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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0013

PubMed

21460081, J Bacteriol. 2011 Jun;193(11):2838-50. doi: 10.1128/JB.00222-11. Epub 2011 Apr 1.

Characterization method

Northern Blot,RT-PCR,isothermal titration calorimetry,electrophoretic mobility shift assay

Genomic accession number

DQ868502.2

Nucelotide position range

1561-77747

Substrate

arabinan

Loci

ACE73663.1-ABI49957.1

Species

Geobacillus stearothermophilus/1422

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

araP - ACE73663.1 1561 - 2569 (+) DQ868502.2:3122-4130 -
araS - ACE73664.1 2602 - 4378 (+) DQ868502.2:4163-5939 -
araT - ACE73665.1 4525 - 5740 (+) DQ868502.2:6086-7301 -
araE - ACE73666.1 5918 - 7007 (+) DQ868502.2:7479-8568 -
- - ACE73667.1 6668 - 8129 (-) DQ868502.2:8229-9690 -
IE1 - ACE73668.1 8370 - 9738 (+) DQ868502.2:9931-11299 -
araG - ACE73669.1 10187 - 11729 (+) DQ868502.2:11748-13290 -
araH - ACE73670.1 11730 - 12954 (+) DQ868502.2:13291-14515 -
araR - ACE73671.1 13259 - 14354 (+) DQ868502.2:14820-15915 -
araD - ACE73672.1 14447 - 15134 (+) DQ868502.2:16008-16695 -
araB - ACE73673.1 15150 - 16845 (+) DQ868502.2:16711-18406 -
araA - ACE73674.1 16858 - 18352 (+) DQ868502.2:18419-19913 -
abp - ACE73675.1 18791 - 19640 (+) DQ868502.2:20352-21201 -
abnB - ACE73676.1 21149 - 22097 (+) DQ868502.2:22710-23658 -
abnE - ACE73677.1 22424 - 23789 (+) DQ868502.2:23985-25350 -
abnF - ACE73678.1 23875 - 24802 (+) DQ868502.2:25436-26363 -
abnJ - ACE73679.1 24801 - 25710 (+) DQ868502.2:26362-27271 -
abnA - ACE73680.1 25739 - 28286 (+) DQ868502.2:27300-29847 -
abfB - ACE73681.1 28549 - 30070 (+) DQ868502.2:30110-31631 -
abfA - ACE73682.1 30396 - 31905 (+) DQ868502.2:31957-33466 -
araJ - ACE73683.1 31968 - 32964 (+) DQ868502.2:33529-34525 -
araK - ACE73684.1 32982 - 34035 (+) DQ868502.2:34543-35596 -
araL - ACE73685.1 34039 - 34861 (+) DQ868502.2:35600-36422 -
araM - ACE73686.1 34941 - 36072 (+) DQ868502.2:36502-37633 -
araN - ACE73687.1 36081 - 38010 (+) DQ868502.2:37642-39571 -
xynD - ABI49930.1 38551 - 40279 (+) DQ868502.2:40112-41840 -
xynC - ABI49931.1 40271 - 41051 (+) DQ868502.2:41832-42612 -
xynE - ABI49932.1 41155 - 42481 (+) DQ868502.2:42716-44042 -
xynF - ABI49933.1 42543 - 43413 (+) DQ868502.2:44104-44974 -
xynG - ABI49934.1 43427 - 44294 (+) DQ868502.2:44988-45855 -
xylM - ABI49935.1 44486 - 45455 (+) DQ868502.2:46047-47016 -
axe1 - ABI49936.1 45478 - 46093 (+) DQ868502.2:47039-47654 -
xynB2 - ABI49956.1 46172 - 48290 (+) DQ868502.2:47733-49851 -
xynA2 - ABI49937.2 48292 - 49288 (+) DQ868502.2:49853-50849 -
- - ABI49960.1 50052 - 51510 (+) DQ868502.2:51613-53071 -
aguF - ABI49938.1 53022 - 54105 (+) DQ868502.2:54583-55666 -
aguG - ABI49939.1 54120 - 55011 (+) DQ868502.2:55681-56572 -
aguA - ABI49940.1 55028 - 57068 (+) DQ868502.2:56589-58629 -
xynB1 - ABI49941.1 57083 - 58598 (+) DQ868502.2:58644-60159 -
kdgK - ABI49942.1 58629 - 59574 (+) DQ868502.2:60190-61135 -
kdgA - ABI49943.1 59589 - 60240 (+) DQ868502.2:61150-61801 -
uxuR - ABI49944.1 60304 - 61054 (+) DQ868502.2:61865-62615 -
uxaC - ABI49945.1 61090 - 62512 (+) DQ868502.2:62651-64073 -
uxuA - ABI49946.1 62519 - 63635 (+) DQ868502.2:64080-65196 -
uxuB - ABI49947.1 63610 - 64456 (+) DQ868502.2:65171-66017 -
orfA - ABI49948.1 64532 - 65177 (+) DQ868502.2:66093-66738 -
orfB - ABI49949.1 65448 - 65964 (+) DQ868502.2:67009-67525 -
- - ABI49958.1 66145 - 67399 (+) DQ868502.2:67706-68960 -
orfC - ABI49950.1 67391 - 68192 (+) DQ868502.2:68952-69753 -
xynA - ABI49951.1 68529 - 69877 (-) DQ868502.2:70090-71438 -
xynX - ABI49952.1 70384 - 71056 (+) DQ868502.2:71945-72617 -
axe2 - ABI49953.1 71229 - 71889 (+) DQ868502.2:72790-73450 -
xynB3 - ABI49959.1 71933 - 73541 (+) DQ868502.2:73494-75102 -
xylA - ABI49954.1 73649 - 74987 (+) DQ868502.2:75210-76548 -
xylB - ABI49955.1 74994 - 76503 (+) DQ868502.2:76555-78064 -
orfD - ABI49957.1 77273 - 77747 (+) DQ868502.2:78834-79308 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1562 - 2569 (+) TC: gnl|TC-DB|G4FGN5|3.A.1.2.20 Yes
- 2603 - 4378 (+) TC: gnl|TC-DB|F4LXP4|8.A.59.2.1 Yes
- 4526 - 5740 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 5919 - 7007 (+) TC: gnl|TC-DB|P25548|3.A.1.2.5 Yes
- 6669 - 8129 (-) other Yes
- 8371 - 9738 (+) other Yes
- 10188 - 11729 (+) TC: gnl|TC-DB|O05176|3.A.1.2.5 Yes
- 11731 - 12954 (+) TC: gnl|TC-DB|O05177|3.A.1.2.5 Yes
- 13260 - 14354 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0043758 Yes
- 14448 - 15134 (+) other Yes
- 15151 - 16845 (+) other Yes
- 16859 - 18352 (+) other Yes
- 18792 - 19640 (+) other Yes
- 21150 - 22097 (+) CAZyme: GH43_5|GH43 Yes
- 22425 - 23789 (+) STP: STP|SBP_bac_1 Yes
- 23876 - 24802 (+) TC: gnl|TC-DB|Q7WWQ9|3.A.1.1.20 Yes
- 24802 - 25710 (+) TC: gnl|TC-DB|Q9X9R5|3.A.1.1.23 Yes
- 25740 - 28286 (+) CAZyme: GH43|GH43_4 Yes
- 28550 - 30070 (+) CAZyme: GH51 Yes
- 30397 - 31905 (+) CAZyme: GH51 Yes
- 31969 - 32964 (+) other Yes
- 32983 - 34035 (+) other Yes
- 34040 - 34861 (+) other Yes
- 34942 - 36072 (+) other Yes
- 36082 - 38010 (+) CAZyme: GH127 Yes
- 38552 - 40279 (+) TC: gnl|TC-DB|F4LXP4|8.A.59.2.1 Yes
- 40272 - 41051 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 41156 - 42481 (+) STP: STP|SBP_bac_1 Yes
- 42544 - 43413 (+) TC: gnl|TC-DB|Q8RJU9|3.A.1.1.18 Yes
- 43428 - 44294 (+) TC: gnl|TC-DB|G4FGN6|3.A.1.1.41 Yes
- 44487 - 45455 (+) other Yes
- 45479 - 46093 (+) CAZyme: CE4 Yes
- 46173 - 48290 (+) CAZyme: GH52 Yes
- 48293 - 49288 (+) CAZyme: GH10 Yes
- 50053 - 51510 (+) other Yes
- 53023 - 54105 (+) TC: gnl|TC-DB|Q09LY7|3.A.1.1.9 Yes
- 54121 - 55011 (+) TC: gnl|TC-DB|Q09LY6|3.A.1.1.9 Yes
- 55029 - 57068 (+) CAZyme: GH67 Yes
- 57084 - 58598 (+) CAZyme: GH39 Yes
- 58630 - 59574 (+) STP: STP|PfkB Yes
- 59590 - 60240 (+) other Yes
- 60305 - 61054 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 Yes
- 61091 - 62512 (+) other Yes
- 62520 - 63635 (+) other Yes
- 63611 - 64456 (+) other Yes
- 64533 - 65177 (+) TC: gnl|TC-DB|G4PA66|9.B.28.1.5 Yes
- 65449 - 65964 (+) other Yes
- 66146 - 67399 (+) other Yes
- 67392 - 68192 (+) STP: STP|AAA Yes
- 68530 - 69768 (-) other Yes
- 70385 - 71056 (+) other Yes
- 71230 - 71889 (+) other Yes
- 71934 - 73541 (+) CAZyme: GH43_11 Yes
- 73650 - 74987 (+) CDS No
- 74995 - 76503 (+) CDS No
- 77274 - 77747 (+) CDS No

PUL ID

PUL0013

PubMed

21460081, J Bacteriol. 2011 Jun;193(11):2838-50. doi: 10.1128/JB.00222-11. Epub 2011 Apr 1.

Title

The L-Arabinan utilization system of Geobacillus stearothermophilus.

Author

Shulami S, Raz-Pasteur A, Tabachnikov O, Gilead-Gropper S, Shner I, Shoham Y

Abstract

Geobacillus stearothermophilus T-6 is a thermophilic soil bacterium that has a 38-kb gene cluster for the utilization of arabinan, a branched polysaccharide that is part of the plant cell wall. The bacterium encodes a unique three-component regulatory system (araPST) that includes a sugar-binding lipoprotein (AraP), a histidine sensor kinase (AraS), and a response regulator (AraT) and lies adjacent to an ATP-binding cassette (ABC) arabinose transport system (araEGH). The lipoprotein (AraP) specifically bound arabinose, and gel mobility shift experiments showed that the response regulator, AraT, binds to a 139-bp fragment corresponding to the araE promoter region. Taken together, the results showed that the araPST system appeared to sense extracellular arabinose and to activate a specific ABC transporter for arabinose (AraEGH). The promoter regions of the arabinan utilization genes contain a 14-bp inverted repeat motif resembling an operator site for the arabinose repressor, AraR. AraR was found to bind specifically to these sequences, and binding was efficiently prevented in the presence of arabinose, suggesting that arabinose is the molecular inducer of the arabinan utilization system. The expression of the arabinan utilization genes was reduced in the presence of glucose, indicating that regulation is also mediated via a catabolic repression mechanism. The cluster also encodes a second putative ABC sugar transporter (AbnEFJ) whose sugar-binding lipoprotein (AbnE) was shown to interact specifically with linear and branched arabino-oligosaccharides. The final degradation of the arabino-oligosaccharides is likely carried out by intracellular enzymes, including two alpha-l-arabinofuranosidases (AbfA and AbfB), a beta-l-arabinopyranosidase (Abp), and an arabinanase (AbnB), all of which are encoded in the 38-kb cluster.