDS Page, Staining, Labeling, Glycoproteomics, Western Blot, Molecular Weight, Marker