Biology subjects

Pandiyan, A.

Publications and source records attributed to Pandiyan, A..

3 recordsLinked to original sources

bioRxiv2024

Re-examination of the taxonomic status of the Antarctic Pseudomonas syringae Lz4W isolate and proposal to rename it as a novel species Pseudomonas cryophila sp. nov.

A taxonomic re-evaluation of the Antarctic psychrotrophic bacterium Pseudomonas syringae Lz4W was performed in the light of its available genome sequence and due to a revision in the key phenotypic characteristics that are in conflict with the "syringae" group of Pseudomonads. A 16S rRNA gene sequence based phylogenetic analysis suggested that Lz4WT strain belongs to "fragi" cluster of Pseudomonas species, with closest similarity (99.72%) to the type strain P. deceptionensis M1T. However, in silico analysis of the Lz4W genome sequence using SpecI (species identification tools), ANI (average nucleotide identity), and GBDP (Genome Blast Distance phylogeny) methods suggest that Lz4WT strain cannot be delineated with any of the type strains of "fragi" cluster of species. Based on predictive low DNA-DNA hybridization value (<29.9%) and differences in phenotypic features with the related species we suggest that Lz4WT is a novel species under the Pseudomonas genus, and we propose that the strain be named as Pseudomonas cryophila sp. nov. The type strain is Lz4WT (=CFBP 8403T =KCTC 42933T =LMG 29591T =MTCC 673T).

microbiology↗

bioRxiv2024

Pathological R-loops in bacteria from engineered expression of endogenous antisense RNAs whose synthesis is ordinarily terminated by Rho

In many bacteria, the essential factors Rho and NusG mediate termination of synthesis of nascent transcripts (including antisense RNAs) which are not being simultaneously translated. It has been proposed that in Rhos absence toxic RNA-DNA hybrids (R-loops) may be generated from nascent untranslated transcripts; and genome-wide mapping studies in Escherichia coli have identified putative loci of R-loop formation from more than 100 endogenous antisense transcripts that are synthesized only in a Rho-deficient strain. Here we provide evidence that engineered expression in wild-type E. coli of several such individual antisense regions on a plasmid or the chromosome generates R-loops that, in an RNase H-modulated manner, serve to disrupt genome integrity. Rho inhibition was associated with increased prevalence of antisense R-loops also in Xanthomonas oryzae pv. oryzae and Caulobacter crescentus. Our results confirm the essential role of Rho in several bacterial genera for prevention of toxic R-loops from pervasive yet cryptic endogenous antisense transcripts. Engineered antisense R-looped regions may be useful for studies on both site-specific impediments to bacterial chromosomal replication and the mechanisms of their resolution.

microbiology↗

bioRxiv2023

Exoribonuclease RNase R protects Antarctic Pseudomonas syringae Lz4W from DNA damage and oxidative stress

RNase R is a highly processive, 3 -5 exoribonuclease involved in RNA degradation, maturation, and processing in bacteria. In Pseudomonas syringae Lz4W, RNase R interacts with RNase E to form the RNA degradosome complex and is essential for growth at low temperature. RNase R is also implicated in general stress response in many bacteria. We show here that the deletion mutant of rnr gene (encoding RNase R) of P. syringae is highly sensitive to various DNA damaging agents and oxidative stress. RNase R is a multidomain protein comprised of CSD, RNB and S1 domains. We investigated the role of each domain of RNase R and its exoribonuclease activity in nucleic acid damage and oxidative stress response. Our results revealed that the RNB domain alone without its exoribonuclease activity is sufficient to protect against DNA damage and oxidative stress. We also show that the association of RNase R with the degradosome complex is not required for this function. Our study has discovered for the first time a hitherto unknown role of RNase R in protecting P. syringae Lz4W against DNA damage and oxidative stress. ImportanceBacterial exoribonucleases play a crucial role in RNA maturation, degradation, quality control and turnover. In this study, we have uncovered a previously unknown role of 3-5 exoribonuclease RNase R of P. syringae Lz4W in DNA damage and oxidative stress response. Here, we show that neither the exoribonuclease function of RNase R, nor its association with the RNA degradosome complex is essential for this function. Interestingly, in P. syringae Lz4W, hydrolytic RNase R exhibits physiological roles similar to phosphorolytic 3-5 exoribonuclease PNPase of E. coli. Our data suggest that during the course of evolution, mesophilic E. coli and psychrotrophic P. syringae have apparently swapped these exoribonucleases to adapt to their respective environmental growth conditions.

microbiology↗