Barbe, J. | Search bioRxiv

bioRxiv2026

Early-life optimization of mitochondrial aerobic metabolism: high efficiency to grow fast, yet at no oxidative cost

Variation in mitochondrial aerobic metabolism has been suggested to underlie variation in interindividual performance. Mitochondrial efficiency quantifies, directly or indirectly, the amount of adenosine triphosphate (ATP) produced relative to O2 consumption. High mitochondrial efficiency is theoretically beneficial by providing more ATP per amount of resource consumed, but may come at the cost of increased reactive oxygen species (ROS) production damaging tissues through oxidative stress. Mitochondrial efficiency is a plastic trait but how it changes through postnatal development remains unknown. We hypothesized that strong selective pressure could lead to an increased mitochondrial efficiency to support fast growth but incur an oxidative cost. We tested this hypothesis by quantifying mitochondrial aerobic metabolism, efficiency and ROS production through postnatal growth in Japanese quail (Coturnix japonica), in two highly aerobic tissues: skeletal and cardiac muscles. Mitochondrial efficiency was indeed higher during peak growth in both tissues, but this was surprisingly associated with markedly lower ROS production. This high efficiency was likely achieved via both a lower proton leak and a higher contribution of complex I to respiration. These results show that enhancing mitochondrial efficiency may be important to support growth, but suggest the presence of unexpected ROS mitigation processes during early-life growth.

physiology↗

bioRxiv2020

Recurrent mobilization of ancestral and novel variants of the chromosomal di-hydrofolate reductase gene drives the emergence of clinical resistance to trimethoprim

2.Trimethoprim is a synthetic antibacterial agent that targets folate biosynthesis by competitively binding to the di-hydrofolate reductase enzyme (DHFR). Trimethoprim is often administered synergistically with sulfonamide, another chemotherapeutic agent targeting the di-hydro-pteroate synthase (DHPS) enzyme in the same pathway. Clinical resistance to both drugs is widespread and mediated by enzyme variants capable of performing their biological function without binding to these drugs. These mutant enzymes were assumed to have arisen after the discovery of these synthetic drugs, but recent work has shown that genes conferring resistance to sulfonamide were present in the bacterial pangenome millions of years ago. Here we apply phylogenetics and comparative genomics methods to study the largest family of mobile trimethoprim resistance genes (dfrA). We show that most of the dfrA genes identified to date map to two large clades that likely arose from independent mobilization events. In contrast to sulfonamide resistance (sul) genes, we find evidence of recurrent mobilization in dfrA genes. Phylogenetic evidence allows us to identify novel dfrA genes in the emerging pathogen Acinetobacter baumannii, and we confirm their resistance phenotype in vitro. We also identify a cluster of dfrA homologs in cryptic plasmid and phage genomes, but we show that these enzymes do not confer resistance to trimethoprim. Our methods also allow us to pinpoint the chromosomal origin of previously reported dfrA genes, and we show that many of these ancient chromosomal genes also confer resistance to trimethoprim. Our work reveals that trimethoprim resistance predated the clinical use of this chemotherapeutic agent, but that novel mutations have likely also arisen and become mobilized following its widespread use within and outside the clinic. This work hence confirms that resistance to novel drugs may already be present in the bacterial pangenome, and stresses the importance of rapid mobilization as a fundamental element in the emergence and global spread of resistance determinants. 3. Impact statementAntibiotic resistance is a pressing and global phenomenon. It is well-established that resistance to conventional antibiotics emerged millions of years ago in either antibiotic-producing bacteria or their competitors. Resistance to synthetic chemotherapeutic agents cannot be explained by this paradigm, since these drugs are not naturally produced. Resistance is hence assumed to have evolved rapidly following the clinical introduction of these drugs. Recently we showed that resistance to one such drug, sulfonamide, evolved not recently, but millions of years ago, suggesting that the diversity of bacterial genomes may well contain genes conferring resistance to drugs yet to be developed. Here we analyze the origin of resistance to trimethoprim, another chemotherapeutic agent developed in the 1960s. Using phylogenetic methods, we identify new variants of the trimethoprim resistance genes that had not previously been reported, and we trace the chromosomal origins for a number of already known resistance variants. Our results show that resistance to trimethoprim is very diverse and has originated both from recent mutations and from preexisting ancient variants. These results stress the importance of gene mobilization mechanisms as the main drivers of the current antibiotic resistance phenomenon. 4. Data summary- The scripts used for data collection and analysis can be obtained at the GitHub ErillLab repository (https://github.com/ErillLab/). - The Bayesian phylogenetic tree can be visualitzed online on iTOL (https://itol.embl.de/tree/855674159451585133078) [1]. - The authors confirm all other supporting data has been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2018

Origin of the mobile di-hydro-pteroate synthase gene determining sulfonamide resistance in clinical isolates

Sulfonamides are synthetic chemotherapeutic agents that work as competitive inhibitors of the di-hydro-pteroate synthase (DHPS) enzyme, encoded by the folP gene. Resistance to sulfonamides is widespread in the clinical setting and predominantly mediated by plasmid- and integron-borne sul1-3 genes encoding mutant DHPS enzymes that do not bind sulfonamides. In spite of their clinical importance, the genetic origin of sul1-3 genes remains unknown. Here we analyze sul genes and their genetic neighborhoods to uncover sul signature elements that enable the elucidation of their genetic origin. We identify a protein sequence Sul motif associated with sul-encoded proteins, as well as consistent association of a phosphoglucosamine mutase gene (glmM) with the sul2 gene. We identify chromosomal folP genes bearing these genetic markers in two bacterial families: the Rhodobiaceae and the Leptospiraceae. Bayesian phylogenetic inference of FolP/Sul and GlmM protein sequences clearly establishes that sul1-2 and sul3 genes originated as a mobilization of folP genes present in, respectively, the Rhodobiaceae and the Leptospiraceae, and indicate that the Rhodobiaceae folP gene was transferred from the Leptospiraceae. Analysis of %GC content in folP/sul gene sequences supports the phylogenetic inference results and indicates that the emergence of the Sul motif in chromosomally-encoded FolP proteins is ancient and considerably predates the clinical introduction of sulfonamides. In vitro assays reveal that both the Rhodobiaceae and the Leptospiraceae, but not other related chromosomally-encoded FolP proteins confer resistance in a sulfonamide-sensitive Escherichia coli background, indicating that the Sul motif is associated with sulfonamide resistance. Given the absence of any known natural sulfonamides targeting DHPS, these results provide a novel perspective on the emergence of resistance to synthetic chemotherapeutic agents, whereby preexisting resistant variants in the vast bacterial pangenome may be rapidly selected for and mobilized upon the clinical introduction of novel chemotherapeuticals.

microbiology↗