1887

Microbiology Society logo

Volume 148, Issue 8

Identification and characterization of novel small RNAs in the – intergenic region of the genome Free

Abstract

A novel RNA species was isolated from , and its sequence was determined and mapped to its genetic position. This RNA was termed BS190 RNA from the length of its mature form (190 nt), and the gene encoding it is located within the – intergenic region of the genome. Northern blotting revealed that the novel RNA species is transcribed in vegetative cells as a larger precursor (BS201 RNA, 201 nt). After transcription, the 5′ end of the precursor is processed to generate the mature form, BS190 RNA. A computer-aided prediction of the secondary structure of BS190 RNA showed that it can be folded into a single hairpin structure with some bulge structures. The authors found that the growth rate of a ΔBS190 mutant strain of was reduced when compared to the wild-type. A phylogenetic comparison of the sequence of the BS190 RNA gene with sequences from the databases suggests that RNA related to BS190 RNA appears to be encoded in the genomes of and

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): non-coding RNA , RNA processing , RNA secondary structure , scRNA, small cytoplasmic RNA , sRNA, small RNA and tmRNA, transfer-message RNA
© Microbiology Society
Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-148-8-2591
2002-08-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/148/8/1482591a.html?itemId=/content/journal/micro/10.1099/00221287-148-8-2591&mimeType=html&fmt=ahah

References

  1. Altuvia S., Wagner E. G. H. 2000; Switching on and off with RNA. Proc Natl Acad Sci USA 97:9824–9826 [CrossRef]
     [Google Scholar]
  2. Altuvia S., Weinstein-Fischer D., Zhang A., Postow L., Storz G. 1997; A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. Cell 90:43–53 [CrossRef]
     [Google Scholar]
  3. Altuvia S., Zhang A., Argaman L., Tiwari A., Storz G. 1998; The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding. EMBO J 17:6069–6075 [CrossRef]
     [Google Scholar]
  4. Ando Y., Asari S., Suzuma S., Yamane K., Nakamura K. 2002; Expression of a small RNA, BS203 RNA, from the yocI–yocJ intergenic region of Bacillus subtilis genome. FEMS Microbiol Lett 207:29–33
     [Google Scholar]
  5. Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner E. G. H., 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]
  6. Bernstein H. D., Poritz M. A., Strub K., Hoben P. J., Brenner S., Walter P. 1989; Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle. Nature 340:482–486 [CrossRef]
     [Google Scholar]
  7. Bourgaize D. B., Fournier M. J. 1987; Initiation of translation is impaired in E. coli cells deficient in 4·5S RNA. Nature 325:281–284 [CrossRef]
     [Google Scholar]
  8. Brown S. 1987; Mutations in the gene for EF-G reduce the requirement for 4·5S RNA in the growth of E. coli . Cell 49:825–833 [CrossRef]
     [Google Scholar]
  9. Brown S., Fournier M. J. 1984; The 4·5S RNA gene of Escherichia coli is essential for cell growth. J Mol Biol 178:533–550 [CrossRef]
     [Google Scholar]
  10. Chen J.-H., Le S.-Y., Shapiro B., Currey K. M., Maizel J. V. 1990; A computational procedure for assessing the significance of RNA secondary structure. Comput Appl Biosci 6:7–18
     [Google Scholar]
  11. Dandekar T., Hentze M. W. 1995; Finding the hairpin in the haystack: searching for RNA motifs. Trends Genet 11:45–50 [CrossRef]
     [Google Scholar]
  12. Eddy S. R. 1999; Noncoding RNA genes. Curr Opin Genet Dev 9:695–699 [CrossRef]
     [Google Scholar]
  13. Erdmann V. A., Barciszewska M. Z., Szymanski M., Hochberg A., de Groot N., Barciszewski J. 2001; The non-coding RNAs as riboregulators. Nucleic Acids Res 29:189–193 [CrossRef]
     [Google Scholar]
  14. Gorodkin J., Knudsen B., Zwieb C., Samuelsson T. 2001; SRPDB (Signal Recognition Particle Database. Nucleic Acids Res 29:169–170 [CrossRef]
     [Google Scholar]
  15. Guerout-Fleury A. M., Shazand K., Frandsen N., Stragier P. 1995; Antibiotic-resistance cassettes for Bacillus subtilis . Gene 167:335–336 [CrossRef]
     [Google Scholar]
  16. Jovine L., Hainzl T., Oubridge C., Scott W. G., Li J., Sixma T. K., Wonacott A., Skarzynski T., Nagai K. 2000; Crystal structure of the Ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4·5S RNA. Structure Fold Des 8:527–540 [CrossRef]
     [Google Scholar]
  17. Kirsebom L. A. 2001; Escherichia coli ribonuclease P. Methods Enzymol 342:77–92
     [Google Scholar]
  18. Lankenau S., Corces V. G., Lankenau D. H. 1994; The Drosophila micropia retrotransposon encodes a testis-specific antisense RNA complementary to reverse transcriptase. Mol Cell Biol 14:1764–1775
     [Google Scholar]
  19. Le S.-Y., Chen J.-H., Maizel J. V. 1989; Thermodynamic stability and statistical significance of potential stem–loop structures situated at the frameshift sites of retroviruses. Nucleic Acids Res 17:6143–6152 [CrossRef]
     [Google Scholar]
  20. Lowe T. M., Eddy S. R. 1997; tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964 [CrossRef]
     [Google Scholar]
  21. Majdalani N., Cunning C., Sledjeski D., Elliott T., Gottesman S. 1998; DsrA RNA regulates translation of RpoS message by an anti-sense mechanism, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci USA 95:12462–12467 [CrossRef]
     [Google Scholar]
  22. Muto A., Ushida C., Himeno H. 1998; A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem Sci 23:25–29 [CrossRef]
     [Google Scholar]
  23. Nakamura K., Nishiguchi M., Minemura M., Honda K., Yamane K. 1994; Small cytoplasmic RNA of Bacillus brevis : transcriptional and phylogenetic analysis. Microbiology 140:493–498 [CrossRef]
     [Google Scholar]
  24. Nakamura K., Fujii Y., Shibata T., Yamane K. 1999; Depletion of Escherichia coli 4·5S RNA leads to an increase in the amount of protein elongation factor EF-G associated with ribosomes. Eur J Biochem 259:543–550 [CrossRef]
     [Google Scholar]
  25. Nuyts S., Van Mellaert L., Lambin P., Anne J. 2001; Efficient isolation of total RNA from Clostridium without DNA contamination. J Microbiol Methods 44:235–238 [CrossRef]
     [Google Scholar]
  26. Poritz M. A., Strub K., Walter P. 1988; Human SRP RNA and E. coli 4·5S RNA contain a highly homologous structural domain. Cell 55:4–6 [CrossRef]
     [Google Scholar]
  27. Rivas E., Klein R. J., Jones T. A., Eddy S. R. 2001; Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 11:1369–1373 [CrossRef]
     [Google Scholar]
  28. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  29. Shibata T., Fujii Y., Nakamura Y., Nakamura K., Yamane K. 1996; Identification of protein synthesis elongation factor G as a 4·5S RNA-binding protein in Escherichia coli . J Biol Chem 271:13162–13168 [CrossRef]
     [Google Scholar]
  30. Storz G. 1999; An RNA thermometer. Genes Dev 13:633–636 [CrossRef]
     [Google Scholar]
  31. Stroud R. M., Walter P. 1999; Signal sequence recognition and protein targeting. Curr Opin Struct Biol 9:754–759 [CrossRef]
     [Google Scholar]
  32. Tetart F., Bouche J. P. 1992; Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules. Mol Microbiol 6:615–620 [CrossRef]
     [Google Scholar]
  33. Wassarman K. M., Storz G. 2000; 6S RNA regulates E. coli polymerase activity. Cell 101:613–623 [CrossRef]
     [Google Scholar]
  34. Wassarman K. M., Zhang A., Storz G. 1999; Small RNAs in Escherichia coli . Trends Microbiol 7:37–45 [CrossRef]
     [Google Scholar]
  35. Wassarman K. M., Repoila F., Rosenow C., Storz G., Gottesman S. 2001; Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15:1637–1651 [CrossRef]
     [Google Scholar]
  36. Wightman B., Ha I., Ruvikun G. 1993; Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans . Cell 75:855–862 [CrossRef]
     [Google Scholar]
  37. Zhang A., Altuvia S., Tiwari A., Argaman L., Hengge-Aronis R., Storz G. 1998; The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J 17:6061–6068 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-148-8-2591
Loading
Identification and characterization of novel small RNAs in the aspS–yrvM intergenic region of the Bacillus subtilis genome
Microbiology 148, 2591 (2002); https://doi.org/10.1099/00221287-148-8-2591
/content/journal/micro/10.1099/00221287-148-8-2591
/content/journal/micro/10.1099/00221287-148-8-2591
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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