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Caractérisation Bioinformatique Des Nouvelles Protéines Mitochondriales Chez Les Moules D'eau Douce

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Caractérisation Bioinformatique Des Nouvelles Protéines Mitochondriales Chez Les Moules D'eau Douce Université de Montréal Caractérisation bioinformatique des nouvelles protéines mitochondriales chez les moules d’eau douce (Bivalvia : Unionoida). par Alyssa Mitchell Département de sciences biologiques Faculté des arts et des sciences Mémoire présenté à la Faculté des arts et des sciences en vue de l’obtention du grade de M.Sc. en sciences biologiques Décembre, 2015 © Alyssa Mitchell, 2015 Résumé Malgré que le contenu des génomes mitochondriaux animaux soit dit bien conservé, des nouveaux gènes mitochondriaux ont été identifiés chez plusieurs espèces, surtout des invertébrés. Par exemple, les bivalves exhibant la double transmission uniparentale de leurs génomes mitochondriaux possèdent des nouveaux gènes spécifiques au sexe (M-ORF dans l’ADN de type M, F-ORF dans l’ADN de type F) qui ont été caractérisés in silico chez trois espèces de l’ordre Mytiloida, une espèce de Veneroida et une espèce de Unionoida par une précédente étude. Même si les séquences varient beaucoup entre ces trois ordres, cette étude à montré que des hélices transmembranaires ainsi que des peptides signaux sont conservés pour toutes les séquences. L’étude a aussi montré que les nouveaux gènes pourraient avoir des rôles dans la signalisation cellulaire, le cycle cellulaire et la réponse immunitaire et qu’ils pourraient être le résultat de l’endogénisation de l’ADN viral. Le projet présenté ici a pour but de mieux caractériser ces nouveaux gènes et leur origine potentielle, en plus d’étudier le H-ORF particulier aux hermaphrodites, en ciblant les espèces des unionidés. Les résultats montrent que les hélices transmembranaires et peptides signaux sont conservés chez les unionidés, les protéines semblent être associées à la membrane et être capables de lier des acides nucléiques et protéines, et les fonctions potentielles sont conservées. Les M-ORFs semblent avoir un rôle dans le transport et des processus cellulaires tels que la signalisation, le cycle cellulaire et la division, et l’organisation du cytosquelette. Les F-ORFs semblent être impliqués dans le trafic et transport cellulaire et la réponse immunitaire. Finalement, les H-ORFs semblent être des glycoprotéines structurales avec des rôles dans la signalisation, le transport et la transcription. Les résultats de ce projet pourraient supporter une origine virale ou mitochondriale pour ces gènes. Mots-clés : double transmission uniparentale, Unionoida, ORFans, mitochondrie, in silico 1 Abstract Although animal mitochondrial gene content is generally considered to be well- conserved, new genes have been identified in a variety of species, particularly invertebrates. For example, bivalves with doubly uniparental inheritance (DUI) of the mitochondrial genome have novel, sex-specific genes (M-ORF in M-type DNA, F-ORF in F-type DNA) which have been characterized in silico in three species of the order Mytiloida, one Veneroida and one Unionoida in a previous study. Although they are highly variable across these three orders, this study found conserved N-terminal signal peptides and transmembrane helices across all species. The study also showed that the new genes may and have roles in cell signaling, cell cycle, and immune response, and that they may be the result of endogenization of viral DNA. This project aimed to better characterize these novel genes and their potential origin as well as the H-ORF specific to hermaphrodites by focusing on the Unionoida. The pattern of conserved transmembrane helices and signal peptides is present across the species studied, all proteins seem to be membrane associated and able to bind nucleic acids and proteins, and potential functions are conserved as well. M-ORFs seem to have a role in transport and cellular processes such as signalling, cell cycle and division, and cytoskeleton organisation. F-ORFs are predicted to be involved in cellular traffic and transport and immune response. Finally, H- ORFs appear to be structural glycoproteins which may be involved in signalling, transport and transcription. The results of this project support either a viral or a mitochondrial origin for these genes. Keywords : doubly uniparental inheritance, Unionoida, ORFans, mitochondria, in silico 2 Table des matières Résumé ........................................................................................................................................ 1 Abstract ....................................................................................................................................... 2 Table des matières ....................................................................................................................... 3 Liste des tableaux ........................................................................................................................ 5 Liste des figures .......................................................................................................................... 8 Liste des abréviations et sigles .................................................................................................... 9 Remerciements .......................................................................................................................... 11 Chapitre 1 : Introduction générale ............................................................................................ 13 Section 1.1 : La mitochondrie et son génome ....................................................................... 13 Section 1.2 : La double transmission uniparentale ............................................................... 14 Section 1.3 : Les moules d’eau douce (Unionoida) .............................................................. 16 Section 1.4 : Nouveautés et nouveaux gènes ........................................................................ 18 Section 1.5 : Objectifs et hypothèses .................................................................................... 22 Chapitre 2 : In silico analyses of mitochondrial ORFans in freshwater mussels (Bivalvia: Unionoida) provide framework for future studies of their origin and function. ....................... 23 Section 2.1: Introduction ....................................................................................................... 23 Section 2.2: Materials and methods ...................................................................................... 26 Section 2.2.1: Sequences used in the analyses .................................................................. 26 Section 2.2.2: Analyses of ORFan sequences and protein secondary structures .............. 30 Section 2.2.3: Functional analyses of ORFan proteins ..................................................... 30 Section 2.3: Results ............................................................................................................... 31 Section 2.3.1: Rate of evolution of ORFan genes and proteins ........................................ 31 Section 2.3.2: Conserved structures in ORFan protein sequences .................................... 40 3 Section 2.3.3: Motif and functional domain scans: frequently recurring HHpred hits and potential ligand-binding sites ............................................................................................ 44 Section 2.3.4: Prediction of molecular function: hits to viral proteins ............................. 47 Section 2.3.5: Prediction of molecular function: hits to mitochondrial proteins .............. 51 Section 2.3.6: Profile HMM – sequence comparisons for F-ORFs and M-ORFs ............ 53 Section 2.3.7: Prediction of molecular function (all sequences, all programs except hmmsearch ) ...................................................................................................................... 54 Section 2.4: Discussion and conclusion ................................................................................ 57 Section 2.4.1: Evolution of freshwater mussel ORFan sequences and protein structures ....................................................................................................................................... 57 Section 2.4.2: Conserved motifs and domains: mitochondrial export of ORFan proteins ....................................................................................................................................... 59 Section 2.4.3: Putative origin for freshwater mussel mitochondrial ORFans ............... 61 Section 2.4.4: Predicted functions for freshwater mussel mitochondrial ORFans ....... 64 Section 2.4.5: Conclusions and future directions .......................................................... 67 Chapitre 3 : Discussion, perspectives et conclusion ................................................................. 69 Section 3.1 : Conservation des séquences et structures des ORFans .................................... 69 Section 3.2 : Exportation des ORFans de la mitochondrie ................................................... 70 Section 3.3 : Fonctions potentielles ...................................................................................... 72 Section 3.4 : DUI et conflit génomique ................................................................................ 73 Section 3.5 : Unionoida ......................................................................................................... 74 Bibliographie ............................................................................................................................. 76 Appendice 1 : L’approche bioinformatique .............................................................................
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