Intracellular peroxynitrite perturbs redox balance, bioenergetics, and Fe-S cluster homeostasis in Mycobacterium tuberculosis.

The ability of Mycobacterium tuberculosis (Mtb) to tolerate nitric oxide (NO) and superoxide (O) produced by phagocytes contributes to its success as a human pathogen. Recombination of NO and O generates peroxynitrite (ONOO), a potent oxidant produced inside activated macrophages causing lethality in diverse organisms. While the response of Mtb toward NO and O is well established, how Mtb responds to ONOO remains unclear.

Cysteine desulfurase (IscS)-mediated fine-tuning of bioenergetics and SUF expression prevents hypervirulence.

Iron-sulfur (Fe-S) biogenesis requires multiprotein assembly systems, SUF and ISC, in most prokaryotes. () encodes a complete SUF system, the depletion of which was bactericidal. The ISC operon is truncated to a single gene (cysteine desulfurase), whose function remains uncertain.

Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models.

Attempts to understand gene regulation by global transcription factors have largely been limited to expression studies under binary conditions of presence and absence of the transcription factor. Studies addressing genome-wide transcriptional responses to changing transcription factor concentration at high resolution are lacking. Here, we create a data set containing the entire Escherichia coli transcriptome in Luria-Bertani (LB) broth as it responds to 10 different cAMP concentrations spanning the biological range.

Emergence of networks of shared restriction-modification systems in phage-bacteria ecosystems.

Restriction-modification (RM) systems are the most ubiquitous bacterial defence systems against bacteriophages. Using genome sequence data, we showed that RM systems are often shared among bacterial strains in a structured way. Examining the network of interconnections between bacterial strains within genera, we found that many strains share more RM systems than expected compared with a suitable null model.

Replication-Dependent Organization Constrains Positioning of Long DNA Repeats in Bacterial Genomes.

Bacterial genome organization is primarily driven by chromosomal replication from a single origin of replication. However, chromosomal rearrangements, which can disrupt such organization, are inevitable in nature. Long DNA repeats are major players mediating rearrangements, large and small, via homologous recombination.

Global pleiotropic effects in adaptively evolved lacking CRP reveal molecular mechanisms that define the growth physiology.

Evolution facilitates emergence of fitter phenotypes by efficient allocation of cellular resources in conjunction with beneficial mutations. However, system-wide pleiotropic effects that redress the perturbations to the apex node of the transcriptional regulatory networks remain unclear. Here, we elucidate that absence of global transcriptional regulator CRP in results in alterations in key metabolic pathways under glucose respiratory conditions, favouring stress- or hedging-related functions over growth-enhancing functions.

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.

Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair.

DNA double-strand breaks (DSBs) are a threat to genome stability. In all domains of life, DSBs are faithfully fixed via homologous recombination. Recombination requires the presence of an uncut copy of duplex DNA which is used as a template for repair.

Whole-Genome Sequencing of sp. Strain RSMS, a Highly Efficient Tributyl Phosphate-Degrading Bacterium.

sp. strain RSMS was described earlier as an efficient degrader of tributyl phosphate, an organic pollutant. This report describes the generation and annotation of the genome sequence of sp.

Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria.

The evolution of regulatory networks in Bacteria has largely been explained at macroevolutionary scales through lateral gene transfer and gene duplication. Transcription factors (TF) have been found to be less conserved across species than their target genes (TG). This would be expected if TFs accumulate mutations faster than TGs.

Laboratory Evolution Experiments Help Identify a Predominant Region of Constitutive Stable DNA Replication Initiation.

The bacterium can initiate replication in the absence of the replication initiator protein DnaA and/or the canonical origin of replication in a background. This phenomenon, which can be primed by R-loops, is called constitutive stable DNA replication (cSDR). Whether DNA replication during cSDR initiates in a stochastic manner through the length of the chromosome or at specific sites and how can find adaptations to loss of fitness caused by cSDR remain inadequately answered.

Early fate of exogenous promoters in E. coli.

Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory.

Targeting redox heterogeneity to counteract drug tolerance in replicating .

The capacity of () to tolerate multiple antibiotics represents a major problem in tuberculosis (TB) management. Heterogeneity in populations is one of the factors that drives antibiotic tolerance during infection. However, the mechanisms underpinning this variation in bacterial population remain poorly understood.

Using stochastic cell division and death to probe minimal units of cellular replication.

The invariant cell initiation mass measured in bacterial growth experiments has been interpreted as a minimal unit of cellular replication. Here we argue that the existence of such minimal units induces a coupling between the rates of stochastic cell division and death. To probe this coupling we tracked live and dead cells in populations treated with a ribosome-targeting antibiotic.

Redox-dependent condensation of the mycobacterial nucleoid by WhiB4.

Oxidative stress response in bacteria is mediated through coordination between the regulators of oxidant-remediation systems (e.g. OxyR, SoxR) and nucleoid condensation (e.

Regulation of Global Transcription in by Rsd and 6S RNA.

In , the sigma factor σ directs RNA polymerase to transcribe growth-related genes, while σ directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ, and the non-coding 6S RNA which binds to the RNA polymerase-σ holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial.

CRISPR-Cas-Mediated Gene Silencing Reveals RacR To Be a Negative Regulator of YdaS and YdaT Toxins in K-12.

Bacterial genomes are rich in horizontally acquired prophages. is an essential gene located in the prophage that is resident in many genomes. Employing a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas-based gene silencing approach, we show that RacR is a negative regulator of the divergently transcribed and adjacent operon in K-12.

Repression of YdaS Toxin Is Mediated by Transcriptional Repressor RacR in the Cryptic Prophage of K-12.

Horizontal gene transfer is a major driving force behind the genomic diversity seen in prokaryotes. The cryptic prophage in K-12 carries the gene for a putative transcription factor RacR, whose deletion is lethal. We have shown that the essentiality of in K-12 is attributed to its role in transcriptionally repressing toxin gene(s) called and , which are adjacent to and coded divergently to .

Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in .

Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics. In our previous work, we used short-term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin, and reported that develops low cost resistance to kanamycin via different point mutations in the translation Elongation Factor-G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes /// Mutations in three of these genes had been discovered in earlier screens for aminoglycoside resistance.

Nucleoid-Associated Proteins: Genome Level Occupancy and Expression Analysis.

The advent of Chromatin Immunoprecipitation sequencing (ChIP-Seq) has allowed the identification of genomic regions bound by a DNA binding protein in-vivo on a genome-wide scale. The impact of the DNA binding protein on gene expression can be addressed using transcriptome experiments in appropriate genetic settings. Overlaying the above two sources of data enables us to dissect the direct and indirect effects of a DNA binding protein on gene expression.

Genomewide Mutational Diversity in Population Evolving in Prolonged Stationary Phase.

Prolonged stationary phase is an approximation of natural environments presenting a range of stresses. Survival in prolonged stationary phase requires alternative metabolic pathways for survival. This study describes the repertoire of mutations accumulating in starving populations in lysogeny broth.

Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology?

Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria.

Gene expression homeostasis and chromosome architecture.

In rapidly growing populations of bacterial cells, including those of the model organism Escherichia coli, genes essential for growth--such as those involved in protein synthesis--are expressed at high levels; this is in contrast to many horizontally-acquired genes, which are maintained at low transcriptional levels. (1) This balance in gene expression states between 2 distinct classes of genes is established by a galaxy of transcriptional regulators, including the so-called nucleoid associated proteins (NAP) that contribute to shaping the chromosome. (2) Besides these active players in gene regulation, it is not too far-fetched to anticipate that genome organization in terms of how genes are arranged on the chromosome, (3) which is the result of long-drawn transactions among genome rearrangement processes and selection, and the manner in which it is structured inside the cell, plays a role in establishing this balance.