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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0221

PubMed

24223817, PLoS One. 2013 Nov 5;8(11):e78507. doi: 10.1371/journal.pone.0078507. eCollection 2013.

Characterization method

fosmid library screen

Genomic accession number

KC246798.1

Nucelotide position range

14700-34417

Substrate

cellulose

Loci

AHF24576.1-AHF24585.1

Species

uncultured bacterium Contig1529/1393449

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - AHF24576.1 0 - 1761 (-) KC246798.1:14700-16461 -
- - AHF24577.1 1765 - 3097 (-) KC246798.1:16465-17797 -
- - AHF24578.1 3117 - 4506 (-) KC246798.1:17817-19206 -
- - AHF24579.1 4883 - 6794 (+) KC246798.1:19583-21494 -
- - AHF24580.1 6843 - 9081 (+) KC246798.1:21543-23781 -
- - AHF24581.1 9686 - 11261 (-) KC246798.1:24386-25961 -
- - AHF24582.1 11377 - 13099 (-) KC246798.1:26077-27799 -
- - AHF24583.1 13143 - 14862 (-) KC246798.1:27843-29562 -
- - AHF24584.1 14891 - 17690 (-) KC246798.1:29591-32390 -
- - AHF24585.1 17726 - 19718 (-) KC246798.1:32426-34418 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1761 (-) CAZyme: GH35 Yes
- 1766 - 3097 (-) other Yes
- 3118 - 4506 (-) CAZyme: GH105 Yes
- 4884 - 6794 (+) other Yes
- 6844 - 9081 (+) CAZyme: GH3 Yes
- 9687 - 11261 (-) CAZyme: GH5_4 Yes
- 11378 - 13099 (-) other Yes
- 13144 - 14862 (-) other Yes
- 14892 - 17690 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 17727 - 19718 (-) CDS No

PUL ID

PUL0221

PubMed

24223817, PLoS One. 2013 Nov 5;8(11):e78507. doi: 10.1371/journal.pone.0078507. eCollection 2013.

Title

Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows.

Author

Wang L, Hatem A, Catalyurek UV, Morrison M, Yu Z

Abstract

The ruminal microbial community is a unique source of enzymes that underpin the conversion of cellulosic biomass. In this study, the microbial consortia adherent on solid digesta in the rumen of Jersey cattle were subjected to an activity-based metagenomic study to explore the genetic diversity of carbohydrolytic enzymes in Jersey cows, with a particular focus on cellulases and xylanases. Pyrosequencing and bioinformatic analyses of 120 carbohydrate-active fosmids identified genes encoding 575 putative Carbohydrate-Active Enzymes (CAZymes) and proteins putatively related to transcriptional regulation, transporters, and signal transduction coupled with polysaccharide degradation and metabolism. Most of these genes shared little similarity to sequences archived in databases. Genes that were predicted to encode glycoside hydrolases (GH) involved in xylan and cellulose hydrolysis (e.g., GH3, 5, 9, 10, 39 and 43) were well represented. A new subfamily (S-8) of GH5 was identified from contigs assigned to Firmicutes. These subfamilies of GH5 proteins also showed significant phylum-dependent distribution. A number of polysaccharide utilization loci (PULs) were found, and two of them contained genes encoding Sus-like proteins and cellulases that have not been reported in previous metagenomic studies of samples from the rumens of cows or other herbivores. Comparison with the large metagenomic datasets previously reported of other ruminant species (or cattle breeds) and wallabies showed that the rumen microbiome of Jersey cows might contain differing CAZymes. Future studies are needed to further explore how host genetics and diets affect the diversity and distribution of CAZymes and utilization of plant cell wall materials.