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«Ανάλυση Μιτοχονδριακών Γονιδιωμάτων Με Έμφαση Στη Μελέτη Γενετικών Στοιχείων Που Εμπλέκονται Στην Οργάνωση Και Μεταγραφή Του Mtdna Στους Pezizomycotina»

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«Ανάλυση Μιτοχονδριακών Γονιδιωμάτων Με Έμφαση Στη Μελέτη Γενετικών Στοιχείων Που Εμπλέκονται Στην Οργάνωση Και Μεταγραφή Του Mtdna Στους Pezizomycotina» ΕΛΛΗΝΙΚΗ ΔΗΜΟΚΡΑΤΙΑ Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών ΣΧΟΛΗ ΘΕΤΙΚΩΝ ΕΠΙΣΤΗΜΩΝ ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ ΠΡΟΓΡΑΜΜΑ ΜΕΤΑΠΤΥΧΙΑΚΩΝ ΣΠΟΥΔΩΝ «ΒΙΟΠΛΗΡΟΦΟΡΙΚΗ» ΔΙΠΛΩΜΑΤΙΚΗ ΕΡΓΑΣΙΑ «Ανάλυση μιτοχονδριακών γονιδιωμάτων με έμφαση στη μελέτη γενετικών στοιχείων που εμπλέκονται στην οργάνωση και μεταγραφή του mtDNA στους Pezizomycotina» Ντερτιλή Μαρία Βιολόγος, Τμήμα Βιολογίας, Σχολή Θετικών Επιστημών, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών ΑΘΗΝΑ 2016 ~ II ~ HELLENIC REPUBLIC National and Kapodistrian University of Athens SCHOOL OF SCIENCE FACULTY OF BIOLOGY MASTER IN “BIOINFORMATICS” Master Diploma Thesis « Analysis of mitochondrial genomes with emphasis in the study of the genetic elements that interfere with the organization and the transcription of the mtDNA in Pezizomycotina » Ntertilis Maria Biologist, Faculty of Biology, School of Science, National and Kapodistrian University of Athens ATHENS 2016 ~ III ~ ΕΛΛΗΝΙΚΗ ΔΗΜΟΚΡΑΤΙΑ Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών ΣΧΟΛΗ ΘΕΤΙΚΩΝ ΕΠΙΣΤΗΜΩΝ ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ ΠΡΟΓΡΑΜΜΑ ΜΕΤΑΠΤΥΧΙΑΚΩΝ ΣΠΟΥΔΩΝ «ΒΙΟΠΛΗΡΟΦΟΡΙΚΗ» ΔΙΠΛΩΜΑΤΙΚΗ ΕΡΓΑΣΙΑ « Ανάλυση μιτοχονδριακών γονιδιωμάτων με έμφαση στη μελέτη γενετικών στοιχείων που εμπλέκονται στην οργάνωση και μεταγραφή του mtDNA στους Pezizomycotina» Τριμελής εξεταστική επιτροπή Καθηγητής Κωνσταντίνος Ε. Βοργιάς (Επιβλέπων) Τομέας Βιοχημείας και Μοριακής Βιολογίας, Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών Επίκουρη Καθηγήτρια Αικατερίνη-Μαρία Παππά Τομέας Γενετικής και Βιοτεχνολογίας, Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών Επίκουρη Καθηγήτρια Βασιλική Α. Οικονομίδου Τομέας Βιολογίας Κυττάρου και Βιοφυσικής, Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών ~ IV ~ ΠΕΡΙΕΧΟΜΕΝΑ Πρόλογος VΙ Περιεχόμενα VIΙ Περίληψη VIII Summary X 1. Εισαγωγή 1 1.1 Το Μιτοχονδριακό Γονιδίωμα 1 1.1.1 Γενικά χαρακτηριστικά 1 1.1.2 Η εξέλιξη των μιτοχονδρίων 5 1.1.3 Η οργάνωση των μιτοχονδριακών γονιδιωμάτων 7 1.1.4 Η οργάνωση των μιτοχονδριακών γονιδιωμάτων στους μύκητες 8 1.2 Οι μηχανισμοί συντήρησης και ρύθμισης της έκφρασης του μιτοχονδριακού γονιδιώματος 12 1.2.1 Η αντιγραφή του μιτοχονδριακού γονιδιώματος 12 1.2.2 Η μεταγραφή του μιτοχονδριακού γονιδιώματος 15 1.2.2.1 Η μεταγραφή του mtDNA στον άνθρωπο 15 1.2.2.2 Η μεταγραφή του mtDNA στις ζύμες και η ωρίμανση των πολυσιστρονικών μεταγράφων 20 1.3 Πρόβλεψη υποκινητών 27 1.4 Μύκητες 29 1.5 Η φυλογένεση και το μιτοχονδριακό γονιδίωμα των μυκήτων 32 1.6 Στόχος 35 2. Υλικά και Μέθοδοι 37 2.1 Χαρακτηρισμός μιτοχονδριακών γονιδιωμάτων 37 2.2 Φυλογενετικά δέντρα 41 2.3 Στοιχίσεις διαγονιδιακών περιοχών 42 2.4 Πρόβλεψη υποκινητών 43 3. Αποτελέσματα 45 3.1 Η βάση δεδομένων MitoFun 45 3.2 Φυλογενετικά δέντρα 52 3.3 Πρόβλεψη υποκινητών 53 4. Συζήτηση 87 5. Βιβλιογραφία 97 ΠΑΡΑΡΤΗΜΑ 120 ~ VII ~ ΠΕΡΙΛΗΨΗ Τα μιτοχόνδρια είναι οργανίδια ζωτικής σημασίας για τις κυτταρικές λειτουργίες σε όλους τους ευκαρυωτικούς οργανισμούς τόσο στην κυτταρική ανάπτυξη όσο και στον κυτταρικό θάνατο. Θεωρείται πως έχουν προέλθει έπειτα από ενδοσυμβίωση του πρόγονου ευκαρυωτικού κυττάρου με α-πρωτεοβακτήρια. Η ενδοσυμβίωση είχε ως αποτέλεσμα η πλειοψηφία των αρχικών μιτοχονδριακών γονιδίων να μεταναστεύσουν στον πυρήνα. Τα εναπομείναντα γονίδια οργανώθηκαν στο DNA του οργανιδίου, και για αυτό το μιτοχόνδριο χαρακτηρίζεται ως ημιαυτόνομο οργανίδιο. Τα γονίδια αυτά κωδικοποιούν ένα σύνολο υπομονάδων των συμπλόκων για την οξειδωτική φωσφορυλίωση και την ATP συνθετάση, που ευθύνεται για το μεγαλύτερο ποσοστό της παραγωγής ΑΤΡ στα κύτταρα των ευκαρυωτικών οργανισμών. Η διατήρηση και έκφραση του μιτοχονδριακού γονιδιώματος (mtDNA) απαιτεί ένα πλήθος πρωτεϊνών, οι οποίες είναι πυρηνικά κωδικοποιούμενες, μεταφράζονται στο κυτταρόπλασμα και μεταφέρονται στα μιτοχόνδρια. Οι μύκητες αποτελούν μια ξεχωριστή ομάδα οργανισμών. Είναι ευκαρυωτικοί οργανισμοί, ετερότροφοι, που τυπικά έχουν ένα θαλλό που λέγεται μυκήλιο και αποτελείται από διακλαδισμένα σωληνοειδή νημάτια, τις υφές. Οι μύκητες είναι αρκετά επιτυχείς οργανισμοί διότι έχουν καταφέρει να αποικήσουν σε κάθε είδος περιβάλλοντος. Εφόσον δεν φωτοσυνθέτουν, μπορούν να καταλάβουν ακόμα και σκοτεινούς βιότοπους και να αναπτυχθούν προς κάθε κατεύθυνση και σε κάθε είδος υποστρώματος. Ταυτόχρονα, παράγουν τεράστιους αριθμούς σπορίων, τα οποία απελευθερώνονται και διασπείρονται με μεγάλη αποτελεσματικότητα. Με αποτέλεσμα κάθε οικολογική θέση, είτε βρίσκεται στον αέρα, είτε στο έδαφος είτε στο νερό, όχι μόνο αποικείται από μύκητες αλλά περιλαμβάνει και εξαιρετικά μεγάλο αριθμό ειδών μυκήτων. Σύμφωνα με τα σύγχρονα δεδομένα τα μιτοχονδριακά γονιδιώματα παρέχουν πληροφορίες σχετικά με τη γενετική, ταξινομική, εξελικτική και φυλογενετική μελέτη των μυκήτων. Το ενδιαφέρον του mtDNA εστιάζεται στη συνύπαρξη της συντηρητικότητας των λειτουργιών του, με τη διαφορετικότητα της δομής και σύστασης (γονιδιακή οργάνωση, εσώνια) στα διάφορα είδη μυκήτων. Τα μυκητιακά mtDNAs φέρουν συνήθως γονίδια που κωδικοποιούν (α) 14 πρωτεΐνες για την αναπνοή και παραγωγή ΑΤΡ, (β) 2 rRNA και (γ) 25 κατά μέσο όρο tRNAs. Στην παρούσα Διπλωματική εργασία μελετήθηκαν 126 mtDNAs, εκ των οποίων τρία επισημάνθηκαν εξ’ ολοκλήρου, εμπλουτίζοντας την βάση δεδομένων MitoFun που είχε αναπτυχθεί νωρίτερα για την ολοκληρωμένη και σωστή παρουσίαση των γνωστών mtDNA των μυκήτων. Αναλύθηκαν οι αλληλουχίες, διορθώθηκαν τα λάθη και εμπλουτίστηκαν οι εγγραφές που ήταν ελλιπείς. Προκειμένου να μελετηθεί ο μηχανισμός της ρύθμισης της έκφρασης των mtDNAs, μελετήθηκαν τα γονιδιώματα που ανήκουν στο Φύλο των Ασκομυκήτων (223 ~ VIII ~ γνωστά mtDNAs) και έμφαση δόθηκε στο Υπόφυλο Pezizomycotina (100 γνωστά mtDNAs). Οι πρωτεϊνικές αλληλουχίες των γονιδίων όλων των μιτοχονδριακών γονιδιωμάτων (287) χρησιμοποιήθηκαν για την κατασκευή φυλογενετικών δένδρων που αναδεικνύουν τις εξελικτικές σχέσεις των οργανισμών που τα φέρουν. Επιβεβαιώθηκε μέσα από αυτήν την φυλογένεση η σημαντικότητα των mtDNAs στις εξελικτικές μελέτες και η περιεκτικότητα της πληροφορίας που αυτά φέρουν. Μελετήθηκε η συνταινικότητα των γονιδιωμάτων καθώς φάνηκε πως η γονιδιακή οργάνωση μπορεί να προδιαγράφει το περιεχόμενο των πολυσιστρονικών μεταγράφων. Επίσης αξιοποιήθηκαν οι διαγονιδιακές περιοχές προκειμένου να εντοπιστούν οι ρυθμιστικές περιοχές που παίζουν ρόλο στην μεταγραφή των γονιδιωμάτων. Οι διαγονιδιακές περιοχές στην ανιούσα θέση των γονιδίων cox1, cob και nad4L από 71 επιλεγμένα στελέχη απομονώθηκαν και στοιχήθηκαν προκειμένου να εντοπιστούν οι συντηρητικές περιοχές που πιθανά να φέρουν την αλληλουχία του υποκινητή. Επιπλέον μελετήθηκαν οι επαναλαμβανόμενες αλληλουχίες DNA των διαγονιδιακών αυτών περιοχών και τα ανοικτά πλαίσια ανάγνωσης που αυτές μπορεί να φέρουν. Αποτέλεσμα των παραπάνω ήταν ο σχεδιασμός ενός αλγορίθμου σε γλώσσα προγραμματισμού perl, ο οποίος μπορεί να προβλέπει τη δυνητική θέση ενός υποκινητή σε ένα μιτοχονδριακό γονιδίωμα. Μετά την δοκιμή του αλγορίθμου σε 27 γονιδιώματα οργανισμών που ανήκουν στο Υπόφυλο Pezizomycotina, διαπιστώθηκαν πιθανές θέσεις έναρξης της μεταγραφής, όπως στην ανιούσα θέση των γονιδίων rns, rnl, cox1, cob, που έχουν αναφερθεί στην βιβλιογραφία αλλά και νέες πιθανές θέσεις όπως αυτές στην ανιούσα θέση των γονιδίων nad1, nad4, nad6, atp9, cox3. Ο παραπάνω αλγόριθμος θα μπορούσε να αποτελέσει ένα χρήσιμο εργαλείο που θα οδηγούσε σε γρηγορότερα και αποδοτικότερα πειραματικά δεδομένα που θα επιβεβαιώσουν τις in silico προβλέψεις που αφορούν την ρύθμιση της γονιδιακής μετάφρασης και έκφρασης των μιτοχονδριακών γονιδιωμάτων των μυκήτων. ~ IX ~ SUMMARY Mitochondria are vital organelles to cell growth and cellular death in all eukaryotic organisms. Their origin is proposed to be a result of the endosymbiosis of the eukaryotic ancestor with α-proteobacteria. The endosymbiosis and the consequent evolution forced the majority of the mitochondrial genes to migrate to the nucleus. The remaining genes were organized within the DNA of the organelle, and thus, mitochondria are called semiautonomous. The genes which are located within the mitochondrial genome (mt DNA), encode for a number of proteins that participate in the formation of the complexes of oxidative phosphorylation and of ATP synthase, which is responsible for the majority of the ATP production in eukaryotic cells. The maintenance and expression of the mitochondrial genome (mtDNA) require a number of proteins, who are encoded in the nucleus, translated in the cytoplasm and then transferred to the mitochondria. Fungi are a special group of organisms. They are eukaryotic, heterotrophic organisms that typically have a thallus that it is called mycelium and consists of branched tubular filaments, the hyphae. Fungi are adaptable organisms since they have managed to inhabit in any kind of environment. They do not photosynthesize and thus, they can grow even in dark habitats, in all substrates. At the same time, they produce a large number of spores, which are spread with great effectiveness. So any habitat, whether on air, on ground or in water is inhabited by fungi which are taxonomically placed to a large number of different species. According to many recent articles, mitochondrial genomes can provide information about the genetics, taxonomy, evolution and phylogenetic analyses of fungi. MtDNA contains genes responsible for conserved functions but also present an extreme divergence in structure and composition (gene order, introns) in different species of fungi. Fungal mtDNAs usually carry genes that encode for (a) 14 proteins that participate in respiration and production of ATP, (b) 2 rRNAs and (c) an average of 25 tRNAs. In this master thesis,
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