Gene Symbol: rnr
Description: exoribonuclease R, RNase R
Alias: ECK4175, JW5741, vacB, yjeC
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. Awano N, Xu C, Ke H, Inoue K, Inouye M, Phadtare S. Complementation analysis of the cold-sensitive phenotype of the Escherichia coli csdA deletion strain. J Bacteriol. 2007;189:5808-15 pubmed
    ..These results suggest that the primary role of CsdA in cold acclimation of cells is in mRNA decay and that its helicase activity is pivotal for promoting degradation of mRNAs stabilized at low temperature. ..
  2. Liang W, Malhotra A, Deutscher M. Acetylation regulates the stability of a bacterial protein: growth stage-dependent modification of RNase R. Mol Cell. 2011;44:160-6 pubmed publisher
    ..These findings indicate that acetylation can regulate the stability of a bacterial protein. ..
  3. Awano N, Rajagopal V, Arbing M, Patel S, Hunt J, Inouye M, et al. Escherichia coli RNase R has dual activities, helicase and RNase. J Bacteriol. 2010;192:1344-52 pubmed publisher
    ..We further demonstrated that RNase R exhibits helicase activity in vitro independent of its RNase activity. Our results shed light on the unique properties of RNase R and how it is distinct from other exoribonucleases in E. coli. ..
  4. Karzai A, Sauer R. Protein factors associated with the SsrA.SmpB tagging and ribosome rescue complex. Proc Natl Acad Sci U S A. 2001;98:3040-4 pubmed
  5. Cheng Z, Deutscher M. Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II. J Biol Chem. 2002;277:21624-9 pubmed
    ..molecular mass of approximately 95 kDa, in close agreement with its expected size based on the sequence of the rnr gene. RNase R was most active at pH 7.5-9.5 in the presence of 0.1-0.5 mm Mg(2+) and 50-500 mm KCl...
  6. Cairrao F, Cruz A, Mori H, Arraiano C. Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA. Mol Microbiol. 2003;50:1349-60 pubmed
    ..Transcriptional studies reveal that the rnr gene is co-transcribed with flanking genes as an operon induced under cold shock...
  7. Cheng Z, Deutscher M. An important role for RNase R in mRNA decay. Mol Cell. 2005;17:313-8 pubmed
    ..These data demonstrate that RNase R, which is widespread in prokaryotes and eukaryotes, is an important participant in mRNA decay. ..
  8. Andrade J, Hajnsdorf E, Regnier P, Arraiano C. The poly(A)-dependent degradation pathway of rpsO mRNA is primarily mediated by RNase R. RNA. 2009;15:316-26 pubmed publisher
    ..Moreover, this regulation is shown to occur despite the presence of PNPase. Similar results were observed with the rpsT mRNA. This report shows that polyadenylation favors in vivo the RNase R-mediated pathways of RNA degradation. ..
  9. Liang W, Deutscher M. Ribosomes regulate the stability and action of the exoribonuclease RNase R. J Biol Chem. 2013;288:34791-8 pubmed publisher
    ..Inhibition of RNase R binding to ribosomes leads to slower growth and a massive increase in RNA degradation. These studies indicate a previously unknown role for ribosomes in cellular homeostasis. ..

More Information


  1. Matos R, Barbas A, Arraiano C. RNase R mutants elucidate the catalysis of structured RNA: RNA-binding domains select the RNAs targeted for degradation. Biochem J. 2009;423:291-301 pubmed publisher
    ..These results can have important implications for the study of poly(A)-dependent RNA degradation mechanisms. ..
  2. Zheng Y, Roberts R, Kasif S. Segmentally variable genes: a new perspective on adaptation. PLoS Biol. 2004;2:E81 pubmed
    ..Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment. ..
  3. Purusharth R, Madhuri B, Ray M. Exoribonuclease R in Pseudomonas syringae is essential for growth at low temperature and plays a novel role in the 3' end processing of 16 and 5 S ribosomal RNA. J Biol Chem. 2007;282:16267-77 pubmed
    ..Mutants of P. syringae with inactivated rnr gene (encoding RNase R) are cold-sensitive and die upon incubation at 4 degrees C, a phenotype that can be ..
  4. Matos R, Barbas A, Gomez Puertas P, Arraiano C. Swapping the domains of exoribonucleases RNase II and RNase R: conferring upon RNase II the ability to degrade ds RNA. Proteins. 2011;79:1853-67 pubmed publisher
    ..Finally, we show that the RNase R C-terminal Lysine-rich region is involved in the degradation of double-stranded substrates in an RNase II context, probably by unwinding the substrate before it enters into the catalytic cavity. ..
  5. Vincent H, Deutscher M. Insights into how RNase R degrades structured RNA: analysis of the nuclease domain. J Mol Biol. 2009;387:570-83 pubmed publisher
    ..On the basis of these data, we propose a model in which tight binding within the nuclease domain allows RNase R to capitalize on the natural thermal breathing of an RNA duplex to degrade structured RNAs. ..
  6. Carpousis A. The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol. 2007;61:71-87 pubmed
  7. Amblar M, Barbas A, Gomez Puertas P, Arraiano C. The role of the S1 domain in exoribonucleolytic activity: substrate specificity and multimerization. RNA. 2007;13:317-27 pubmed
    ..In addition, we show that the S1 domain from PNPase is able to induce the trimerization of the RNaseII-PNP hybrid protein, indicating that this domain can have a role in the biogenesis of multimers. ..
  8. Vincent H, Deutscher M. Substrate recognition and catalysis by the exoribonuclease RNase R. J Biol Chem. 2006;281:29769-75 pubmed
    ..Based on these data and a homology model of RNase R, derived from the structure of the closely related enzyme, RNase II, we present a model for how RNase R interacts with its substrates and degrades RNA. ..
  9. Richards J, Mehta P, Karzai A. RNase R degrades non-stop mRNAs selectively in an SmpB-tmRNA-dependent manner. Mol Microbiol. 2006;62:1700-12 pubmed
  10. Cheng Z, Zuo Y, Li Z, Rudd K, Deutscher M. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J Biol Chem. 1998;273:14077-80 pubmed
    b>vacB, a gene previously shown to be required for expression of virulence in Shigella and enteroinvasive Escherichia coli, has been found to encode the 3'-5' exoribonuclease, RNase R. Thus, cloning of E...
  11. Pobre V, Arraiano C. Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli. BMC Genomics. 2015;16:72 pubmed publisher
    ..the total RNA (RNA-Seq) from wild-type cells and from mutants for each of the exoribonucleases (∆rnb, ∆rnr and ∆pnp)...
  12. Barbas A, Matos R, Amblar M, López Viñas E, Gomez Puertas P, Arraiano C. New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end product. J Biol Chem. 2008;283:13070-6 pubmed publisher
    ..Our findings improve the present model for RNA degradation by the RNase II family of enzymes. ..
  13. Malecki M, Bárria C, Arraiano C. Characterization of the RNase R association with ribosomes. BMC Microbiol. 2014;14:34 pubmed publisher
    ..This study leads us to conclude that RNase R can interact with ribosomal proteins and that this interaction may be a result of this enzyme involvement in the ribosome quality control. ..
  14. Kasai T, Gupta R, Schlessinger D. Exoribonucleases in wild type Escherichia coli and RNase II-deficient mutants. J Biol Chem. 1977;252:8950-6 pubmed
  15. Liang W, Deutscher M. A novel mechanism for ribonuclease regulation: transfer-messenger RNA (tmRNA) and its associated protein SmpB regulate the stability of RNase R. J Biol Chem. 2010;285:29054-8 pubmed publisher
    ..These data define a previously unknown regulatory process in which the stability of an RNase is determined by its interaction with an RNA and an RNA-associated protein. ..
  16. Andrade J, Cairrao F, Arraiano C. RNase R affects gene expression in stationary phase: regulation of ompA. Mol Microbiol. 2006;60:219-28 pubmed
    ..This work is the first report of RNase R activity on a full length mRNA. In the absence of RNase R in a single rnr mutant, higher levels of ompA mRNA are found as a consequence of the stabilization of ompA full transcript...
  17. Hossain S, Malhotra A, Deutscher M. The Helicase Activity of Ribonuclease R Is Essential for Efficient Nuclease Activity. J Biol Chem. 2015;290:15697-706 pubmed publisher
    ..These findings indicate that the helicase activity plays an essential role in the catalytic efficiency of RNase R. ..
  18. Salguero I, Acedo E, Guzmán E. Overlap of replication rounds disturbs the progression of replicating forks in a ribonucleotide reductase mutant of Escherichia coli. Microbiology. 2011;157:1955-67 pubmed publisher
    Ribonucleotide reductase (RNR) is the only enzyme specifically required for the synthesis of deoxyribonucleotides (dNTPs)...
  19. Hossain S, Deutscher M. Helicase Activity Plays a Crucial Role for RNase R Function in Vivo and for RNA Metabolism. J Biol Chem. 2016;291:9438-43 pubmed publisher
    ..These findings indicate that the intrinsic helicase activity of RNase R is required for its proper functioning in vivo and for effective RNA metabolism. ..
  20. Pagba C, McCaslin T, Veglia G, Porcelli F, Yohannan J, Guo Z, et al. A tyrosine-tryptophan dyad and radical-based charge transfer in a ribonucleotide reductase-inspired maquette. Nat Commun. 2015;6:10010 pubmed publisher
    In class 1a ribonucleotide reductase (RNR), a substrate-based radical is generated in the α2 subunit by long-distance electron transfer involving an essential tyrosyl radical (Y122O·) in the β2 subunit...
  21. Jain C. Identification and characterization of growth suppressors of Escherichia coli strains lacking phosphorolytic ribonucleases. J Bacteriol. 2009;191:5622-7 pubmed publisher
    ..These results suggest that the requirement for phosphorolytic RNases for robust cellular growth and efficient ribosome assembly can be bypassed by increased expression of hydrolytic RNases. ..
  22. Liang W, Deutscher M. Post-translational modification of RNase R is regulated by stress-dependent reduction in the acetylating enzyme Pka (YfiQ). RNA. 2012;18:37-41 pubmed publisher
    ..We find that RNase R in cold-shocked cells also lacks the acetyl modification due to the absence of Pka. These data indicate that RNase R stability depends on Pka, which itself is regulated under stress conditions. ..
  23. Cairrao F, Arraiano C. The role of endoribonucleases in the regulation of RNase R. Biochem Biophys Res Commun. 2006;343:731-7 pubmed
    ..RNase E is necessary for the decay of intermediary products that arise from the maturation of transcripts from the rnr operon. RNase G and RNase III do not seem to have a primary role in the processing of the rnr transcripts...
  24. Chu L, Hsieh T, Golzarroshan B, Chen Y, Agrawal S, Yuan H. Structural insights into RNA unwinding and degradation by RNase R. Nucleic Acids Res. 2017;45:12015-12024 pubmed publisher
    ..Thus, RNase R is a proficient enzyme, capable of concurrently binding, unwinding and degrading structured RNA in a highly processive manner during RNA decay. ..
  25. Liang W, Deutscher M. Transfer-messenger RNA-SmpB protein regulates ribonuclease R turnover by promoting binding of HslUV and Lon proteases. J Biol Chem. 2012;287:33472-9 pubmed publisher
    ..RNase R in stationary phase or in cold-shocked cells is not acetylated, and thereby remains stable. Such a regulatory mechanism, dependent on protein acetylation, has not been observed previously in bacterial cells...
  26. Awano N, Inouye M, Phadtare S. RNase activity of polynucleotide phosphorylase is critical at low temperature in Escherichia coli and is complemented by RNase II. J Bacteriol. 2008;190:5924-33 pubmed publisher
  27. Deutscher M. Maturation and degradation of ribosomal RNA in bacteria. Prog Mol Biol Transl Sci. 2009;85:369-91 pubmed publisher
    ..The second focus of this review is to describe these degradative reactions, the RNases that carry them out, and the conditions that initiate the turnover process. ..
  28. Sundermeier T, Ge Z, Richards J, Dulebohn D, Karzai A. Studying tmRNA-mediated surveillance and nonstop mRNA decay. Methods Enzymol. 2008;447:329-58 pubmed publisher
    ..2003; Kihara et al., 1996; Makino et al., 1999; Maurizi et al., 1990; Shotland et al., 2000). In addition, we present biochemical and genetic assays to study the various aspects of the trans-translation mechanism. ..
  29. Vincent H, Deutscher M. The roles of individual domains of RNase R in substrate binding and exoribonuclease activity. The nuclease domain is sufficient for digestion of structured RNA. J Biol Chem. 2009;284:486-94 pubmed publisher
    RNase R and RNase II are the two representatives from the RNR family of processive, 3' to 5' exoribonucleases in Escherichia coli. Although RNase II is specific for single-stranded RNA, RNase R readily degrades through structured RNA...
  30. Windbichler N, von Pelchrzim F, Mayer O, Csaszar E, Schroeder R. Isolation of small RNA-binding proteins from E. coli: evidence for frequent interaction of RNAs with RNA polymerase. RNA Biol. 2008;5:30-40 pubmed
    ..Our observations show that RNA polymerase is able to bind and react with many different RNAs and we suggest that RNAs are involved in transcriptional regulation more frequently than anticipated. ..
  31. Suzuki H, Zuo Y, Wang J, Zhang M, Malhotra A, Mayeda A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res. 2006;34:e63 pubmed
    ..Further analysis of the intronic RNA pool from a specific tissue or cell will provide insights into the global profile of alternative splicing. ..
  32. Chen C, Deutscher M. Elevation of RNase R in response to multiple stress conditions. J Biol Chem. 2005;280:34393-6 pubmed
    ..Its dramatic increase under multiple stress conditions suggests extensive remodeling of structured RNA in response to the altered environment. ..
  33. Polissi A, De Laurentis W, Zangrossi S, Briani F, Longhi V, Pesole G, et al. Changes in Escherichia coli transcriptome during acclimatization at low temperature. Res Microbiol. 2003;154:573-80 pubmed
    ..Interestingly, we found that PNPase both negatively and positively modulated the transcript abundance of some of these genes, thus suggesting a complex role of PNPase in controlling cold adaptation. ..
  34. Wolfe S, Smith J. Nucleotide sequence and analysis of the purA gene encoding adenylosuccinate synthetase of Escherichia coli K12. J Biol Chem. 1988;263:19147-53 pubmed
    ..The purA control region did not resemble the control regions of the other known pur loci. ..
  35. Tobe T, Sasakawa C, Okada N, Honma Y, Yoshikawa M. vacB, a novel chromosomal gene required for expression of virulence genes on the large plasmid of Shigella flexneri. J Bacteriol. 1992;174:6359-67 pubmed
    ..was assigned to a NotI chromosomal restriction map, confirming that the virulence-associated locus, designated vacB, is a new locus on the chromosome...