Journal: The Journal of biological chemistry

Article Title: Biochemical and structural basis of sialic acid utilization by gut microbes.

doi: 10.1016/j.jbc.2023.102989

Figure Lengend Snippet: Figure 3. Structural characteristics of sialic acid catabolic enzymes from gut bacteria. A, crystal structure of B. thetaiotaomicron VPI-5482 sialidase with catalytic domain in teal and proposed CBM40 domain in wheat (PDB 4BBW). The active site is indicated by a red sphere. Close-up of the active site shows the catalytic residues in orange and the arginine triad in green. In gray is the aligned crystal structure of S. pneumoniae NanA (PDB 2YA5) with sialic acid bound in yellow. B, composite structure of R. gnavus IT-sialidase RgNanH. The catalytic domain in complex with 2,7-anhydro-Neu5Ac and inserted domain, pink and light blue, respectively (PDB 4X4A), and in green the CBM40 domain in complex with 2,3-sialyllactose (PDB 6ER3). The resi- dues responsible for reaction specificity are highlighted with a yellow surface. The VPI-5482 sialidase is aligned in teal for comparison. C, 9-O- acetylesterase from P. vulgatus (PDB: 7PZG). The SGNH motif is highlighted with a pink surface and the canonical catalytic in orange in the active-site close-up. PDB, Protein Data Bank.

Article Snippet: Both ATCC 29149 and ATCC 35913 strains R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source (131).

Techniques: Bacteria, Comparison

Journal: The Journal of biological chemistry

Article Title: Biochemical and structural basis of sialic acid utilization by gut microbes.

doi: 10.1016/j.jbc.2023.102989

Figure Lengend Snippet: Figure 5. Schematic representation of the sialic acid metabolic path- ways identified in gut bacteria. A, E. coli Neu5Ac metabolism. B, B. fragilis Neu5Ac metabolism. C, R. gnavus 2,7-anhydro-Neu5Ac metabolism. Differ- ence in the pathways are highlighted: orange, 2,7-anhydro-Neu5Ac meta- bolic pathway; green, “E. coli” Neu5Ac metabolic pathway; blue, B. fragilis Neu5Ac metabolic pathway.

Article Snippet: Both ATCC 29149 and ATCC 35913 strains R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source (131).

Techniques: Bacteria

Journal: The Journal of biological chemistry

Article Title: Biochemical and structural basis of sialic acid utilization by gut microbes.

doi: 10.1016/j.jbc.2023.102989

Figure Lengend Snippet: Figure 6. Structural characteristics of 2,7-anhydro-Neu-5Ac metabolic enzymes. Once transported inside R. gnavus ATCC 29149 cells (A) RgNanOx converts 2,7-anhydro-Neu5Ac into Neu5Ac with the aid of an NAD cofactor. The NAD cofactor and a bound citrate molecule are shown in yellow and green, respectively (PDB 6Z3C). B, Neu5Ac is subsequently converted to ManNAc and pyruvate by RgNanA. Neu5Ac in its open-chain ketone form is shown bound in the active site with catalytic residues in green (PDB 6RD1). For clarity, the surface representation has been omitted from the active site due to its buried nature. PDB, Protein Data Bank.

Article Snippet: Both ATCC 29149 and ATCC 35913 strains R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source (131).

Techniques:

Journal:

Article Title: Ruminococcin A, a New Lantibiotic Produced by a Ruminococcus gnavu s Strain Isolated from Human Feces

doi: 10.1128/AEM.67.9.4111-4118.2001

Figure Lengend Snippet: Bacterial strains: sensitivity to RumA and metronidazole a

Article Snippet: Other strains were from culture collections: ATCC (American Type Culture Collection, Manassas, Va.), CIP (Collection Institut Pasteur, Paris, France), NCTC (National Collection of Type Cultures, London, United Kingdom), and VPI (Virginia Polytechnic Institute, Blacksburg). table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Species Strain Culture medium MIC (μg/ml) of agent: Prepurified RumA Metronidazole Bacteroides putredenis ATCC 29800 BHI-YH NI ∗ 3.0 Bacteroides thetaiotaomicron ATCC 29148 BHI-YH NI ∗ 12.5 Bacteroides vulgatus ATCC 8482 BHI-YH 600 12.5 Bacteroides fragilis ATCC 25285 BHI-YH NI ∗ NI ∗∗ Bifidobacterium adolescentis ATCC 15703 BHI-YH 150 NI ∗∗ Bifidobacterium breve ATCC 15700 BHI-YH 300 NI ∗∗ Bifidobacterium catenulatum ATCC 27539 BHI-YH 150 NI ∗∗ B. longum ATCC 15707 BHI-YH 75 NI ∗∗ Enterococcus faecalis CIP 76117 BHI-YH NI ∗ NT Eubacterium contortum ATCC 25540 BHI-YH 32.5 1.5 Ruminococcus obeum ATCC 29174 BHI-YH 32.5 1.5 R. torques ATCC 27756 BHI-YH 300 NT R. gnavus ATCC 29149 BHI-YH 75 12.5 C. nexile ATCC 27757 BHI-YH 150 3.0 C. oroticum ATCC 13619 BHI-YH 600 6.25 C. perfringens CpA BHI-YH 75 25 C. difficile serogroup A B-1 BHI-YH 75 6.25 C. difficile serogroup C C253 BHI-YH 75 6.25 C. difficile serogroup D ATCC 43598 BHI-YH 150 6.25 C. difficile serogroup F M-1 BHI-YH 150 12.5 C. difficile serogroup S3 79685 BHI-YH 75 6.25 C. difficile ATCC 43255 BHI-YH 150 6.25 C. botulinum type A CIP 38 TGY 75 NT C. botulinum type B NCTC 7273 TGY 75 NT C. botulinum type E NCTC 8266 TGY 75 NT C. sordellii VPI 9048 BHI-YH 150 NT C. bifermentans NCTC 506 BHI-YH 75 NT C. septicum ATCC 12464 BHI-YH 150 NT C. sporogenes ATCC 19404 BHI-YH 300 NT B. cereus Z4222, TZ415 J agar 75 NT B. cereus Z4234, K1231, P2101 J agar 150 NT B. cereus K1166, L2104, P2174, Z421, P21S J agar NI ∗ NT Open in a separate window a In this test, a Sep-pack-purified RumA containing 600 μg of total protein per ml was used.

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