Discovery of Small Regulatory RNAs Extends Our Understanding of Gene Regulation in the Acidithiobacillus Genus


Article Preview

Small regulatory RNAs (srRNAs) control gene expression in Bacteria, usually at the posttranscriptional level, by acting as antisense RNAs that bind targeted mRNAs or by interacting with regulatory proteins. srRNAs are involved in the regulation of a large variety of processes such as plasmid replication, transposition and global genetic circuits that respond to environmental changes. Since their discovery a few years ago, it has become apparent that they are prolific and widespread. In this study, we describe bioinformatic approaches to srRNA discovery in the biomining microorganisms Acidithiobacillus ferrooxidans, A. caldus and A. thiooxidans. Intergenic regions of the annotated genomes were extracted and computationally searched for srRNAs. Candidate srRNAs that were associated with predicted sigma 70 promoters and/or rho-independent terminators were chosen for further study. The resulting potential srRNAs include known examples from other microorganisms and some novel candidates and reveal interesting underlying biology of the Acidithiobacillus genus.



Advanced Materials Research (Volumes 20-21)

Edited by:

Axel Schippers, Wolfgang Sand, Franz Glombitza and Sabine Willscher




A. Shmaryahu and D. S. Holmes, "Discovery of Small Regulatory RNAs Extends Our Understanding of Gene Regulation in the Acidithiobacillus Genus", Advanced Materials Research, Vols. 20-21, pp. 535-538, 2007

Online since:

July 2007




[1] N. Delihas: Mol. Microbiol. Vol. 15 (1995), p.411.

[2] E.G. H Wagner and S. Brantl: Trends Biochem. Sci. Vol. 23 (1998), p.451.

[3] D.H. Lenz, K. C Mok, B. N Lilley, R. V Kulkarni, N. S Wingreen and B.L. Bassler: Cell Vol 118 (2004), p.69.

[4] J.C. Carrington and V. Ambros: Science Vol. 301 (2003), p.336.

[5] M. T McManus and P. A Sharp: Nat. Rev. Genet. Vol. 3 (2003), p.737.

[6] G. Storz: Science Vol. 296 (2002), p.1260 B. A.

[7] L. Argaman, R. Hershberg, J. Vogel, G. Bejerano, E.G.H. Wagner, H. Margalit and S. Altuvia: Current Biol. Vol. 11 (2001), p.941.


[8] K.M. Wassarman, F. Repoila, C. Rosenow, G. Storz and S. Gottesman: Genes Dev. Vol. 15 (2001), p.1637.

[9] R.J. Carter, I. Dubchak and S.R. Holbrook: Nucl. Acids Res. Vol. 29 (2001), p.3928.

[10] E. Rivas, R.J. Klein, T.A. Jones and S.R. Eddy: Current Biol. Vol. 11 (2001), p.1369.

[11] C. Kingsford, K. Ayanbule and S.L. Salzberg: Genome Biology Vol. 8 (2007), R22 12] V. Gopalan, A. Vioque and S. Altman: J. Biol. Chem. Vol. 277 (2002), p.6759.

[13] A.W. Karzai, E.D. Roche and R. T Sauer: Nat. Struct. Biol. Vol. 7 (2000), p.449.

[14] S. Gottesman, E. Roche, Y.N. Zhou and R.T. Sauer: Genes Dev. Vol. 12 (1998), p.1338.

[15] K.M. Wassarman, G. Storz: Cell Vol. 101 (2002), p.613.

[16] A.E. Trotochaud and K.M. Wassarman: Nat. Struct. Mol. Biol. Vol. 12 (2005), p.313.

[17] J.E. Barrick, N. Sudarsan, Z. Weinberg, W.L. Ruzzo and R.R. Breaker: RNA Vol. 11 (2005), p.774.