Experts and Doctors on bacterial rna in Bethesda, Maryland, United States

Summary

Locale: Bethesda, Maryland, United States
Topic: bacterial rna

Top Publications

  1. Carlson B, Hatfield D. Transfer RNAs that insert selenocysteine. Methods Enzymol. 2002;347:24-39 pubmed
  2. Rosta E, Woodcock H, Brooks B, Hummer G. Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. J Comput Chem. 2009;30:1634-41 pubmed publisher
    ..The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations. ..
  3. Wassarman K, Repoila F, Rosenow C, Storz G, Gottesman S. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 2001;15:1637-51 pubmed
    ..The approaches used here should allow identification of small RNAs in other organisms. ..
  4. Veres Z, Stadtman T. A purified selenophosphate-dependent enzyme from Salmonella typhimurium catalyzes the replacement of sulfur in 2-thiouridine residues in tRNAs with selenium. Proc Natl Acad Sci U S A. 1994;91:8092-6 pubmed
    ..A labeled compound in the nucleoside mixture was coeluted with authentic 5-methylaminomethyl-2-selenouridine...
  5. Munavar H, Zhou Y, Gottesman S. Analysis of the Escherichia coli Alp phenotype: heat shock induction in ssrA mutants. J Bacteriol. 2005;187:4739-51 pubmed
    ..Thus, ssrA and faa each suppress two lon mutant phenotypes but by somewhat different mechanisms, with heat shock induction playing a major role. ..
  6. Lewis D, Adhya S. Axiom of determining transcription start points by RNA polymerase in Escherichia coli. Mol Microbiol. 2004;54:692-701 pubmed
    ..The cAMP-CRP complex, which stimulates P1 and represses P2, did not affect the tsp selection process. The rules of tsp selection by RNA polymerase containing sigma70 in gal and pyr promoters discussed here may be applicable to others. ..
  7. Miles S, Carpenter B, Gancz H, Merrell D. Helicobacter pylori apo-Fur regulation appears unconserved across species. J Microbiol. 2010;48:378-86 pubmed publisher
    ..These data suggest that despite the conservation among bacterial Fur proteins, H. pylori Fur contains unique structure/function features that make it novel in comparison to Fur from other species. ..
  8. Potrykus K, Murphy H, Chen X, Epstein J, Cashel M. Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL. Nucleic Acids Res. 2010;38:1636-51 pubmed publisher
    ..Although GraL overexpression induces >/=3-fold transcriptional changes of over 100 genes, a direct target remains elusive. ..
  9. Piszczek G, Rozycki J, Singh S, Ginsburg A, Maurizi M. The molecular chaperone, ClpA, has a single high affinity peptide binding site per hexamer. J Biol Chem. 2005;280:12221-30 pubmed
    ..Because only one protein at a time can be unfolded and translocated by ClpA hexamers, restricting the number of peptides initially bound should avoid nonproductive binding of substrates and aggregation of partially processed proteins. ..

More Information

Publications44

  1. Mass E, Majdalani N, Gottesman S. Regulatory roles for small RNAs in bacteria. Curr Opin Microbiol. 2003;6:120-4 pubmed
    ..Small RNAs can both positively and negatively regulate translation, can simultaneously regulate multiple mRNA targets, and can change the pattern of polarity within an operon...
  2. Heredia Moya J, Kirk K. Synthesis of beta-(S-methyl)thioaspartic acid and derivatives. Bioorg Med Chem. 2008;16:5908-13 pubmed publisher
    ..Following this key transformation, we were able to prepare protected beta-(S-methyl)thioaspartic acid derivative suitable for peptide coupling. ..
  3. Keiser P, Coulibaly Y, Kubofcik J, Diallo A, Klion A, Traore S, et al. Molecular identification of Wolbachia from the filarial nematode Mansonella perstans. Mol Biochem Parasitol. 2008;160:123-8 pubmed publisher
  4. Kunkle C, Schmitt M. Comparative analysis of hmuO function and expression in Corynebacterium species. J Bacteriol. 2007;189:3650-4 pubmed
    ..diphtheriae hmuO promoter shows both significant iron repression and heme-dependent activation. These findings indicate that variability in HmuO function and expression exists among Corynebacterium species. ..
  5. Fozo E, Hemm M, Storz G. Small toxic proteins and the antisense RNAs that repress them. Microbiol Mol Biol Rev. 2008;72:579-89, Table of Contents pubmed publisher
  6. Moon K, Gottesman S. A PhoQ/P-regulated small RNA regulates sensitivity of Escherichia coli to antimicrobial peptides. Mol Microbiol. 2009;74:1314-30 pubmed publisher
    ..sRNAs have previously been shown to regulate many outer membrane proteins. This work demonstrates that LPS, a major contributor of bacterial interactions with mammalian cells, is also subject to regulation by sRNAs. ..
  7. Fozo E, Makarova K, Shabalina S, Yutin N, Koonin E, Storz G. Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res. 2010;38:3743-59 pubmed publisher
    ..Our results suggest that type I toxin-antitoxin modules are much more widely distributed among bacteria than previously appreciated. ..
  8. Mass E, Gottesman S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A. 2002;99:4620-5 pubmed publisher
  9. Decker K, Hinton D. The secret to 6S: regulating RNA polymerase by ribo-sequestration. Mol Microbiol. 2009;73:137-40 pubmed publisher
    ..Several residues that interact with 6S RNA are ones previously known to interact with protein activators of Esigma(70). Their work adds 6S RNA to the growing list of factors that can regulate Esigma(70) by interacting with region 4. ..
  10. Fozo E, Kawano M, Fontaine F, Kaya Y, Mendieta K, Jones K, et al. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol Microbiol. 2008;70:1076-93 pubmed publisher
    ..Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell. ..
  11. Ranquet C, Gottesman S. Translational regulation of the Escherichia coli stress factor RpoS: a role for SsrA and Lon. J Bacteriol. 2007;189:4872-9 pubmed
    ..We suggest that SsrA may indirectly improve RpoS translation by limiting ribosome stalling and depletion of some component of the translation machinery. ..
  12. Sledjeski D, Gupta A, Gottesman S. The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli. EMBO J. 1996;15:3993-4000 pubmed
    ..dsrA expression is also increased at low temperatures. These results suggest a new role for RpoS during exponential growth at low temperatures, mediated by DsrA. ..
  13. Sarubbi E, Rudd K, Cashel M. Basal ppGpp level adjustment shown by new spoT mutants affect steady state growth rates and rrnA ribosomal promoter regulation in Escherichia coli. Mol Gen Genet. 1988;213:214-22 pubmed
  14. Mandin P, Gottesman S. A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system. Mol Microbiol. 2009;72:551-65 pubmed publisher
    ..One small RNA, RybC, was found to negatively regulate the expression of dpiB. Using mutants in the dpiB-lacZ fusion and compensatory mutations in the RybC sRNA, we demonstrate that RybC directly base pairs with the dpiBA mRNA. ..
  15. Lewis D, Komissarova N, Le P, Kashlev M, Adhya S. DNA sequences in gal operon override transcription elongation blocks. J Mol Biol. 2008;382:843-58 pubmed publisher
    ..It also explains the synthesis of gal enzymes in the absence of inducer for biosynthetic reactions. ..
  16. James T, Cashel M, Hinton D. A mutation within the ? subunit of Escherichia coli RNA polymerase impairs transcription from bacteriophage T4 middle promoters. J Bacteriol. 2010;192:5580-7 pubmed publisher
    ..Our results suggest that the presence of MotA and AsiA may impair the function of this loop or that this portion of the ? subunit may influence interactions among MotA, AsiA, and RNA polymerase. ..
  17. Singh S, Grimaud R, Hoskins J, Wickner S, Maurizi M. Unfolding and internalization of proteins by the ATP-dependent proteases ClpXP and ClpAP. Proc Natl Acad Sci U S A. 2000;97:8898-903 pubmed
    ..ClpX preferentially targets motifs exposed in specific proteins. As the protein is unfolded by ClpX, additional motifs are exposed that facilitate its retention and favor its translocation to ClpP for degradation. ..
  18. Weisberg R. Transcription by moonlight: structural basis of an extraribosomal activity of ribosomal protein S10. Mol Cell. 2008;32:747-8 pubmed publisher
    ..2008) show that S10 protein can function in the ribosome or the transcript elongation complex with minimal structural change, providing new insights into the roles of S10 and NusB in transcript elongation. ..
  19. McCullen C, Benhammou J, Majdalani N, Gottesman S. Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation. J Bacteriol. 2010;192:5559-71 pubmed publisher
  20. Thompson K, Rhodius V, Gottesman S. SigmaE regulates and is regulated by a small RNA in Escherichia coli. J Bacteriol. 2007;189:4243-56 pubmed
    ..Based on the plasmid screens, NsrR, a repressor sensitive to nitric oxide, was also found to negatively regulate sigma(E)-dependent promoters in an RseA-independent fashion. ..
  21. Chattoraj D. Tryptophanase in sRNA control of the Escherichia coli cell cycle. Mol Microbiol. 2007;63:1-3 pubmed
    ..Targeting a catabolic enzyme to buy time for recombination is an amazing example of adaptation, which illustrates the power of a selfish element (a plasmid in this case) to exploit the host cell machinery to its advantage. ..
  22. Jaroniec C, Boisbouvier J, Tworowska I, Nikonowicz E, Bax A. Accurate measurement of 15N-13C residual dipolar couplings in nucleic acids. J Biomol NMR. 2005;31:231-41 pubmed
  23. Anantharaman V, Aravind L. The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism. Genome Biol. 2002;3:RESEARCH0061 pubmed
    ..Identification of this versatile domain in numerous proteins could aid investigation of unexplored aspects of their biology. ..
  24. Palmer R, Diaz P, Kolenbrander P. Rapid succession within the Veillonella population of a developing human oral biofilm in situ. J Bacteriol. 2006;188:4117-24 pubmed
    ..Changes in community structure can occur very rapidly in natural biofilm development, and we suggest that this process may influence evolution within this ecosystem...
  25. Waters L, Storz G. Regulatory RNAs in bacteria. Cell. 2009;136:615-28 pubmed publisher
    ..Here, we review the known mechanisms and roles of regulatory RNAs, highlight emerging themes, and discuss remaining questions. ..
  26. Majdalani N, Hernandez D, Gottesman S. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol Microbiol. 2002;46:813-26 pubmed
    ..This work suggests a new signal for RpoS translation and extends the global regulation effected by the RcsC/RcsB system to coregulation of RpoS with capsule and FtsZ. ..
  27. Mandin P, Gottesman S. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J. 2010;29:3094-107 pubmed publisher
    ..ArcZ directly represses, and is repressed by, arcB transcription, providing a negative feedback loop that may affect functioning of the ArcA-ArcB regulon. ..
  28. Zhang A, Altuvia S, Tiwari A, Argaman L, Hengge Aronis R, Storz G. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J. 1998;17:6061-8 pubmed
    ..Co-immunoprecipitation and gel mobility shift experiments revealed that the OxyS RNA binds Hfq, suggesting that OxyS represses rpoS translation by altering Hfq activity. ..
  29. Sledjeski D, Gottesman S. A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1995;92:2003-7 pubmed
    ..coli. Since the stimulation of rcsA transcription by this small RNA does not depend on any sequences from within the rcsA transcript, DsrA acts, either directly or indirectly, on rcsA transcription initiation. ..
  30. Gottesman S. Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet. 2005;21:399-404 pubmed
    ..Because these non-coding RNAs act post-transcriptionally, they impose a regulatory step that is independent of and epistatic to any transcriptional signals for their target mRNAs. ..
  31. Majdalani N, Vanderpool C, Gottesman S. Bacterial small RNA regulators. Crit Rev Biochem Mol Biol. 2005;40:93-113 pubmed
    ..Homologs of CsrA and related regulatory RNAs have been implicated in the regulation of gluconeogenesis, biofilm formation,and virulence factor expression in plant and human pathogens. ..
  32. Kawano M, Reynolds A, Miranda Rios J, Storz G. Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res. 2005;33:1040-50 pubmed
    ..In addition, we identified a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5' or 3' ends of the mRNAs with perfect complementarity. ..
  33. Vanderpool C, Gottesman S. Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol. 2004;54:1076-89 pubmed
    ..Decreased ptsG mRNA results in decreased production of glucose transport machinery, thus limiting further accumulation of glucose phosphate. ..
  34. Ortega J, Lee H, Maurizi M, Steven A. Alternating translocation of protein substrates from both ends of ClpXP protease. EMBO J. 2002;21:4938-49 pubmed
  35. Altuvia S, Zhang A, Argaman L, Tiwari A, Storz G. The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding. EMBO J. 1998;17:6069-75 pubmed
    ..We examined the mechanism of OxyS repression of fhlA and found that the OxyS RNA inhibits fhlA translation by pairing with a short sequence overlapping the Shine-Dalgarno sequence, thereby blocking ribosome binding/translation. ..