Biology subjects

Varshney, U.

Publications and source records attributed to Varshney, U..

5 recordsLinked to original sources

bioRxiv2026

Evidence for a regulatory role of the evolutionarily conserved sequence complementarity between tRNAs

The tRNAs are non-coding RNAs (ncRNAs) known for their classical role in decoding mRNAs. Analysis of tRNA sequences from Escherichia coli revealed pairwise similarities for different combinations of tRNAs, as well as complementarities between some tRNA pairs. To explore the physiological significance of the complementarities between the tRNAs, we investigated the pair of tRNAs encoded by lysT (encoding an abundant tRNA, tRNALysT), and argU (encoding a rare tRNA, tRNAArgU). We show that tRNALysT and tRNAArgU anneal to form a heterodimer in vitro. The heterodimerisation is prevented by the presence of DNA oligomers complementary to the interacting sequences, in a dose dependent manner. Consistent with the notion of sequestration of tRNAArgU by tRNALysT, while the overexpression of tRNAArgU did not impact the culture growth, that of tRNALysT did. The tRNALysT mediated inhibition of the culture growth was enhanced at a lower temperature. The AGA minigene (decoded by tRNAArgU) mediated toxicity and hybrid phage ({lambda}imm-P22) growth on ssrA (tmRNA) strains was also consistent with the sequestration of tRNAArgU by tRNALysT. Also, we observed tRNA-derived fragments (tRFs) from tRNALysT and tRNAArgU, which too might facilitate tRNAArgU sequestration. Taken together, these observations support a novel regulatory role of the evolutionary conserved complementarities between tRNAs.

genetics↗

bioRxiv2025

LuxS/AI-2 signaling in Salmonella Typhimurium regulates phoP/phoQ to protect against acidic pH for enhanced survival in macrophages

The intestinal milieu is largely characterized by the complex array of chemical compounds produced through the metabolic activity of resident microbiota. Enteric pathogens like Salmonella, which have evolved refined mechanisms to persist within this environment, utilize these microbial metabolites and self-produce quorum molecules as molecular cues to identify ecological niches and modulate their survival and virulence strategies. Salmonella quorum sensing involves producing and detecting Autoinducer-2 (AI-2) signaling molecules. Our research reveals that Salmonella Typhimurium enhances AI-2 biosynthesis and transport under acidic conditions, aiding environmental adaptation and facilitating pathogenesis in macrophages. AI-2 signaling regulates the pH-sensing two-component system genes, phoP/phoQ, ensuring cytosolic pH homeostasis, survival, and acid tolerance. It also involves regulating the lysine/cadaverine-mediated acid tolerance response and maintaining bacterial cytosolic pH. Furthermore, we show that the repressor LsrR protein, apart from the lsr promoter, binds to only one strand of the phoP promoter via its Y25 and R43 amino acids to negatively modulate phoP expression. Additionally this signaling ameliorates the intracellular survival by modulating Salmonella Pathogenicity Island-2 (SPI-2) regulators (ssrA/ssrB) and SPI-2 effector expression via PhoP. Mouse models demonstrate that AI-2 signaling is essential for colonizing the primary and secondary infection sites, showcasing its critical role in pathogenesis and low pH survival mechanisms in Salmonella.

microbiology↗

bioRxiv2025

Mycobacterial MutT1 mediated dephosphorylation of the sensor kinases reveals a new link in the regulation of the two-component signaling in bacteria

Bacterial pathogens such as Mycobacterium tuberculosis majorly rely on two-component signaling (TCS) systems to sense and generate adaptive responses to the dynamic and stressful host environment. TCS comprises a sensor histidine kinase (SK) that perceives the environmental signal, and a response regulator (RR) that modulates the target gene expression. TCS occurs via a phosphotransfer event from SK to RR. However, the mechanisms that regulate phosphotransfer events are not well understood. We explored the role of MutT1, originally characterized to hydrolyze oxidized GTP (8-oxo-GTP) and dGTP (8-oxo-dGTP), in TCS regulation. Unlike other MutT proteins, mycobacterial MutT1 comprises two domains (N-terminal domain, NTD; and C-terminal domain, CTD). Structurally, MutT1 NTD is like MutT proteins in other organisms. However, the MutT1 CTD is similar to E. coli SixA, a histidine phosphatase with an RHG motif. We show that MutT1 CTD dephosphorylates many SKs and impacts expression of their target genes, highlighting the role of MutT1 in regulating TCS. These novel findings are of special significance because they provide us with an extrinsic phosphatase mechanism to reset TCS signaling. The study reveals an intricate interplay between an enzyme that sanitizes the cellular nucleotide pool, and bacterial signaling pathways, offering insights into the adaptation mechanisms.

cell biology↗

bioRxiv2024

An unusual activity of mycobacterial MutT1 Nudix hydrolase domain as a protein phosphatase regulates nucleoside diphosphate kinase (NDK) function

MutT proteins are Nudix hydrolases characterized by the presence of a Nudix box, GX5EX7REUXEEXGU, where U is a bulky hydrophobic residue and X is any residue. Major MutT proteins hydrolyse 8-oxo-(d)GTP (8-oxo-GTP or 8-oxo-dGTP) to the corresponding 8-oxo-(d)GMP, preventing their incorporation into nucleic acids. Mycobacterial MutT1 comprises an N-terminal domain (NTD) harbouring the Nudix box motif, and a C-terminal domain (CTD) harbouring the RHG histidine phosphatase motif. Interestingly, unlike other MutTs, the MutT1 hydrolyses the mutagenic 8-oxo-(d)GTP to corresponding 8-oxo-(d)GDP. Nucleoside diphosphate kinase (NDK), a conserved protein, carries out reversible conversion of (d)NDPs to (d)NTPs through phospho-NDK (NDK-Pi) intermediate. Recently, we showed that NDK-Pi converts 8-oxo-dGDP to 8-oxo-dGTP and escalates A to C mutations in a MutT deficient Escherichia coli. We now show that both Mycobacterium tuberculosis MutT1, and M. smegmatis MutT1, through their NTD (Nudix hydrolase motifs) function as protein phosphatase to regulate the levels of NDK-Pi to NDK and prevent it from catalysing conversion of (d)NDPs to (d)NTPs (including conversion of 8-oxo-dGDP to 8-oxo-dGTP). To corroborate this function, we show that MsmMutT1 decreases A to C mutations in E. coli under the conditions of EcoNDK overexpression. ImportanceMutT proteins, having a Nudix box domain, hydrolyse the mutagenic 8-oxo-dGTP to 8-oxo-dGMP. However, mycobacterial MutT (MutT1) comprises an N-terminal domain (NTD) harboring a Nudix box, and a C-terminal domain (CTD) harboring an RHG histidine phosphatase. Unlike other MutTs, mycobaterial MutT1 hydrolyses 8-oxo-dGTP to 8-oxo-dGDP. Nucleoside diphosphate kinase (NDK), a conserved protein, converts 8-oxo-dGDP to 8-oxo-dGTP through phospho-NDK (NDK-Pi) intermediate, and escalates A to C mutations. Here, we show that the mycobacterial MutT1 is unprecedented in that its NTD (Nudix box), functions as protein phosphatase to regulate NDK-Pi levels and prevents it from converting dNDPs to dNTPs (including 8-oxo-dGDP to 8-oxo-dGTP conversion). In addition, mycobacterial MutT1 decreases A to C mutations in Escherichia coli under the conditions of NDK overexpression.

molecular biology↗

bioRxiv2022

GWAS and functional studies implicate a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis

The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis (GWAS) using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, for the first time, we identified a strong association between the mutations in the DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis (Msm) and Mtb. Results show that variant mutations abrogated the function of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. Notably, in an in vivo Guinea pig infection model, the MutY variant outcompeted the wild-type strain. Collectively, we show that novel variant mutations in the DNA repair genes abrogate their function and contribute to better survival under antibiotic/host stress conditions.

microbiology↗