Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

Background Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and families within the phylum Annelida are still represented by a single specimen of a single species. The genus of interstitial annelids Ophryotrocha (Dorvilleidae, Errantia, Annelida) is among these neglected groups, despite its extensive use as model organism in numerous studies on the evolution of life history, physiological and ecological traits. To compensate for the paucity of genomic information in this genus, we here obtained novel complete mitochondrial genomes of six Ophryotrocha species using next generation sequencing. In addition, we investigated the evolution of the reproductive mode in the Ophryotrocha genus using a phylogeny based on two mitochondrial markers (COXI and 16S rDNA) and one nuclear fragment (Histone H3). Results Surprisingly, gene order was not conserved among the six Ophryotrocha species investigated, and varied greatly as compared to those found in other annelid species within the class Errantia. The mitogenome phylogeny for the six Ophryotrocha species displayed a separation of gonochoric and hermaphroditic species. However, this separation was not observed in the phylogeny based on the COX1, 16S rDNA, and H3 genes. Parsimony and Bayesian ancestral trait reconstruction indicated that gonochorism was the most parsimonious ancestral reproductive mode in Ophryotrocha spp. Conclusions Our results highlight the remarkably high level of gene order variation among congeneric species, even in annelids. This encourages the need for additional mitogenome sequencing of annelid taxa in order to properly understand its mtDNA evolution, high biodiversity and phylogenetic relationships. -- Keywords : Molecular phylogeny ; Dorvilleidae ; Mitogenome ; Next generation sequencing ; Model species ; Reproductive mode

Mitochondrial bioenergetic and genomic flexibilities in birds

Les oiseaux sont des organismes endothermes faisant preuve d’une flexibilité métabolique remarquable en réponse aux contraintes énergétiques inhérentes à leur mode de vie. Cette flexibilité est notamment stimulée lors de transitions nutritionnelles pour adapter leur intensité métabolique selon les ressources énergétiques disponibles, est déterminante pour la survie chez ces animaux. Les mitochondries constituant le principal carrefour métabolique, en permettant l’essentiel de la production d’ATP cellulaire, sont largement impliquées dans les modulations observées au cours d’un jeûne et lors de la réalimentation. Le but de cette thèse était d’étudier la flexibilité de la fonction mitochondriale face à un jeûne alimentaire et lors de la réalimentation chez le canard de Barbarie. Plusieurs aspects allant de la bioénergétique, à l’organisation anatomique jusqu’à la génomique et l’évolution des espèces ont été analysés pour mieux comprendre les modulations impliquées et leurs interrelations potentielles pour ajuster le fonctionnement mitochondrial aux contraintes énergétiques. Une 1ère étude a décrit la cinétique de l’installation d’un hypométabolisme musculaire associé à l’augmentation de l’efficacité bioénergétique mitochondriale en réponse au jeûne, avec une acclimatation maximale après 3 jours. L’étude en parallèle du remodelage des réseaux grâce à une double approche par anticorps et microscopie confocale a montré une flexibilité bidirectionnelle de l’organisation des réseaux de mitochondries musculaires, avec une fusion accrue au tout début du jeûne précédant une fragmentation accrue après 4 jours. Une 2ème étude a montré l’implication potentielle de l’activité de la monoxyde d’azote synthase (NOS) mitochondriale dans les modulations de la bioénergétique mitochondriale induites par le jeûne alimentaire. L’activité de la NOS mitochondriale est accrue par le jeûne et sa modulation in vitro reproduit de façon rapidement réversible sur des mitochondries musculaires d’oiseaux nourris les effets induits par le jeûne alimentaire. Une 3ème étude a exploré la flexibilité du génome mitochondrial pour détecter la présence de cadres ouverts de lecture (ORF) codant pour des peptides bioactifs, similaires à ceux qui chez les mammifères sont codés par les gènes 12S et 16S et sont métaboliquement actifs. Les analyses génétiques ont mis en évidence chez les oiseaux la présence d’ORFs incorporés dans le gène codant pour l’ARNr 16S et dont l’évolution moléculaire est similaire à celle des gènes mitochondriaux codant pour des sous-unités de la chaîne respiratoire. Parmi les ORFs détectés, certains correspondent à ceux décrits chez les mammifères (humanine, SHLP6). Une 4ème étude a montré que la très forte conservation chez les mammifères, les oiseaux et les ectothermes terrestres, des ORFs situés sur le gène 16S ne peut être un artéfact lié à une contrainte imposée par la structure de l’ARNr codé, n’étant pas retrouvée sur des simulations de séquences générées en tenant compte de la structure secondaire et tertiaire. Chez les 3 groupes de vertébrés étudiés, l’ORF codant pour l’humanine, un peptide identifié chez l’homme, a subi au cours de l’évolution une pression de sélection purifiante maintenant sa composition en acides aminés. Ce travail souligne la remarquable flexibilité bioénergétique et génomique des mitochondries chez les oiseaux qui peut contribuer aux ajustements de l’activité énergétique lors des transitions nutritionnelles. Les résultats obtenus ont ouvert un nouveau champ d’investigations sur les nouveaux peptides codés par le génome mitochondrial et dont les rôles biologiques restent à explorerBirds are endotherms that exhibit a remarkable metabolic flexibility in response to energetic constraints related to their lifestyles. This flexibility is notably involved during nutritional transitions in order to adjust metabolic intensity to the available energy resources, a prerequisite for survival. Mitochondria, that produce most of cellular ATP production, are involved in the modulations observed during a fast and during refeeding. The aim of this thesis was to investigate the flexibility of mitochondrial functions in response to fasting and refeeding in Muscovy ducks (Cairina moschata). Several aspects, ranging from bioenergetics and anatomical organization to genomics and evolution of species, were analysed to better understand the modulations involved to adjust mitochondrial functioning to energy constraints. A first study described the kinetics of the installation of fasting-induced muscle hypometabolism and the associated improved mitochondrial bioenergetics efficiency and showed that maximum acclimation was reached after 3 days. Mitochondrial networks remodelling, investigated by antibodies (Western blot) and confocal microscopy, showed a bidirectional flexibility with an increased fusion at the beginning of the fast preceding an increased fragmentation observable after 4 days of fasting. A second study suggested the potential involvement of a nitric oxide synthase (NOS) activity detected in mitochondrial fractions in the modulations of mitochondrial bioenergetics induced by fasting. The activity of mitochondrial NOS was found to be increased by fasting and its in vitro modulation mimicked the effects induced by fasting in nourished birds, in a rapid and reversible manner. A third study explored the flexibility of the mitochondrial genome in order to detect the presence of open reading frames (ORF) potentially encoding bioactive peptides similar to those described in mammals and that are encoded by small regions included in the 12S and 16S genes. Our genetic analyses demonstrated the presence of ORFs incorporated into the 16S rRNA coding gene of most avian species. The molecular evolution of these ORFs among bird species was found to be similar to that calculated for all mitochondrial genes coding for subunits of the respiratory chain. Among the detected ORFs, some corresponded to those described in mammals (humanin and SHLP6) but others had never been described. A fourth study showed that the very strong nucleotide conservation of ORFs located in the 16S gene, and observed in mammals, birds and terrestrial ectotherms, was not an artifact linked to a constraint imposed by the structure of the encoded rRNA. Indeed, the strong nucleotide conservation was not found on alignments of sequences generated by simulations of evolution that took into account the secondary and tertiary structures of 16S rRNA. In the 3 groups of vertebrates, the ORF coding humanin, a peptide identified in humans, underwent a specific negative selection pressure in order to maintain its amino-acid composition during evolution. In conclusion, this thesis highlighted the remarkable bioenergetics and genomic flexibilities of mitochondrial function in birds, which could contribute to the metabolic adjustments required during nutritional transitions. Our results have also opened up a new field of investigation concerning the putative peptides encoded by the mitochondrial genome and their biological roles remain to be explore

Comparative genomic analysis identifies small open reading frames (sORFs) with peptide-encoding features in avian 16S rDNA

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Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates

International audienceBivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1–2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies have shown that mitochondrial DNA mutation rates are linked to lifespan in vertebrate species, but no study has explored this in invertebrates. To this end, we performed a Bayesian Phylogenetic Covariance model of evolution analysis using 12 mitochondrial protein-coding genes of 76 bivalve species. Three life history traits (maximum longevity, generation time and mean temperature tolerance) were tested against 1) synonymous substitution rates (dS), 2) conservative amino acid replacement rates (Kc) and 3) ratios of radical over conservative amino acid replacement rates (Kr/Kc). Our results confirm the already known correlation between longevity and generation time and show, for the first time in an invertebrate class, a significant negative correlation between dS and longevity. This correlation was not as strong when generation time and mean temperature tolerance variations were also considered in our model (marginal correlation), suggesting a confounding effect of these traits on the relationship between longevity and mtDNA substitution rate. By confirming the negative correlation between dS and longevity previously documented in birds and mammals, our results provide support for a general pattern in substitution rates

Threshold effect in the H2O2 production of skeletal muscle mitochondria during fasting and refeeding

International audienceUnder nutritional deprivation, the energetic benefits of reducing mitochondrial metabolism are often associated with enhanced harmful pro-oxidant effects and a subsequent long-term negative impact on cellular integrity. However, the flexibility of mitochondrial functioning under stress has rarely been explored during the transition from basal non-phosphorylating to maximal phosphorylating oxygen consumption. Here, we experimentally tested whether ducklings (Cairina moscnata), fasted for 6 days and subsequently refed for 3 days, exhibited modifications to their mitochondrial fluxes, i.e. oxygen consumption, ATP synthesis, reactive oxygen species generation (ROS) and associated ratios, such as the electron leak (% ROS/O) and the oxidative cost of ATP production (% ROS/ATP). This was carried out at different steady-state rates of oxidative phosphorylation in both pectoralis (glycolytic) and gastrocnemius (oxidative) muscles. Fasting induced a decrease in the rates of oxidative phosphorylation and maximal ROS release. These changes were completely reversed by 3 days of refeeding. Yet, the fundamental finding of the present study was the existence of a clear threshold in ROS release and associated ratios, which remained low until a low level of mitochondrial activity was reached (30-40% of maximal oxidative phosphorylation activity)

Hormetic response triggers multifaceted anti-oxidant strategies in immature king penguins (Aptenodytes patagonicus)

International audienceRepeated deep dives are highly pro-oxidative events for air-breathing aquatic foragers such as penguins. At ␣edging, the transition from a strictly terrestrial to a marine lifestyle may therefore trigger a complex set of anti-oxidant responses to prevent chronic oxidative stress in immature penguins but these pro- cesses are still unde␣ned. By combining in vivo and in vitro approaches with transcriptome analysis, we investigated the adaptive responses of sea-acclimatized (SA) immature king penguins (Aptenodytes pa- tagonicus) compared with pre-␣edging never-immersed (NI) birds. In vivo, experimental immersion into cold water stimulated a higher thermogenic response in SA penguins than in NI birds, but both groups exhibited hypothermia, a condition favouring oxidative stress. In vitro, the pectoralis muscles of SA birds displayed increased oxidative capacity and mitochondrial protein abundance but unchanged reactive oxygen species (ROS) generation per g tissue because ROS production per mitochondria was reduced. The genes encoding oxidant-generating proteins were down-regulated in SA birds while mRNA abundance and activity of the main antioxidant enzymes were up-regulated. Genes encoding proteins involved in repair mechanisms of oxidized DNA or proteins and in degradation processes were also up-regulated in SA birds. Sea life also increased the degree of fatty acid unsaturation in muscle mitochondrial membranes resulting in higher intrinsic susceptibility to ROS. Oxidative damages to protein or DNA were reduced in SA birds. Repeated experimental immersions of NI penguins in cold-water partially mimicked the effects of acclimatization to marine life, modi␣ed the expression of fewer genes related to oxidative stress but in a similar way as in SA birds and increased oxidative damages to DNA. It is concluded that the multi- faceted plasticity observed after marine life may be crucial to maintain redox homeostasis in active tissues subjected to high pro-oxidative pressure in diving birds. Initial immersions in cold-water may initiate an hormetic response triggering essential changes in the adaptive antioxidant response to marine life