1887

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.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.27041-0
2004-11-01
2019-11-18
Loading full text...

Full text loading...

/deliver/fulltext/micro/150/11/mic1503571.html?itemId=/content/journal/micro/10.1099/mic.0.27041-0&mimeType=html&fmt=ahah

References

  1. Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  2. Bardonnet, N. & Blanco, C. ( 1992; ). uidA antibiotic resistance cassettes for insertion mutagenesis, gene fusion and genetic constructions. FEMS Microbiol Lett 93, 243–248.
    [Google Scholar]
  3. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Rapp, B. A. & Wheeler, D. L. ( 2000; ). GenBank. Nucleic Acids Res 28, 15–18.[CrossRef]
    [Google Scholar]
  4. Bledig, S. A., Ramseier, T. M. & Saier, M. H., Jr ( 1996; ). FruR mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli. J Bacteriol 178, 280–283.
    [Google Scholar]
  5. Blot, N., Berrier, C., Hugouvieux-Cotte-Pattat, N., Ghazi, A. & Condemine, G. ( 2002; ). The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family. J Biol Chem 277, 7936–7944.[CrossRef]
    [Google Scholar]
  6. Condemine, G. ( 2000; ). Characterization of SotA and SotB, two Erwinia chrysanthemi proteins which modify isopropyl-beta-d-thiogalactopyranoside and lactose induction of the Escherichia coli lac promoter. J Bacteriol 182, 1340–1345.[CrossRef]
    [Google Scholar]
  7. Condemine, G. & Robert-Baudouy, J. ( 1987; ). 2-Keto-3-deoxygluconate transport system in Erwinia chrysanthemi. J Bacteriol 169, 1972–1978.
    [Google Scholar]
  8. Condemine, G., Dorel, C., Hugouvieux-Cotte-Pattat, N. & Robert-Baudouy, J. ( 1992; ). Some of the out genes involved in the secretion of pectate lyases in Erwinia chrysanthemi are regulated by KdgR. Mol Microbiol 6, 3199–3211.[CrossRef]
    [Google Scholar]
  9. Elliott, A. C., Sinnott, M. L., Smith, P. J., Bommuswamy, J., Guo, Z., Hall, B. G. & Zhang, Y. ( 1992; ). The catalytic consequences of experimental evolution. Studies on the subunit structure of the second (ebg) beta-galactosidase of Escherichia coli, and on catalysis by ebgAB, an experimental evolvant containing two amino acid substitutions. Biochem J 282, 155–164.
    [Google Scholar]
  10. Felsenstein, J. ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef]
    [Google Scholar]
  11. Fuhrman, L. K., Wanken, A., Nickerson, K. W. & Conway, T. ( 1998; ). Rapid accumulation of intracellular 2-keto-3-deoxy-6-phosphogluconate in an Entner–Doudoroff aldolase mutant results in bacteriostasis. FEMS Microbiol Lett 159, 261–266.[CrossRef]
    [Google Scholar]
  12. Gage, D. J. & Long, S. R. ( 1998; ). Alpha-galactoside uptake in Rhizobium meliloti: isolation and characterization of agpA, a gene encoding a periplasmic binding protein required for melibiose and raffinose utilization. J Bacteriol 180, 5739–5748.
    [Google Scholar]
  13. Gelfand, M. S. ( 2003; ). Computational identification of regulatory sites in DNA sequences. In Artificial Intelligence and Heuristic Methods in Bioinformatics, pp. 148–172. Edited by P. Frasconi & R. Shamir. Amsterdam: IOS Press.
  14. Gelfand, M. S. & Laikova, O. N. ( 2003; ). Prolegomena to the evolution of transcriptional regulation in bacterial genomes. In Frontiers in Computational Genomics, pp. 195–216. Edited by E. V. Koonin & M. Y. Galperin. Wymondham: Caister Academic Press.
  15. Gelfand, M. S., Novichkov, P. S., Novichkova, E. S. & Mironov, A. A. ( 2000; ). Comparative analysis of regulatory patterns in bacterial genomes. Brief Bioinform 1, 357–371.[CrossRef]
    [Google Scholar]
  16. Hashimoto, W., Kobayashi, E., Nankai, H., Sato, N., Miya, T., Kawai, S. & Murata, K. ( 1999; ). Unsaturated glucuronyl hydrolase of Bacillus sp. GL1: novel enzyme prerequisite for metabolism of unsaturated oligosaccharides produced by polysaccharide lyases. Arch Biochem Biophys 368, 367–374.[CrossRef]
    [Google Scholar]
  17. Hofmann, K. & Stoffel, W. ( 1993; ). TMbase – A database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler 374, 166.
    [Google Scholar]
  18. Hugouvieux-Cotte-Pattat, N. ( 2004; ). The RhaS activator controls the Erwinia chrysanthemi 3937 genes rhiN, rhiT and rhiE involved in rhamnogalacturonan catabolism. Mol Microbiol 51, 1361–1374.[CrossRef]
    [Google Scholar]
  19. Hugouvieux-Cotte-Pattat, N. & Reverchon, S. ( 2001; ). Two transporters TogT and TogMNAB are responsible for oligogalacturonide uptake in Erwinia chrysanthemi 3937. Mol Microbiol 41, 1125–1132.
    [Google Scholar]
  20. Hugouvieux-Cotte-Pattat, N. & Robert-Baudouy, J. ( 1989; ). Isolation of Erwinia chrysanthemi mutants altered in pectinolytic enzyme production. Mol Microbiol 3, 1587–1597.[CrossRef]
    [Google Scholar]
  21. Hugouvieux-Cotte-Pattat, N., Dominguez, H. & Robert-Baudouy, J. (1992; ). Environmental conditions affect the transcription of the pectinase genes of Erwinia chrysanthemi 3937. J Bacteriol 174, 7807–7818.
    [Google Scholar]
  22. Hugouvieux-Cotte-Pattat, N., Condemine, G., Nasser, W. & Reverchon, S. ( 1996; ). Regulation of pectinolysis in Erwinia chrysanthemi. Annu Rev Microbiol 50, 213–257.[CrossRef]
    [Google Scholar]
  23. Hugouvieux-Cotte-Pattat, N., Blot, N. & Reverchon, S. ( 2001; ). Identification of TogMNAB, an ABC transporter which mediates the uptake of pectic oligomers in Erwinia chrysanthemi 3937. Mol Microbiol 41, 1113–1123.
    [Google Scholar]
  24. Hvorup, R. N., Winnen, B., Chang, A. B., Jiang, Y., Zhou, X. F. & Saier, M. H. ( 2003; ). The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily. Eur J Biochem 270, 799–813.[CrossRef]
    [Google Scholar]
  25. James, V. & Hugouvieux-Cotte-Pattat, N. ( 1996; ). Regulatory systems modulating the transcription of the pectinase genes of Erwinia chrysanthemi are conserved in Escherichia coli. Microbiology 142, 2613–2619.[CrossRef]
    [Google Scholar]
  26. Liu, Y., Jiang, G., Cui, Y., Mukherjee, A., Ma, W. L. & Chatterjee, A. K. ( 1999; ). KdgREcc negatively regulates genes for pectinases, cellulase, protease, HarpinEcc, and a global RNA regulator in Erwinia carotovora subsp. carotovora. J Bacteriol 181, 2411–2421.
    [Google Scholar]
  27. Miller, J. H. ( 1972; ). Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  28. Mironov, A. A., Koonin, E. V., Roytberg, M. A. & Gelfand, M. S. ( 1999; ). Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res 27, 2981–2989.[CrossRef]
    [Google Scholar]
  29. Mironov, A. A., Vinokurova, N. P. & Gel'fand, M. S. ( 2000; ). Software for analyzing bacterial genomes. Mol Biol 34, 253–262.
    [Google Scholar]
  30. Nasser, W. & Reverchon, S. ( 2002; ). H-NS-dependent activation of pectate lyases synthesis in the phytopathogenic bacterium Erwinia chrysanthemi is mediated by the PecT repressor. Mol Microbiol 43, 733–748.[CrossRef]
    [Google Scholar]
  31. Nasser, W., Reverchon, S. & Robert-Baudouy, J. ( 1992; ). Purification and functional characterization of the KdgR protein, a major repressor of pectinolysis genes of Erwinia chrysanthemi. Mol Microbiol 6, 257–265.[CrossRef]
    [Google Scholar]
  32. Nasser, W., Awade, A. C., Reverchon, S. & Robert-Baudouy, J. ( 1993; ). Pectate lyase from Bacillus subtilis: molecular characterization of the gene, and properties of the cloned enzyme. FEBS Lett 335, 319–326.[CrossRef]
    [Google Scholar]
  33. Nasser, W., Reverchon, S., Condemine, G. & Robert-Baudouy, J. ( 1994; ). Specific interactions of Erwinia chrysanthemi KdgR repressor with different operators of genes involved in pectinolysis. J Mol Biol 236, 427–440.[CrossRef]
    [Google Scholar]
  34. Nasser, W., Robert-Baudouy, J. & Reverchon, S. ( 1997; ). Antagonistic effect of CRP and KdgR in the transcription control of the Erwinia chrysanthemi pectinolysis genes. Mol Microbiol 26, 1071–1082.[CrossRef]
    [Google Scholar]
  35. Negre, D., Oudot, C., Prost, J. F., Murakami, K., Ishihama, A., Cozzone, A. J. & Cortay, J. C. ( 1998; ). FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli. J Mol Biol 276, 355–365.[CrossRef]
    [Google Scholar]
  36. Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. ( 1997; ). Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10, 1–6.[CrossRef]
    [Google Scholar]
  37. Niersbach, M., Kreuzaler, F., Geerse, R. H., Postma, P. W. & Hirsch, H. J. ( 1992; ). Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase. Mol Gen Genet 231, 332–336.
    [Google Scholar]
  38. Nomura, K., Nasser, W. & Tsuyumu, S. ( 1999; ). Self-regulation of Pir, a regulatory protein responsible for hyperinduction of pectate lyase in Erwinia chrysanthemi EC16. Mol Plant–Microbe Interact 5, 385–390.
    [Google Scholar]
  39. Oh, M. K., Rohlin, L., Kao, K. C. & Liao, J. C. ( 2002; ). Global expression profiling of acetate-grown Escherichia coli. J Biol Chem 277, 13175–13183.[CrossRef]
    [Google Scholar]
  40. Resibois, A., Colet, M., Faelen, M., Schoonejans, E. & Toussaint, A. ( 1984; ). PhiEC2, a new generalised transducing phage of Erwinia chrysanthemi. Virology 137, 102–112.[CrossRef]
    [Google Scholar]
  41. Reverchon, S., Expert, D., Robert-Baudouy, J. & Nasser, W. ( 1997; ). The cyclic AMP receptor protein is the main activator of the pectinolysis genes in Erwinia chrysanthemi. J Bacteriol 179, 3500–3508.
    [Google Scholar]
  42. Robert-Baudouy, J., Nasser, W., Condemine, G., Reverchon, S., Shevchik, V. E. & Hugouvieux-Cotte-Pattat, N. ( 2000; ). Regulation of pectinase gene expression in Erwinia chrysanthemi. Plant–Microbe Interact 5, 221–268.
    [Google Scholar]
  43. Rodionov, D. A., Mironov, A. A., Rakhmaninova, A. B. & Gelfand, M. S. ( 2000; ). Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria. Mol Microbiol 38, 673–683.[CrossRef]
    [Google Scholar]
  44. Roeder, D. L. & Collmer, A. ( 1985; ). Marker-exchange mutagenesis of pectate lyase isozyme gene in Erwinia chrysanthemi. J Bacteriol 164, 51–56.
    [Google Scholar]
  45. Sabnis, N. A., Yang, H. & Romeo, T. ( 1995; ). Pleiotropic regulation of central carbohydrate metabolism in Escherichia coli via the gene csrA. J Biol Chem 270, 29096–29104.[CrossRef]
    [Google Scholar]
  46. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning. A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  47. Surgey, N., Robert-Baudouy, J. & Condemine, G. ( 1996; ). The Erwinia chrysanthemi pecT gene regulates pectinase gene expression. J Bacteriol 178, 1593–1599.
    [Google Scholar]
  48. Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. ( 2000; ). The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28, 33–36.[CrossRef]
    [Google Scholar]
  49. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  50. Thomson, N. R., Nasser, W., McGowan, S., Sebaihia, M. & Salmond, G. P. ( 1999; ). Erwinia carotovora has two KdgR-like proteins belonging to the IclR family of transcriptional regulators: identification and characterization of the RexZ activator and the KdgR repressor of pathogenesis. Microbiology 145, 1531–1545.[CrossRef]
    [Google Scholar]
  51. Yew, W. S. & Gerlt, J. A. ( 2002; ). Utilization of l-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. J Bacteriol 184, 302–306.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.27041-0
Loading
/content/journal/micro/10.1099/mic.0.27041-0
Loading

Data & Media loading...

Supplements

vol. , part 11, pp. 3571-3590

A table of predicted CRP sites for KdgR-regulated genes in enterobacteria and sp. operons is available hereas an Acrobat PDF file.



PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error