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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0374

PubMed

19734309, J Bacteriol. 2009 Nov;191(22):6960-7. doi: 10.1128/JB.00594-09. Epub 2009 Sep 4.

Characterization method

microarray,qPCR

Genomic accession number

CP002038.1

Nucelotide position range

1781030-1785659

Substrate

melibiose

Loci

rafRAB

Species

Dickeya dadantii/204038

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rafR Dda3937_03030 ADM97864.1 0 - 1047 (+) CP002038.1:1781030-1782077 -
rafA Dda3937_03029 ADM97865.1 1166 - 3296 (+) CP002038.1:1782196-1784326 3.2.1.22
rafB Dda3937_03028 ADM97866.1 3349 - 4630 (+) CP002038.1:1784379-1785660 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

rafR 1 - 1047 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 No
rafA 1167 - 3296 (+) CAZyme: GH36 Yes
rafB 3350 - 4630 (+) TC: gnl|TC-DB|P96517|2.A.1.5.4 Yes

PUL ID

PUL0374

PubMed

19734309, J Bacteriol. 2009 Nov;191(22):6960-7. doi: 10.1128/JB.00594-09. Epub 2009 Sep 4.

Title

Catabolism of raffinose, sucrose, and melibiose in Erwinia chrysanthemi 3937.

Author

Hugouvieux-Cotte-Pattat N, Charaoui-Boukerzaza S

Abstract

Erwinia chrysanthemi (Dickeya dadantii) is a plant pathogenic bacterium that has a large capacity to degrade the plant cell wall polysaccharides. The present study reports the metabolic pathways used by E. chrysanthemi to assimilate the oligosaccharides sucrose and raffinose, which are particularly abundant plant sugars. E. chrysanthemi is able to use sucrose, raffinose, or melibiose as a sole carbon source for growth. The two gene clusters scrKYABR and rafRBA are necessary for their catabolism. The phenotypic analysis of scr and raf mutants revealed cross-links between the assimilation pathways of these oligosaccharides. Sucrose catabolism is mediated by the genes scrKYAB. While the raf cluster is sufficient to catabolize melibiose, it is incomplete for raffinose catabolism, which needs two additional steps that are provided by scrY and scrB. The scr and raf clusters are controlled by specific repressors, ScrR and RafR, respectively. Both clusters are controlled by the global activator of carbohydrate catabolism, the cyclic AMP receptor protein (CRP). E. chrysanthemi growth with lactose is possible only for mutants with a derepressed nonspecific lactose transport system, which was identified as RafB. RafR inactivation allows the bacteria to the assimilate the novel substrates lactose, lactulose, stachyose, and melibionic acid. The raf genes also are involved in the assimilation of alpha- and beta-methyl-D-galactosides. Mutations in the raf or scr genes did not significantly affect E. chrysanthemi virulence. This could be explained by the large variety of carbon sources available in the plant tissue macerated by E. chrysanthemi.