Biology subjects

Matange, N.

Publications and source records attributed to Matange, N..

5 recordsLinked to original sources

bioRxiv2026

Divergent genotype-phenotype maps determine the capacity for adaptation to antibiotics among Enterobacteria

What dictates the extent to which a bacterial strain can evolve under antibiotic pressure remains poorly defined, despite its implications for the effectiveness of antibiotics in clinical practice. In this study, we compare the evolution of Escherichia coli and Klebsiella aerogenes, two medically relevant members of Enterobacteriaceae, under colistin and trimethoprim selection. We discover that the mere presence of effector genes of resistance, as well as conserved gene regulatory architecture, do not necessarily translate to similar evolvabilities during antibiotic challenge. Instead genotype-phenotype maps of adaptive mutations, which can diverge at different biological levels, govern how effectively a strain evolves resistance. Both, E. coli and K. aerogenes, demonstrated strikingly parallel capacities for adaptation to trimethoprim, as a result of conserved mechanisms of resistance, including drug target modification and efflux. On the other hand, E. coli was driven to extinction by colistin, while K. aerogenes was able to evolve a high level of colistin resistance. Like the better studied K. pneumoniae, K. aerogenes acquired mutations in the BasSR (also called PmrAB) and PhoQP two-component signalling pathways under colistin selection. These mutations increased the expression of chromosomally-encoded lipopolysaccharide (LPS) modifiers, EptA and Arn. Similar mutations in E. coli were unable to confer protection against colistin, despite successfully up-regulating homologous effectors genes. However, expression of MCR-1, a horizontally acquired EptA-homolog found in clinical strains, conferred high level colistin resistance to E. coli. This difference in the intrinsic capacity to adapt to colistin was reflected in frequencies of resistance among clinical isolates from around the world. It also altered the dependency of Escherichia and Klebsiella species on horizontal gene acquisition for colistin resistance. Our study highlights the importance of understanding pathogen-specific genotype-phenotype maps of drug resistance to better predict long-term effectiveness of antibiotic therapies and define resistance-proof treatment strategies.

microbiology↗

bioRxiv2025

Engineering Escherichia coli FAD synthetase for the biosynthesis of FAD nucleotide analogues results in aminoglycoside antibiotic tolerance

Cofactors such as flavin adenine dinucleotide (FAD), nicotinamide adenine dinucleotide, coenzyme A, and S-adenosylmethionine cofactors share a common adenosine moiety that is generally not considered to contribute directly to catalysis. In FAD biosynthesis, the adenosine group is installed by the flavin mononucleotide adenylyltransferase (FMNAT) domain of the bifunctional FAD synthetase using FMN and ATP. This study explores the nucleotide selectivity of the Escherichia coli FMNAT domain and physiological effects of FAD nucleotide analogues synthesized with cellular nucleotides other than ATP. First, we engineer the FAD synthetase enzyme at an active site loop to produce FAD nucleotide analogues. Chromosomal substitution of the wild-type E. coli FAD synthetase with the mutated version results in the intracellular synthesis of these noncanonical FAD nucleotide analogues and confers tolerance to aminoglycoside antibiotics. Upon investigating their potential downstream metabolic roles, we find that their biosynthesis perturbs cellular metabolism and they could bind to a range of E. coli enzymes. These findings validate the FMNAT domain loop as a viable site for cofactor engineering, with potential for synthetic biology applications. Finally, the observed correlation between FAD analogue production and increased tolerance to aminoglycosides reveals novel metabolic mechanisms underlying antibiotic sensitivity.

microbiology↗

bioRxiv2024

Proteostasis modulates gene dosage evolution in antibiotic-resistant bacteria

Evolution of gene expression frequently drives antibiotic resistance in bacteria. We had previously (Patel and Matange, eLife, 2021) shown that, in Escherichia coli, mutations at the mgrB locus were beneficial under trimethoprim exposure and led to overexpression of dihydrofolate reductase (DHFR), encoded by the folA gene. Here, we show that DHFR levels are further enhanced by spontaneous duplication of a genomic segment encompassing folA and spanning hundreds of kilobases. This duplication was rare in wild type E. coli. However, its frequency was elevated in a lon-knockout strain, altering the mutational landscape early during trimethoprim adaptation. We then exploit this system to investigate the relationship between trimethoprim pressure and folA copy number. During long-term evolution, folA duplications were frequently reversed. Reversal was slower under antibiotic pressure, first requiring the acquisition of point mutations in DHFR or its promoter. Unexpectedly, despite resistance-conferring point mutations, some populations under high trimethoprim pressure maintained folA duplication to compensate for low abundance DHFR mutants. We find that evolution of gene dosage depends on expression demand, which is generated by antibiotic and exacerbated by proteolysis of drug-resistant mutants of DHFR. We propose a novel role for proteostasis as a determinant of copy number evolution in antibiotic-resistant bacteria.

genetics↗

bioRxiv2023

Adaptive and maladaptive consequences of deregulation in a bacterial gene regulatory network

The archetypal PhoQP two-component system from Enterobacteria regulates crucial pathways like magnesium homeostasis in Escherichia coli and virulence factor expression in Salmonella enterica. Previously we had reported that a laboratory strain of E. coli rapidly accumulated loss-of-function mutations in the mgrB gene, a negative feedback regulator of PhoQP, when evolved in the presence of the antibiotic trimethoprim. Hyperactive PhoQP enhanced the expression of dihydrofolate reductase (folA), target of trimethoprim, resulting in antibiotic tolerance. Here we ask, firstly, how important are mutations in mgrB for trimethoprim resistance? Using laboratory evolution, we show that trimethoprim resistance evolves by different mutational trajectories under condition of high and low PhoQP activity. Mutations in mgrB are only fixed when PhoQP is active. Importantly, loss of functional MgrB, though itself only mildly beneficial, enhances the fixation probability of trimethoprim-resistant bacteria under selection and this can be explained by epistasis between mgrB and folA loci. As a result, the activation status of PhoQP directly impacts how fast resistance is acquired by evolving populations of E. coli. Secondly, we investigate why negative feedback may be needed in the PhoQP system. We show that under drug-free conditions MgrB is required to mitigate the fitness costs of pervasive gene dysregulation by hyperactive PhoQP. Using RNA-seq transcriptomics and genetic analyses, we demonstrate that PhoQP-hyperactivation perturbs the balance of RpoS and RpoD-regulated transcriptional programs, and spontaneous mutations in rpoS rectify this imbalance. We propose that deregulation can be adaptive or maladaptive depending on the environmental context and this explain the evolution of negative feedback in bacterial gene regulatory networks.

microbiology↗

bioRxiv2021

Adaptation and Compensation in a Bacterial Gene Regulatory Network Evolving Under Antibiotic Selection

Gene regulatory networks allow organisms to generate coordinated responses to environmental challenges. In bacteria, regulatory networks are re-wired and re-purposed during evolution, though the relationship between selection pressures and evolutionary change is poorly understood. In this study, we discover that early evolutionary response of Escherichia coli to the antibiotic trimethoprim involves de-repression of PhoPQ signalling, a Mg2+-sensitive two-component system, by inactivation of the MgrB feedback-regulatory protein. We report that de-repression of PhoPQ confers trimethoprim-tolerance to E. coli by hitherto unrecognized transcriptional up-regulation of dihydrofolate reductase (DHFR), target of trimethoprim. As a result, mutations in mgrB precede and facilitate the evolution of drug resistance. Using laboratory evolution, genome sequencing and mutation re-construction, we show that populations of E. coli challenged with trimethoprim are faced with the evolutionary choice of transitioning from tolerant to resistant by mutations in DHFR, or compensating for the fitness costs of PhoPQ de-repression by inactivating the RpoS sigma factor, itself a PhoPQ-target. Outcomes at this evolutionary branch-point are determined by strength of antibiotic selection, such that high pressures favour resistance, while low pressures favour cost-compensation. Our results relate evolutionary changes in bacterial gene regulatory networks to strength of selection and provide mechanistic evidence to substantiate this link.

microbiology↗