JOSIP SKEJO - OBRANA DOKTORSKOG RADA

Naslov: Reconstruction of the Last Eukaryotic Common Ancestor by Cladistic and Phylogenetic Approach

(Rekonstrukcija zajedničkoga pretka eukariota kladističkim i filogenetičkim pristupom)

Četvrtak, 26. svibanj 2022. godine u 15,00 sati u predavaonici Biološkog odsjeka PMF-a, BO 1, Rooseveltov trg 6, Zagreb

Povjerenstvo za obranu:

Prof. dr. sc. Jasna Hrenović, PMF, Zagreb

Prof. dr. sc. Marija Heffer, Sveučilište u Osijeku, Medicinski fakultet

Prof. dr. sc. Ivan Mijaković, Chalmers University of Technology, Švedska

Zamjena: prof. dr. sc. Kristian Vlahoviček, PMF, Zagreb

Mentor 1: izv. prof. dr. sc. Damjan Franjević, PMF, Zagreb

Mentor 2: prof. dr. sc. William F. Martin, Heinrich Heine University Düsseldorf

Sažetak:

Raznolikost i organizacija eukariotskih stanica danas su tako dobro poznati da je već prihvaćena teorija da je LECA (engl. Last Eukaryotic Common Ancestor, Posljednji zajednički predak eukariota) imao mitohondrij, jezgru, unutarstaničnu mrežu membrana, spol, mejozu i eukariotski životni ciklus. Prokarioti ne posjeduju spomenuta obilježja. Usprkos dobrom poznavanju građe, postanak eukariota i dalje je nerazjašnjen. Ne zna se je li mitohondrij ušao u arheju prije ili nakon formacije jezgre; je li LECA imao samo jednu ili više jezgara; koliko je LECA imao dupliciranih gena ni koje im je porijeklo. Često se pogrešno koristi terminologija sistematike, a moderni radovi najčešće ne pokrivaju mnogo svojti. Ciljevi ove disertacije su teoretski raspraviti terminologiju sistematike, s naglaskom na definiciju eukariota; te istražiti organizaciju genoma, morfologiju i fiziologiju LECA-e praktičnim analizama. Eukarioti su definirani kao monofiletska i holofiletska skupina polifiletskog postanka. Zbog hibridnog postanka eukariota i bakterije i arheje su parafiletske i monofiletske skupine. LECA je imao mnogo duplikacija, a najviše ih potječu od bakterija što ide u prilog hipotezi da je mitohondrij bio prisutan tijekom eukariogeneze. Osim plastidnih gena koji su porijeklom iz cijanobakterija, nisu pronađeni jedinstveni geni niti u jednoj supergrupi što znači da su veliki gubitci dijelova genoma i duplikacije gena glavne sile evolucije eukariotskog genoma. Višejezgrene stanice učestale su među eukariotima. Na stablu eukariota označena je prisutnost i odsutnost višejezgrenih stanica te otvorena i zatvorena dioba jezgre. Rekonstrukcija predačkih svojstava nije odbacila pretpostavke da je LECA bio višejezgreni spolni organizam s mitohondrijima i zatvorenom diobom, što znači da je vjerojatno bio sličan današnjim aseptičnim gljivama i sluznjačama. Potvrđeno je da LECA nije imao plastide te da nije bio poliploidan. Suprotno uvriježenom mišljenju, LECA najvjerojatnije nije bio jednojezgreni organizam i prema tome jednojezgreni jednostanični eukarioti vjerojatno predstavljaju visokospecijalizirane organizme, od kojih neki možda čak potječu od LECA-inih gameta.

The organization and diversity of the eukaryotic cells are well documented, so it is a scientific theory that LECA (the Last Eukaryotic Common Ancestor) harbored mitochondrion, nucleus, endoplasmic reticulum, sex, meiosis, and eukaryotic life cycle. None of these traits has been found in prokaryotes. The origin of the eukaryotic traits is, however, still an unresolved issue. It is questionable whether the mitochondrion entered the archaeal host prior to the nucleus formation or later; it has never been systematically studied if LECA had a single or many nuclei; it has not been quantified how many gene duplications there were in LECA, and what is their origin. Cladistic terminology is often misapplied in molecular evolution and studies are rarely based on taxon-rich sampling. This dissertation, hence, discusses cladistics and its interpretation in theory with an emphasis on the definition of eukaryotes. Main focus of dissertation is analyses of genome organization, morphology, and physiology of LECA. Eukaryotes are defined as a monophyletic, holophyletic group with polyphyletic, reticulated origin. Because of this and because mitochondria and the nucleus are not regarded as prokaryotes, both Bacteria and Archaea are paraphyletic and monophyletic. Many duplications were present in LECA, Bacteria-derived ones being prevalent, favoring the mitochondria-early hypothesis. Except for the genes from plastid acquisition, no specific genes were found within eukaryotic supergroups, suggesting that differential loss and genome duplications are the major forces of the eukaryotic evolution. The ubiquity of the multinucleate state across the eukaryotic domain is presented. Traits annotated on the eukaryotic tree were multinucleate state presence and absence, open vs. closed nuclear division, and 'control traits' known to be ancestral (presence of sex, mitochondria) or known not to be ancestral to LECA (plastid, polyploidy). Ancestral state reconstruction did not reject the hypothesis that LECA was multinucleated, likely similar to modern aseptate fungi or myxomycetes, and that it exhibited closed nuclear division. It is confirmed that LECA was sexual, mitochondriate, haploid, and did not have plastids. The results of ancestral state reconstruction indicate that, contrary to popular beliefs, LECA was not a uninucleate cell, from which it follows that uninuclear eukaryotes possibly represent highly specialized forms, of which some might even have originated a long time ago from LECA's gametes.