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PlantCAZyme
Cite: NAR/gkaa742 2020

Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL General Information

Literature Information

PUL ID

PUL0763

PubMed

39636128, Appl Environ Microbiol. 2025 Jan 31;91(1):e0175924. doi: 10.1128/aem.01759-24. Epub 2024 Dec 5.

Characterization method

RNA-seq,qRT-PCR,gas chromatography,mass spectrometry,thin-layer chromatography

Genomic accession number

NZ_CP102288.1

Nucelotide position range

3309626-3319524

Substrate

Hemicellulose

Loci

NQ544_13890-NQ544_13915

Species

Segatella copri DSM 18205/537011

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- NQ544_RS13890 WP_040553739.1 0 - 1911 (-) NZ_CP102288.1:3309626-3311537 -
- NQ544_RS13895 WP_006849123.1 2272 - 2431 (+) NZ_CP102288.1:3311898-3312057 -
- NQ544_RS13900 WP_006849124.1 2549 - 5066 (+) NZ_CP102288.1:3312175-3314692 -
- NQ544_RS13905 WP_208855011.1 5109 - 5784 (+) NZ_CP102288.1:3314735-3315410 -
- NQ544_RS13910 - 5804 - 7295 (+) NZ_CP102288.1:3315430-3316921 -
- NQ544_RS13915 WP_006849128.1 7361 - 9899 (+) NZ_CP102288.1:3316987-3319525 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1911 (-) CAZyme: CE6|CE1 No
- 2273 - 2431 (+) CDS No
- 2550 - 5066 (+) CAZyme: GH43_2|CBM6|GH8 No
- 5110 - 5784 (+) CDS No
- 7362 - 9899 (+) CAZyme: GH31_4 No

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PUL ID

PUL0763

PubMed

39636128, Appl Environ Microbiol. 2025 Jan 31;91(1):e0175924. doi: 10.1128/aem.01759-24. Epub 2024 Dec 5.

Title

Transcriptional delineation of polysaccharide utilization loci in the human gut commensal Segatella copri DSM18205 and co-culture with exemplar Bacteroides species on dietary plant glycans.

Author

Panwar D, Briggs J, Fraser ASC, Stewart WA, Brumer H

Abstract

There is growing interest in members of the genus Segatella (family Prevotellaceae) as members of a well-balanced human gut microbiota (HGM). Segatella are particularly associated with the consumption of a diet rich in plant polysaccharides comprising dietary fiber. However, understanding of the molecular basis of complex carbohydrate utilization in Segatella species is currently incomplete. Here, we used RNA sequencing (RNA-seq) of the type strain Segatella copri DSM 18205 (previously Prevotella copri CB7) to define precisely individual polysaccharide utilization loci (PULs) and associated carbohydrate-active enzymes (CAZymes) that are implicated in the catabolism of common fruit, vegetable, and grain polysaccharides (viz. mixed-linkage beta-glucans, xyloglucans, xylans, pectins, and inulin). Although many commonalities were observed, several of these systems exhibited significant compositional and organizational differences vis-a-vis homologs in the better-studied Bacteroides (sister family Bacteroidaceae), which predominate in post-industrial HGM. Growth on beta-mannans, beta(1, 3)-galactans, and microbial beta(1, 3)-glucans was not observed, due to an apparent lack of cognate PULs. Most notably, S. copri is unable to grow on starch, due to an incomplete starch utilization system (Sus). Subsequent transcriptional profiling of bellwether Ton-B-dependent transporter-encoding genes revealed that PUL upregulation is rapid and general upon transfer from glucose to plant polysaccharides, reflective of de-repression enabling substrate sensing. Distinct from previous observations of Bacteroides species, we were unable to observe clearly delineated substrate prioritization on a polysaccharide mixture designed to mimic in vitro diverse plant cell wall digesta. Finally, co-culture experiments generally indicated stable co-existence and lack of exclusive competition between S. copri and representative HGM Bacteroides species (Bacteroides thetaiotaomicron and Bacteroides ovatus) on individual polysaccharides, except in cases where corresponding PULs were obviously lacking. IMPORTANCE: There is currently a great level of interest in improving the composition and function of the human gut microbiota (HGM) to improve health. The bacterium Segatella copri is prevalent in people who eat plant-rich diets and is therefore associated with a healthy lifestyle. On one hand, our study reveals the specific molecular systems that enable S. copri to proliferate on individual plant polysaccharides. On the other, a growing body of data suggests that the inability of S. copri to grow on starch and animal glycans, which dominate in post-industrial diets, as well as host mucin, contributes strongly to its displacement from the HGM by Bacteroides species, in the absence of direct antagonism.