Dr. J. Krishna Leela

Scopus Publications

Topoisomerase i essentiality, dnaa-independent chromosomal replication, and transcription-replication conflict in escherichia coli
J. Krishna Leela, Nalini Raghunathan, J. Gowrishankar
Journal of Bacteriology, 2021
In all life forms, double-helical DNA exists in a topologically supercoiled state. The enzymes DNA gyrase and topoisomerase I act, respectively, to introduce and to relax negative DNA supercoils in Escherichia coli .
Corrigendum to: Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination: RNase E pathways and Rho-dependent transcription termination (Molecular Microbiology, (2011), 82, 6, (1330-1348), 10.1111/j.1365-2958.2011.07895.x)
K. Anupama, J. Krishna Leela, J. Gowrishankar
Molecular Microbiology, 2019
In the above article, authors compiled Figure 3B incorrectly by inadvertently using the same image for a pair of panels depicting growth of isogenic nusG+ and nusG::Kan strains under permissive conditions (that is, with IPTG supplementation at 30°). The correct image for Figure 3B is shown below. The authors sincerely apologize for this error and emphasize that it does not affect the conclusions reported in the paper.
A new role for Escherichia coli Dam DNA methylase in prevention of aberrant chromosomal replication
Nalini Raghunathan, Sayantan Goswami, Jakku K Leela, Apuratha Pandiyan, Jayaraman Gowrishankar
Nucleic Acids Research, 2019
The Dam DNA methylase of Escherichia coli is required for methyl-directed mismatch repair, regulation of chromosomal DNA replication initiation from oriC (which is DnaA-dependent), and regulation of gene expression. Here, we show that Dam suppresses aberrant oriC-independent chromosomal replication (also called constitutive stable DNA replication, or cSDR). Dam deficiency conferred cSDR and, in presence of additional mutations (Δtus, rpoB*35) that facilitate retrograde replication fork progression, rescued the lethality of ΔdnaA mutants. The DinG helicase was required for rescue of ΔdnaA inviability during cSDR. Viability of ΔdnaA dam derivatives was dependent on the mismatch repair proteins, since such viability was lost upon introduction of deletions in mutS, mutH or mutL; thus generation of double strand ends (DSEs) by MutHLS action appears to be required for cSDR in the dam mutant. On the other hand, another DSE-generating agent phleomycin was unable to rescue ΔdnaA lethality in dam+ derivatives (mutS+ or ΔmutS), but it could do so in the dam ΔmutS strain. These results point to a second role for Dam deficiency in cSDR. We propose that in Dam-deficient strains, there is an increased likelihood of reverse replication restart (towards oriC) following recombinational repair of DSEs on the chromosome.
Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli
Nalini Raghunathan, Rajvardhan M Kapshikar, Jakku K Leela, Jillella Mallikarjun, Philippe Bouloc, Jayaraman Gowrishankar
Nucleic Acids Research, 2018
Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.
Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli
J. Krishna Leela, Aisha H. Syeda, K. Anupama, J. Gowrishankar
Proceedings of the National Academy of Sciences of the United States of America, 2013
Two pathways of transcription termination, factor-independent and -dependent, exist in bacteria. The latter pathway operates on nascent transcripts that are not simultaneously translated and requires factors Rho, NusG, and NusA, each of which is essential for viability of WT Escherichia coli . NusG and NusA are also involved in antitermination of transcription at the ribosomal RNA operons, as well as in regulating the rates of transcription elongation of all genes. We have used a bisulfite-sensitivity assay to demonstrate genome-wide increase in the occurrence of RNA-DNA hybrids (R-loops), including from antisense and read-through transcripts, in a nusG missense mutant defective for Rho-dependent termination. Lethality associated with complete deficiency of Rho and NusG (but not NusA) was rescued by ectopic expression of an R-loop-helicase UvsW, especially so on defined growth media. Our results suggest that factor-dependent transcription termination subserves a surveillance function to prevent translation-uncoupled transcription from generating R-loops, which would block replication fork progression and therefore be lethal, and that NusA performs additional essential functions as well in E. coli . Prevention of R-loop–mediated transcription-replication conflicts by cotranscriptional protein engagement of nascent RNA is emerging as a unifying theme among both prokaryotes and eukaryotes.
R-loops in bacterial transcription: Their causes and consequences
J Gowrishankar, J Krishna Leela, K Anupama
Transcription, 2013
Nascent untranslated transcripts in bacteria are prone to generating RNA-DNA hybrids (R-loops); Rho-dependent transcription termination acts to reduce their prevalence. Here we discuss the mechanisms of R-loop formation and growth inhibition in bacteria.
Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination
K. Anupama, J. Krishna Leela, J. Gowrishankar
Molecular Microbiology, 2011
Summary The endonuclease RNase E of Escherichia coli is essential for viability, but deletion of its C‐terminal half (CTH) is not lethal. RNase E preferentially acts on 5′‐monophosphorylated RNA whose generation from primary transcripts is catalysed by RppH, but ΔRppH strains are viable. Here we show that the RNase E‐ΔCTH ΔRppH combination is lethal, and that the lethality is suppressed by rho or nusG mutations impairing Rho‐dependent transcription termination. Lethality was correlated with defects in bulk mRNA decay and tRNA processing, which were reversed by the rho suppressor. Lethality suppression was dependent on RNase H1 or the helicase UvsW of phage T4, both of which act to remove RNA–DNA hybrids (R‐loops). The rho and nusG mutations also rescued inviability of a double alteration R169Q (that abolishes 5′‐sensing) with ΔCTH in RNase E, as also that of conditional RNase E deficiency. We suggest that the ΔCTH alteration leads to loss of a second 5′‐end‐independent pathway of RNase E action. We further propose that an increased abundance of R‐loops in the rho and nusG mutants, although ordinarily inimical to growth, contributes to rescue the lethality associated with loss of the two RNase E cleavage pathways by providing an alternative means of RNA degradation.
Studies on xanthan production from Xanthomonas campestris
J. Krishna Leela, Gita Sharma
Bioprocess Engineering, 2000

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