Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.
In the plant-pathogenic enterobacterium Erwinia chrysanthemi, almost all known genes involved in pectin catabolism are controlled by the transcriptional regulator KdgR. In this study, the comparative genomics approach was used to analyse the KdgR regulon in completely sequenced genomes of eight enterobacteria, including Erw. chrysanthemi, and two Vibrio species. Application of a signal recognition procedure complemented by operon structure and protein sequence analysis allowed identification of new candidate genes of the KdgR regulon. Most of these genes were found to be controlled by the cAMP-receptor protein, a global regulator of catabolic genes. At the next step, regulation of these genes in Erw. chrysanthemi was experimentally verified using in vivo transcriptional fusions and an attempt was made to clarify the functional role of the predicted genes in pectin catabolism. Interestingly, it was found that the KdgR protein, previously known as a repressor, positively regulates expression of two new members of the regulon, phosphoenolpyruvate synthase gene ppsA and an adjacent gene, ydiA, of unknown function. Other predicted regulon members, namely chmX, dhfX, gntB, pykF, spiX, sotA, tpfX, yeeO and yjgK, were found to be subject to classical negative regulation by KdgR. Possible roles of newly identified members of the Erw. chrysanthemi KdgR regulon, chmX, dhfX, gntDBMNAC, spiX, tpfX, ydiA, yeeO, ygjV and yjgK, in pectin catabolism are discussed. Finally, complete reconstruction of the KdgR regulons in various gamma-proteobacteria yielded a metabolic map reflecting a globally conserved pathway for the catabolism of pectin and its derivatives with variability in transport and enzymic capabilities among species. In particular, possible non-orthologous substitutes of isomerase KduI and a new oligogalacturonide transporter in the Vibrio species were detected.
Rodionov
Dmitry A
DA
State Scientific Centre GosNIIGenetika, Moscow, 117545, Russia.
Gelfand
Mikhail S
MS
Institute for Problems of Information Transmission, Russian Academy of Sciences, Bolshoy Karetny per. 19, Moscow GSP-4, 127994, Russia.|State Scientific Centre GosNIIGenetika, Moscow, 117545, Russia.
Hugouvieux-Cotte-Pattat
Nicole
N
Unité de Microbiologie et Génétique - Composante INSA, UMR CNRS-INSA-UCB 5122, bat Lwoff, 10 rue Dubois, Domaine Scientifique de la Doua, 69622 Villeurbanne Cedex, France.
D019677:Artificial Gene Fusion; D001426:Bacterial Proteins / Q000235:genetics / Q000502:physiology*; D002373:Cyclic AMP Receptor Protein / Q000378:metabolism; D016974:Dickeya chrysanthemi / Q000235:genetics*; D004755:Enterobacteriaceae / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter / Q000502:physiology; D009004:Monosaccharide Transport Proteins / Q000235:genetics; D009876:Operon; D010368:Pectins / Q000378:metabolism; D016973:Pectobacterium carotovorum / Q000235:genetics; D017866:Phosphotransferases (Paired Acceptors) / Q000235:genetics; D010802:Phylogeny; D018085:Regulon; D012097:Repressor Proteins / Q000502:physiology*; D012486:Salmonella typhimurium / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000502:physiology*; D014158:Transcription, Genetic; D014733:Vibrio / Q000235:genetics*; D014736:Vibrio parahaemolyticus / Q000235:genetics; D041261:Vibrio vulnificus / Q000235:genetics; D015008:Yersinia enterocolitica / Q000235:genetics; D015010:Yersinia pestis / Q000235:genetics
D001426:Bacterial Proteins; D002373:Cyclic AMP Receptor Protein; C098628:KdgR protein, Erwinia chrysanthemi; D009004:Monosaccharide Transport Proteins; D012097:Repressor Proteins; C404569:SotA protein, Erwinia chrysanthemi; D014157:Transcription Factors; D010368:Pectins; D017866:Phosphotransferases (Paired Acceptors); C022509:pyruvate, water dikinase