Biology subjects

Wigneshweraraj, S.

Publications and source records attributed to Wigneshweraraj, S..

5 recordsLinked to original sources

bioRxiv2026

A nucleic acid host factor enables optimal phage replication in Escherichia coli

Host acquisition by bacteriophages (phages) often entails modulation, appropriation, or inhibition of components and processes central to bacterial gene expression. Small non-coding RNAs (sRNAs) are major regulators of RNA fate and frequently rely on the conserved RNA chaperone Hfq to engage their cognate targets. Although phages are known to encode specialised proteins and sRNAs to manipulate host gene expression, it has remained unclear whether they also co-opt host-encoded sRNAs for their own regulatory needs. We show that transcriptome-wide Hfq-mediated RNA-RNA interactions are broadly destabilised during T2 phage infection of Escherichia coli. We further demonstrate that the conserved bacterial sRNA ArcZ is co-opted by T2 to promote expression of a conserved phage operon that includes a protein which inhibits a bacterial restriction-modification system. ArcZ achieves this by preventing RNase E-mediated degradation of the transcript originating from the phage operon. Our study provides the first evidence of an evolutionary strategy in which a phage leverages a nucleic acid host factor to fulfil its own gene expression requirements.

microbiology↗

bioRxiv2025

Pleiotropic functions of glutathione in the adaptive response to long-term nitrogen starvation in Escherichia coli

Nitrogen (N) is essential for bacterial growth, and adaptation to N starvation involves extensive reprogramming of gene expression. A hallmark subcellular feature in long-term N starved Escherichia coli cells is the presence of biomolecular condensates of the major bacterial RNA regulator Hfq. The Hfq condensates, which accumulate gradually during N starvation, contribute to adaptation by modulating RNA metabolism and central metabolic pathways. Metabolites play central roles in stress responses, often acting as modulators of protein function to support survival and recovery. Glutathione (GSH), a universal stress protectant, has broad roles in bacterial stress adaptation, yet its function during N starvation remains unexplored. Using a GSH-deficient mutant ({Delta}gshAB), we show that GSH is required for optimal survival and recovery from prolonged N starvation. We reveal that GSH regulates the temporal dynamics of Hfq condensation and dissipation during starvation and recovery, respectively, via an as-yet unknown mechanism. Notably, these two functions of GSH appear mutually exclusive, highlighting its pleiotropic role in the adaptive response to N starvation that potentially extends its canonical function as a stress protectant. IMPORTANCENitrogen is a vital nutrient that bacteria need to grow. When nitrogen becomes scarce, bacteria must quickly adjust how their genes are used to survive. In Escherichia coli, one of the key changes during long-term nitrogen starvation is the formation of tiny structures inside the cell called Hfq condensates, which help manage genetic information flow and metabolism. Small molecules called metabolites play important roles in helping bacteria cope with stress, and one such molecule, glutathione (GSH), is known to protect cells under various stress conditions. However, its role during nitrogen starvation is not known. In this study, we used a mutant strain of E. coli that cannot produce GSH and found that these bacteria struggle to survive and recover from nitrogen starvation. We also discovered that GSH helps control when and how Hfq condensates form and disappear. Although, these two functions of GSH seem to be unrelated, our study highlights the versatile role of GSH in helping bacteria adapt to nitrogen stress.

microbiology↗

bioRxiv2021

The association between Hfq and RNase E in long-term nitrogen starved Escherichia coli

Under conditions of nutrient adversity, bacteria adjust metabolism to minimise cellular energy usage. This is often achieved by controlling the synthesis and degradation of RNA. In Escherichia coli, RNase E is the central enzyme involved in RNA degradation and serves as a scaffold for the assembly of the multiprotein complex known as the RNA degradosome. The activity of RNase E against specific mRNAs can also be regulated by the action of small RNAs (sRNA). In this case, the ubiquitous bacterial chaperone Hfq bound to sRNAs can interact with the RNA degradosome for the sRNA guided degradation of target RNAs. The RNA degradosome and Hfq have never been visualised together in live bacteria. We now show that in long-term nitrogen starved E. coli, both RNase E and Hfq co-localise in a single, large focus. This subcellular assembly, which we refer to as the H-body, forms by a liquid-liquid phase separation type mechanism and includes components of the RNA degradosome, namely, the helicase RhlB and the exoribonuclease polynucleotide phosphorylase. The results support the existence of an hitherto unreported subcellular compartmentalisation of a process(s) associated with RNA management in stressed bacteria.

microbiology↗

bioRxiv2018

A role for a conserved kinase in the transcriptional control of methionine biosynthesis in Escherichia coli experiencing sustained nitrogen starvation

The initial adaptive transcriptional response to nitrogen (N) starvation in Escherichia coli involves large-scale alterations to the transcriptome mediated by the transcription activator, NtrC. One of the NtrC-activated genes is yeaG, which encodes a conserved bacterial kinase. Although it is known that YeaG is required for optimal survival under sustained N starvation, the molecular basis by which YeaG benefits N starved E. coli remains elusive. By combining transcriptomics with targeted metabolomics analyses, we demonstrate that the methionine biosynthesis pathway becomes transcriptionally dysregulated in{Delta} yeaG bacteria experiencing sustained N starvation. This results in the aberrant and energetically costly biosynthesis of methionine and associated metabolites under sustained N starvation with detrimental consequences to cell viability. It appears the activity of the master transcriptional repressor of methionine biosynthesis genes, MetJ, is compromised in{Delta} yeaG bacteria under sustained N starvation, resulting in transcriptional derepression of MetJ-regulated genes. The results suggest that YeaG is a novel regulatory factor and functions as a molecular brake in the transcriptional control of both the NtrC-regulon and methionine biosynthesis genes in E. coli experiencing sustained N starvation.

microbiology↗

bioRxiv2017

Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli

Many bacterial adaptive responses to changes in growth conditions due to biotic and abiotic factors involve reprogramming of gene expression at the transcription level. The bacterial RNA polymerase (RNAP), which catalyzes transcription, can thus be considered as the major mediator of cellular adaptive strategies. But how do bacteria respond if a stress factor directly compromises the activity of the RNAP? We used a phage-derived small protein to specifically perturb bacterial RNAP activity in exponentially growing Escherichia coli. Using cytological profiling, tracking RNAP behavior at single-molecule level and transcriptome analysis, we reveal that adaptation to conditions that directly perturb bacterial RNAP performance can result in a biphasic growth behavior and thereby confer the adapted bacterial cells an enhanced ability to tolerate diverse antibacterial stresses. The results imply that while synthetic transcriptional rewiring may confer bacteria with the intended desirable properties, such approaches may also collaterally allow them to acquire undesirable traits.

microbiology↗