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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0249

PubMed

17449691, Appl Environ Microbiol. 2007 Jun;73(12):3803-13. doi: 10.1128/AEM.00147-07. Epub 2007 Apr 20.

Characterization method

microarray

Genomic accession number

NC_000964.3

Nucelotide position range

761662-776790

Substrate

rhamnogalacturonan

Loci

BSU06970-BSU07080

Species

Bacillus subtilis/1423

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

yesO BSU_06970 NP_388578.2 0 - 1284 (+) NC_000964.3:761662-762946 -
rhgP BSU_06980 NP_388579.1 1280 - 2210 (+) NC_000964.3:762942-763872 -
rhgQ BSU_06990 NP_388580.1 2213 - 3104 (+) NC_000964.3:763875-764766 -
rhgH BSU_07000 NP_388581.1 3119 - 4154 (+) NC_000964.3:764781-765816 3.2.1.172
rhgR BSU_07010 NP_388582.1 4176 - 6462 (+) NC_000964.3:765838-768124 -
rhgT BSU_07020 NP_388583.1 6475 - 7174 (+) NC_000964.3:768137-768836 3.1.1.-
yesU BSU_07030 NP_388584.1 7166 - 7829 (+) NC_000964.3:768828-769491 -
yesV BSU_07040 NP_388585.1 7825 - 8452 (+) NC_000964.3:769487-770114 -
rhgW BSU_07050 NP_388586.1 8572 - 10435 (+) NC_000964.3:770234-772097 4.2.2.23
rhgX BSU_07060 NP_388587.1 10480 - 12319 (+) NC_000964.3:772142-773981 4.2.2.24
yesY BSU_07070 NP_388588.1 12476 - 13130 (+) NC_000964.3:774138-774792 3.1.1.-
rhgZ BSU_07080 NP_388589.1 13137 - 15129 (+) NC_000964.3:774799-776791 3.2.1.67

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

yesO 1 - 1284 (+) STP: STP|SBP_bac_1 No
rhgP 1281 - 2210 (+) TC: gnl|TC-DB|Q93KC0|3.A.1.1.11 Yes
rhgQ 2214 - 3104 (+) TC: gnl|TC-DB|Q93KB9|3.A.1.1.11 Yes
rhgH 3120 - 4154 (+) CAZyme: GH105 Yes
rhgR 4177 - 6462 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
rhgT 6476 - 7174 (+) CAZyme: CE12 Yes
yesU 7167 - 7829 (+) other Yes
yesV 7826 - 8452 (+) TC: gnl|TC-DB|G4PA66|9.B.28.1.5 Yes
rhgW 8573 - 10435 (+) CAZyme: PL11_1|CE12|PL11 Yes
rhgX 10481 - 12319 (+) CAZyme: PL11_1|PL11 Yes
yesY 12477 - 13130 (+) CAZyme: CE12 Yes
rhgZ 13138 - 15129 (+) CAZyme: GH42 Yes

PUL ID

PUL0249

PubMed

17449691, Appl Environ Microbiol. 2007 Jun;73(12):3803-13. doi: 10.1128/AEM.00147-07. Epub 2007 Apr 20.

Title

Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization.

Author

Ochiai A, Itoh T, Kawamata A, Hashimoto W, Murata K

Abstract

Plant cell wall degradation is a premier event when Bacillus subtilis, a typical saprophytic bacterium, invades plants. Here we show the degradation system of rhamnogalacturonan type I (RG-I), a component of pectin from the plant cell wall, in B. subtilis strain 168. Strain 168 cells showed a significant growth on plant cell wall polysaccharides such as pectin, polygalacturonan, and RG-I as a carbon source. DNA microarray analysis indicated that three gene clusters (yesOPQRSTUVWXYZ, ytePQRST, and ybcMOPST-ybdABDE) are inducibly expressed in strain 168 cells grown on RG-I. Cells of an industrially important bacterium, B. subtilis strain natto, fermenting soybeans also express the gene cluster including the yes series during the assimilation of soybean used as a carbon source. Among proteins encoded in the yes cluster, YesW and YesX were found to be novel types of RG lyases releasing disaccharide from RG-I. Genetic and enzymatic properties of YesW and YesX suggest that strain 168 cells secrete YesW, which catalyzes the initial cleavage of the RG-I main chain, and the resultant oligosaccharides are converted to disaccharides through the extracellular exotype YesX reaction. The disaccharide is finally degraded into its constituent monosaccharides through the reaction of intracellular unsaturated galacturonyl hydrolases YesR and YteR. This enzymatic route for RG-I degradation in strain 168 differs significantly from that in plant-pathogenic fungus Aspergillus aculeatus. This is, to our knowledge, the first report on the bacterial system for complete RG-I main chain degradation.