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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0456

PubMed

20622018, J Biol Chem. 2010 Sep 24;285(39):30261-73. doi: 10.1074/jbc.M110.141788. Epub 2010 Jul 9.

Characterization method

microarray,RNA-Seq

Genomic accession number

ADWO01000021.1,ADWO01000020.1

Nucelotide position range

1-5954,1-18196

Substrate

xylan

Loci

PBR_RS03345-PBR_RS03360+PBR_RS02950-PBR_RS02990

Species

Prevotella bryantii/77095

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- PBR_RS03345 WP_008760065.1 0 - 2566 (-) ADWO01000021.1:1-2566 -
- PBR_RS03350 WP_006281697.1 2592 - 3966 (-) ADWO01000021.1:2593-3966 -
- PBR_RS03355 WP_006281698.1 4100 - 5009 (+) ADWO01000021.1:4101-5009 -
- PBR_RS03360 WP_155815414.1 5297 - 5954 (+) ADWO01000021.1:5298-5954 -
- PBR_RS02950 WP_162091544.1 5954 - 6597 (-) ADWO01000020.1:1-641 -
- PBR_RS02955 WP_006281618.1 6606 - 9741 (-) ADWO01000020.1:653-3787 -
- PBR_RS14860 WP_094448662.1 10344 - 11907 (-) ADWO01000020.1:4391-6748 -
- PBR_RS02965 WP_039869720.1 12973 - 17080 (+) ADWO01000020.1:7059-11126 -
- PBR_RS02970 WP_006281621.1 17228 - 18188 (-) ADWO01000020.1:11275-12234 -
- PBR_RS02975 WP_039869723.1 18270 - 19380 (-) ADWO01000020.1:12317-13393 -
- PBR_RS02980 WP_006281623.1 19411 - 20809 (-) ADWO01000020.1:13458-14855 -
- PBR_RS02985 WP_039869725.1 20811 - 21996 (-) ADWO01000020.1:14858-16015 -
- PBR_RS02990 WP_006281625.1 22260 - 24150 (+) ADWO01000020.1:16307-18196 -

Cluster number

2

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2566 (-) CDS No
- 2593 - 3966 (-) TC: gnl|TC-DB|P96710|2.A.1.1.55 Yes (cluster 1)
- 4101 - 5009 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes (cluster 1)
- 5298 - 5954 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes (cluster 1)
- 5955 - 6597 (-) other Yes (cluster 1)
- 6607 - 9741 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes (cluster 1)
- 10345 - 11907 (-) CAZyme: CE6|GH43_10|GH43 Yes (cluster 1)
- 12974 - 17080 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No
- 17229 - 18188 (-) CAZyme: GH43_1|GH43 Yes (cluster 2)
- 18271 - 19380 (-) CAZyme: GH10 Yes (cluster 2)
- 19412 - 20809 (-) TC: gnl|TC-DB|P94488|2.A.2.3.2 Yes (cluster 2)
- 20812 - 21996 (-) other Yes (cluster 2)
- 22261 - 24150 (+) CAZyme: GH67 Yes (cluster 2)

PUL ID

PUL0456

PubMed

20622018, J Biol Chem. 2010 Sep 24;285(39):30261-73. doi: 10.1074/jbc.M110.141788. Epub 2010 Jul 9.

Title

Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes.

Author

Dodd D, Moon YH, Swaminathan K, Mackie RI, Cann IK

Abstract

Enzymatic depolymerization of lignocellulose by microbes in the bovine rumen and the human colon is critical to gut health and function within the host. Prevotella bryantii B(1)4 is a rumen bacterium that efficiently degrades soluble xylan. To identify the genes harnessed by this bacterium to degrade xylan, the transcriptomes of P. bryantii cultured on either wheat arabinoxylan or a mixture of its monosaccharide components were compared by DNA microarray and RNA sequencing approaches. The most highly induced genes formed a cluster that contained putative outer membrane proteins analogous to the starch utilization system identified in the prominent human gut symbiont Bacteroides thetaiotaomicron. The arrangement of genes in the cluster was highly conserved in other xylanolytic Bacteroidetes, suggesting that the mechanism employed by xylan utilizers in this phylum is conserved. A number of genes encoding proteins with unassigned function were also induced on wheat arabinoxylan. Among these proteins, a hypothetical protein with low similarity to glycoside hydrolases was shown to possess endoxylanase activity and subsequently assigned to glycoside hydrolase family 5. The enzyme was designated PbXyn5A. Two of the most similar proteins to PbXyn5A were hypothetical proteins from human colonic Bacteroides spp., and when expressed each protein exhibited endoxylanase activity. By using site-directed mutagenesis, we identified two amino acid residues that likely serve as the catalytic acid/base and nucleophile as in other GH5 proteins. This study therefore provides insights into capture of energy by xylanolytic Bacteroidetes and the application of their enzymes as a resource in the biofuel industry.