Experts and Doctors on exoribonucleases in Miami, Florida, United States

Summary

Locale: Miami, Florida, United States
Topic: exoribonucleases

Top Publications

  1. Zuo Y, Vincent H, Zhang J, Wang Y, Deutscher M, Malhotra A. Structural basis for processivity and single-strand specificity of RNase II. Mol Cell. 2006;24:149-56 pubmed
    ..The presence of the clamp and the narrow channel provides an explanation for the processivity of RNase II and for why its action is limited to single-stranded RNA. ..
  2. 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...
  3. Fiedler T, Vincent H, Zuo Y, Gavrialov O, Malhotra A. Purification and crystallization of Escherichia coli oligoribonuclease. Acta Crystallogr D Biol Crystallogr. 2004;60:736-9 pubmed
    ..5, b = 91.5, c = 111.1 A). This crystal (Zn-ApUp-Orn) belongs to the P6(5) space group and has three oligoribonuclease molecules per asymmetric unit. ..
  4. 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
    ..We also show that the nuclease domain of RNase R binds RNA more tightly than the nuclease domain of RNase II. This tighter binding may help to explain the difference in catalytic properties between RNase R and RNase II. ..
  5. 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. ..
  6. 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. ..
  7. 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. ..
  8. 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. ..
  9. 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. ..

More Information

Publications33

  1. Ezraty B, Dahlgren B, Deutscher M. The RNase Z homologue encoded by Escherichia coli elaC gene is RNase BN. J Biol Chem. 2005;280:16542-5 pubmed
    ..These data correct a previous misassignment for the gene encoding RNase BN. Based on the fact that the original RNase BN mutation has now been identified, we propose that the elaC gene be renamed rbn. ..
  2. Zuo Y, Deutscher M. Mechanism of action of RNase T. I. Identification of residues required for catalysis, substrate binding, and dimerization. J Biol Chem. 2002;277:50155-9 pubmed
    ..These data define the domains necessary for RNase T action, and together with information in the accompanying article, have led to the formulation of a detailed model for the structure and mechanism of action of RNase T. ..
  3. 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. ..
  4. Jain C. Novel role for RNase PH in the degradation of structured RNA. J Bacteriol. 2012;194:3883-90 pubmed publisher
    ..Overall, these results indicate that RNase PH plays a novel role in the degradation of structured RNAs and provides a potential explanation for the growth defects caused by an absence of the phosphorolytic RNases. ..
  5. Zuo Y, Deutscher M. The DNase activity of RNase T and its application to DNA cloning. Nucleic Acids Res. 1999;27:4077-82 pubmed
    ..This property of RNase T suggested that it might be a useful enzyme for blunt-ended DNA cloning. We show here that RNase T provides much higher cloning efficiency than the currently used mung bean nuclease. ..
  6. 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. ..
  7. 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
    ..The identification of the vacB gene product as RNase R should aid in understanding how the virulence phenotype in enterobacteria is expressed and regulated. On the basis of this information we propose that vacB be renamed rnr...
  8. 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. ..
  9. Sulthana S, Deutscher M. Multiple exoribonucleases catalyze maturation of the 3' terminus of 16S ribosomal RNA (rRNA). J Biol Chem. 2013;288:12574-9 pubmed publisher
    ..These findings, together with the earlier discovery that RNases E and G are the 5'-processing enzymes, completes the catalogue of RNases involved in maturation of Escherichia coli 16S rRNA. ..
  10. Dutta T, Deutscher M. Catalytic properties of RNase BN/RNase Z from Escherichia coli: RNase BN is both an exo- and endoribonuclease. J Biol Chem. 2009;284:15425-31 pubmed publisher
    ..These data suggest that RNase BN may differ from other members of the RNase Z family, and they provide important information to be considered in identifying a physiological role for this enzyme. ..
  11. 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. ..
  12. 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. ..
  13. Zuo Y, Deutscher M. Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res. 2001;29:1017-26 pubmed
    ..This analysis may serve as a useful first step for developing a nomenclature for this group of enzymes. ..
  14. Zhang X, Zhu L, Deutscher M. Oligoribonuclease is encoded by a highly conserved gene in the 3'-5' exonuclease superfamily. J Bacteriol. 1998;180:2779-81 pubmed
    ..On the basis of these data, we propose that yjeR be renamed orn. Orthologs of oligoribonuclease are present in a wide range of organisms, extending up to humans. ..
  15. 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. ..
  16. Zuo Y, Deutscher M. The physiological role of RNase T can be explained by its unusual substrate specificity. J Biol Chem. 2002;277:29654-61 pubmed
    ..The substrate specificity described here helps to explain why the different substrates yield different products, and why certain RNA molecules are not substrates at all. ..
  17. Callahan C, Neri Cortes D, Deutscher M. Purification and characterization of the tRNA-processing enzyme RNase BN. J Biol Chem. 2000;275:1030-4 pubmed
    ..However, since tRNA molecules with incorrect residues within the -CCA sequence are not normally produced in E. coli, the role of RNase BN in uninfected cells remains to be determined. ..
  18. Zuo Y, Deutscher M. Mechanism of action of RNase T. II. A structural and functional model of the enzyme. J Biol Chem. 2002;277:50160-4 pubmed
    ..These data explain why RNase T must dimerize to function. The model provides a detailed framework on which to explain the mechanism of action of RNase T. ..
  19. Schmier B, Seetharaman J, Deutscher M, Hunt J, Malhotra A. The structure and enzymatic properties of a novel RNase II family enzyme from Deinococcus radiodurans. J Mol Biol. 2012;415:547-59 pubmed publisher
    ..These data indicate that DrII is the RNase II of D. radiodurans and that its structure and catalytic properties are distinct from those of other related enzymes. ..
  20. Zuo Y, Zheng H, Wang Y, Chruszcz M, Cymborowski M, Skarina T, et al. Crystal structure of RNase T, an exoribonuclease involved in tRNA maturation and end turnover. Structure. 2007;15:417-28 pubmed
    ..The catalytic residues in these two enzymes are organized very similarly to the catalytic domain of the third DEDD family exoribonuclease in E. coli, RNase D, which is monomeric. ..
  21. Li Z, Pandit S, Deutscher M. 3' exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc Natl Acad Sci U S A. 1998;95:2856-61 pubmed
    ..A model is proposed that identifies a structural feature present in all the small, stable RNAs of E. coli, and describes how this structure together with the RNases influences the common mechanism for 3' maturation. ..
  22. Chen C, Deutscher M. RNase R is a highly unstable protein regulated by growth phase and stress. RNA. 2010;16:667-72 pubmed publisher
    ..These data demonstrate that RNase R is subject to regulation by a novel, posttranslational mechanism that may have important implications for our complete understanding of RNA metabolism. ..
  23. Ghosh S, Deutscher M. Oligoribonuclease is an essential component of the mRNA decay pathway. Proc Natl Acad Sci U S A. 1999;96:4372-7 pubmed
    ..Inasmuch as close homologues of the orn gene are found in a wide range of eukaryotes, extending up to humans, these findings raise the possibility that oligoribonuclease also participates in mRNA degradation in these organisms. ..
  24. 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
    ..Although the in vivo function of RNase R is not known, its ability to digest certain natural RNAs may explain why it is maintained in E. coli together with RNase II. ..