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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0225

PubMed

23150581, Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19786-91. doi: 10.1073/pnas.1211002109. Epub 2012 Nov 12.

Characterization method

RT-PCR

Genomic accession number

NZ_DS990130.1

Nucelotide position range

72558-132837

Substrate

agarose

Loci

BACPLE_RS08560-BACPLE_RS08735

Species

Bacteroides plebeius/310297

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BACPLE_RS08560 WP_007560909.1 0 - 1284 (-) NZ_DS990130.1:72558-73842 -
- BACPLE_RS08565 WP_009121375.1 1264 - 3591 (-) NZ_DS990130.1:73822-76149 -
- BACPLE_RS08570 WP_007560915.1 3771 - 4722 (-) NZ_DS990130.1:76329-77280 -
- BACPLE_RS08575 WP_007560917.1 4748 - 5957 (-) NZ_DS990130.1:77306-78515 -
- BACPLE_RS08580 WP_007560919.1 5965 - 8521 (-) NZ_DS990130.1:78523-81079 -
- BACPLE_RS08585 WP_007560921.1 8559 - 11115 (-) NZ_DS990130.1:81117-83673 -
- BACPLE_RS08590 WP_007560923.1 11235 - 12723 (-) NZ_DS990130.1:83793-85281 -
- BACPLE_RS08595 WP_007560925.1 12765 - 14208 (-) NZ_DS990130.1:85323-86766 -
- BACPLE_RS08600 WP_007560927.1 14237 - 15254 (-) NZ_DS990130.1:86795-87812 -
fucP BACPLE_RS08605 WP_007560929.1 15291 - 16545 (-) NZ_DS990130.1:87849-89103 -
- BACPLE_RS08610 WP_025018820.1 16541 - 17465 (-) NZ_DS990130.1:89099-90023 -
- BACPLE_RS08615 WP_007560932.1 17476 - 18409 (-) NZ_DS990130.1:90034-90967 -
- BACPLE_RS08620 WP_007560934.1 18449 - 18833 (-) NZ_DS990130.1:91007-91391 -
- BACPLE_RS19300 WP_007560936.1 19026 - 19200 (-) NZ_DS990130.1:91584-91758 -
- BACPLE_RS08625 WP_147345519.1 19262 - 19742 (-) NZ_DS990130.1:91820-92300 -
- BACPLE_RS08630 WP_007560940.1 19854 - 21426 (-) NZ_DS990130.1:92412-93984 -
- BACPLE_RS08635 WP_040312745.1 21446 - 23759 (-) NZ_DS990130.1:94004-96317 -
- BACPLE_RS08640 WP_007560944.1 23846 - 25577 (-) NZ_DS990130.1:96404-98135 -
- BACPLE_RS08645 WP_007560946.1 25640 - 26153 (-) NZ_DS990130.1:98198-98711 -
- BACPLE_RS08650 WP_007560950.1 26390 - 26882 (-) NZ_DS990130.1:98948-99440 -
- BACPLE_RS08655 WP_007560951.1 26928 - 27894 (-) NZ_DS990130.1:99486-100452 -
- BACPLE_RS19305 WP_007560953.1 28295 - 28490 (-) NZ_DS990130.1:100853-101048 -
- BACPLE_RS08660 WP_007560957.1 28900 - 30211 (-) NZ_DS990130.1:101458-102769 -
- BACPLE_RS08665 WP_007560960.1 30216 - 32403 (-) NZ_DS990130.1:102774-104961 -
- BACPLE_RS08670 WP_117892265.1 32453 - 34277 (-) NZ_DS990130.1:105011-106835 -
- BACPLE_RS08675 WP_007560964.1 34372 - 34927 (-) NZ_DS990130.1:106930-107485 -
- BACPLE_RS08680 WP_007560966.1 34942 - 36667 (-) NZ_DS990130.1:107500-109225 -
- BACPLE_RS18590 WP_007560968.1 36672 - 38709 (-) NZ_DS990130.1:109230-111267 -
- BACPLE_RS08695 WP_007560970.1 38728 - 41827 (-) NZ_DS990130.1:111286-114385 -
- BACPLE_RS08700 WP_007560972.1 41959 - 45931 (-) NZ_DS990130.1:114517-118489 -
- BACPLE_RS08705 WP_007560974.1 46195 - 47368 (-) NZ_DS990130.1:118753-119926 -
- BACPLE_RS08710 WP_117652420.1 47392 - 48976 (-) NZ_DS990130.1:119950-121534 -
- BACPLE_RS08715 WP_117652469.1 48980 - 50759 (-) NZ_DS990130.1:121538-123317 -
- BACPLE_RS08720 WP_007560980.1 51069 - 51972 (+) NZ_DS990130.1:123627-124530 -
- BACPLE_RS08725 WP_007560982.1 52075 - 53707 (-) NZ_DS990130.1:124633-126265 -
- BACPLE_RS08730 WP_081458114.1 53718 - 56781 (-) NZ_DS990130.1:126276-129339 -
- BACPLE_RS08735 WP_117652419.1 57019 - 60280 (-) NZ_DS990130.1:129577-132838 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1284 (-) TF: DBD-Pfam|HTH_8,DBD-SUPERFAMILY|0037176 No
- 3772 - 4722 (-) CAZyme: GH16_16 Yes
- 4749 - 5957 (-) CAZyme: GH117|GH117 Yes
- 5966 - 8521 (-) CAZyme: GH2 Yes
- 8560 - 11115 (-) CAZyme: GH2 Yes
- 11236 - 12723 (-) other Yes
- 12766 - 14208 (-) other Yes
- 14238 - 15254 (-) other Yes
fucP 15292 - 16545 (-) TC: gnl|TC-DB|P11551|2.A.1.7.1 Yes
- 16542 - 17465 (-) other Yes
- 17477 - 18409 (-) other Yes
- 18450 - 18833 (-) other Yes
- 19027 - 19200 (-) other Yes
- 19263 - 19742 (-) other Yes
- 19855 - 21426 (-) CAZyme: GH50 Yes
- 21447 - 23759 (-) CAZyme: GH105|GH154 Yes
- 23847 - 25577 (-) other Yes
- 25641 - 26153 (-) other Yes
- 26391 - 26882 (-) other Yes
- 26929 - 27894 (-) CAZyme: GH16_12 Yes
- 28296 - 28490 (-) other Yes
- 28901 - 30211 (-) other Yes
- 30217 - 32403 (-) CAZyme: GH86 Yes
- 32454 - 34277 (-) CAZyme: GH86 Yes
- 34373 - 34927 (-) other Yes
- 34943 - 36667 (-) other Yes
- 36673 - 38709 (-) other Yes
- 38729 - 41827 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 41960 - 45931 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 46196 - 47368 (-) other Yes
- 47393 - 48976 (-) other Yes
- 48981 - 50759 (-) CAZyme: GH29 Yes
- 51070 - 51972 (+) CAZyme: GH16_14 Yes
- 52076 - 53707 (-) other Yes
- 53719 - 56781 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 57020 - 60280 (-) CAZyme: GH2 Yes

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PUL ID

PUL0225

PubMed

23150581, Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19786-91. doi: 10.1073/pnas.1211002109. Epub 2012 Nov 12.

Title

Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes.

Author

Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB

Abstract

Humans host an intestinal population of microbes--collectively referred to as the gut microbiome--which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant polysaccharides. The question then arises as to if and how the microbiome adapts to new carbohydrate sources when modern humans change eating habits. Recent metagenome analysis of microbiomes from healthy American, Japanese, and Spanish populations identified putative CAZymes obtained by horizontal gene transfer from marine bacteria, which suggested that human gut bacteria evolved to degrade algal carbohydrates-for example, consumed in form of sushi. We approached this hypothesis by studying such a polysaccharide utilization locus (PUL) obtained by horizontal gene transfer by the gut bacterium Bacteroides plebeius. Transcriptomic and growth experiments revealed that the PUL responds to the polysaccharide porphyran from red algae, enabling growth on this carbohydrate but not related substrates like agarose and carrageenan. The X-ray crystallographic and biochemical analysis of two proteins encoded by this PUL, BACPLE_01689 and BACPLE_01693, showed that they are beta-porphyranases belonging to glycoside hydrolase families 16 and 86, respectively. The product complex of the GH86 at 1.3 A resolution highlights the molecular details of porphyran hydrolysis by this new porphyranase. Combined, these data establish experimental support for the argument that CAZymes and associated genes obtained from extrinsic microbes add new catabolic functions to the human gut microbiome.