PUL ID

PUL0530

PubMed

22205877, PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.

Characterization method

microarray, qPCR

Genomic accession number

AE015928.1

Nucelotide position range

1194776-1298373

Substrate

rhamnogalacturonan

Loci

BT0977-BT1030

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_0977 AAO76084.1 0 - 252 (-) AE015928.1:1194776-1195028 -
- BT_0978 AAO76085.1 334 - 826 (-) AE015928.1:1195110-1195602 -
- BT_0979 AAO76086.1 1062 - 4158 (-) AE015928.1:1195838-1198934 -
- BT_0980 AAO76087.1 4225 - 5908 (-) AE015928.1:1199001-1200684 -
- BT_0981 AAO76088.1 5971 - 10390 (-) AE015928.1:1200747-1205166 -
- BT_0982 AAO76089.1 10647 - 10899 (-) AE015928.1:1205423-1205675 -
- BT_0983 AAO76090.1 11128 - 13777 (-) AE015928.1:1205904-1208553 -
- BT_0984 AAO76091.1 13805 - 16217 (-) AE015928.1:1208581-1210993 -
- BT_0985 AAO76092.1 16226 - 17660 (-) AE015928.1:1211002-1212436 -
- BT_0986 AAO76093.1 17662 - 20980 (-) AE015928.1:1212438-1215756 -
- BT_0987 AAO76094.1 21103 - 22618 (-) AE015928.1:1215879-1217394 -
- BT_0988 AAO76095.1 22781 - 25433 (-) AE015928.1:1217557-1220209 -
- BT_0989 AAO76096.1 25553 - 26921 (-) AE015928.1:1220329-1221697 -
- BT_0990 AAO76097.1 26917 - 27604 (-) AE015928.1:1221693-1222380 -
- BT_0991 AAO76098.1 27666 - 28143 (+) AE015928.1:1222442-1222919 -
- BT_0992 AAO76099.1 28164 - 31017 (-) AE015928.1:1222940-1225793 -
- BT_0993 AAO76100.1 31068 - 34347 (-) AE015928.1:1225844-1229123 -
- BT_0994 AAO76101.1 34702 - 36202 (+) AE015928.1:1229478-1230978 -
- BT_0995 AAO76102.1 36198 - 37044 (-) AE015928.1:1230974-1231820 -
- BT_0996 AAO76103.1 37257 - 41514 (-) AE015928.1:1232033-1236290 -
- BT_0997 AAO76104.1 41626 - 44248 (-) AE015928.1:1236402-1239024 -
- BT_0998 AAO76105.1 44545 - 46978 (+) AE015928.1:1239321-1241754 -
- BT_0999 AAO76106.1 47017 - 47563 (+) AE015928.1:1241793-1242339 -
- BT_1000 AAO76107.1 48045 - 50454 (-) AE015928.1:1242821-1245230 -
- BT_1001 AAO76108.1 50659 - 52849 (-) AE015928.1:1245435-1247625 -
- BT_1002 AAO76109.1 52869 - 54729 (-) AE015928.1:1247645-1249505 -
- BT_1003 AAO76110.1 54748 - 56845 (-) AE015928.1:1249524-1251621 -
- BT_1004 AAO76111.1 56980 - 57754 (-) AE015928.1:1251756-1252530 -
- BT_1005 AAO76112.1 58167 - 58425 (+) AE015928.1:1252943-1253201 -
- BT_1006 AAO76113.1 58451 - 59180 (-) AE015928.1:1253227-1253956 -
- BT_1007 AAO76114.1 59413 - 60205 (-) AE015928.1:1254189-1254981 -
- BT_1008 AAO76115.1 60271 - 61060 (-) AE015928.1:1255047-1255836 -
- BT_1009 AAO76116.1 61065 - 62004 (-) AE015928.1:1255841-1256780 -
- BT_1010 AAO76117.1 62286 - 64761 (+) AE015928.1:1257062-1259537 -
- BT_1011 AAO76118.1 64774 - 65977 (+) AE015928.1:1259550-1260753 -
- BT_1012 AAO76119.1 66013 - 67465 (+) AE015928.1:1260789-1262241 -
- BT_1013 AAO76120.1 67457 - 71330 (+) AE015928.1:1262233-1266106 -
- BT_1014 AAO76121.1 71408 - 72929 (-) AE015928.1:1266184-1267705 -
- BT_1015 AAO76122.1 73480 - 74368 (+) AE015928.1:1268256-1269144 -
- BT_1016 AAO76123.1 74355 - 75138 (-) AE015928.1:1269131-1269914 -
- BT_1017 AAO76124.1 75308 - 77270 (-) AE015928.1:1270084-1272046 -
- BT_1018 AAO76125.1 77307 - 78645 (-) AE015928.1:1272083-1273421 -
- BT_1019 AAO76126.1 78681 - 81453 (-) AE015928.1:1273457-1276229 -
- BT_1020 AAO76127.1 81575 - 84905 (-) AE015928.1:1276351-1279681 -
- BT_1021 AAO76128.1 84956 - 85808 (-) AE015928.1:1279732-1280584 -
- BT_1022 AAO76129.1 86129 - 86798 (-) AE015928.1:1280905-1281574 -
- BT_1023 AAO76130.1 86871 - 88611 (-) AE015928.1:1281647-1283387 -
- BT_1024 AAO76131.1 88837 - 91135 (-) AE015928.1:1283613-1285911 -
- BT_1025 AAO76132.1 91121 - 94430 (-) AE015928.1:1285897-1289206 -
- BT_1026 AAO76133.1 94462 - 95908 (-) AE015928.1:1289238-1290684 -
- BT_1027 AAO76134.1 96000 - 96186 (-) AE015928.1:1290776-1290962 -
- BT_1028 AAO76135.1 96556 - 98731 (-) AE015928.1:1291332-1293507 -
- BT_1029 AAO76136.1 98784 - 102093 (-) AE015928.1:1293560-1296869 -
- BT_1030 AAO76137.1 102122 - 103598 (-) AE015928.1:1296898-1298374 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 252 (-) CDS No
- 335 - 826 (-) STP: STP|Sigma70_r2,STP|Sigma70_r4_2 No
- 1063 - 4158 (-) CDS No
- 4226 - 5908 (-) CAZyme: PL1|CE8|PL1_2 Yes
- 5972 - 10390 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 10648 - 10899 (-) other Yes
- 11129 - 13777 (-) CAZyme: GH2 Yes
- 13806 - 16217 (-) CAZyme: GH139 Yes
- 16227 - 17660 (-) other Yes
- 17663 - 20980 (-) CAZyme: GH106 Yes
- 21104 - 22618 (-) other Yes
- 22782 - 25433 (-) TC: gnl|TC-DB|P36640|3.A.3.4.1 Yes
- 25554 - 26921 (-) STP: STP|HisKA,STP|HATPase_c Yes
- 26918 - 27604 (-) TF: DBD-Pfam|Trans_reg_C Yes
- 27667 - 28143 (+) other Yes
- 28165 - 31017 (-) CAZyme: GH2 Yes
- 31069 - 34347 (-) CAZyme: GH2 Yes
- 34703 - 36202 (+) STP: STP|HisKA,STP|HATPase_c Yes
- 36199 - 37044 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 37258 - 41514 (-) CAZyme: GH137|GH2|CBM57 Yes
- 41627 - 44248 (-) CAZyme: GH138 Yes
- 44546 - 46978 (+) TC: gnl|TC-DB|Q93N33|2.A.21.9.2 Yes
- 47018 - 47563 (+) other Yes
- 48046 - 50454 (-) other Yes
- 50660 - 52849 (-) CAZyme: GH78 Yes
- 52870 - 54729 (-) CAZyme: GH141 Yes
- 54749 - 56845 (-) CAZyme: GH127 Yes
- 56981 - 57754 (-) other Yes
- 58168 - 58425 (+) other Yes
- 58452 - 59180 (-) STP: STP|Nitroreductase Yes
- 59414 - 60205 (-) other Yes
- 60272 - 61060 (-) other Yes
- 61066 - 62004 (-) other Yes
- 62287 - 64761 (+) CAZyme: GH95 Yes
- 64775 - 65977 (+) CAZyme: GH105 Yes
- 66014 - 67465 (+) CAZyme: GH140 Yes
- 67458 - 71330 (+) CAZyme: GH78|GH33|CBM67 Yes
- 71409 - 72929 (-) other Yes
- 73481 - 74368 (+) other Yes
- 74356 - 75138 (-) other Yes
- 75309 - 77270 (-) other Yes
- 77308 - 78645 (-) CAZyme: GH28 Yes
- 78682 - 81453 (-) CAZyme: GH78|CBM67 Yes
- 81576 - 84905 (-) CAZyme: GH143|GH142 Yes
- 84957 - 85808 (-) CAZyme: GH43_18|GH43 Yes
- 86130 - 86798 (-) other Yes
- 86872 - 88611 (-) CAZyme: PL1|CE8|PL1_2 Yes
- 88838 - 91135 (-) other Yes
- 91122 - 94430 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 94463 - 95908 (-) other Yes
- 96001 - 96186 (-) other Yes
- 96557 - 98731 (-) other Yes
- 98785 - 102093 (-) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 102123 - 103598 (-) CDS No

PUL ID

PUL0530

PubMed

22205877, PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.

Title

Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts.

Author

Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, Abbott DW, Henrissat B, Gilbert HJ, Bolam DN, Gordon JI

Abstract

Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs) that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target unique suites of available polysaccharides, a theme that likely applies to disparate bacteria from the gut and other habitats.