Filogenomska analiza lizocimov pri evkariontih

Štukelj, Sabina (author), Kordiš, Dušan (mentor), Župunski, Vera (comentor)

Lizocimi so bakteriolitični encimi, ki so prisotni pri skoraj vseh organizmih in virusih, kjer hidrolizirajo peptidoglikane. Predstavljajo pomembno komponento prirojenega imunskega sistema za obrambo pred bakterijami. Lizocimi spadajo v obsežno proteinsko naddružino glikozidnih hidrolaz. V okviru svoje raziskave sem se osredotočila na pet glavnih družin lizocimov, ki so razširjeni pri evkariontih in poskušala razložiti potek njihove evolucije s pomočjo filogenomske analize. Analizirala sem naslednje družine lizocimov: GH22i (i-tip lizocima), GH22c (c-tip lizocima), GH23 (g-tip lizocima), GH24 (fagni lizocim) in GH25 (1,4-beta-N-acetilmuraminidaza). Namen magistrske naloge je bil pridobiti nove podatke o razširjenosti lizocimskih družin pri evkariontih in s pomočjo teh podatkov ter doslej znanih podatkov razložiti evolucijo posameznih družin lizocimov. Zaradi slabe zastopanosti najstarejših skupin živali v podatkovnih bazah, sem pridobila največ novih podatkov za spužve (Porifera), ožigalkarje (Cnidaria), rebrače (Ctenophora) in plakozoje (Placozoa). Za pridobivanje in analizo podatkov sem uporabila raziskovalne metode filogenomike, filogenetike, primerjalne genomike, bioinformatike in strukturnega modeliranja. Novi podatki so omogočili identifikacijo evolucijskih mehanizmov (horizontalni genski prenos in funkcionalna diverzifikacija) ter določitev časa nastanka družin GH22c, GH22i in GH23 pri evkariontih, ki so se pojavile v predniku živali. S pomočjo filogenetske analize sem prikazala razširjenost in evolucijo posameznih lizocimskih družin ter v filogenetsko drevo umestila predstavnike najstarejših skupin živali, ki so bili pri dosedanjih analizah izključeni. Najbolj divergentna zaporedja predstavnikov lizocimskih družin iz spužev oz. ožigalkarjev, na osnovi najmanjše podobnosti z doslej znanimi lizocimskimi zaporedji, sem uporabila za strukturno modeliranje s programom I-TASSER in tako pridobila podatke o ohranjenosti lizocimske domene pri vseh petih družinah ter ohranjenosti motiva β-lasnične zanke pri družinah GH22c, GH22i in GH23. Novi podatki so pokazali več primerov horizontalnega prenosa lizocimskih genov iz bakterij na evkarionte pri družinah GH24 in GH25 ter izgubo gena za c-tip lizocima pri glistah, mehkužcih, kolobarnikih, preprostih strunarjih, plaščarjih in piškurjih.

• Language: Slovenian
• Keywords: Lizocimi, antimikrobni peptidi, konvergentna evolucija, horizontalni genski prenos
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2019
• PID: 20.500.12556/RUL-113325
• COBISS.SI-ID: 1538509763
• Publication date in RUL: 20.12.2019

Secondary language

• Language: English
• Title: Phylogenomic analysis of lysozymes in eukaryotes

Abstract

Lysozymes are bacteriolytic enzymes which are present in almost all organisms and viruses where they hydrolyse peptidoglycans. They serve as a key component of the innate immune system for the defence against bacteria. Lysozymes are a part of a large protein superfamily of glycoside hydrolases. I have focused my analysis on five main lysozyme families which are present in eukaryotes: GH22i (i-type lysozyme), GH22c (c-type lysozyme), GH23 (g-type lysozyme), GH24 (phage lysozyme) and GH25 (1,4-beta-N-acetylmuraminidase). The objective of my Master's thesis was to acquire new informations regarding the distribution of lysozyme families in eukaryotes and to explain the evolution of individual lysozyme families. The oldest animal lineages are poorly represented in proteome databases therefore a large part of the newly acquired data focused on sponges (Porifera), Cnidarians, Ctenophores and Placozoans. I have used diverse methods of phylogenomics, phylogenetics, bioinformatics and structural modelling for the analysis of the new lysozyme data. The new information enabled the identification of evolutionary mechanisms (Horizontal gene transfer and functional diversification) along with the timing of the origin of GH22c, GH22i and GH23 families in eukaryotes which emerged in the ancestor of all animals. The phylogenetic analysis has demonstrated the distribution and evolution of individual lysozyme families and involved the representatives of the oldest animal lineages, which were not analysed before. For structural modelling with the program I-TASSER I have used the most divergent sequences of lysozyme families from sponges or cnidarians, based on the lowest similarity with previously known lysozyme sequences. The newly acquired data provided information about the conserved lysozyme domain in all five families and the conserved β-hairpin motif in GH22c, GH22i and GH23 families. The newly acquired data has shown multiple cases of horizontal gene transfer of lysozyme genes from bacteria to eukaryotes in GH24 and GH25 families and c-type lysozyme gene loss in nematodes, molluscs, annelids, hemichordates, urochordates and lampreys.

• Keywords: Lysozymes, antimicrobial peptides, convergent evolution, horizontal gene transfer