1887

Abstract

The ability to recognize and predict non- promoters in the alphaproteobacteria is not well developed. In this study, 25 experimentally verified promoter sequences were compiled and used to predict the location of other related promoters in the genome. Fourteen candidate predictions were targeted for verification and of these at least 12 proved to be genuine promoters. As a result, the experimental identification of 12 novel promoters linked to genes , , , , , , , , and three tRNA genes is reported. In all, 99 predicted and verified promoters are reported, including those linked with 13 tRNA genes, eight ribosomal protein genes and a number of other physiologically important or essential genes. On the basis of sequence conservation and a mutational analysis of promoter activity, the −35 and −10 consensus for these promoters is 5-CTTGAC-N-CTATAT. This promoter structure, which seems to be widely conserved amongst several other genera in the alphaproteobacteria, shares significant similarity with, but is skewed by a 1 nt step from, the canonical promoter. Perhaps this difference is responsible for the observation that promoters are often poorly expressed in . In this regard, expression data from plasmid-borne -reporter fusions to eight of the promoters verified in this work revealed that while these promoters were very active in and only very low, near-background activity was detected in .

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2006-06-01
2024-03-29
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References

  1. Aiyar S. E, Gourse R. L, Ross W. 1998; Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit. Proc Natl Acad Sci U S A 95:14652–14657 [CrossRef]
    [Google Scholar]
  2. Allaway D, Schofield N. A, Leonard M. E, Gilardoni L, Finan T. M, Poole P. S. 2001; Use of differential fluorescence induction and optical trapping to isolate environmentally induced genes. Environ Microbiol 3:397–406 [CrossRef]
    [Google Scholar]
  3. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner E. G, Margalit H, Altuvia S. 2001; Novel small RNA-encoding genes in the intergenic regions of Escherichia coli . Curr Biol 11:941–950 [CrossRef]
    [Google Scholar]
  4. Bae Y. M, Holmgren E, Crawford I. P. 1989; Rhizobium meliloti anthranilate synthase gene: cloning, sequence, and expression in Escherichia coli . J Bacteriol 171:3471–3478
    [Google Scholar]
  5. Beck C, Marty R, Klausli S, Hennecke H, Gottfert M. 1997; Dissection of the transcription machinery for housekeeping genes of Bradyrhizobium japonicum . J Bacteriol 179:364–369
    [Google Scholar]
  6. Chai Y, Winans S. C. 2005; A small antisense RNA downregulates expression of an essential replicase protein of an Agrobacterium tumefaciens Ti plasmid. Mol Microbiol 56:1574–1585 [CrossRef]
    [Google Scholar]
  7. Chen S, Lesnik E. A, Hall T. A, Sampath R, Griffey R. H, Ecker D. J, Blyn L. B. 2002; A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems 65:157–177 [CrossRef]
    [Google Scholar]
  8. DelVecchio V. G, Kapatral V, Elzer P, Patra G, Mujer C. V. 2002; The genome of Brucella melitensis . Vet Microbiol 90:587–592 [CrossRef]
    [Google Scholar]
  9. Dombrecht B, Marchal K, Vanderleyden J, Michiels J. 2002; Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales . Genome Biol 3: RESEARCH0076
    [Google Scholar]
  10. Dsouza M, Larsen N, Overbeek R. 1997; Searching for patterns in genomic data. Trends Genet 13:497–498
    [Google Scholar]
  11. Fisher R. F, Brierley H. L, Mulligan J. T, Long S. R. 1987; Transcription of Rhizobium meliloti nodulation genes. Identification of a nodD transcription initiation site in vitro and in vivo . J Biol Chem 262:6849–6855
    [Google Scholar]
  12. Galibert F, Finan T. M, Long S. R. 53 other authors 2001; The composite genome of the legume symbiont Sinorhizobium meliloti . Science 293:668–672 [CrossRef]
    [Google Scholar]
  13. Gustafson A. M, O'Connell K. P, Thomashow M. F. 2002; Regulation of Sinorhizobium meliloti 1021 rrnA -reporter gene fusions in response to cold shock. Can J Microbiol 48:821–830 [CrossRef]
    [Google Scholar]
  14. Halling S. M, Peterson-Burch B. D, Bricker B. J, Zuerner R. L, Qing Z, Li L. L, Kapur V, Alt D. P, Olsen S. C. 2005; Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis . J Bacteriol 187:2715–2726 [CrossRef]
    [Google Scholar]
  15. Harley C. B, Reynolds R. P. 1987; Analysis of E. coli promoter sequences. Nucleic Acids Res 15:2343–2361 [CrossRef]
    [Google Scholar]
  16. Izquierdo J, Venkova-Canova T, Ramirez-Romero M. A, Tellez-Sosa J, Hernandez-Lucas I, Sanjuan J, Cevallos M. A. 2005; An antisense RNA plays a central role in the replication control of a repC plasmid. Plasmid 54:259–277 [CrossRef]
    [Google Scholar]
  17. Kaneko T, Nakamura Y, Sato S. 14 other authors 2002; Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 (supplement). DNA Res 9:225–256 [CrossRef]
    [Google Scholar]
  18. Leong S. A, Williams P. H, Ditta G. S. 1985; Analysis of the 5′ regulatory region of the gene for delta-aminolevulinic acid synthetase of Rhizobium meliloti . Nucleic Acids Res 13:5965–5976 [CrossRef]
    [Google Scholar]
  19. Lisser S, Margalit H. 1993; Compilation of E. coli mRNA promoter sequences. Nucleic Acids Res 21:1507–1516 [CrossRef]
    [Google Scholar]
  20. MacLellan S. R, Smallbone L. A, Sibley C. D, Finan T. M. 2005; The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids. Mol Microbiol 55:611–623
    [Google Scholar]
  21. Osteras M, Driscoll B. T, Finan T. M. 1995; Molecular and expression analysis of the Rhizobium meliloti phosphoenolpyruvate carboxykinase (pckA) gene. J Bacteriol 177:1452–1460
    [Google Scholar]
  22. Papp P. P. 2004; tRNA gene containing an attachment site of a temperate phage is functional: proof by converting attB to amber suppressor. GenBank accession no. AJ698943
    [Google Scholar]
  23. Paulsen I. T, Seshadri R, Nelson K. E. 28 other authors 2002; The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A 99:13148–13153 [CrossRef]
    [Google Scholar]
  24. Ronson C. W, Nixon B. T, Albright L. M, Ausubel F. M. 1987; Rhizobium meliloti ntrA (rpoN) gene is required for diverse metabolic functions. J Bacteriol 169:2424–2431
    [Google Scholar]
  25. Ross W, Aiyar S. E, Salomon J, Gourse R. L. 1998; Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J Bacteriol 180:5375–5383
    [Google Scholar]
  26. Thony B, Hennecke H. 1989; The −24/−12 promoter comes of age. FEMS Microbiol Rev 5:341–357
    [Google Scholar]
  27. Venkova-Canova T, Soberon N. E, Ramirez-Romero M. A, Cevallos M. A. 2004; Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure. Mol Microbiol 54:1431–1444 [CrossRef]
    [Google Scholar]
  28. Wood D. W, Setubal J. C, Kaul R. 49 other authors 2001; The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317–2323 [CrossRef]
    [Google Scholar]
  29. Zacharias M, Goringer H. U, Wagner R. 1990; The signal for growth rate control and stringent sensitivity in E. coli is not restricted to a particular sequence motif within the promoter region. Nucleic Acids Res 18:6271–6275 [CrossRef]
    [Google Scholar]
  30. Zacharias M, Theissen G, Bradaczek C, Wagner R. 1991; Analysis of sequence elements important for the synthesis and control of ribosomal RNA in E coli . Biochimie 73:699–712 [CrossRef]
    [Google Scholar]
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