PUL ID

PUL0558

PubMed

28329766, Nature. 2017 Apr 6;544(7648):65-70. doi: 10.1038/nature21725. Epub 2017 Mar 22.

Characterization method

gene deletion mutant and growth assay, growth assay, enzyme activity assay

Genomic accession number

AE015928.1

Nucelotide position range

1200747-1298373

Substrate

rhamnogalacturonan

Loci

BT0981-BT1030

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_0981 AAO76088.1 0 - 4419 (-) AE015928.1:1200747-1205166 -
- BT_0982 AAO76089.1 4676 - 4928 (-) AE015928.1:1205423-1205675 -
- BT_0983 AAO76090.1 5157 - 7806 (-) AE015928.1:1205904-1208553 -
- BT_0984 AAO76091.1 7834 - 10246 (-) AE015928.1:1208581-1210993 -
- BT_0985 AAO76092.1 10255 - 11689 (-) AE015928.1:1211002-1212436 -
- BT_0986 AAO76093.1 11691 - 15009 (-) AE015928.1:1212438-1215756 -
- BT_0987 AAO76094.1 15132 - 16647 (-) AE015928.1:1215879-1217394 -
- BT_0988 AAO76095.1 16810 - 19462 (-) AE015928.1:1217557-1220209 -
- BT_0989 AAO76096.1 19582 - 20950 (-) AE015928.1:1220329-1221697 -
- BT_0990 AAO76097.1 20946 - 21633 (-) AE015928.1:1221693-1222380 -
- BT_0991 AAO76098.1 21695 - 22172 (+) AE015928.1:1222442-1222919 -
- BT_0992 AAO76099.1 22193 - 25046 (-) AE015928.1:1222940-1225793 -
- BT_0993 AAO76100.1 25097 - 28376 (-) AE015928.1:1225844-1229123 -
- BT_0994 AAO76101.1 28731 - 30231 (+) AE015928.1:1229478-1230978 -
- BT_0995 AAO76102.1 30227 - 31073 (-) AE015928.1:1230974-1231820 -
- BT_0996 AAO76103.1 31286 - 35543 (-) AE015928.1:1232033-1236290 -
- BT_0997 AAO76104.1 35655 - 38277 (-) AE015928.1:1236402-1239024 -
- BT_0998 AAO76105.1 38574 - 41007 (+) AE015928.1:1239321-1241754 -
- BT_0999 AAO76106.1 41046 - 41592 (+) AE015928.1:1241793-1242339 -
- BT_1000 AAO76107.1 42074 - 44483 (-) AE015928.1:1242821-1245230 -
- BT_1001 AAO76108.1 44688 - 46878 (-) AE015928.1:1245435-1247625 -
- BT_1002 AAO76109.1 46898 - 48758 (-) AE015928.1:1247645-1249505 -
- BT_1003 AAO76110.1 48777 - 50874 (-) AE015928.1:1249524-1251621 -
- BT_1004 AAO76111.1 51009 - 51783 (-) AE015928.1:1251756-1252530 -
- BT_1005 AAO76112.1 52196 - 52454 (+) AE015928.1:1252943-1253201 -
- BT_1006 AAO76113.1 52480 - 53209 (-) AE015928.1:1253227-1253956 -
- BT_1007 AAO76114.1 53442 - 54234 (-) AE015928.1:1254189-1254981 -
- BT_1008 AAO76115.1 54300 - 55089 (-) AE015928.1:1255047-1255836 -
- BT_1009 AAO76116.1 55094 - 56033 (-) AE015928.1:1255841-1256780 -
- BT_1010 AAO76117.1 56315 - 58790 (+) AE015928.1:1257062-1259537 -
- BT_1011 AAO76118.1 58803 - 60006 (+) AE015928.1:1259550-1260753 -
- BT_1012 AAO76119.1 60042 - 61494 (+) AE015928.1:1260789-1262241 -
- BT_1013 AAO76120.1 61486 - 65359 (+) AE015928.1:1262233-1266106 -
- BT_1014 AAO76121.1 65437 - 66958 (-) AE015928.1:1266184-1267705 -
- BT_1015 AAO76122.1 67509 - 68397 (+) AE015928.1:1268256-1269144 -
- BT_1016 AAO76123.1 68384 - 69167 (-) AE015928.1:1269131-1269914 -
- BT_1017 AAO76124.1 69337 - 71299 (-) AE015928.1:1270084-1272046 -
- BT_1018 AAO76125.1 71336 - 72674 (-) AE015928.1:1272083-1273421 -
- BT_1019 AAO76126.1 72710 - 75482 (-) AE015928.1:1273457-1276229 -
- BT_1020 AAO76127.1 75604 - 78934 (-) AE015928.1:1276351-1279681 -
- BT_1021 AAO76128.1 78985 - 79837 (-) AE015928.1:1279732-1280584 -
- BT_1022 AAO76129.1 80158 - 80827 (-) AE015928.1:1280905-1281574 -
- BT_1023 AAO76130.1 80900 - 82640 (-) AE015928.1:1281647-1283387 -
- BT_1024 AAO76131.1 82866 - 85164 (-) AE015928.1:1283613-1285911 -
- BT_1025 AAO76132.1 85150 - 88459 (-) AE015928.1:1285897-1289206 -
- BT_1026 AAO76133.1 88491 - 89937 (-) AE015928.1:1289238-1290684 -
- BT_1027 AAO76134.1 90029 - 90215 (-) AE015928.1:1290776-1290962 -
- BT_1028 AAO76135.1 90585 - 92760 (-) AE015928.1:1291332-1293507 -
- BT_1029 AAO76136.1 92813 - 96122 (-) AE015928.1:1293560-1296869 -
- BT_1030 AAO76137.1 96151 - 97627 (-) AE015928.1:1296898-1298374 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 4419 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 No
- 4677 - 4928 (-) CDS No
- 5158 - 7806 (-) CAZyme: GH2 Yes
- 7835 - 10246 (-) CAZyme: GH139 Yes
- 10256 - 11689 (-) other Yes
- 11692 - 15009 (-) CAZyme: GH106 Yes
- 15133 - 16647 (-) other Yes
- 16811 - 19462 (-) TC: gnl|TC-DB|P36640|3.A.3.4.1 Yes
- 19583 - 20950 (-) STP: STP|HisKA,STP|HATPase_c Yes
- 20947 - 21633 (-) TF: DBD-Pfam|Trans_reg_C Yes
- 21696 - 22172 (+) other Yes
- 22194 - 25046 (-) CAZyme: GH2 Yes
- 25098 - 28376 (-) CAZyme: GH2 Yes
- 28732 - 30231 (+) STP: STP|HisKA,STP|HATPase_c Yes
- 30228 - 31073 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 31287 - 35543 (-) CAZyme: GH2|CBM57|GH137 Yes
- 35656 - 38277 (-) CAZyme: GH138 Yes
- 38575 - 41007 (+) TC: gnl|TC-DB|Q93N33|2.A.21.9.2 Yes
- 41047 - 41592 (+) other Yes
- 42075 - 44483 (-) other Yes
- 44689 - 46878 (-) CAZyme: GH78 Yes
- 46899 - 48758 (-) CAZyme: GH141 Yes
- 48778 - 50874 (-) CAZyme: GH127 Yes
- 51010 - 51783 (-) other Yes
- 52197 - 52454 (+) other Yes
- 52481 - 53209 (-) STP: STP|Nitroreductase Yes
- 53443 - 54234 (-) other Yes
- 54301 - 55089 (-) other Yes
- 55095 - 56033 (-) other Yes
- 56316 - 58790 (+) CAZyme: GH95 Yes
- 58804 - 60006 (+) CAZyme: GH105 Yes
- 60043 - 61494 (+) CAZyme: GH140 Yes
- 61487 - 65359 (+) CAZyme: CBM67|GH33|GH78 Yes
- 65438 - 66958 (-) other Yes
- 67510 - 68397 (+) other Yes
- 68385 - 69167 (-) other Yes
- 69338 - 71299 (-) other Yes
- 71337 - 72674 (-) CAZyme: GH28 Yes
- 72711 - 75482 (-) CAZyme: CBM67|GH78 Yes
- 75605 - 78934 (-) CAZyme: GH142|GH143 Yes
- 78986 - 79837 (-) CAZyme: GH43_18|GH43 Yes
- 80159 - 80827 (-) other Yes
- 80901 - 82640 (-) CAZyme: CE8|PL1_2|PL1 Yes
- 82867 - 85164 (-) other Yes
- 85151 - 88459 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 88492 - 89937 (-) other Yes
- 90030 - 90215 (-) other Yes
- 90586 - 92760 (-) other Yes
- 92814 - 96122 (-) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 96152 - 97627 (-) CDS No

PUL ID

PUL0558

PubMed

28329766, Nature. 2017 Apr 6;544(7648):65-70. doi: 10.1038/nature21725. Epub 2017 Mar 22.

Title

Complex pectin metabolism by gut bacteria reveals novel catalytic functions.

Author

Ndeh D, Rogowski A, Cartmell A, Luis AS, Basle A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O'Neil MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, Gilbert HJ

Abstract

The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities. The degradation system informs revision of the current structural model of rhamnogalacturonan-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycan in the human diet.