Biology subjects

Breton, S.

Publications and source records attributed to Breton, S..

15 recordsLinked to original sources

bioRxiv2025

Alterations to cellular metabolism are linked to multiple natural parasite infections across populations of a freshwater fish

Exposure to environmental stressors can induce physiological responses in organisms, which can lead to population-level differences in physiological traits. However, the mechanisms underlying these responses both within individuals and among populations are often unknown. Parasite infections, in particular, are important biotic stressors that can induce a range of effects in hosts, including altered whole-organism metabolism. However, few studies have explored sub-cellular alterations to metabolic performance across both an individual infection gradient and population-level differences in infection prevalence. We compared mitochondrial enzyme activities across five distinct populations of pumpkinseed sunfish (Lepomis gibbosus) differing in the prevalence of cestode and trematode parasites. Overall, we found that enzymes from the OXPHOS pathway (cytochrome c oxidase, NADH dehydrogenase and coenzyme Q : cytochrome c oxidoreductase), the anaerobic pathway (lactate dehydrogenase), the TCA cycle (citrate synthase) and lipid metabolism (carnitine palmitoyl transferase) were positively correlated with parasite density with trends depending on the organ, parasite species and host population studied. Our results suggest complex and nuanced relationships among infections and host physiological performance and provide strong evidence of parasite-induced alterations to mitochondrial metabolism which may explain previously reported whole-organism responses to infections.

ecology↗

bioRxiv2025

Evaluation of parasitic contamination and effects on estimates of mitochondrial enzymatic activities in infected fish livers

Parasites can impair host performance through various physiological processes, including alterations to host metabolism. Since mitochondria are responsible for cellular energy production, it is likely that disruptions in host cellular metabolism contribute to changes in metabolism at the organismal level. However, some studies investigating parasite-induced alteration in cellular metabolism have not taken the presence of parasites in the target tissues into account, potentially biasing results. It is therefore critical to confirm that the measured enzyme activities reflect those of the hosts rather than the parasites themselves. Here, we tested a parasite extraction protocol to evaluate the extent to which parasite contamination impacts estimates of cellular enzyme activities in hepatic tissues of wild pumpkinseed sunfish (Lepomis gibbosus) infected with bass tapeworm cestodes (Proteocephalus ambloplitis). We tested four treatments: uninfected livers, cleaned infected livers, infected livers (repopulated) and parasites alone. We then compared the activity of key metabolic enzymes among groups. PCR tests were used to assess parasitic contamination of samples after applying the parasite extraction protocol on hepatic tissue. Enzyme activities of cleaned livers and contaminated livers were similar despite PCR tests revealing contamination. The intensity of cestode infection also did not influence enzyme activity, which suggests that parasite presence in liver tissues does not impact the accuracy of the enzyme activity estimates. These results suggest that studying the organs of heavily parasitized individuals is possible. Nevertheless, we recommend that our cleaning protocol is applied to infected organs to avoid any perception of biases in highly infected individuals.

ecology↗

bioRxiv2024

MTALTCO1: a 259 amino acid long mtDNA-encoded alternative protein that challenges conventional understandings of mitochondrial genomics.

Mitochondrial alternative Open Reading Frames (ORFs) substantially broaden the functional scope traditionally attributed to mitochondrial DNA, encoding peptides and proteins that participate in diverse cellular processes. These newly identified ORFs are embedded within annotated sequences, both coding and non-coding, and reveal layers of overlapping genetic information. We here report the discovery of MTALTCO1, a 259 amino-acid protein, the longest mitochondrial alternative protein identified to date, encoded by an ORF located within the human cytochrome oxidase 1 gene, in the +3 reading frame. We confirm the expression and mitochondrial origin of MTALTCO1 through multiple independent lines of evidence, including a custom-designed antibody, mass spectrometry-derived peptides, sequence analysis, and inhibitors of mitochondrial expression. Despite encoding AGR codons as arginine, contrary to the prevailing view that these function as stop codons in the vertebrate mitochondrial genetic code, MTALTCO1 shows strong evidence of mitochondrial translation, challenging established models of mitochondrial codon usage and gene expression. Co-immunoprecipitations and pull-down assays delineate MTALTCO1s interaction landscape across major cellular pathways. Lastly, we present the first in-depth analysis of conservation for a mitochondrial alternative ORF overlapping a reference protein-coding gene and discuss the results in light of MTALTCO1s suggested role in protein scaffolding.

molecular biology↗

bioRxiv2024

Acclimation temperature and parasite infection drive metabolic changes in a freshwater fish at different biological scales

O_LIEnvironmental stressors such as elevated temperature and parasite infection can impact individual energy metabolism. However, organismal responses to co-occurring stressors and their effects across biological scales remain unexplored despite the importance of integrative studies for accurately predicting the resilience of natural populations in changing environments. C_LIO_LIUsing wild-caught, naturally parasitized pumpkinseed sunfish, Lepomis gibbosus, we quantified changes in cellular and whole-organism metabolism in response to temperature and parasite infection. We acclimated pumpkinseeds for three weeks at 20{degrees}C, 25{degrees}C, or 30{degrees}C before measuring whole-organism oxygen uptake ([M]O2) using intermittent flow-respirometry to quantify maximal and standard metabolic rates (MMR and SMR, respectively) and aerobic scope (AS). We also measured the maximal activity of enzymes (citrate synthase (CS), respiratory complexes I + III and IV of the electron transport system, and lactate dehydrogenase (LDH)) linked with cellular bioenergetics in fish heart, brain, spleen and gills using spectrophotometry. C_LIO_LIWe found no interactions between acclimation temperatures and parasite intensity on cellular or whole-organism metabolism. However, both stressors were independently related to fish metabolism, with differing impacts across biological scales. C_LIO_LIWhereas MMR increased with acclimation temperature, this was not mirrored by increasing SMR or decreasing AS, suggesting thermal compensation across acclimation temperatures at the whole-organism level. C_LIO_LIOn a cellular level, acclimation responses were similar across organs, with maximal activity of all enzymes decreasing with increasing acclimation temperature. However, LDH activity remained higher than aerobic enzyme activities (CS, ETS complexes I + III and IV) across acclimation temperatures and organs, especially in gills, where LDH activity drastically increased at 30{degrees}C. This may indicate a stronger reliance on anaerobic metabolism to sustain whole-organism metabolic performance. C_LIO_LIFish with greater trematode infection had lower MMR and AS. There were no relationships between parasite intensity and SMR nor maximal enzyme activity. C_LIO_LIOur work shows that co-occurring stressors have distinct impacts on fish metabolism: parasites are primarily related to whole-organism metabolism while temperature impacts metabolism across biological scales. This highlights that interactions among co-occurring stressors are important for ecological realism and accurate predictions regarding population resilience to environmental changes. C_LI

physiology↗

bioRxiv2023

Investigating the role of mitochondrial membrane potential in paternal inheritance of mitochondria

The process of oxidative phosphorylation (OXPHOS) in mitochondria depends on an electrochemical gradient known as the mitochondrial membrane potential ({Delta}{psi}m). Reflecting high functionality, elevated {Delta}{psi}m usually depicts healthy mitochondria and contribute to organelle selection. This study investigates whether mitochondrial properties linked with bioenergetics, such as {Delta}{psi}m, may play a role in paternal inheritance of mitochondria. More specifically, how sperm {Delta}{psi}m responds to egg chemoattractants in bivalves characterized by distinct mitochondrial inheritance patterns: strict maternal inheritance (SMI) and doubly uniparental inheritance (DUI), the latter displaying sex-specific transmission of paternal mitochondrial DNA (mtDNA). Sperm {Delta}{psi}m was examined in four bivalve species: Mytilus edulis and Ruditapes philippinarum (DUI), plus Mercenaria mercenaria and Mya arenaria (SMI). In absence of oocytes, sperm {Delta}{psi}m did not vary between the two groups. However, we revealed an increase in {Delta}{psi}m following egg detection only in sperm bearing paternally-derived mitochondria (DUI). This suggests, along with bioenergetic changes, that {Delta}{psi}m modulation might be a specific property of DUI paternal mitochondria, possibly implicated in their unique ability to be sex-specifically transmitted.

evolutionary biology↗

bioRxiv2023

In vitro proliferation of Mytilus edulis male germ cell progenitors

Our understanding of basic cellular processes has mostly been provided by mammalian cell culture, and by some non-mammalian vertebrate and few invertebrate cell culture models. Developing reliable culture conditions for non-model organisms is essential to allow investigation of more unusual cellular processes. Here, we investigate how cells isolated from different tissues of the marine mussel Mytilus edulis thrive and survive in vitro in the hope of establishing a suitable laboratory model for the investigation of cellular mechanisms specific to these bivalve mollusks. We found that cells dissociated from male mantle tissue attached to the culture vessels and proliferated well in vitro, whereas all other cell types, although remaining viable, did not maintain divisions over three to four weeks in culture. We used antibodies against the germ-line marker DEAD-box helicase 4 (DDX4), also known as VASA, and the epithelial cell marker cytokeratin to distinguish different cell types in culture. DDX4-positive cells were the only cells that significantly proliferated in culture, and only from male tissue samples. Overall, the culture conditions described here allow an efficient selection of male germ cells that could be used to study specific cellular mechanisms in vitro.

cell biology↗

bioRxiv2022

Mitochondrial metabolism and body condition of naturally infected sunfish (Lepomis gibbosus)

Parasites can affect host behavior, cognition, locomotion, body condition and many other physiological traits. Changes to host aerobic metabolism are likely responsible for these parasite-induced performance alterations. Whole-organism metabolic rate is underpinned by cellular energy metabolism driven most prominently by the mitochondria. However, few studies have explored how mitochondrial enzymatic activity relates to body condition and parasite infection despite being a putative site for metabolic disruptions related to health status. We studied correlations among natural parasite infection, host body condition and the activity of key mitochondrial enzymes in target organs from wild-caught pumpkinseed sunfish (Lepomis gibbosus) to better understand the cellular responses of fish hosts to endoparasite infection. Enzymatic activities in the gills, spleen, and brain of infected fish were not significantly related to parasite infection or host body condition. However, the activity of cytochrome C oxidase, an enzyme involved in oxidative phosphorylation, in fish hearts was higher in individuals with lower body condition. Activities of citrate synthase, complexes I and III and carnitine palmitoyltransferase were also significantly different among organ types. These results provide preliminary information regarding the likely mitochondrial pathways affecting host body condition, the maintenance energetic requirements of different organs and their specific dependency on particular mitochondrial pathways. These results help pave the way for future studies on the effects of parasite infection on mitochondrial metabolism.

ecology↗

bioRxiv2022

Evolutionary trajectories are contingent on mitonuclear interactions

Critical mitochondrial functions, including cellular respiration, rely on frequently interacting components expressed from both the mitochondrial and nuclear genomes. The fitness of eukaryotic organisms depends on a tight collaboration between both genomes. In the face of an elevated rate of evolution in the mitochondrial genome, current models predict that maintenance of mitonuclear compatibility relies on compensatory evolution of the nuclear genome. Mitonuclear interactions would therefore exert an influence on evolutionary trajectories. One prediction from this model is that the same nuclear genomes but evolving with different mitochondrial haplotypes would follow distinct molecular paths towards higher fitness peaks. To test this prediction, we submitted 1344 populations derived from seven mitonuclear genotypes of Saccharomyces cerevisiae to more than 300 generations of experimental evolution in conditions that either select for a mitochondrial function, or that do not strictly require respiration for survival. Performing high-throughput phenotyping and whole-genome sequencing on independently evolved individuals isolated from endpoint populations, we identified numerous examples of gene-level evolutionary convergence among populations with the same mitonuclear background. Phenotypic and genotypic data on strains derived from this evolution experiment identify the nuclear genome and the environment as the main determinants of evolutionary divergence, but also show a modulating role for the mitochondrial genome exerted both directly and via interactions with the two other components. We finally recapitulated a subset of prominent loss-of-function alleles in the ancestral backgrounds and confirmed a generalized pattern of mitonuclear-specific and highly epistatic fitness effects. Together, these results demonstrate how mitonuclear interactions can dictate evolutionary divergence of populations with identical starting nuclear genotypes.

evolutionary biology↗

bioRxiv2022

MTALTND4, a second protein coded by nd4 impacts mitochondrial bioenergetics

Recent evidence suggests that the coding potential of the mitogenome is underestimated. We found a downstream alternative ATG initiation codon in the +3 reading frame of the human mitochondrial nd4 gene. This newly characterized alternative open reading frame (altORF) encodes a 99-amino acids long polypeptide, MTALTND4, which is conserved in primates. This small protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts mitochondrial physiology. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.

molecular biology↗

bioRxiv2022

Global phylogeography of marine Synechococcus in coastal areas reveals strikingly different communities than in the open ocean

Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome dataset of the Ocean Sampling Day (June 21st 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study tackles the main differences between open-ocean and coastal communities worldwide.

microbiology↗

bioRxiv2022

Discordant population structure inferred from male- and female-type mtDNAs from Limecola balthica, a bivalve species characterized by doubly uniparental inheritance of mitochondria

Doubly Uniparental Inheritance (DUI) of mitochondria is a remarkable exception to the Strictly Maternal Inheritance (SMI) in metazoans. In species characterized by DUI --almost exclusively gonochoric bivalve mollusks--females (F) transmit mitochondria to offspring of both sexes, while males (M) pass on their mitochondria exclusively to their sons. Under DUI, males are heteroplasmic, somatic tissues containing F-transmitted mtDNA and gametic cells containing M-transmitted mtDNAs. The aforementioned transmission routes make M- and F-transmitted mtDNA interesting as sex-specific markers which can differ in their effective population sizes, mutation rates, and selective constraints. For these reasons, looking at both markers can provide significant insights into the genetic structure of populations and investigate its determinants. In this study, we document differences in genetic diversity, divergence, inter-populational differentiation and biogeographic structure between M- and F-type cox1 mt genes in the Baltic tellin (Macoma balthica) to test whether cox1m and cox1f genes bear the marks of similar phylogeographic histories. These markers were sequenced for 302 male individuals sampled from the North Sea to the Gironde Estuary (Southern France) encompassing the intra-subspecific M. b. rubra hybrid zone in the Gulf of Saint Malo. Both genes supported a scenario of cladogenesis of M.b. rubra clades prior to the last glacial maximum. Nucleotide diversity and net divergence were over twice higher in cox1m compared to cox1f. Genetic differentiation between northern and southern populations was nearly 3 times higher at cox1m compared to cox1f (global {Phi}ST = 0.345 and 0.126 respectively) and the geographic localization of the strongest genetic break significantly differed between the markers (Finistere Peninsula at cox1f; Cotentin Peninsula at cox1m, [~]250 km apart). A higher mutation rate, relaxed negative selection and differences in effective population sizes (depending on locations) at cox1m could explain differences in population genetic structure. As both F- and M-type mtDNAs interact with nuclear genes for oxidative phosphorylation and ATP production, geographical discordances in genetic clines in a context of secondary contact could be linked to mito-nuclear genetic incompatibilities.

evolutionary biology↗

bioRxiv2021

Targeting the chemokine receptor CXCR4 with histamine analogue to reduce inflammation in juvenile arthritis: a proof of concept for COVID-19 therapeutic approach

Among immune cells, activated monocytes play a detrimental role in chronic and viral-induced inflammatory pathologies. The uncontrolled activation of monocytes and the subsequent excessive production of inflammatory factors damage bone-cartilage joints in Juvenile Idiopathic Arthritis (JIA), a childhood rheumatoid arthritis (RA) disease. Inflammatory monocytes also exert a critical role in the cytokine storm induced by SARS-CoV2 infection in severe COVID-19 patients. The moderate beneficial effect of current therapies and clinical trials highlights the need of alternative strategies targeting monocytes to treat RA and COVID-19 pathologies. Here, we show that targeting CXCR4 with small amino compound such as the histamine analogue clobenpropit (CB) inhibits spontaneous and induced-production of a set of key inflammatory cytokines by monocytes isolated from blood and synovial fluids of JIA patients. Moreover, daily intraperitoneal CB treatment of arthritic mice results in significant decrease in circulating inflammatory cytokine levels, immune cell infiltrates, joints erosion, and bone resorption leading to reduction of disease progression. Finally, we provide the prime evidence that the exposure of whole blood from hospitalized COVID-19 patients to CB significantly reduces levels of key cytokine-storm-associated factors including TNF-, IL-6 and IL-1{beta}. These overall data show that targeting CXCR4 with CB-like molecules may represent a promising therapeutic option for chronic and viral-induced inflammatory diseases.

immunology↗

bioRxiv2020

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2,4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

genomics↗

bioRxiv2018

Hybrid de novo assembly of the draft genome of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida).

Freshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecological value and unique \"doubly uniparental inheritance\" mode of mitochondrial DNA transmission of freshwater mussels. The genome described here was obtained by combining high coverage short reads (65X genome coverage of Illumina paired-end and 11X genome coverage of mate-pairs sequences) with low coverage Pacific Biosciences long reads (0.3X genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54Gb (366,926 scaffolds, N50 = 6.5Kb, with 2.3% of \"N\" nucleotides), representing 86% of the predicted genome size of 1.80Gb, while over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Given the repeated genetic bottlenecks of V. ellipsiformis populations as a result of glaciations events, heterozygosity was also found to be remarkably low (0.6%), in contrast to most other sequenced bivalve species. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.

genomics↗

bioRxiv2017

Transcriptomes of major renal collecting-duct cell types in mouse identified by single-cell RNA-Seq

Prior RNA sequencing (RNA-Seq) studies have identified complete transcriptomes for most renal epithelial cell types. The exceptions are the cell types that make up the renal collecting duct, namely intercalated cells (ICs) and principal cells (PCs), which account for only a small fraction of the kidney mass, but play critical physiological roles in the regulation of blood pressure, extracellular fluid volume and extracellular fluid composition. To enrich these cell types, we used fluorescence-activated cell sorting (FACS) that employed well established lectin cell surface markers for PCs and type B ICs, as well as a newly identified cell surface marker for type A ICs, viz. c-Kit. Single-cell RNA-Seq using the 1C- and PC-enriched populations as input enabled identification of complete transcriptomes of A-ICs, B-ICs and PCs. The data were used to create a freely-accessible online gene-expression database for collecting duct cells. This database allowed identification of genes that are selectively expressed in each cell type including cell-surface receptors, transcription factors, transporters and secreted proteins. The analysis also identified a small fraction of hybrid cells expressing both aquapor{inverted exclamation}n-2 and either anion exchanger 1 or pendrin transcripts. In many cases, mRNAs for receptors and their ligands were identified in different cells (e.g. Notch2 chiefly in PCs vs Jag1 chiefly in ICs) suggesting signaling crosstalk among the three cell types. The identified patterns of gene expression among the three types of collecting duct cells provide a foundation for understanding physiological regulation and pathophysiology in the renal collecting duct.\n\nSIGNIFICANCE STATEMENTA long-term goal in mammalian biology is to identify the genes expressed in every cell type of the body. In kidney, the expressed genes (\"transcriptome\") of all epithelial cell types have already been identified with the exception of the cells that make up the renal collecting duct, responsible for regulation of blood pressure and body fluid composition. Here, a technique called \"single-cell RNA-Seq\" was used in mouse to identify transcriptomes for the major collecting-duct cell types: type A intercalated cells, type B intercalated cells and principal cells. The information was used to create a publicly-accessible online resource. The data allowed identification of genes that are selectively expressed in each cell type, informative for cell-level understanding of physiology and pathophysiology.

physiology↗