1887

Abstract

Purine nucleotides are either synthesized from 5-phosphoribosyl-1-pyrophosphate (PRPP) or salvaged from the environment. In , transcription of the synthesis operons, and , has genetically been shown to be activated by the PurR protein when bound to a conserved PurBox motif present on the DNA at a fixed distance from the promoter −10 element. PurR contains a PRPP-binding site, and activation occurs when the intracellular PRPP pool is high as a consequence of low exogenous purine nucleotide pools. By an iterative approach of bioinformatics searches and motif optimization, 21 PurR-regulated genes were identified and used in a redefinition of the PurBox consensus sequence. In the process a new motif, the double-PurBox, which is present in a number of promoters and contains two partly overlapping PurBox motifs, was established. Transcriptional fusions were used to analyse wild-type promoters and promoters with inactivating PurBox mutations to confirm the relevance of the PurBox motifs as PurR-binding sites. The promoters of several operons were shown to be devoid of any −35 sequence, and found to be completely dependent on PurR-mediated activation. This suggests that binding of the PurR protein to the PurBox takes over the role of the −35 sequence. The study has expanded the PurR regulon to include promoters in nucleotide metabolism, C compound metabolism, phosphonate transport, pyrophosphatase activity, (p)ppGpp metabolism, and translation-related functions. Of special interest is the presence of PurBox motifs in promoters, suggesting a novel connection between nucleotide availability and the translational machinery.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.059576-0
2012-08-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/158/8/2026.html?itemId=/content/journal/micro/10.1099/mic.0.059576-0&mimeType=html&fmt=ahah

References

  1. Andersen P. S., Martinussen J., Hammer K. ( 1996). Sequence analysis and identification of the pyrKDbF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis. J Bacteriol 178:5005–5012[PubMed]
    [Google Scholar]
  2. Bera A. K., Zhu J., Zalkin H., Smith J. L. ( 2003). Functional dissection of the Bacillus subtilis pur operator site. J Bacteriol 185:4099–4109 [View Article][PubMed]
    [Google Scholar]
  3. Beresford T., Condon S. ( 1991). Cloning and partial characterization of genes for ribosomal ribonucleic acid in Lactococcus lactis subsp. lactis . FEMS Microbiol Lett 62:319–323 [View Article][PubMed]
    [Google Scholar]
  4. Beresford T., Condon S. ( 1993). Physiological and genetic regulation of rRNA synthesis in Lactococcus . J Gen Microbiol 139:2009–2017[PubMed] [CrossRef]
    [Google Scholar]
  5. Bertani G. ( 1951). Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli . J Bacteriol 62:293–300[PubMed]
    [Google Scholar]
  6. Beyer N. H., Roepstorff P., Hammer K., Kilstrup M. ( 2003). Proteome analysis of the purine stimulon from Lactococcus lactis . Proteomics 3:786–797 [View Article][PubMed]
    [Google Scholar]
  7. Bochner B. R., Ames B. N. ( 1982). Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography. J Biol Chem 257:9759–9769[PubMed]
    [Google Scholar]
  8. Bolotin A., Wincker P., Mauger S., Jaillon O., Malarme K., Weissenbach J., Ehrlich S. D., Sorokin A. ( 2001). The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 11:731–753 [View Article][PubMed]
    [Google Scholar]
  9. Cho B. K., Federowicz S. A., Embree M., Park Y. S., Kim D., Palsson B. O. ( 2011). The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res 39:6456–6464 [View Article][PubMed]
    [Google Scholar]
  10. Costantino N., Court D. L. ( 2003). Enhanced levels of λRed-mediated recombinants in mismatch repair mutants. Proc Natl Acad Sci U S A 100:15748–15753 [View Article][PubMed]
    [Google Scholar]
  11. Crooks G. E., Hon G., Chandonia J. M., Brenner S. E. ( 2004). WebLogo: a sequence logo generator. Genome Res 14:1188–1190 [View Article][PubMed]
    [Google Scholar]
  12. Gasson M. J. ( 1983). Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J Bacteriol 154:1–9[PubMed]
    [Google Scholar]
  13. Gasson M. J., Godon J. J., Pillidge C. J., Eaton T. J., Jury K., Shearman C. A. ( 1995). Characterization and exploitation of conjugation in Lactococcus lactis . Int Dairy J 5:757–762 [View Article]
    [Google Scholar]
  14. Gitton C., Meyrand M., Wang J., Caron C., Trubuil A., Guillot A., Mistou M. Y. ( 2005). Proteomic signature of Lactococcus lactis NCDO763 cultivated in milk. Appl Environ Microbiol 71:7152–7163 [View Article][PubMed]
    [Google Scholar]
  15. Guédon E., Jamet E., Renault P. ( 2002). Gene regulation in Lactococcus lactis: the gap between predicted and characterized regulators. Antonie van Leeuwenhoek 82:93–112 [View Article][PubMed]
    [Google Scholar]
  16. Haugen S. P., Berkmen M. B., Ross W., Gaal T., Ward C., Gourse R. L. ( 2006). rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase. Cell 125:1069–1082 [View Article][PubMed]
    [Google Scholar]
  17. Helmann J. D. ( 1995). Compilation and analysis of Bacillus subtilis σA-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res 23:2351–2360 [View Article][PubMed]
    [Google Scholar]
  18. Hove-Jensen B., Rosenkrantz T. J., Haldimann A., Wanner B. L. ( 2003). Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways. J Bacteriol 185:2793–2801 [View Article][PubMed]
    [Google Scholar]
  19. Jendresen C. B., Kilstrup M., Martinussen J. ( 2011). A simplified method for rapid quantification of intracellular nucleoside triphosphates by one-dimensional thin-layer chromatography. Anal Biochem 409:249–259 [View Article][PubMed]
    [Google Scholar]
  20. Jensen P. R., Hammer K. ( 1993). Minimal requirements for exponential growth of Lactococcus lactis . Appl Environ Microbiol 59:4363–4366[PubMed]
    [Google Scholar]
  21. Jensen P. R., Hammer K. ( 1998). The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl Environ Microbiol 64:82–87[PubMed]
    [Google Scholar]
  22. Jensen K. F., Dandanell G., Hove Jensen B., Willemoes M. ( 2008). Nucleotides, nucleosides, and nucleobases. Escherichia coli and Salmonella: Cellular and Molecular Biology Böck A., Curtiss R. III, Kaper J. B., Karp P. D., Neidhardt F. C., Nyström T., Slauch J. M., Squires C. L. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  23. Kilstrup M., Martinussen J. ( 1998). A transcriptional activator, homologous to the Bacillus subtilis PurR repressor, is required for expression of purine biosynthetic genes in Lactococcus lactis . J Bacteriol 180:3907–3916[PubMed]
    [Google Scholar]
  24. Kilstrup M., Jessing S. G., Wichmand-Jørgensen S. B., Madsen M., Nilsson D. ( 1998). Activation control of pur gene expression in Lactococcus lactis: proposal for a consensus activator binding sequence based on deletion analysis and site-directed mutagenesis of purC and purD promoter regions. J Bacteriol 180:3900–3906[PubMed]
    [Google Scholar]
  25. Kilstrup M., Hammer K., Ruhdal Jensen P., Martinussen J. ( 2005). Nucleotide metabolism and its control in lactic acid bacteria. FEMS Microbiol Rev 29:555–590 [View Article][PubMed]
    [Google Scholar]
  26. Kolb A., Busby S., Buc H., Garges S., Adhya S. ( 1993). Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 62:749–797 [View Article][PubMed]
    [Google Scholar]
  27. Kumar A., Grimes B., Fujita N., Makino K., Malloch R. A., Hayward R. S., Ishihama A. ( 1994). Role of the σ70 subunit of Escherichia coli RNA polymerase in transcription activation. J Mol Biol 235:405–413 [View Article][PubMed]
    [Google Scholar]
  28. Martinussen J., Wadskov-Hansen S. L., Hammer K. ( 2003). Two nucleoside uptake systems in Lactococcus lactis: competition between purine nucleosides and cytidine allows for modulation of intracellular nucleotide pools. J Bacteriol 185:1503–1508 [View Article][PubMed]
    [Google Scholar]
  29. Martinussen J., Sørensen C., Jendresen C. B., Kilstrup M. ( 2010). Two nucleoside transporters in Lactococcus lactis with different substrate specificities. Microbiology 156:3148–3157 [View Article][PubMed]
    [Google Scholar]
  30. Moll I., Grill S., Gualerzi C. O., Bläsi U. ( 2002). Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control. Mol Microbiol 43:239–246 [View Article][PubMed]
    [Google Scholar]
  31. Nilsson D., Kilstrup M. ( 1998). Cloning and expression of the Lactococcus lactis purDEK genes, required for growth in milk. Appl Environ Microbiol 64:4321–4327[PubMed]
    [Google Scholar]
  32. Nygaard P., Duckert P., Saxild H. H. ( 1996). Role of adenine deaminase in purine salvage and nitrogen metabolism and characterization of the ade gene in Bacillus subtilis . J Bacteriol 178:846–853[PubMed]
    [Google Scholar]
  33. Rajagopal L., Vo A., Silvestroni A., Rubens C. E. ( 2005). Regulation of purine biosynthesis by a eukaryotic-type kinase in Streptococcus agalactiae . Mol Microbiol 56:1329–1346 [View Article][PubMed]
    [Google Scholar]
  34. Saxild H. H., Nygaard P. ( 1991). Regulation of levels of purine biosynthetic enzymes in Bacillus subtilis: effects of changing purine nucleotide pools. J Gen Microbiol 137:2387–2394[PubMed] [CrossRef]
    [Google Scholar]
  35. Saxild H. H., Brunstedt K., Nielsen K. I., Jarmer H., Nygaard P. ( 2001). Definition of the Bacillus subtilis PurR operator using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD, and pbuO . J Bacteriol 183:6175–6183 [View Article][PubMed]
    [Google Scholar]
  36. Schneider T. D., Stephens R. M. ( 1990). Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18:6097–6100 [View Article][PubMed]
    [Google Scholar]
  37. Shin B. S., Stein A., Zalkin H. ( 1997). Interaction of Bacillus subtilis purine repressor with DNA. J Bacteriol 179:7394–7402[PubMed]
    [Google Scholar]
  38. Terzaghi B. E., Sandine W. E. ( 1975). Improved medium for lactic streptococci and their bacteriophages. Appl Microbiol 29:807–813[PubMed]
    [Google Scholar]
  39. Thomason L., Court D. L., Bubunenko M., Costantino N., Wilson H., Datta S., Oppenheim A. ( 2007a). Recombineering: genetic engineering in bacteria using homologous recombination. Curr Protoc Mol Biol Chapter 1:1–, 16[PubMed]
    [Google Scholar]
  40. Thomason L. C., Costantino N., Shaw D. V., Court D. L. ( 2007b). Multicopy plasmid modification with phage λRed recombineering. Plasmid 58:148–158 [View Article][PubMed]
    [Google Scholar]
  41. Travers A. A. ( 1980). Promoter sequence for stringent control of bacterial ribonucleic acid synthesis. J Bacteriol 141:973–976[PubMed]
    [Google Scholar]
  42. Tulloch D. L., Finch L. R., Hillier A. J., Davidson B. E. ( 1991). Physical map of the chromosome of Lactococcus lactis subsp. lactis DL11 and localization of six putative rRNA operons. J Bacteriol 173:2768–2775[PubMed]
    [Google Scholar]
  43. Wegmann U., O’Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M. J. & other authors ( 2007). Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 189:3256–3270 [View Article][PubMed]
    [Google Scholar]
  44. Weng M., Nagy P. L., Zalkin H. ( 1995). Identification of the Bacillus subtilis pur operon repressor. Proc Natl Acad Sci U S A 92:7455–7459 [View Article][PubMed]
    [Google Scholar]
  45. Zomer A. L., Buist G., Larsen R., Kok J., Kuipers O. P. ( 2007). Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 189:1366–1381 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.059576-0
Loading
/content/journal/micro/10.1099/mic.0.059576-0
Loading

Data & Media loading...

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