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Gene Review

ssrA  -  miscRNA

Escherichia coli O157:H7 str. Sakai

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Disease relevance of ssrA

  • In E. coli, the adaptor SspB tethers ssrA-tagged substrates to the ClpXP protease, causing a modest increase in their rate of degradation [1].
  • Using various ssrA alleles, we demonstrate the importance of SsrA charging on the ribosome for controlling Mu prophage repression [2].
  • The PAI is 39.5 kb in size, has low %G+C (35%), contains putative integrase and transposase genes, is flanked by att sites, and inserts near a 10Sa RNA gene (ssrA), suggesting it may be of bacteriophage origin [3].
  • Both forms of the protein displayed equivalent stability in the slow-growing species Mycobacterium bovis bacille Calmette-Guerin (BCG), suggesting differing recognition of the ssrA-encoded peptides in slow- and fast-growing mycobacteria [4].
  • We report that tmRNA is essential in Neisseria gonorrhoeae [5].

High impact information on ssrA

  • The tag appears to be added to the carboxyl terminus of the nascent polypeptide chain by cotranslational switching of the ribosome from the damaged messenger RNA to ssrA RNA [6].
  • This tripartite structure--an ssrA-tag binding and dimerization domain, a flexible linker, and a short peptide module that docks with ClpX--allows SspB to deliver tagged substrates to ClpXP without interfering with their denaturation or degradation [7].
  • ClpXP is a protease involved in DNA damage repair, stationary-phase gene expression, and ssrA-mediated protein quality control [8].
  • We report that native Escherichia coli tmRNA interacts specifically with native or synthetic E.coli tRNA alanine (tRNA(Ala)) in vitro, alanine being the first codon of the tmRNA internal open reading frame [9].
  • The reading frame of tmRNA is determined differently from all other known reading frames in that the first translated codon is not specified by a particular tRNA anticodon [10].

Chemical compound and disease context of ssrA


Biological context of ssrA

  • Disruption of the gene encoding 10Sa RNA (ssrA) caused a reduction in the rate of cell growth, which was especially apparent at 45 degrees C, and a reduction in motility on semisolid agar [13].
  • Analysis of the Escherichia coli Alp phenotype: heat shock induction in ssrA mutants [14].
  • We show that sipB391, previously located to the 57-min region of the E. coli chromosome, is a large deletion that extends into the 3' end of ssrA, a gene encoding the small stable 10Sa RNA [15].
  • The 10Sa RNA gene (ssrA) has been located between 2,760 and 2,761 kilobases on the E. coli genome [16].
  • We find that ssrA mutants alone significantly induce the heat shock response [14].

Anatomical context of ssrA

  • These functions are facilitated by transfer-messenger RNA (tmRNA, also called 10Sa RNA or SsrA RNA), a small stable RNA molecule encoded by the SsrA gene found in bacteria, chloroplasts and mitochondria [17].
  • The cyanelle of the primitive alga Cyanophora paradoxa is the only photosynthetic organelle where the ribonucleoprotein nature of this enzyme has been functionally proven. tmRNA is another highly structured RNA: it can be aminoacylated with alanine, which is then incorporated into a tag peptide encoded on the same RNA molecule [18].
  • tmRNA decreases the bactericidal activity of aminoglycosides and the susceptibility to inhibitors of cell wall synthesis [19].

Associations of ssrA with chemical compounds

  • When the G.U pair (G3.U357) in 10Sa RNA, which may be equivalent to the determinant G.U pair of alanine tRNA, was changed to a G.A or G.C pair, the ability to complement the phenotypic mutations of the delta ssrA strain was lost [13].
  • We have investigated directionality in the ClpA/ClpP-mediated reaction by using two substrate proteins bearing the COOH-terminal ssrA recognition element, each labeled near the NH(2) or COOH terminus with fluorescent probes [20].
  • Although A-site-cleaved mRNAs were not detected, tmRNA-mediated ssrA tagging after SecM glycine 165 was observed [21].
  • Inactivation of transfer mRNA (tmRNA) (encoded by ssrA), coupled with a multicopy kanamycin resistance determinant, suppressed both lon phenotypes and restored the rapid degradation of SulA [14].
  • The native E.coli tmRNA contains two modified nucleosides, 5-methyluridine and pseudouridine [22].

Physical interactions of ssrA


Other interactions of ssrA


Analytical, diagnostic and therapeutic context of ssrA

  • By PCR analysis and sequencing, it was shown that this integrative element is present in a number of non-O157 STEC serotypes and in non-STEC strains, where it is located at the 3'-end of the chromosomal ssrA gene [26].
  • From Escherichia coli cells with a deletion in the ssrA gene that encodes 10Sa RNA after treatment with a mutagen, we isolated two temperature-sensitive mutants, which we designated TS15 and TS101 [27].
  • Together with comparative sequence analysis, these findings yielded a three-dimensional model of the tRNA-like domain of E. coli tmRNA [25].
  • Covariations, identified by sequence alignment with nine other tmRNA sequences, suggest the presence of several tertiary interactions, including pseudoknots [28].
  • Gel mobility shift assays demonstrated that tmRNA(Delta90-299), a truncated tmRNA derivative lacking pseudoknots 2-4, has the same affinity for the Escherichia coli and Aquifex aeolicus SmpB proteins as the intact E. coli tmRNA [29].


  1. Engineering controllable protein degradation. McGinness, K.E., Baker, T.A., Sauer, R.T. Mol. Cell (2006) [Pubmed]
  2. The tRNA function of SsrA contributes to controlling repression of bacteriophage Mu prophage. Ranquet, C., Geiselmann, J., Toussaint, A. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  3. A Vibrio cholerae pathogenicity island associated with epidemic and pandemic strains. Karaolis, D.K., Johnson, J.A., Bailey, C.C., Boedeker, E.C., Kaper, J.B., Reeves, P.R. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  4. Destabilized green fluorescent protein for monitoring transient changes in mycobacterial gene expression. Triccas, J.A., Pinto, R., Britton, W.J. Res. Microbiol. (2002) [Pubmed]
  5. Charged tmRNA but not tmRNA-mediated proteolysis is essential for Neisseria gonorrhoeae viability. Huang, C., Wolfgang, M.C., Withey, J., Koomey, M., Friedman, D.I. EMBO J. (2000) [Pubmed]
  6. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Keiler, K.C., Waller, P.R., Sauer, R.T. Science (1996) [Pubmed]
  7. Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. Wah, D.A., Levchenko, I., Rieckhof, G.E., Bolon, D.N., Baker, T.A., Sauer, R.T. Mol. Cell (2003) [Pubmed]
  8. Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Flynn, J.M., Neher, S.B., Kim, Y.I., Sauer, R.T., Baker, T.A. Mol. Cell (2003) [Pubmed]
  9. Transfer RNA(Ala) recognizes transfer-messenger RNA with specificity; a functional complex prior to entering the ribosome? Gillet, R., Felden, B. EMBO J. (2001) [Pubmed]
  10. Resuming translation on tmRNA: a unique mode of determining a reading frame. Williams, K.P., Martindale, K.A., Bartel, D.P. EMBO J. (1999) [Pubmed]
  11. A nickel complex cleaves uridine in folded RNA structures: application to E. coli tmRNA and related engineered molecules. Hickerson, R.P., Watkins-Sims, C.D., Burrows, C.J., Atkins, J.F., Gesteland, R.F., Felden, B. J. Mol. Biol. (1998) [Pubmed]
  12. Amino acid acceptor identity switch of Escherichia coli tmRNA from alanine to histidine in vitro. Nameki, N., Tadaki, T., Muto, A., Himeno, H. J. Mol. Biol. (1999) [Pubmed]
  13. A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Komine, Y., Kitabatake, M., Yokogawa, T., Nishikawa, K., Inokuchi, H. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  14. Analysis of the Escherichia coli Alp phenotype: heat shock induction in ssrA mutants. Munavar, H., Zhou, Y., Gottesman, S. J. Bacteriol. (2005) [Pubmed]
  15. Role for 10Sa RNA in the growth of lambda-P22 hybrid phage. Retallack, D.M., Johnson, L.L., Friedman, D.I. J. Bacteriol. (1994) [Pubmed]
  16. Location of a gene (ssrA) for a small, stable RNA (10Sa RNA) in the Escherichia coli chromosome. Oh, B.K., Chauhan, A.K., Isono, K., Apirion, D. J. Bacteriol. (1990) [Pubmed]
  17. Quality control of the elongation step of protein synthesis by tmRNP. Wower, J., Wower, I.K., Kraal, B., Zwieb, C.W. J. Nutr. (2001) [Pubmed]
  18. In vitro and in vivo processing of cyanelle tmRNA by RNase P. Gimple, O., Schön, A. Biol. Chem. (2001) [Pubmed]
  19. tmRNA decreases the bactericidal activity of aminoglycosides and the susceptibility to inhibitors of cell wall synthesis. Luidalepp, H., Hallier, M., Felden, B., Tenson, T. RNA biology (2005) [Pubmed]
  20. ClpA mediates directional translocation of substrate proteins into the ClpP protease. Reid, B.G., Fenton, W.A., Horwich, A.L., Weber-Ban, E.U. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  21. Prolyl-tRNAPro in the A-site of SecM-arrested Ribosomes Inhibits the Recruitment of Transfer-messenger RNA. Garza-S??nchez, F., Janssen, B.D., Hayes, C.S. J. Biol. Chem. (2006) [Pubmed]
  22. Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches. Felden, B., Hanawa, K., Atkins, J.F., Himeno, H., Muto, A., Gesteland, R.F., McCloskey, J.A., Crain, P.F. EMBO J. (1998) [Pubmed]
  23. Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu. Rudinger-Thirion, J., Giegé, R., Felden, B. RNA (1999) [Pubmed]
  24. Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli. Barends, S., Wower, J., Kraal, B. Biochemistry (2000) [Pubmed]
  25. Three-dimensional folding of the tRNA-like domain of Escherichia coli tmRNA. Zwieb, C., Guven, S.A., Wower, I.K., Wower, J. Biochemistry (2001) [Pubmed]
  26. Genetic structure and chromosomal integration site of the cryptic prophage CP-1639 encoding Shiga toxin 1. Creuzburg, K., Köhler, B., Hempel, H., Schreier, P., Jacobs, E., Schmidt, H. Microbiology (Reading, Engl.) (2005) [Pubmed]
  27. 10Sa RNA complements the temperature-sensitive phenotype caused by a mutation in the phosphoribosyl pyrophosphate synthetase (prs) gene in Escherichia coli. Ando, H., Kitabatake, M., Inokuchi, H. Genes Genet. Syst. (1996) [Pubmed]
  28. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). Felden, B., Himeno, H., Muto, A., McCutcheon, J.P., Atkins, J.F., Gesteland, R.F. RNA (1997) [Pubmed]
  29. SmpB: a protein that binds to double-stranded segments in tmRNA and tRNA. Wower, J., Zwieb, C.W., Hoffman, D.W., Wower, I.K. Biochemistry (2002) [Pubmed]
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