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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0067

PubMed

31420336, Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15.

Characterization method

bicinchoninic acid (BCA) reducing-sugar assay,enzymatic product analysis,affinity gel electrophoresis,isothermal titration calorimetry

Genomic accession number

GL891979.1

Nucelotide position range

376649-402405

Substrate

xyloglucan

Loci

HMPREF9455_00294-HMPREF9455_00304

Species

Dysgonomonas gadei/156974

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- HMPREF9455_00294 EGJ99261.1 0 - 2502 (-) GL891979.1:376649-379151 -
- HMPREF9455_00295 EGJ99262.1 2637 - 4110 (-) GL891979.1:379286-380759 -
- HMPREF9455_00296 EGJ99263.1 4197 - 6009 (-) GL891979.1:380846-382658 -
- HMPREF9455_00297 EGJ99264.1 6065 - 7709 (-) GL891979.1:382714-384358 -
- HMPREF9455_00298 EGJ99265.1 7721 - 10841 (-) GL891979.1:384370-387490 -
- HMPREF9455_00299 EGJ99266.1 10896 - 13731 (-) GL891979.1:387545-390380 -
- HMPREF9455_00300 EGJ99267.1 13941 - 18057 (+) GL891979.1:390590-394706 -
- HMPREF9455_00301 EGJ99268.1 18205 - 20566 (+) GL891979.1:394854-397215 -
- HMPREF9455_00302 EGJ99269.1 21182 - 21290 (+) GL891979.1:397831-397939 -
- HMPREF9455_00303 EGJ99270.1 21391 - 23596 (+) GL891979.1:398040-400245 -
- HMPREF9455_00304 EGJ99271.1 24164 - 25757 (+) GL891979.1:400813-402406 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2502 (-) CAZyme: GH2 Yes
- 2638 - 4110 (-) CAZyme: GH5_4|GH5 Yes
- 4198 - 6009 (-) other Yes
- 6066 - 7709 (-) TC: gnl|TC-DB|Q5LEN2|8.A.46.1.4 Yes
- 7722 - 10841 (-) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 10897 - 13731 (-) CAZyme: GH31 Yes
- 13942 - 18057 (+) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 18206 - 20566 (+) CAZyme: GH95 Yes
- 21183 - 21290 (+) other Yes
- 21392 - 23596 (+) CAZyme: GH3 Yes
- 24165 - 25757 (+) CAZyme: GH43_12 Yes

PUL ID

PUL0067

PubMed

31420336, Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15.

Title

Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity.

Author

Dejean G, Tauzin AS, Bennett SW, Creagh AL, Brumer H

Abstract

Genome sequencing has revealed substantial variation in the predicted abilities of individual species within animal gut microbiota to metabolize the complex carbohydrates comprising dietary fiber. At the same time, a currently limited body of functional studies precludes a richer understanding of how dietary glycan structures affect the gut microbiota composition and community dynamics. Here, using biochemical and biophysical techniques, we identified and characterized differences among recombinant proteins from syntenic xyloglucan utilization loci (XyGUL) of three Bacteroides and one Dysgonomonas species from the human gut, which drive substrate specificity and access to distinct polysaccharide side chains. Enzymology of four syntenic glycoside hydrolase family 5 subfamily 4 (GH5_4) endo-xyloglucanases revealed surprising differences in xyloglucan (XyG) backbone cleavage specificity, including the ability of some homologs to hydrolyze congested branched positions. Further, differences in the complement of GH43 alpha-l-arabinofuranosidases and GH95 alpha-l-fucosidases among syntenic XyGUL confer distinct abilities to fully saccharify plant species-specific arabinogalactoxyloglucan and/or fucogalactoxyloglucan. Finally, characterization of highly sequence-divergent cell surface glycan-binding proteins (SGBPs) across syntenic XyGUL revealed a novel group of XyG oligosaccharide-specific SGBPs encoded within select BacteroidesIMPORTANCE The catabolism of complex carbohydrates that otherwise escape the endogenous digestive enzymes of humans and other animals drives the composition and function of the gut microbiota. Thus, detailed molecular characterization of dietary glycan utilization systems is essential both to understand the ecology of these complex communities and to manipulate their compositions, e.g., to benefit human health. Our research reveals new insight into how ubiquitous members of the human gut microbiota have evolved a set of microheterogeneous gene clusters to efficiently respond to the structural variations of plant xyloglucans. The data here will enable refined functional prediction of xyloglucan utilization among diverse environmental taxa in animal guts and beyond.