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Sidney Kushner

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Distinguished Research Professor
Ph.D. (1970) Brandeis University
  • Who's Who in America
  • 2013 Lamar Dodd Award Recipient, University of Georgia
  • 2013 Division H Lecturer by the American Society for Microbiology
  • Chair-Elect of Division H, American Society of Microbiology, 2012-2013
  • Fellow, American Academy for the Advancement of Science
  • American Men and Women in Science
  • Fellow, American Academy of Microbiology
  • Excellence in Undergraduate Research Mentoring Award, Center for Undergraduate Research Opportunities, University of Georgia, 2005
  • SREB Faculty Mentor of the Year, 2004
  • Creative Research Medal, University of Georgia, 1987
  • Grant Support -
    • "Analysis of E. coli Ribonucleases and RNA Metabolism," NIH
  • Research Interests -
    • We are using a combination of genetic, biochemical, bioinformatics and RNA-seq approaches to analyze the post-transcriptional control of gene expression in the model prokaryote, Escherichia coli. These studies include examining the biological role of polyadenylation in bacteria, determining the multiple pathways by which primary transfer RNA (tRNA) transcripts are processed into their mature forms, outlining the enzymatic steps in converting primary 30S ribosomal RNA (rRNA) transcripts into their mature 16S, 23S and 5S components, examining the mechanisms of mRNA decay and processing, and understanding how small regulatory RNAs (sRNAs) help control gene expression.  Other research interests include various aspects of using Escherichia coli as a host for expressing eukaryotic proteins and DNA repair. 
Selected Publications:
  • Mohanty, B. K. and S. R. Kushner. 2019.  Analysis of post-transcriptional RNA metabolism in prokaryotes.  Methods, 155:124-130.

  • Mohanty, B.K. and S. R. Kushner. 2019.  New insights into the relationship between tRNA processing and polyadenylation in Escherichia coli.  Trends in Genetics, 35:434-445.

  • Kushner, Sidney R.  2018. Messenger RNA in Prokaryotes. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0000874.pub4.

  • Mohanty, B.K. and S. R. Kushner.  2018. Enzymes Involved in Post-transcriptional RNA Metabolism in Gram-negative bacteria. Microbiology Spectrum, 6:RWR-0011-2017. Doi:10.1128/microbiolspec.RWR-0011-2017.

  • Bowden, K. E., Wiese, N.S., Perwez, T., Mohanty, B.K., and S.R. Kushner.  2017.  The rph-1 encoded truncated RNase PH protein inhibits RNase P maturation of pre-tRNAs with short leader sequences in the absence of RppH.  Journal of Bacteriology, 199: UNSP e00301-17.

  • Mildenhall, K.B., Wiese, N., Chung, D., Maples, V.F., Mohanty, B. K., and S. R. Kushner. 2016.  RNase E-based degradosome modulates polyadenylation of mRNAs after Rho-independent transcription terminators in Escherichia coli.  Molecular Microbiology, 101:645-655

  • Mohanty, B. K., Petree, J. R., and S. R. Kushner.  2016.  Endonucleolytic cleavages by RNase E generate the mature 3' termini of the three proline tRNAs in Escherichia coli.  Nucleic Acids Res., 44:6350-62

  • Mohanty, B. K. and S. R. Kushner.  2016.  Regulation of mRNA decay in bacteria.  Annual Review of Microbiology, 70, 25-44.

  • Kushner, S.R. 2016.  Poly(A) tails.  Reference Module in Life Sciences, Elsevier Press,

  • Neidhardt, F. C., and S. R. Kushner.  Escherichia coli.  Reference Module in Life Sciences, Elsevier Press.

  • Kushner, S. R.  2015.  Polyadenylation in E. coli: A 20 year odyssey.  RNA, 21:673-674.
  • Agrawal, A., Mohanty, B. K., and S. R. Kushner. 2014.  Processing of the seven valine tRNAs in Escherichia coli involves novel features of RNase P.  Nucleic Acids Res., 42:11166-11179.
  • Mohanty, B. K. and S.R. Kushner.  2014.  In vivo Analysis of Polyadenylation in Prokaryotes. Methods in Molecular Biology 1125, Polyadenylation: Methods and Protocols, J. Rorbach and A. J. Bobrowicz, eds., Humana Press, pp. 229-249.
  • Mohanty, B. K. and S. R. Kushner.  2013.  Deregulation of poly(A) polymerase I in Escherichia coli inhibits protein synthesis and leads to cell death.  Nucleic Acids Res., 41:1757-1766.
  • Mohanty, B. K., Maples, V. F., and S. R. Kushner.  2012. Polyadenylation helps regulate functional tRNA levels in Escherichia coli. Nucleic Acids Res., 40:4589-4603.
  • Stead, M.B., Agrawal, A., Bowden, K.E., Nasir, R., Mohanty, B.K., Meagher, R.B., and S.R. Kushner. 2012.  RNAsnap™: a rapid, quantitative and inexpensive method for isolating total RNA from bacteria. Nucleic Acids Res., 40:e156.
  • Stead, M.B., S. Marshburn, J. Mitra, L.P. Castillo, D. Ray, H. van Bakel, T.R. Hughes and S. R. Kushner. 2011. Analysis of Escherichia coli RNase E and RNase III activity using tiling microarrays. Nucleic Acids Res. 39:3188-3203.
  • Mohanty, B.K. and S.R. Kushner. 2010. Bacterial/archaeal/organellar polyadenylation. WIREs RNA 2: 256-276.
  • Mohanty, B.K. and S.R. Kushner. 2010. Processing of the Escherichia coli leuX tRNA transcript, encoding tRNALeu5, requires either the 3’ - 5’ exoribonucleases polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator. Nucleic Acids Research 38: 597-607.
  • Chung, D.-H., Z. Min, B.-C. Wang and S.R. Kushner. 2010. Single amino acid changes in the predicted RNase H domain of coli RNase G lead to complementation of RNase E deletion mutants. RNA 16: 1371-1385.
  • Tran, T.T., F. Zhou, S. Marshburn, M. Stead, S.R. Kushner and Z. Xu. 2009. De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinformatics 25: 2897-2905.
  • Carabetta, V.J., B.K. Mohanty, S.R. Kushner and T.J. Silhavy. 2009. The response regulator SprE (RssB) modulates polyadenylation and mRNA stability in Escherichia coli. J. Bacteriology 191: 6812-6821.
  • Mohanty, B.K., H. Giladi, V. Maples and S.R. Kushner. 2008. Pp. 3-29. Analysis of RNA Decay, Processing, and Polyadenylation in Escherichia coli and Other Prokaryotes. In Methods in Enzymology, volume 447. L.E. Maquat and C.M. Arraiano (eds.). Academic Press, Burlington.
  • Mohanty, B.K. and S.R. Kushner. 2008. Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli. Nucleic Acids Research 36: 364-375.
  • Perwez, T., D. Hami, V. Maples, Z. Min, B.-C.Wang and S.R. Kushner. 2008. Intragenic suppressors of temperature-sensitive rne mutations lead to the dissociation of RNase E activity on mRNA and tRNA substrates in Escherichia coli. Nucleic Acids Research 36: 5306-5318.
  • Kushner, S.R. 2007. Chapter 4.6.4. Messenger RNA decay. In, Escherichia coli and Salmonella: cellular and molecular biology. A. Böck, R. Curtis III., Gross, C.A., J.B. Kaper, F.C. Neidhardt, T. Nyström, K.E, Rudd, and C. L. Squires (eds.). American Society for Microbiology Press, Washington, DC.
  • Mohanty, B.K. and S.R. Kushner. 2007. Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. Nucleic Acids Research 35: 7614-25.
  • Mohanty, B.K. and S.R. Kushner. 2006. The majority of E. coli mRNAs undergo post-transcriptional modification in exponentially growing cells. Nucleic Acids Research 34: 5695-5704.
  • Suzuki, K., P. Babitske, S.R. Kushner, and T. Romeo. 2006. Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes and Development 20: 2605-2617.
  • Perwez, T.  and S.R. Kushner. 2006. RNase Z in Escherichia coli plays a significant role in mRNA decay. Molec. Microbiol. 60: 723-737.
  • Kushner, S.R. 2004. mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem. IUBMB Life 56: 585-594.
  • Mohanty, B.K., V.F. Maples and S.R. Kushner. 2004. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Molec. Microbiol. 54: 645-658.

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