Distinguished Research Professor
Ph.D. (1970) Brandeis University
See my Laboratory Home Page
In all biological systems, RNA molecules--including messenger RNAs (mRNAs), or noncoding RNAs such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) or small regulatory RNAs (sRNAs)--serve as intermediates to help regulate the conversion of the genetic information contained within a cell’s DNA into functional proteins. My laboratory is currently employing a combination of genetic, molecular biological, genomic, proteomic, bioinformatic, and biochemical approaches to develop a better understanding of the mechanisms involved in the processing, maturation and decay of all types of RNA molecules in E. coli. In addition, we also are examining the biological role of polyadenylation in bacteria, in part by employing genomic arrays. Beyond the work on RNA metabolism, my laboratory continues its genetic and biochemical analysis of DNA repair, mutagenesis, and genetic recombination in E. coli. In particular, we are now working on understanding the role of DNA helicase II in DNA repair, spontaneous mutagenesis and DNA replication. Other interests include the expression of cloned eukaryotic genes in prokaryotic hosts.
- Stead, M.B., A. Agrawal, K.E. Bowen, R. Nasir, B.K. Mohanty, R.B. Meagher and S.R. Kushner. 2012. RNAsnapTM: a rapid, quantitative and inexpensive method for isolating total RNA from bacteria. Nucleic Acids Res. 40: e156.
- Mohanty, B.K. and S.R. Kushner. 2012. 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., V.F. Maples and S. R. Kushner. 2012. Polyadenylation helps regulate functional tRNA levels in Escherichia coli. Nucleic Acids Res. doi: 10.1093/nar/gks006.
- Stead, M.B., S. Marshburn, B.K. Mohanty, 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 in vivo Using Tiling Microarrays. Nucleic Acids Res. 39: 3188-203.
- 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 Escherichia 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.
- Kushner, S.R. 2004. mRNA decay and processing. Pp. 327-345 In: The Bacterial Chromosome. N.P. Higgins (ed). ASM Press, Washington, DC.
- Mohanty, B.K. and S.R. Kushner. 2003. Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Molec. Microbiol. 50: 645-658.
- Ow, M.C., T. Perwez and S.R. Kushner. 2003. RNase G of Escherichia coli exhibits only limited functional overlap with its essential homologue, RNase E. Molec. Microbiol. 49: 607-622.
- Kushner, S.R. 2002. mRNA decay in Escherichia coli comes of age. J. Bacteriol. 184: 4658-4665.
- Ow, M.C., Q. Liu, B.K. Mohanty, M.E. Andrew, V.F. Maples and S.R. Kushner. 2002. RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the rne gene from three promoters. Molec. Microbiol. 43: 159-172.
- Ow, M.C. and S.R. Kushner. 2002. Initiation of tRNA maturation by RNase E is essential for cell viability in Escherichia coli. Genes and Development 16: 1102-1115.
- Mohanty, B.K. and S.R. Kushner. 2000. Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli. Molec. Microbiol. 36: 982-994.
- Bügl, H., E.B. Fauman, B.L. Staker, F-Z. Zheng, S.R. Kushner, M.A. Saper, J.C.A. Bardwell and U. Jakob. 2000. RNA methylation under heat shock control. Molecular Cell 6: 349-360.
- Mohanty, B.K. and S.R. Kushner. 2000. Polynucleotide phosphorylase functions both as a 3' --> 5' exonuclease and a poly(A) polymerase in in Escherichia coli. Proc. Natl. Acad. Sci. USA 97: 11966-11971.
- Ow, M.C., Q. Liu and S.R. Kushner. 2000. Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly. Molec. Microbiol. 38: 854-866.