Biology subjects

Cariou, M.

Publications and source records attributed to Cariou, M..

6 recordsLinked to original sources

bioRxiv2026

Metabolic reorganization shapes the dynamics of a water kefir microbial community

Microbial fermentations emerge from the collective activity of interacting species whose relative abundances, metabolic functions, and environmental constraints continuously change over time. Water kefir provides a tractable model to investigate how multispecies communities coordinate their metabolic activities during fermentation. Here, we combined time-resolved community profiling, physicochemical measurements, metabolite quantification, and controlled co-culture assays to characterize the dynamics of a water kefir consortium comprising 19 detected microbial species. Our results reveal that water kefir fermentation is not adequately described as a simple succession of independently acting microbial groups. Instead, the community undergoes a reproducible reorganization of its collective metabolism around 20 h of fermentation. This transition marks a shift from an early regime characterized by the accumulation of soluble sugars and ethanol to a later regime dominated by enhanced sugar consumption and lactate production. Controlled interaction assays further showed that bacterial partners can alter carbon-use behaviour in Saccharomyces cerevisiae, highlighting the capacity of interspecies interactions to reshape metabolic phenotypes within the consortium. Together, these results support an ecological view of water kefir fermentation in which community-wide metabolic reorganization emerges from the interplay between microbial interactions, resource availability, and environmental change.

microbiology↗

bioRxiv2023

Discovery of new endogenous viral elements in campoplegine wasps (Ichneumonidae, Campopleginae, Campoplex) suggests a widespread nudivirus domestication event

Viral endogenization events in the genomes of parasitoid wasps have led to the production of immunosuppressive particles that are injected into the host and that either contain DNA encoding virulence effectors or virulence proteins, essential for parasitism success. In some Campopleginae (Ichneumonidae) wasps, viral endogenisation involves the production of large dsDNA ichnoviruses encoding several dozens of rep virulence genes, to the exception of Venturia canescens. Instead, V. canescens harbours an endogenous nudivirus producing Virus-Like-Particles (VLPs) in which virulence proteins are wrapped into viral envelopes. Here, we described that this nudiviral domestication event is more ancient and widespread than previously thought as we identified homologous alphanudivirus sequences in the genomes of three Campopleginae species belonging to the genera Campoplex and Rimphoctona. We showed that Campoplex capitator produces morphologically similar VLPs to those of V. canescens with almost the same viral protein content. Strikingly, the virulence proteins are however different, suggesting that VLPs allow a high versatility in the molecular strategies used by the wasps in response to host selection pressures. Furthermore, a marked expansion of serpin and rep genes is present in Campoplex capitator, with one serpin and several REP proteins identified as major VLP components using proteomics. REP proteins are also well-described virulence factors initially shown to be delivered into hosts via the expression of rep genes coded by ichnovirus DNA. In Campoplex capitator, these proteins are packaged into nudivirus-derived VLPs indicating that convergent use of virulence factors can imply endogenous viruses of different origin and with different delivery mechanisms.

evolutionary biology↗

bioRxiv2023

Stable Structures or poly(A)-binding protein loading protect cellular and viral RNAs against ISG20-mediated decay

ISG20 is an interferon-induced 3-to-5 RNA exonuclease that acts as a broad antiviral factor. At present, the features that expose RNA to ISG20 remain unclear, although recent studies have pointed to the modulatory role of epitranscriptomic modifications in the susceptibility of target RNAs to ISG20. These findings raise the question as to how cellular RNAs, on which these modifications are abundant, cope with ISG20. To obtain an unbiased perspective on this topic, we used RNAseq and biochemical assays to identify elements that regulate the behavior of RNAs against ISG20. The results we have obtained indicate that poly(A)-binding protein (PABP1) loading on the RNA 3 tail provides a primal protection against ISG20, easily explaining the overall protection of cellular mRNAs observed by RNAseq. The second element we uncovered is provided by terminal stem-loop RNA structures, that have been associated to ISG20 protection before, but that we re-examine here systematically to define the stabilities that tilt the balance between resistance and susceptibility to ISG20. Given that these elements are present on cellular mRNAs, but can be co-opted by viruses as well, these results shed new light on the complex interplay that regulates the susceptibility of different classes of viruses against ISG20.

microbiology↗

bioRxiv2022

Distinct evolutionary trajectories of SARS-CoV-2 interacting proteins in bats and primates identify important host determinants of COVID-19

The COVID-19 pandemic is caused by SARS-CoV-2, a novel coronavirus that spilled from the bat reservoir. Despite numerous clinical trials and vaccines, the burden remains immense, and the host determinants of SARS-CoV-2 susceptibility and COVID-19 severity remain largely unknown. Signatures of positive selection detected by comparative functional-genetic analyses in primate and bat genomes can uncover important and specific adaptations that occurred at virus-host interfaces. Here, we performed high-throughput evolutionary analyses of 334 SARS- CoV-2 interacting proteins to identify SARS-CoV adaptive loci and uncover functional differences between modern humans, primates and bats. Using DGINN (Detection of Genetic INNovation), we identified 38 bat and 81 primate proteins with marks of positive selection. Seventeen genes, including the ACE2 receptor, present adaptive marks in both mammalian orders, suggesting common virus-host interfaces and past epidemics of coronaviruses shaping their genomes. Yet, 84 genes presented distinct adaptations in bats and primates. Notably, residues involved in ubiquitination and phosphorylation of the inflammatory RIPK1 have rapidly evolved in bats but not primates, suggesting different inflammation regulation versus humans. Furthermore, we discovered residues with typical virus-host arms-race marks in primates, such as in the entry factor TMPRSS2 or the autophagy adaptor FYCO1, pointing to host-specific in vivo important interfaces that may be drug targets. Finally, we found that FYCO1 sites under adaptation in primates are those associated with severe COVID-19, supporting their importance in pathogenesis and replication. Overall, we identified functional adaptations involved in SARS- CoV-2 infection in bats and primates, critically enlightening modern genetic determinants of virus susceptibility and severity. Key findingsO_LIEvolutionary history of 334 SARS-CoV-2 interacting proteins (VIPs) in bats and primates identifying how the past has shaped modern viral reservoirs and humans - results publicly-available in an online resource. C_LIO_LIIdentification of 81 primate and 38 bat VIPs with signatures of adaptive evolution. The common ones among species delineate a core adaptive interactome, while the ones displaying distinct evolutionary trajectories enlighten host lineage-specific determinants. C_LIO_LIEvidence of primate specific adaptation of the entry factor TMPRSS2 pointing to its host- specific in vivo importance and predicting molecular interfaces. C_LIO_LIFYCO1 sites associated with severe COVID-19 in human (GWAS) display hallmarks of ancient adaptive evolution in primates, highlighting its importance in SARS-CoV-2 replication or pathogenesis and differences with the bat reservoir. C_LIO_LIIdentification of adaptive evolution in the bats multifunctional RIPK1 at residues that may differentially regulate inflammation. C_LI

evolutionary biology↗

bioRxiv2020

Homologous chromosomes in asexual rotifer Adineta vaga suggest automixis

The several hundreds of species of bdelloid rotifers are notorious because they represent an ancient clade comprising only asexual lineages1. Moreover, most bdelloid species have the ability to withstand complete desiccation and high doses of ionizing radiation, being able to repair their DNA after massive genome breakage2. To better understand the impact of long-term asexuality and DNA breakage on genome evolution, a telomere-to-tolemere reference genome assembly of a bdelloid species is critical3, 4. Here we present the first, high quality chromosome-scale genome assembly for the bdelloid A. vaga validated using three complementary assembly procedures combined with chromosome conformation capture (Hi-C) data. The different assemblies reveal the same genome architecture and using fluorescent in situ hybridization (FISH), we demonstrate that the A. vaga genome is composed of six pairs of homologous chromosomes, compatible with meiosis. Moreover, the synteny between homoeologous (or ohnologous) chromosomes is also preserved, confirming their paleotetraploidy. The diploid genome structure of A. vaga and the presence of very long homozygous tracts show that recombination between homologous chromosomes occurs in this ancient asexual scandal, either during DSB repair or during meiotic pairing. These homozygosity tracts are mainly observed towards the chromosome ends in the clonal A. vaga suggesting signatures of a parthenogenetic mode of reproduction equivalent to central fusion automixis, in which homologous chromosomes are not segregated during the meiotic division.

evolutionary biology↗

bioRxiv2017

The global impact of Wolbachia on mitochondrial diversity and evolution

The spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. Although suggested by a few case studies, the global consequences of this process on mitochondrial diversity and evolution remains to be assessed. Here we address this question using a mapping of Wolbachia acquisition / extinction events on a large mitochondrial DNA tree, including over 1,000 species. We show that the presence of Wolbachia is associated with a twofold reduction in silent mitochondrial polymorphism, and a 13% increase in non-synonymous substitution rates. These findings validate the conjecture that the widespread distribution of Wolbachia infections throughout arthropods impacts the effective population size of mitochondria. These effects might in part explain the disconnection between genetic diversity and demographic population size in mitochondria, and also fuel red-queen-like cytonuclear coevolution through the fixation of deleterious mitochondrial alleles.

evolutionary biology↗