1887

Abstract

As in other bacteria, 3′-tails are added post-transcriptionally to RNA. These tails are heteropolymeric, and although there are several candidates, the enzyme responsible for their synthesis has not been definitively identified. This paper reports on three candidates for this role. First, it is confirmed that the product of gene , although it bears significant sequence similarity to poly(A) polymerase I, is a tRNA nucleotidyltransferase, not a poly(A) polymerase. It is further shown that encodes an RNase PH homologue that possesses the polymerization and phosphorolysis activities expected for enzymes of that family. RNase PH can add poly(A) tails to a model RNA transcript . However, disruption of the RNase PH gene has no effect on RNA 3′-tail length or composition in ; thus, RNase PH does not function as the RNA 3′-polyribonucleotide polymerase [poly(A) polymerase] in that organism. These results strongly suggest that the enzyme responsible for RNA 3′-tail synthesis in and other streptomycetes is polynucleotide phosphorylase (PNPase). Moreover, this study shows that both PNPase and the product of are essential. It is possible that the dual functions of PNPase in the synthesis and degradation of RNA 3′-tails make it indispensable in .

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.28363-0
2006-03-01
2019-10-22
Loading full text...

Full text loading...

/deliver/fulltext/micro/152/3/627.html?itemId=/content/journal/micro/10.1099/mic.0.28363-0&mimeType=html&fmt=ahah

References

  1. Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A. M. & 40 other authors ( 2002; ). Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141–147.[CrossRef]
    [Google Scholar]
  2. Bierman, M., Logan, R., O'Brien, K., Seno, E. T., Rao, R. N. & Shoner, B. E. ( 1992; ). Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. Gene 116, 43–49.[CrossRef]
    [Google Scholar]
  3. Bradford, M. M. ( 1976; ). A rapid and sensitive method for the quantitation of microgram quantities of protein using the principle of protein-dye binding. Anal Biochem 72, 248–254.[CrossRef]
    [Google Scholar]
  4. Bralley, P. & Jones, G. H. ( 2001; ). Poly(A) polymerase activity and RNA polyadenylation in Streptomyces coelicolor A3(2). Mol Microbiol 40, 1155–1164.[CrossRef]
    [Google Scholar]
  5. Bralley, P. & Jones, G. H. ( 2002; ). cDNA cloning confirms the polyadenylation of RNA decay intermediates in Streptomyces coelicolor. Microbiology 148, 1421–1425.
    [Google Scholar]
  6. Bralley, P. & Jones, G. H. ( 2003; ). Overexpression of the polynucleotide phosphorylase gene (pnp) of Streptomyces antibioticus affects mRNA stability and poly(A) tail length but not ppGpp levels. Microbiology 149, 2173–2182.[CrossRef]
    [Google Scholar]
  7. Bralley, P. & Jones, G. H. ( 2004; ). Organization and expression of the polynucleotide phosphorylase gene (pnp) of Streptomyces: processing of pnp transcripts in Streptomyces antibioticus. J Bacteriol 186, 3160–3172.[CrossRef]
    [Google Scholar]
  8. Bralley, P., Chang, S. A. & Jones, G. H. ( 2005; ). A phylogeny of bacterial nucleotidyltransferases: Bacillus halodurans contains two tRNA nucleotidyltransferases. J Bacteriol 187, 5927–5936.[CrossRef]
    [Google Scholar]
  9. Campos-Guillén, J., Bralley, P., Jones, G. H., Bechhofer, D. H. & Almeda-Alvarez, G. ( 2005; ). Addition of poly(A) and heteropolymeric 3′-ends in Bacillus subtilis wild-type and PNPase-deficient strains. J Bacteriol 187, 4698–4706.[CrossRef]
    [Google Scholar]
  10. Cao, G. J. & Sarkar, N. ( 1992; ). Identification of the gene for an Escherichia coli poly(A) polymerase. Proc Natl Acad Sci U S A 89, 10380–10384.[CrossRef]
    [Google Scholar]
  11. Carpousis, A. J., Vanzo, N. F. & Raynal, L. C. ( 1999; ). mRNA degradation: a tale of poly(A) and multiprotein machines. Trends Genet 15, 24–28.[CrossRef]
    [Google Scholar]
  12. Chang, S. A., Bralley, P. & Jones, G. H. ( 2005; ). The absB gene encodes a double-strand specific endoribonuclease that cleaves the readthrough transcript of the rspO-pnp operon in Streptomyces coelicolor. J Biol Chem 280, 33213–33219.[CrossRef]
    [Google Scholar]
  13. Cheng, Z. F. & Deutscher, M. P. ( 2005; ). An important role for RNase R in mRNA decay. Mol Cell 17, 313–318.[CrossRef]
    [Google Scholar]
  14. Coburn, G. A. & Mackie, G. A. ( 1999; ). Degradation of mRNA in Escherichia coli: an old problem with some new twists. Prog Nucleic Acids Res Mol Biol 62, 55–105.
    [Google Scholar]
  15. Deutscher, M. ( 1995; ). tRNA processing nucleases. In tRNA: Structure, Biosynthesis and Function, pp. 51–65. Edited by D. Söll & U. L. RajBhandary. Washington, DC: American Society for Microbiology.
  16. Deutscher, M., Marshall, G. T. & Cudny, H. ( 1988; ). RNase PH: an Escherichia coli phosphate-dependent nuclease distinct from polynucleotide phosphorylase. Proc Natl Acad Sci U S A 85, 4710–4714.[CrossRef]
    [Google Scholar]
  17. Gust, B., Challis, G. L., Fowler, K., Kieser, T. & Chater, K. F. ( 2003; ). PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc Natl Acad Sci U S A 100, 1541–1546.[CrossRef]
    [Google Scholar]
  18. Hagège, J. M. & Cohen, S. N. ( 1997; ). A developmentally regulated Streptomyces endoribonuclease resembles ribonuclease of Escherichia coli. Mol Microbiol 25, 1077–1090.[CrossRef]
    [Google Scholar]
  19. He, L., Soderbom, F., Wagner, E. G., Binnie, U., Binns, N. & Masters, M. ( 1993; ). PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids. Mol Microbiol 9, 1131–1142.[CrossRef]
    [Google Scholar]
  20. Holm, L. & Sander, C. ( 1995; ). DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem Sci 20, 345–347.[CrossRef]
    [Google Scholar]
  21. Hsieh, C.-J. & Jones, G. H. ( 1995; ). Nucleotide sequence, transcriptional analysis and glucose regulation of the phenoxazinone synthase gene from Streptomyces antibioticus. J Bacteriol 177, 5740–5747.
    [Google Scholar]
  22. Jones, G. H. & Bibb, M. J. ( 1996; ). Guanosine pentaphosphate synthetase from Streptomyces antibioticus is also a polynucleotide phosphorylase. J Bacteriol 178, 4281–4288.
    [Google Scholar]
  23. Jones, G. H., Symmons, M. F., Hankins, J. S. & Mackie, G. A. ( 2003; ). Overexpression and purification of untagged polynucleotide phosphorylases. Protein Expr Purif 32, 202–209.[CrossRef]
    [Google Scholar]
  24. Kalapos, M. P., Cao, G. J., Kushner, S. R. & Sarkar, N. ( 1994; ). Identification of a second poly(A) polymerase in Escherichia coli. Biochem Biophys Res Commun 198, 459–465.[CrossRef]
    [Google Scholar]
  25. Kieser, Y., Bibb, M. J., Buttner, M. J., Chater, K. F. & Hopwood, D. A. ( 2000; ). Practical Streptomyces Genetics. Norwich: John Innes Foundation.
  26. Laemmli, U. ( 1970; ). Cleavage of structural protein during the assembly of the head of bacteriophage T4. Nature 227, 680–685.[CrossRef]
    [Google Scholar]
  27. Lee, K. & Cohen, S. N. ( 2001; ). A Streptomyces coelicolor functional analog of E. coli RNase E shows evolutionary shuffling of catalytic and PNPase domains. In Proceedings of the 12th International Symposium on the Biology of Actinomycetes, p. 66.
  28. Mohanty, B. K. & Kushner, S. R. ( 1999a; ). Residual polyadenylation in poly(A) polymerase I (pcnB) mutants of Escherichia coli does not result from the activity encoded by the f310 gene. Mol Microbiol 34, 1109–1119.[CrossRef]
    [Google Scholar]
  29. Mohanty, B. K. & Kushner, S. R. ( 1999b; ). Analysis of the function of Escherichia coli poly(A) polymerase in RNA metabolism. Mol Microbiol 34, 1094–1108.[CrossRef]
    [Google Scholar]
  30. Mohanty, B. K. & Kushner, S. R. ( 2000a; ). Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli. Mol Microbiol 36, 982–994.[CrossRef]
    [Google Scholar]
  31. Mohanty, B. K. & Kushner, S. R. ( 2000b; ). Polynucleotide phosphorylase functions both as a 3′-5′ exonuclease and a poly(A) polymerase in Escherichia coli. Proc Natl Acad Sci U S A 97, 11966–11971.[CrossRef]
    [Google Scholar]
  32. O'Connor, T. J., Kanellis, P. & Nodwell, J. R. ( 2002; ). The ramC gene is required for morphogenesis in Streptomyces coelicolor and expressed in a cell type-specific manner under the direct control of RamR. Mol Microbiol 45, 45–57.[CrossRef]
    [Google Scholar]
  33. O'Hara, E. B., Chekanova, J. A., Ingle, C. A., Kushner, Z. R., Peters, E. & Kushner, S. R. ( 1995; ). Polyadenylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci U S A 92, 1807–1811.[CrossRef]
    [Google Scholar]
  34. Ost, K. A. & Deutscher, M. ( 1990; ). RNase PH catalyzes a synthetic reaction, the addition of nucleotides to the 3′-ends of RNA. Biochimie 72, 813–818.[CrossRef]
    [Google Scholar]
  35. Price, B., Adamis, T. & Champness, W. ( 1999; ). A Streptomyces coelicolor antibiotic regulatory gene, absB, encodes an RNase III homolog. J Bacteriol 181, 6142–6151.
    [Google Scholar]
  36. Rauhut, R. & Klug, G. ( 1999; ). mRNA degradation in bacteria. FEMS Microbiol Rev 23, 353–370.[CrossRef]
    [Google Scholar]
  37. Raynal, L. C., Krisch, H. M. & Carpousis, A. J. ( 1998; ). The Bacillus subtilis nucleotidyl transferase is a tRNA CCA-adding enzyme. J Bacteriol 180, 6276–6282.
    [Google Scholar]
  38. Régnier, P. & Arraiano, C. M. ( 2000; ). Degradation of mRNA in bacteria: emergence of ubiquitous features. Bioessays 22, 235–244.[CrossRef]
    [Google Scholar]
  39. Rott, R., Zipor, G., Portnoy, V., Liveanu, V. & Schuster, G. ( 2003; ). RNA polyadenylation and degradation in cyanobacteria are similar to the chloroplast but different from E. coli. J Biol Chem 278, 15771–15777.[CrossRef]
    [Google Scholar]
  40. Sarkar, N. ( 1996; ). Polyadenylation of mRNA in bacteria. Microbiology 142, 3125–3133.[CrossRef]
    [Google Scholar]
  41. Sarkar, N. ( 1997; ). Polyadenylation of mRNA in prokaryotes. Annu Rev Biochem 66, 173–197.[CrossRef]
    [Google Scholar]
  42. Schreier, M. H., Erni, B. & Staehlin, T. ( 1977; ). Initiation of mammalian protein synthesis. I. Purification and characterization of seven initiation factors. J Mol Biol 116, 727–753.[CrossRef]
    [Google Scholar]
  43. Sohlberg, B., Huang, J. & Cohen, S. N. ( 2003; ). The Streptomyces coelicolor polynucleotide phosphorylase homologue, and not the putative poly(A) polymerase can polyadenylate RNA. J Bacteriol 185, 7273–7278.[CrossRef]
    [Google Scholar]
  44. Wen, T., Oussenko, I. A., Pellegrini, O., Bechhofer, D. H. & Condon, C. ( 2005; ). Ribonuclease PH plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors in Bacillus subtilis. Nucleic Acids Res 33, 3636–3643.[CrossRef]
    [Google Scholar]
  45. Yehudai-Resheff, S., Hirsh, M. & Schuster, G. ( 2001; ). Polynucleotide phosphorylase functions as both an exonuclease and a poly(A) polymerase in spinach chloroplasts. Mol Cell Biol 21, 5408–5416.[CrossRef]
    [Google Scholar]
  46. Yue, D., Maizels, N. & Weiner, A. M. ( 1996; ). CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the hyperthermophile Sulfolobus shibatae. RNA 2, 895–908.
    [Google Scholar]
  47. Zhu, L. & Deutscher, M. P. ( 1987; ). tRNA nucleotidyltransferase is not essential for Escherichia coli viability. EMBO J 6, 2473–2477.
    [Google Scholar]
  48. Zuo, Y. & Deutscher, M. ( 2001; ). Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res 29, 1017–1026.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.28363-0
Loading
/content/journal/micro/10.1099/mic.0.28363-0
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