Publications

2022

1. Mohanty B.K. and Kushner S.R. Processing of the alaW alaX operon encoding the Ala2 tRNAs in Escherichia coli requires both RNase E and RNase P.  Mol. Microbiol. October 21, 2022.

2. Mohanty B.K.; Nichols, K. and Kushner S.R. Maturation of the E. coli Glu2, Ile1 and Ala1B tRNAs utilizes a complex processing pathway.  Mol. Microbiol. 118(1-2):30-46, 2022.

3. Mohanty B.K., Maples V. and Kushner S.R. The C nucleotide at the mature 5′ end of the Escherichia coli proline tRNAs is required for the RNase E cleavage specificity at the  3′ terminus as well as functionality, Nucleic Acids Res. 50(3):1639-1649, 2022.

4.  Mohanty B.K. and Kushner S.R. Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism.  Mol. Microbiol. 117(1):121-142, 2022.  Special Issue: Regulating with RNA in Microbes.

2021

1. Mohanty B.K. and Kushner S.R. Regulation of mRNA decay in E. coli.  Crit. Rev. Biochem. & Mol. Microbiol. 2021.

2020

1.  Mohanty B.K., Agrawal A and Kushner S.R. Generation of pre-tRNAs from polycistronic operons is the essential function of RNase P in Escherichia coli.  Nucleic Acids Res. 48(5):2564-2578. 2020.

2019

1. Mohanty B.K. and Kushner S.R. New Insights into the Relationship between tRNA Processing and Polyadenylation in Escherichia coli. Trends in Genetics. 35(6):434-445. 2019.

2. Mohanty B.K. and Kushner S.R. Analysis of post-transcriptional RNA metabolism in prokaryotes. Methods. 155:124-130. 2019.

2018

1. Mohanty B.K. and Kushner S.R.  Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria. Microbiology Spectrum, 6(2): :RWR-0011-2017, doi: 10.1128, 2018.  

2017

1. Bowden KE, Wiese NS, Perwez T, Mohanty BK, Kushner SR.  J. Bacteriol. 200(13):  The rph-1-Encoded Truncated RNase PH Protein Inhibits RNase P Maturation of Pre-tRNAs with Short Leader Sequences in the Absence of RppH.  J. Bacteriol. 199(22), pii: e00301-17. doi: 10.1128, 2017  

2016

1. Mohanty B.K., Petree, J.C. and Kushner S.R.  Endonucleolytic cleavages by RNase E generate the mature 3' termini of the three proline tRNAs in Escherichia coli . Nucleic Acids Res., 44 (13): 6350-62, 2016.

2. Mildenhall, K.B., Wiese, N.; Chung, D. Maples, V.F.; Mohanty, B.K. and Kushner S.R.  RNaseE based Degradosome Modulates Polyadenylation of mrNAs after Rho-Independent Transcription Terminators in Escherichia coli. Mol. Microbiol., 101(4): 645-655, 2016.

3. Mohanty B. K., and Kushner S.R.  Regulation of mRNA Decay in Bacteria.  Ann. Rev. Microbiol., 70:25-44, 2016.  

2014

1. Agrawal, A., Mohanty, B.K. and Kushner S.R.  Processing of the seven valine tRNAs in Escherichia coli involves novel features of RNase P. Nucleic Acids Res., 42 (17): 11166-79, 2014.

2. Mohanty B. K., and Kushner S.R.  In vivo analysis of polyadenylation in prokaryotes.  Methods in Molecular Biology, 1125:229-249, 2014.  

2013

1. Mohanty B.K., and Kushner S.R.  Deregulation of poly(A) polymerase I in Escherichia coli inhibits protein synthesis and leads to cell death. Nucleic Acids Res., 41 (3): 1757-1766, 2013.  

2012

1. Stead, M.B.; Agrawal, A; Bowden, K.E.; Nasir, R; Mohanty, B.K.; Meagher, R.B. and Kushner, S.R.  RNAsnapTM: a rapid, quantitativeand inexpensive, method for isolating total RNA from bacteria.  Nucleic Acids Res., 40(20): e156, 2012.

2. Mohanty, B.K., Maples V; Kushner S.R.  Polyadenylation helps regulate functional tRNA levels in Escherichia coli.  Nucleic Acids Res., 40(10): 4589-4603, 2012.   

2011

1. Stead, M.B.; Marshburn, S; Mohanty, B.K.; Mitra, J; Castillo, L.P.; Ray, D.; van Bakel, H.; Hughes, T.R.; Kushner, S.R.  Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays .  Nucleic Acids Res., 39:3188-3203, 2011. Additional Data  

2010

1. Mohanty, B. K., and  Kushner, S.R.  Bacterial/archaeal/organellar polyadenylation.  WIREs RNA, 2(2):256-276, 2010.

2. Chung, D-H.; Min, Z.; Wang, Bi-C. and Kushner, S.R.  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, 2010.

3. Mohanty, B. K., and  Kushner, S.R.  Processing of the Escherichia coli leuX tRNA transcript, encoding tRNALeu5, requires either the 3'->5' exoribonuclease polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator. Nucleic Acids Res., 38:597-607, 2010.  

2009

1. Tran TT, Zhou F, Marshburn, S., Stead M, Kushner SR, Xu Y.  De novo computational prediction of non-coding RNA genes in prokaryotic genomes.  Bioinformatics, 25:2897-2905, 2009.

2. Carabetta, V.J., Mohanty, B.K., Kushner, S.R. and Silhavy, T.  The response regulator SprE (RssB) modulates polyadenylation and mRNA stability in Escherichia coli. J. Bacteriol., 191:6812-21, 2009.  

2008

1. Mohanty, B.K; Giladi, H; Maples, V.F. and Kushner, S.R.  Analysis of RNA Decay, Processing, and Polyadenylation in Escherichia coli and Other Prokaryotes. In Lynne E. Maquat and Cecilia M. Arraiano, editors:Methods in Enzymology, Vol. 447, Burlington: Academic Press, 2008, pp. 3-29.

2. Tariq Perwez, Danyal Hami, Valerie F. Maples, Zhao Min, Bi-Cheng Wang, and Sidney R. Kushner

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 Res., 36(16):5306-18, 2008.

3. Mohanty, B. K., and S. R. Kushner.  Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli, Nucleic Acids Res., 36(2):364-375, 2008.  

2007

1. Mohanty, B. K., and S. R. Kushner.  Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E.  Nucleic Acids Res., 35(22):7614-7625, 2007.

2. Kushner, S. R.  1 June 2007, posting date. Chapter 4.6.4.  Messenger RNA decay.  In, A. Bock,  R. Curtis III., Gross, C.A., J.B. Kaper, F.C. Neidhardt, T. Nystrom, K.E, Rudd,  and C. L. Squires (ed.),  Escherichia coli and Salmonella: cellular and molecular biology.  http://www.ecosal.org.  American Society for Microbiology Press, Washington, DC.

2006

1. Mohanty, B.K. and Kushner, S.R. Majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells. Nucleic Acids Research, 34(19):5695-5704, 2006. Supplementary materials

2. Suzuki, K., Babitzke, P., Kushner, S.R. and Romeo, T.  Identification of novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E.  Genes and Development, 20:2605-2617, 2006.

3. Perwez, T. and Kushner, S.R.  RNase Z in Escherichia coli plays a significant role in mRNA decay.  Mol. Microbiol., 60(3):723-737, 2006.  

2004

1. Mohanty, B.K. Maples, V.F. and Kushner, S.R. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli.  Mol. Microbiol., 54(4):905-920, 2004.

2. Kushner, S.R. Pre-tRNA Processing and Pre-rRNA Processing in Bacteria, In: Encyclopedia of Biological Chemistry, W.J. Lennarz and M.D. Lane eds., Elsevier, Oxford, Vol. 3, pp. 420-424, 2004.

3. Kushner, S. R. mRNA decay and Processing.  In: The Bacterial Chromosome, Higgins, N.P., ed. ASM Press, Washington, DC, pp. 327-345, 2004  

2003

1. Mohanty, B.K. and Kushner, S.R. Genomic analysis in Escherichia colidemonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay.  Mol. Microbiol., 50(2):645-658, 2003.

Supplementary materials: Table S1, Table S2 2. 

2. Ow, M.C.; Perwez, T. and Kushner, S.R.  RNase G of Escherichicoli exibits only limited functional overlap with its essential homologue, RNase E.  Mol. Microbiol., 49:607-622, 2003.  

2002

1. Mohanty, B.K. and Kushner, S.R. Polyadenylation of Escherichia coli transcripts play an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E.  Mol. Microbiol., 45(5):1315-1324, 2002. 

2.  Kushner, S.R.  mRNA Decay in Escherichia coli Comes of Age.  J. Bacteriol. 184:4658-4665, 2002.

3. Kushner, S. R.  Polyadenylation. In. Encyclopedia of Molecular Biology, On-Line Edition, T. E. Creighton, Ed., John Wiley & Sons, New York. 2002. 

4. Kushner, S. R. Nucleases. In, Encyclopedia of Life Sciences, MacMillan Reference Limited, Stockton Press, London. 2002.

5. Ow, M. C. and S. R. Kushner.  Initiation of tRNA maturation by RNase E is essential for cell viability in Escherichia coli.  Genes and Development, 16:1102-1115, 2002.

6.  Ow, M.C.; Liu, Q.; Mohanty, B.K.; Andrew, M.E.; Maples, V.F. and Kushner, S.R.  RNase E levels in Escherichia    coli are controlled by a complex regulatory system that involves transcription of the rne gene from three promoters.  Mol. Microbiol., 43:159-172, 2002.  

2000

1. Mohanty, B.K. and Kushner, S.R.  Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli.  Mol. Microbiol. 36:982-994, 2000a.

2. Bügl, H., E.B. Fauman, B.L. Staker, F-Z. Zheng, S.R. Kushner, M.A. Saper, J.C.A. Bardwell, and U. Jakob.  RNA methylation under heat shock control.  Molecular Cell, 6:349-360, 2000.

3. Mohanty, B.K. and Kushner, S.R.  Polynucleotide phosphorylase functions both as a 3->5' exonuclease and a poly(A) polymerase in Escherichia coli.  Proc. Natl. Acad. Sci. USA,  97:11966-11971, 2000b.

4. Ow, M.C., Q. Liu, and S. R. Kushner.  Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly.  Molec. Microbiol., 38:854-866, 2000.  

1999

1. Mohanty, B.K. and Kushner, R.  Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism.  Mol. Microbiol. 34(5):1094-1108, 1999a.



2. Mohanty, B.K. and Kushner, R. Residual polyadenylation in poly(A) polymerase I (pcnB ) mutants of Escherichia coli does not result from the activity encoded by the f310 gene. Mol. Microbiol. 34(5):1109-1119, 1999b.

3. Kushner, S. R.   Polyadenylation. In. Encyclopedia of Molecular Biology, T. E. Creighton, Ed., John Wiley & Sons, New York, pp. 1888-1890, 1999.  

1998

1.Zhang, G., E. Deng, L. R. Baugh, and S. R. Kushner.   Identification  and characterization of Escherichia coli DNA helicase II mutants that exhibit increased unwinding efficiency.  J. Bacteriol., 180: 377-387, 1998.

2. Granger, L. L., E. B. O’Hara, R-F. Wang, F.V. Meffen, K. Armstrong., S.D. Yancey, P. Babitzke, and S. R. Kushner. The Escherichia coli mrsC gene is required for cell growth and mRNA decay.  J. Bacteriol., 180: 1920-1928, 1998.

3. Wang, R-F., E.B. O’Hara, M. Aldea, C.I. Bargmann, H. Gromley, and S.R. Kushner. Escherichia coli MrsC is an allele of HflB, encoding a membrane-associated ATPase and protease that is required for mRNA decay. J. Bacteriol., 180: 1929-1938, 1998.