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Συγκριτική Μελέτη Πρωτεϊνών Του Ακραιόφιλου Αρχαίου Metallosphaera Sedula Με Ομόλογες Πρωτεΐνες Άλλων Οργανισμών

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Συγκριτική Μελέτη Πρωτεϊνών Του Ακραιόφιλου Αρχαίου Metallosphaera Sedula Με Ομόλογες Πρωτεΐνες Άλλων Οργανισμών Πτυχιακή Εργασία Συγκριτική μελέτη πρωτεϊνών του ακραιόφιλου αρχαίου Metallosphaera sedula με ομόλογες πρωτεΐνες άλλων οργανισμών Σαμαράς Δημήτριος ΑΕΜ 1664 Επιβλέπουσα Καθηγήτρια: Δρ. Φαδούλογλου Βασιλική Αλεξανδρούπολη 2021 Περιεχόμενα Περιεχόμενα 1 Ευχαριστίες 2 Περίληψη 3 Abstract 4 1. Εισαγωγή 5 1.1. Οι ακραιόφιλοι οργανισμοί 5 Θερμόφιλα 7 Ψυχρόφιλα 8 Οξεόφιλα 9 Αλκαλόφιλα 9 Αλόφιλα 9 1.2. Εφαρμογές στη βιοτεχνολογία 10 1.3. Το αρχαίο Metallosphaera sedula 12 1.4. Σκοπός 13 2. Υλικά και μέθοδοι 14 3. Αποτελέσματα 17 3.1 Αναγωγάση του υδραργύρου 18 3.2 Μηλική αφυδρογονάση 23 3.3 Κιτρική συνθάση 29 3.4 Αποκαρβοξυλάση της 5’-μονοφωσφορικής οροτιδίνης 35 3.5 Δεϋδρατάση του 3-υδροξυπροπιονυλο-CoA 39 3.6 Vacuolar protein sorting 4 AAA-ATPase 44 4. Συμπεράσματα – Συζήτηση 50 5. Βιβλιογραφικές αναφορές 55 6. Παράρτημα 59 1 Ευχαριστίες Σε αυτό το σημείο θα ήθελα να ευχαριστήσω ειλικρινά την επιβλέπουσα καθηγήτριά μου Δρ. Βασιλική Φαδούλογλου που με δέχθηκε στο εργαστήριό της και μου έδωσε την ευκαιρία να εκπονήσω την πτυχιακή μου εργασία υπό την επίβλεψή της. Ήταν διαθέσιμη και πρόθυμη να μου παρέχει οποιαδήποτε βοήθεια και καθοδήγηση κάθε φορά που τη χρειάστηκα. Με την υπομονή και επιμονή που έδειξε με βοήθησε να αποκτήσω θεωρητικές γνώσεις πάνω στο αντικείμενο της εργασίας, μου έδωσε σημαντικά εφόδια για τη μετέπειτα σταδιοδρομία μου, ενώ συνέβαλε και στη γενικότερη βελτίωσή μου ως άνθρωπο και εκκολαπτόμενο επιστήμονα. Φυσικά δε θα μπορούσα να μην ευχαριστήσω την οικογένεια μου που στήριξε και συνεχίζει να στηρίζει την κάθε μου επιλογή και το κάθε μου βήμα. 2 Περίληψη Οι ακραιόφιλοι οργανισμοί (extremophiles) έχουν αναπτύξει πληθώρα μηχανισμών με τους οποίους καθίσταται δυνατή η επιβίωση τους σε περιβάλλοντα όπου επικρατούν ακραίες συνθήκες. Συνθήκες όπως ακραίες τιμές θερμοκρασίας, pH, αλατότητας, πίεσης ή και συνδυασμός αυτών μπορεί να οδηγήσουν στην αποδιάταξη και απώλεια ενεργότητας των πρωτεϊνών με φυσικό επακόλουθο το θάνατο του οργανισμού. Ένας τρόπος με τον οποίο πολλοί οργανισμοί επιβιώνουν σε ακραίες συνθήκες είναι η απομόνωση του εξωτερικού τους περιβάλλοντος από το εσωτερικό τους. Παραδείγματος χάριν, ορισμένοι οξεόφιλοι οργανισμοί διαθέτουν αντλίες με τις οποίες αποβάλουν ιόντα υδρογόνου με αποτέλεσμα να διατηρούν σχέδον ουδέτερο pH στο εσωτερικό τους, ανεξάρτητα με το όξινο pH που επικρατεί στο εξωτερικό τους περιβάλλον. Ωστόσο, πολλές φορές κάτι τέτοιο δεν είναι δυνατόν. Χαρακτηριστικό παράδειγμα αποτελούν οι οργανισμοί που ζουν σε περιβάλλοντα όπου επικρατούν ακραίες θερμοκρασίες. Οι οργανισμοί αυτοί δεν μπορούν να απομονώσουν το εσωτερικό τους από τις ακραίες θερμοκρασίες και επομένως αναγκάστηκαν να αναπτύξουν άλλους μηχανισμούς για να επιβιώσουν. Στους μηχανισμούς αυτούς μπορεί να ενέχονται προσαρμογές της πρωτεϊνικής δομής και αμινοξικής αλληλουχίας, οι οποίες αποσκοπούν στη διατήρηση της σταθερότητας και ενεργότητας των πρωτεϊνών τους κάτω από τις ακραίες συνθήκες στις οποίες ζουν. Στην παρούσα εργασία μελετήσαμε πρωτεΐνες του θερμόφιλου και οξεόφιλου αρχαίου Metallosphaera sedula και τις συγκρίναμε με ομόλογες πρωτεΐνες τους απο μεσόφιλους ή ακραιόφιλους οργανισμούς. Σκοπός μας ήταν ο πιθανός εντοπισμός χαρακτηριστικών που έχουν την τάση να εμφανίζονται ή να απουσιάζουν από πρωτεΐνες που έχουν εξελιχθεί έτσι ώστε να παραμένουν λειτουργικές σε ακραίες συνθήκες. 3 Abstract Extremophilic organisms have developed a wide variety of mechanisms which enable them to survive in environments where the conditions seem incompatible with life to humans. Conditions like extreme temperature, pH, salinity, pressure or a combination of those can lead to the denaturation of proteins and loss of their activity, which naturally leads to the death of the organism. One way which enables organisms to survive extreme conditions is by isolating their external from their internal environment. For example, some acidophiles have proton pumps that allow them to keep their cytoplasm at pH values near neutral, regardless of their extremely acidic external environment. However, this is not always possible. Organisms that live in extremely hot or cold environments is one such example. These organisms cannot shut out heat or cold, so they had to develop different mechanisms to survive. In the mechanisms developed by extremophilic organisms there could be adaptations to the protein structure and amino acid sequence, which aim to the retention of the proteins’ stability and activity under the extreme conditions in which they live. In the present study, we studied proteins of the thermoacidophilic archaeon Metallosphaera sedula and we compared them with homologous proteins from mesophilic or extremophilic organisms. Our goal was to identify protein traits that tend to appear or be absent from specific proteins and could possibly be associated with their ability to remain functional under extreme conditions. 4 1. Εισαγωγή 1.1 Οι ακραιόφιλοι οργανισμοί Η Διεθνής Ένωση Θεωρητικής και Εφαρμοσμένης Χημείας (IUPAC) ορίζει ως κανονικές συνθήκες θερμοκρασίας και πίεσης περιβάλλοντος τους 25oC και 1 atm αντίστοιχα. Ως προς το pH και την αλατότητα, pH 5-9 και αλατότητα που δεν ξεπερνά το 1.2% NaCl (w/v) αποτελούν τιμές ευρέως αποδεκτές ως “φυσιολογικές” (Merino et al. 2019; Schröder et al. 2020). Στον πλανήτη μας υπάρχει πληθώρα περιβαλλόντων όπου τουλάχιστον ένας από τους παραπάνω παράγοντες μπορεί να παίρνει τιμές εκτός αυτών των ορίων. Τέτοιου είδους περιβάλλοντα περιλαμβάνουν ιαματικές πηγές, υδροθερμικές αναβλύσεις και τα ηφαίστεια όπου επικρατεί θερμοκρασία που πλησιάζει ή και ξεπερνά τους 100oC, την Αρκτική και την Ανταρκτική που χαρακτηρίζονται από πολύ χαμηλές θερμοκρασίες, ενώ υπάρχουν και περιβάλλοντα όπως οι έρημοι όπου παρατηρούνται μεγάλες θερμοκρασιακές διακυμάνσεις στη διάρκεια ενός εικοσιτετραώρου. Παράδειγμα αποτελεί η έρημος Σαχάρα όπου η θερμοκρασία μπορεί να κυμαίνεται από τους 50oC την ημέρα στους -4oC κατά τη διάρκεια της νύχτας. Ακραία περιβάλλοντα αποτελούν επίσης τα βάθη των ωκεανών που χαρακτηρίζονται από έλλειψη φωτός και υψηλή πίεση που μπορεί να ξεπερνά τα 110 MPa, όξινες λίμνες όπως η λίμνη Kawah Ijen όπου επικρατεί pH<0.3, καθώς και αλκαλικές λίμνες όπως η λίμνη Bogoria η οποία χαρακτηρίζεται από αλατότητα >40% και pH>10.3 (Peoples et al. 2019; Löhr et al. 2004; Jirsa et al. 2013; Rothschild and Mancinelli 2001;). Ορισμένα από τα περιβάλλοντα αυτά καθώς και η τοποθεσία τους φαίνονται στην Εικόνα 1. 5 Εικόνα 1: Πάνω αριστερά: Η έρημος Σαχάρα, μια έρημος στη νότια Αφρική όπου η θερμοκρασιακή διακύμανση μπορεί να ξεπερνά τους 40oC κατά τη διάρκεια ενός εικοσιτετραώρου. Η τοποθεσία της φαίνεται στο χάρτη της εικόνας με την κόκκινη πινέζα. Πάνω δεξιά: Φωτογραφία από το βυθό της τάφρου των Μαριανών, το βαθύτερο σημείο των Ωκεανών του πλανήτη όπου επικρατεί πολύ υψηλή πίεση και έλλειψη φωτός. Η τοποθεσία της φαίνεται στο χάρτη της εικόνας με την μπλε πινέζα. Κάτω αριστερά: H πιο όξινη λίμνη στον πλανήτη. Η λίμνη Kawah Ijen σχηματίστηκε στον κρατήρα του ηφαιστείου Ijen στην Ινδονησία και η θέση της φαίνεται στο χάρτη με την πράσινη πινέζα. Κάτω δεξιά: Η λίμνη Bogoria, μια λίμνη στην Κένυα στην οποία επικρατεί πολύ υψηλό pH και αλατότητα. Η τοποθεσία της φαίνεται στο χάρτη της εικόνας με την πορτοκαλί πινέζα. 6 Οι άνθρωποι όπως και τα περισσότερα ζώα κατατάσσονται στους μεσόφιλους οργανισμούς, δηλαδή προτιμούν θερμοκρασίες στο εύρος 20-45oC (βέλτιστη ανάπτυξη σε θερμοκρασία 30-39oC) και pH κοντά στο 7 (Schiraldi and De Rosa 2014). Ως εκ τούτου η επιβίωση του ανθρώπου σε ακραία περιβάλλοντα όπως αυτά που αναφέρθηκαν πιο πάνω είναι από πολύ δύσκολη έως αδύνατη. Γνωρίζουμε όμως πως υπάρχει ένας τεράστιος αριθμός οργανισμών που ευδοκιμούν σε περιβάλλοντα όπου επικρατούν ακραίες συνθήκες (Madigan and Marrs 1997). Πέρα από την ικανότητα τους να επιβιώνουν, κάποιοι από τους οργανισμούς αυτούς έχουν εξελιχθεί σε αυτές τις συνθήκες με τρόπο που αδυνατούν να επιβιώσουν σε άλλες συνθήκες. Παραδείγματα τέτοιων οργανισμών αποτελούν το βακτήριο Anaerobranca gottschalkii που αναπτύσσεται μόνο απουσία οξυγόνου (Prowe and Antranikian 2001), το αρχαίο Pyrococcus furiosus που αδυνατεί να αναπτυχθεί σε θερμοκρασία χαμηλότερη των 65oC (Fiala and Stetter 1986) κ.ά. Περισσότεροι ακραιόφιλοι οργανισμοί και λεπτομέρειες για αυτούς μπορούν να βρεθούν στον πίνακα του παραρτήματος τον οποίο κατασκευάσαμε στα πλαίσια της παρούσας εργασίας. Στον πίνακα αυτό υπάρχει ένας μεγάλος αριθμός ακραιόφιλων οργανισμών καθώς και στοιχεία για αυτούς, όπως η επικράτεια στην οποία ανήκουν, οι ακραίες συνθήκες στις οποίες επιβιώνουν, τα μέρη στα οποία εντοπίζονται και η μοριακή βάση της ανθεκτικότητά τους όπου αυτή είναι γνωστή. Οι οργανισμοί που μπορούν να αναπτύσσονται σε ακραίες συνθήκες χωρίζονται σε 2 κατηγορίες. Μια κατηγορία αποτελούν οι οργανισμοί που μπορούν μεν να επιβιώνουν σε ακραίες συνθήκες, αναπτύσσονται όμως βέλτιστα σε φυσιολογικές συνθήκες (extremotolerant). Η δεύτερη κατηγορία αποτελείται από τους ακραιόφιλους οργανισμούς, δηλαδή οργανισμούς που αναπτύσσονται βέλτιστα σε ακραίες συνθήκες (Merino et al. 2019). Οι ακραιόφιλοι οργανισμοί χωρίζονται με τη σειρά τους σε κατηγορίες με βάση τις ιδιαίτερες συνθήκες στις οποίες αναπτύσσονται. Οργανισμοί που αναπτύσσονται σε ακραία χαμηλή ή υψηλή θερμοκρασία ονομάζονται ψυχρόφιλοι και θερμόφιλοι αντίστοιχα. Με την ίδια λογική οργανισμοί που αναπτύσσονται σε πολύ όξινο ή βασικό pH ονομάζονται οξεόφιλοι και αλκαλόφιλοι αντίστοιχα. Οργανισμοί που για την ανάπτυξή τους απαιτούν υψηλή συγκέντρωση άλατος κατατάσσονται στους αλόφιλους οργανισμούς. Άλλες κατηγορίες ακραιόφιλων οργανισμών αποτελούν οι πιεζόφιλοι και
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