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Volume 150, Issue 11

Comparative genomics of the KdgR regulon in 3937 and other gamma-proteobacteria Free

Abstract

In the plant-pathogenic enterobacterium , 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 , and two 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 was experimentally verified using 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 and an adjacent gene, , of unknown function. Other predicted regulon members, namely , , , , , , , and , were found to be subject to classical negative regulation by KdgR. Possible roles of newly identified members of the KdgR regulon, , , , , , , , and , 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 species were detected.

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Keyword(s): CRP, cAMP-receptor protein , DK-I, 5-keto-4-deoxyuronate , DK-II, 2,5-diketo-3-deoxygluconate , GA, galacturonate , KDG, 2-keto-3-deoxygluconate , MCP, methyl-accepting chemotaxis protein , OGA, oligogalacturonate and PGA, polygalacturonate
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2004-11-01
2024-04-24
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Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria
Microbiology 150, 3571 (2004); https://doi.org/10.1099/mic.0.27041-0
/content/journal/micro/10.1099/mic.0.27041-0
/content/journal/micro/10.1099/mic.0.27041-0
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