1887

Abstract

The Cg1547 protein of ATCC 13032 is a member of the LacI/GalR family of DNA-binding transcriptional regulators. A defined deletion in the gene, now designated (uridine utilization regulator), resulted in the mutant strain KB1547. Comparison of gene expression levels in KB1547 and the wild-type strain revealed enhanced expression of the operon genes (ribokinase), (uridine transporter) and (uridine-preferring nucleoside hydrolase). Gene expression of the operon was stimulated by the presence of either uridine or ribose. Growth assays with mutants showed that functional Cg1543 and Cg1545 proteins are essential for the utilization of uridine as the sole carbon source. Transcriptional regulation of the operon is mediated by a 29 bp palindromic sequence composed of two catabolite-responsive element ()-like sequences and located in between the mapped −10 promoter region and the start codon of . A similar sequence was detected in the upstream region of (), coding for a second ribokinase in ATCC 13032. DNA band-shift assays with a streptavidin-tagged UriR protein and labelled oligonucleotides including the -like sequences of and demonstrated the specific binding of the purified regulator . Whole-genome DNA microarray hybridizations comparing the gene expression in KB1547 with that of the wild-type strain revealed that UriR is a pathway-specific repressor of genes involved in uridine utilization in .

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2007/014001-0
2008-04-01
2019-10-22
Loading full text...

Full text loading...

/deliver/fulltext/micro/154/4/1068.html?itemId=/content/journal/micro/10.1099/mic.0.2007/014001-0&mimeType=html&fmt=ahah

References

  1. Arndt, A. & Eikmanns, B. J. ( 2007; ). The alcohol dehydrogenase gene adhA in Corynebacterium glutamicum is subject to carbon catabolite repression. J Bacteriol 189, 7408–7416.[CrossRef]
    [Google Scholar]
  2. Baumbach, J., Brinkrolf, K., Czaja, L. F., Rahmann, S. & Tauch, A. ( 2006; ). CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics 7, 24 [CrossRef]
    [Google Scholar]
  3. Brinkrolf, K., Brune, I. & Tauch, A. ( 2006; ). Transcriptional regulation of catabolic pathways for aromatic compounds in Corynebacterium glutamicum. Genet Mol Res 5, 773–789.
    [Google Scholar]
  4. Brinkrolf, K., Brune, I. & Tauch, A. ( 2007; ). The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum. J Biotechnol 129, 191–211.[CrossRef]
    [Google Scholar]
  5. Brückner, R. & Titgemeyer, F. ( 2002; ). Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol Lett 209, 141–148.[CrossRef]
    [Google Scholar]
  6. Brune, I., Brinkrolf, K., Kalinowski, J., Pühler, A. & Tauch, A. ( 2005; ). The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. BMC Genomics 6, 86 [CrossRef]
    [Google Scholar]
  7. Brune, I., Becker, A., Paarmann, D., Albersmeier, A., Kalinowski, J., Pühler, A. & Tauch, A. ( 2006; ). Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression. J Biotechnol 127, 21–33.[CrossRef]
    [Google Scholar]
  8. Brune, I., Jochmann, N., Brinkrolf, K., Hüser, A. T., Gerstmeir, R., Eikmanns, B. J., Kalinowski, J., Pühler, A. & Tauch, A. ( 2007; ). The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum. J Bacteriol 189, 2720–2733.[CrossRef]
    [Google Scholar]
  9. Daber, R., Stayrook, S., Rosenberg, A. & Lewis, M. ( 2007; ). Structural analysis of lac repressor bound to allosteric effectors. J Mol Biol 370, 609–619.[CrossRef]
    [Google Scholar]
  10. Dondrup, M., Goesmann, A., Bartels, D., Kalinowski, J., Krause, L., Linke, B., Rupp, O., Sczyrba, A., Pühler, A. & other authors ( 2003; ). EMMA: a platform for consistent storage and efficient analysis of microarray data. J Biotechnol 106, 135–146.[CrossRef]
    [Google Scholar]
  11. Dong, F., Spott, S., Zimmermann, O., Kisters-Woike, B., Müller-Hill, B. & Barker, A. ( 1999; ). Dimerisation mutants of Lac repressor. I. A monomeric mutant, L251A, that binds lac operator DNA as a dimer. J Mol Biol 290, 653–666.[CrossRef]
    [Google Scholar]
  12. Eikmanns, B. J. ( 2005; ). Central metabolism: tricarboxylic acid cycle and anaplerotic reactions. In Handbook of Corynebacterium glutamicum, pp. 241–276. Edited by L. Eggeling & M. Bott. Boca Raton, FL: CRC Press.
  13. Fukami-Kobayashi, K., Tateno, Y. & Nishikawa, K. ( 2003; ). Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol Biol Evol 20, 267–277.[CrossRef]
    [Google Scholar]
  14. Grant, S. G., Jessee, J., Bloom, F. R. & Hanahan, D. ( 1990; ). Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A 87, 4645–4649.[CrossRef]
    [Google Scholar]
  15. Han, S. O., Inui, M. & Yukawa, H. ( 2007; ). Expression of Corynebacterium glutamicum glycolytic genes varies with carbon source and growth phase. Microbiology 153, 2190–2202.[CrossRef]
    [Google Scholar]
  16. Herrgård, M. J., Covert, M. W. & Palsson, B. Ø. ( 2004; ). Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol 15, 70–77.[CrossRef]
    [Google Scholar]
  17. Horton, R. M., Hunt, H. D., Ho, S. N., Pullen, J. K. & Pease, L. R. ( 1989; ). Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77, 61–68.[CrossRef]
    [Google Scholar]
  18. Hueck, C. J., Hillen, W. & Saier, M. H., Jr ( 1994; ). Analysis of a cis-active sequence mediating catabolite repression in gram-positive bacteria. Res Microbiol 145, 503–518.[CrossRef]
    [Google Scholar]
  19. Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., De Castro, E., Langendijk-Genevaux, P. S., Pagni, M. & Sigrist, C. J. ( 2006; ). The PROSITE database. Nucleic Acids Res 34, D227–D230.[CrossRef]
    [Google Scholar]
  20. Itou, H., Okada, U., Suzuki, H., Yao, M., Wachi, M., Watanabe, N. & Tanaka, I. ( 2005; ). The CGL2612 protein from Corynebacterium glutamicum is a drug resistance-related transcriptional repressor: structural and functional analysis of a newly identified transcription factor from genomic DNA analysis. J Biol Chem 280, 38711–38719.[CrossRef]
    [Google Scholar]
  21. Kalinowski, J., Bathe, B., Bartels, D., Bischoff, N., Bott, M., Burkovski, A., Dusch, N., Eggeling, L., Eikmanns, B. J. & other authors ( 2003; ). The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins. J Biotechnol 104, 5–25.[CrossRef]
    [Google Scholar]
  22. Keilhauer, C., Eggeling, L. & Sahm, H. ( 1993; ). Isoleucine synthesis in Corynebacterium glutamicum: molecular analysis of the ilvB-ilvN-ilvC operon. J Bacteriol 175, 5595–5603.
    [Google Scholar]
  23. Kim, H. S., Lee, J. H., Lee, W. S. & Bang, W. G. ( 2006; ). Genes encoding ribonucleoside hydrolase 1 and 2 from Corynebacterium ammoniagenes. Microbiology 152, 1169–1177.[CrossRef]
    [Google Scholar]
  24. Kirchner, O. & Tauch, A. ( 2003; ). Tools for genetic engineering in the amino acid-producing bacterium Corynebacterium glutamicum. J Biotechnol 104, 287–299.[CrossRef]
    [Google Scholar]
  25. Kraus, A., Küster, E., Wagner, A., Hoffmann, K. & Hillen, W. ( 1998; ). Identification of a co-repressor binding site in catabolite control protein CcpA. Mol Microbiol 30, 955–963.[CrossRef]
    [Google Scholar]
  26. Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J. & Giegerich, R. ( 2001; ). REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29, 4633–4642.[CrossRef]
    [Google Scholar]
  27. Letek, M., Valbuena, N., Ramos, A., Ordóñez, E., Gil, J. A. & Mateos, L. M. ( 2006; ). Characterization and use of catabolite-repressed promoters from gluconate genes in Corynebacterium glutamicum. J Bacteriol 188, 409–423.[CrossRef]
    [Google Scholar]
  28. Lulko, A. T., Buist, G., Kok, J. & Kuipers, O. P. ( 2007; ). Transcriptome analysis of temporal regulation of carbon metabolism by CcpA in Bacillus subtilis reveals additional target genes. J Mol Microbiol Biotechnol 12, 82–95.[CrossRef]
    [Google Scholar]
  29. Madan Babu, M. & Teichmann, S. A. ( 2003a; ). Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. Trends Genet 19, 75–79.[CrossRef]
    [Google Scholar]
  30. Madan Babu, M. & Teichmann, S. A. ( 2003b; ). Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 31, 1234–1244.[CrossRef]
    [Google Scholar]
  31. Madera, M., Vogel, C., Kummerfeld, S. K., Chothia, C. & Gough, J. ( 2004; ). The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res 32, D235–D239.[CrossRef]
    [Google Scholar]
  32. Mahr, K., Hillen, W. & Titgemeyer, F. ( 2000; ). Carbon catabolite repression in Lactobacillus pentosus: analysis of the ccpA region. Appl Environ Microbiol 66, 277–283.[CrossRef]
    [Google Scholar]
  33. Martínez-Antonio, A., Janga, S. C., Salgado, H. & Collado-Vides, J. ( 2006; ). Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli. Trends Microbiol 14, 22–27.[CrossRef]
    [Google Scholar]
  34. Miles, R. W., Tyler, P. C., Evans, G. B., Furneaux, R. H., Parkin, D. W. & Schramm, V. L. ( 1999; ). Iminoribitol transition state analogue inhibitors of protozoan nucleoside hydrolases. Biochemistry 38, 13147–13154.[CrossRef]
    [Google Scholar]
  35. Nguyen, C. C. & Saier, M. H., Jr ( 1995; ). Phylogenetic, structural and functional analyses of the LacI-GalR family of bacterial transcription factors. FEBS Lett 377, 98–102.[CrossRef]
    [Google Scholar]
  36. Nishio, Y., Nakamura, Y., Kawarabayasi, Y., Usuda, Y., Kimura, E., Sugimoto, S., Matsui, K., Yamagishi, A., Kikuchi, H. & other authors ( 2003; ). Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. Genome Res 13, 1572–1579.[CrossRef]
    [Google Scholar]
  37. Parche, S., Burkovski, A., Sprenger, G. A., Weil, B., Krämer, R. & Titgemeyer, F. ( 2001; ). Corynebacterium glutamicum: a dissection of the PTS. J Mol Microbiol Biotechnol 3, 423–428.
    [Google Scholar]
  38. Pátek, M., Nesvera, J., Guyonvarch, A., Reyes, O. & Leblon, G. ( 2003; ). Promoters of Corynebacterium glutamicum. J Biotechnol 104, 311–323.[CrossRef]
    [Google Scholar]
  39. Price, M. N., Huang, K. H., Alm, E. J. & Arkin, A. P. ( 2005; ). A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 33, 880–892.[CrossRef]
    [Google Scholar]
  40. Resendis-Antonio, O., Freyre-González, J. A., Menchaca-Méndez, R., Gutiérrez-Ríos, R. M., Martínez-Antonio, A., Ávila-Sánchez, C. & Collado-Vides, J. ( 2005; ). Modular analysis of the transcriptional regulatory network of E. coli. Trends Genet 21, 16–20.[CrossRef]
    [Google Scholar]
  41. Rittmann, D., Sorger-Herrmann, U. & Wendisch, V. F. ( 2005; ). Phosphate starvation-inducible gene ushA encodes a 5′ nucleotidase required for growth of Corynebacterium glutamicum on media with nucleotides as the phosphorus source. Appl Environ Microbiol 71, 4339–4344.[CrossRef]
    [Google Scholar]
  42. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
  43. Schäfer, A., Tauch, A., Jäger, W., Kalinowski, J., Thierbach, G. & Pühler, A. ( 1994; ). Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145, 69–73.[CrossRef]
    [Google Scholar]
  44. Shen, X. H., Huang, Y. & Liu, S. J. ( 2005; ). Genomic analysis and identification of catabolic pathways for aromatic compounds in Corynebacterium glutamicum. Microbes Environ 20, 160–167.[CrossRef]
    [Google Scholar]
  45. Sigrell, J. A., Cameron, A. D., Jones, T. A. & Mowbray, S. L. ( 1997; ). Purification, characterization, and crystallization of Escherichia coli ribokinase. Protein Sci 6, 2474–2476.
    [Google Scholar]
  46. Tauch, A., Kirchner, O., Wehmeier, L., Kalinowski, J. & Pühler, A. ( 1994; ). Corynebacterium glutamicum DNA is subjected to methylation-restriction in Escherichia coli. FEMS Microbiol Lett 123, 343–347.[CrossRef]
    [Google Scholar]
  47. Tauch, A., Kassing, F., Kalinowski, J. & Pühler, A. ( 1995; ). The Corynebacterium xerosis composite transposon Tn5432 consists of two identical insertion sequences, designated IS1249, flanking the erythromycin resistance gene ermCX. Plasmid 34, 119–131.[CrossRef]
    [Google Scholar]
  48. Tauch, A., Kirchner, O., Löffler, B., Götker, S., Pühler, A. & Kalinowski, J. ( 2002; ). Efficient electrotransformation of Corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1. Curr Microbiol 45, 362–367.[CrossRef]
    [Google Scholar]
  49. Titgemeyer, F. & Hillen, W. ( 2002; ). Global control of sugar metabolism: a gram-positive solution. Antonie Van Leeuwenhoek 82, 59–71.[CrossRef]
    [Google Scholar]
  50. Weickert, M. J. & Adhya, S. ( 1992; ). A family of bacterial regulators homologous to Gal and Lac repressors. J Biol Chem 267, 15869–15874.
    [Google Scholar]
  51. Weickert, M. J. & Chambliss, G. H. ( 1990; ). Site-directed mutagenesis of a catabolite repression operator sequence in Bacillus subtilis. Proc Natl Acad Sci U S A 87, 6238–6242.[CrossRef]
    [Google Scholar]
  52. Wendisch, V. F. ( 2003; ). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J Biotechnol 104, 273–285.[CrossRef]
    [Google Scholar]
  53. Wendisch, V. F., de Graaf, A. A., Sahm, H. & Eikmanns, B. J. ( 2000; ). Quantitative determination of metabolic fluxes during coutilization of two carbon sources: comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose. J Bacteriol 182, 3088–3096.[CrossRef]
    [Google Scholar]
  54. Winnen, B., Felce, J. & Saier, M. H., Jr ( 2005; ). Genomic analyses of transporter proteins in Corynebacterium glutamicum and Corynebacterium efficiens. In Handbook of Corynebacterium glutamicum, pp. 149–186. Edited by L. Eggeling & M. Bott. Boca Raton, FL: CRC Press.
  55. Yukawa, H., Omumasaba, C. A., Nonaka, H., Kós, P., Okai, N., Suzuki, N., Suda, M., Tsuge, Y., Watanabe, J. & other authors ( 2007; ). Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R. Microbiology 153, 1042–1058.[CrossRef]
    [Google Scholar]
  56. Zuker, M. ( 2003; ). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406–3415.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2007/014001-0
Loading
/content/journal/micro/10.1099/mic.0.2007/014001-0
Loading

Data & Media loading...

Supplements

Oligonucleotides used in the study [ PDF] (17 kb) Differentially expressed genes in KB1547 compared to the wild-type detected by DNA microarray hybridization [ PDF] (164 kb)

PDF

Oligonucleotides used in the study [ PDF] (17 kb) Differentially expressed genes in KB1547 compared to the wild-type detected by DNA microarray hybridization [ PDF] (164 kb)

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