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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0406

PubMed

30315317, ISME J. 2019 Mar;13(3):603-617. doi: 10.1038/s41396-018-0290-y. Epub 2018 Oct 12.

Characterization method

high performance anion exchange chromatography

Genomic accession number

NZ_PXJC01000002.1

Nucelotide position range

246468-268868

Substrate

beta-glucan

Loci

DCP27_RS03160-DCP27_RS03265

Species

Coprothermobacter proteolyticus/35786

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- DCP27_RS03160 WP_004103201.1 0 - 738 (+) NZ_PXJC01000002.1:246468-247206 -
- DCP27_RS03165 WP_011994745.1 749 - 1523 (+) NZ_PXJC01000002.1:247217-247991 -
- DCP27_RS03170 WP_004103205.1 1516 - 2323 (+) NZ_PXJC01000002.1:247984-248791 -
- DCP27_RS03175 WP_107689620.1 2396 - 3410 (-) NZ_PXJC01000002.1:248864-249878 -
- DCP27_RS03180 WP_011994743.1 3459 - 4326 (-) NZ_PXJC01000002.1:249927-250794 -
- DCP27_RS03185 WP_004103212.1 4346 - 6491 (-) NZ_PXJC01000002.1:250814-252959 -
- DCP27_RS03190 WP_004103000.1 6524 - 6674 (-) NZ_PXJC01000002.1:252992-253142 -
- DCP27_RS03195 WP_003520679.1 6677 - 7211 (+) NZ_PXJC01000002.1:253145-253679 -
- DCP27_RS03200 WP_107689621.1 7207 - 9679 (+) NZ_PXJC01000002.1:253675-256147 -
- DCP27_RS03205 WP_004103217.1 9760 - 10171 (+) NZ_PXJC01000002.1:256228-256639 -
- DCP27_RS03210 WP_009052873.1 10167 - 10869 (+) NZ_PXJC01000002.1:256635-257337 -
- DCP27_RS03215 WP_004103221.1 11000 - 11231 (+) NZ_PXJC01000002.1:257468-257699 -
- DCP27_RS03220 WP_056975874.1 11283 - 12843 (+) NZ_PXJC01000002.1:257751-259311 -
- DCP27_RS03225 WP_009052871.1 12812 - 13265 (+) NZ_PXJC01000002.1:259280-259733 -
- DCP27_RS03230 WP_011994748.1 13266 - 14838 (+) NZ_PXJC01000002.1:259734-261306 -
- DCP27_RS03235 WP_107689622.1 15154 - 15529 (+) NZ_PXJC01000002.1:261622-261997 -
cadA DCP27_RS03240 WP_107689623.1 15542 - 17915 (+) NZ_PXJC01000002.1:262010-264383 3.6.3.3
lspA DCP27_RS03245 WP_107689624.1 18001 - 18466 (+) NZ_PXJC01000002.1:264469-264934 3.4.23.36
- DCP27_RS03250 WP_107689625.1 18623 - 19109 (+) NZ_PXJC01000002.1:265091-265577 -
- DCP27_RS03255 WP_058257212.1 19776 - 20355 (+) NZ_PXJC01000002.1:266244-266823 -
- DCP27_RS03260 WP_058259154.1 20393 - 20849 (+) NZ_PXJC01000002.1:266861-267317 -
- DCP27_RS03265 WP_107689626.1 21162 - 22401 (-) NZ_PXJC01000002.1:267630-268869 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 738 (+) TC: gnl|TC-DB|Q0W8T7|3.A.1.144.2 Yes
- 750 - 1523 (+) other Yes
- 1517 - 2323 (+) other Yes
- 2397 - 3410 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 3460 - 4326 (-) CAZyme: GH16 Yes
- 4347 - 6491 (-) CAZyme: GH3 Yes
- 7208 - 9679 (+) CAZyme: GH18 Yes
- 9761 - 10171 (+) TC: gnl|TC-DB|A9BFJ4|1.E.19.1.7 Yes
- 10168 - 10869 (+) other Yes
- 11001 - 11231 (+) other Yes
- 11284 - 12843 (+) other Yes
- 12813 - 13265 (+) other Yes
- 13267 - 14838 (+) other Yes
- 15155 - 15529 (+) TF: DBD-Pfam|HTH_5,DBD-SUPERFAMILY|0043095 Yes
cadA 15543 - 17915 (+) TC: gnl|TC-DB|O32219|3.A.3.6.10 Yes
lspA 18002 - 18466 (+) TC: gnl|TC-DB|B8I766|9.B.105.1.5 Yes
- 18624 - 19109 (+) CDS No
- 19777 - 20355 (+) CDS No
- 20394 - 20849 (+) CDS No
- 21163 - 22401 (-) CDS No

PUL ID

PUL0406

PubMed

30315317, ISME J. 2019 Mar;13(3):603-617. doi: 10.1038/s41396-018-0290-y. Epub 2018 Oct 12.

Title

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus.

Author

Kunath BJ, Delogu F, Naas AE, Arntzen MO, Eijsink VGH, Henrissat B, Hvidsten TR, Pope PB

Abstract

Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C. proteolyticus. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whereas in parallel two novel strains of C. proteolyticus were successfully isolated and sequenced. Annotation of all C. proteolyticus genotypes (two strains and one MAG) revealed their genetic acquisition of carbohydrate-active enzymes (CAZymes), presumably derived from horizontal gene transfer (HGT) events involving polysaccharide-degrading Firmicutes or Thermotogae-affiliated populations that are historically co-located. HGT material included a saccharolytic operon, from which a CAZyme was biochemically characterized and demonstrated hydrolysis of multiple hemicellulose polysaccharides. Finally, temporal genome-resolved metatranscriptomic analysis of SEM1b revealed expression of C. proteolyticus CAZymes at different SEM1b life stages as well as co-expression of CAZymes from multiple SEM1b populations, inferring deeper microbial interactions that are dedicated toward community degradation of cellulose and hemicellulose. We show that C. proteolyticus, a ubiquitous population, consists of closely related strains that have adapted via HGT to presumably degrade both oligo- and longer polysaccharides present in decaying plants and microbial cell walls, thus explaining its dominance in thermophilic anaerobic digesters on a global scale.