A cyanobacterial non-coding RNA, Yfr1, is required for growth under multiple stress conditions

Plant and Cell Physiology

Volumn 48, Issue 9, 2007, Pages 1309-1318

  Nakamura, Takahiro ^a,b   Naito, Kumiko ^a   Yokota, Naoto ^a   Sugita, Chieko ^a   Sugita, Mamoru ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

Author keywords

Cyanobacteria; Functional RNA; Non coding RNA; Stress response; Synechococcus elongatus

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; MESSENGER RNA; UNTRANSLATED RNA;

ARTICLE; BACTERIAL GENE; CHEMISTRY; CONFORMATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; SYNECHOCOCCUS;

BACTERIAL PROTEINS; BASE SEQUENCE; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; RNA, BACTERIAL; RNA, MESSENGER; RNA, UNTRANSLATED; SYNECHOCOCCUS;

CYANOBACTERIA; EUKARYOTA; PROKARYOTA; SYNECHOCOCCUS ELONGATUS; SYNECHOCOCCUS ELONGATUS PCC 6301;

EID: 34548758619     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcm098     Document Type: Article

References (37)

1. Altuvia, S., Weinstein-Fischer, D., Zhang, A., Postow, L. and Storz, G. (1997) A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. Cell 90: 43-53.
2. Andersen, J., Forst, S.A., Zhao, K., Inouye, M. and Delihas, N. (1989) The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli. J. Biol. Chem. 264: 17961-17970.
3. Axmann, I.M., Kensche, P., Vogel, J., Kohl, S., Herzel, H. and Hess, W.R. (2005) Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol. 6: R73.
4. Banta, A.B., Haas, E.S., Brown, J.W. and Pace, N.R. (1992) Sequence of the ribonuclease P RNA gene from the cyanobacterium Anacystis nidulans. Nucleic Acids Res. 20: 911.
5. Davis, B.M., Quinones, M., Pratt, J., Ding, Y. and Waldor, M.K. (2005) Characterization of the small untranslated RNA RyhB and its regulon in Vibrio cholerae. J. Bacteriol. 187: 4005-4014.
6. Duhring, U., Axmann, I.M., Hess, W.R. and Wilde, A. (2006) An internal antisense RNA regulates expression of the photosynthesis gene isiA. Proc. Natl Acad. Sci. USA 103: 7054-7058.
7. Gottesman, S. (2005) Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet. 21: 399-404.
8. Hershberg, R., Altuvia, S. and Margalit, H. (2003) A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 31: 1813-1820.
9. Huttenhofer, A. and Vogel, J. (2006) Experimental approaches to identify non-coding RNAs. Nucleic Acids Res. 34: 635-646.
10. Johansson, J. and Cossart, P. (2003) RNA-mediated control of virulence gene expression in bacterial pathogens. Trends Microbiol. 11: 280-285.
11. Kiledjian, M., Burd, C.G., Görlach, M., Portman, D.S. and Dreyfuss, G. (1994) Structure and function of hnRNP proteins. In RNA-Protein Interactions. Edited by Nagai, K. and Mattaj, I.W. pp. 127-149. IRL Press at Oxford University Press, Oxford.
12. Lenz, D.H., Miller, M.B., Zhu, J., Kulkarni, R.V. and Bassler, B.L. (2005) CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae. Mol. Microbiol. 58: 1186-1202.
13. Lenz, D.H., Mok, K.C., Lilley, B.N., Kulkarni, R.V., Wingreen, N.S. and Bassler, B.L. (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118: 69-82.
14. Moller, T., Franch, T., Hojrup, P., Keene, D.R., Bachinger, H.P., Brennan, R.G. and Valentin-Hansen, P. (2002) Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol. Cell 9: 23-30.
15. Morita, T., Maki, K. and Aiba, H. (2005) RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 19: 2176-2186.
16. Mutsuda, M., Sugiura, M. and Sugita, M. (1999) Physiological characterization of RNA-binding protein-deficient cells from Synechococcus sp. strain PCC7942. Plant Cell Physiol. 40: 1203-1209.
17. Ostberg, Y., Bunikis, I., Bergstrom, S. and Johansson, J. (2004) The etiological agent of Lyme disease, Borrelia burgdorferi, appears to contain only a few small RNA molecules. J. Bacteriol. 186: 8472-8477.
18. Rapp, J.C., Baumgartner, B.J. and Mullet, J. (1992) Quantitative analysis of transcription and RNA levels of 15 barley chloroplast genes. Transcription rates and mRNA levels vary over 300-fold; predicted mRNA stabilities vary 30-fold. J. Biol. Chem. 267: 21404-21411.
19. Shibata, M., Katoh, H., Sonoda, M., Ohkawa, H., Shimoyama, M., Fukuzawa, H., Kaplan, A. and Ogawa, T. (2002) Genes essential to sodium-dependent bicarbonate transport in cyanobacteria: function and phylogenetic analysis. J. Biol. Chem. 277: 18658-18664.
20. Silvaggi, J.M., Perkins, J.B. and Losick, R. (2005) Small untranslated RNA antitoxin in Bacillus subtilis. J. Bacteriol. 187: 6641-6650.
21. Silvaggi, J.M., Perkins, J.B. and Losick, R. (2006) Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J. Bacteriol. 188: 532-541.
22. Stanier, R.Y., Kunisawa, R., Mandel, M. and Cohen-Bazire, G. (1971) Purification and properties of unicellular blue-green algae (order Chroococcales). Bacteriol. Rev. 35: 171-205.
23. Storz, G., Altuvia, S. and Wassarman, K.M. (2005) An abundance of RNA regulators. Annu. Rev. Biochem. 74: 199-217.
24. Storz, G., Opdyke, J.A. and Zhang, A. (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol. 7: 140-144.
25. Sugita, C., Mutsuda, M., Sugiura, M. and Sugita, M. (1999) Target deletion of genes for eukaryotic RNA-binding proteins, Rbp1 and Rbp2, in the cyanobacterium Synechococcus sp. strain PCC7942: Rbp1 is indispensable for cell growth at low temperatures. FEMS Microbiol. Lett. 176: 155-161.
26. Sugita, C., Ogata, K., Shikata, M., Jikuya, H., Takano, J., Furumichi, M., Kanehisa, M., Omata, T., Sugiura, M. and Sugita, M. (2007) Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization. Photosynth. Res. 93: 55-67.
27. Takeshita, S., Sato, M., Toba, M., Masahashi, W. and Hashimoto-Gotoh, T. (1987) High-copy-number and low-copy-number plasmid vectors for lacZ alpha-complementation and chloramphenicol- or kanamycin-resistance selection. Gene 61: 63-74.
28. Tjaden, B., Saxena, R.M., Stolyar, S., Haynor, D.R., Kolker, E. and Rosenow, C. (2002) Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res. 30: 3732-3738.
29. Wassarman, K.M., Repoila, F., Rosenow, C., Storz, G. and Gottesman, S. (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15: 1637-1651.
30. Wassarman, K.M., Zhang, A. and Storz, G. (1999) Small RNAs in Escherichia coli. Trends Microbiol. 7: 37-45.
31. Watanabe, T., Sugita, M. and Sugiura, M. (1998) Identification of 10Sa RNA (tmRNA) homologues from the cyanobacterium Synechococcus sp. strain PCC6301 and related organisms. Biochim. Biophys. Acta 1396: 97-104.
32. Watanabe, T., Sugiura, M. and Sugita, M. (1997) A novel small stable RNA, 6Sa RNA, from the cyanobacterium Synechococcus sp. strain PCC6301. FEBS Lett. 416: 302-306.
33. Wilderman, P.J., Sowa, N.A., FitzGerald, D.J., FitzGerald, P.C., Gottesman, S., Ochsner, U.A. and Vasil, M.L. (2004) Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc. Natl Acad. Sci. USA 101: 9792-9797.
34. Zhang, A., Wassarman, K.M., Ortega, J., Steven, A.C. and Storz, G. (2002) The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell 9: 11-22.
35. Zhang, A., Wassarman, K.M., Rosenow, C., Tjaden, B.C., Storz, G. and Gottesman, S. (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50: 1111-1124.
36. Zhang, P., Battchikova, N., Jansen, T., Appel, J., Ogawa, T. and Aro, E.-M. (2004) Expression and functional roles of the two distinct NDH-1 complexes and the carbon acquisition complex NdhD3/NdhF3/CupA/Sll1735 in Synechocystis sp PCC 6803. Plant Cell 16: 3326-3340.
37. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.