Genomska in evolucijska analiza aerolizinov in aktinoporinov pri najstarejših vretenčarjih

Marondini, Nastja (author), Kordiš, Dušan (mentor), Župunski, Vera (comentor)

Aerolizini in aktinoporini so zanimivi predstavniki toksinov, ki tvorijo pore v membrani. Najbolj so zastopani pri bakterijah, najdemo pa jih tudi pri vretenčarjih. Pri piškurjih je prišlo do velikega povečanja števila genov, ki kodirajo aerolizine in aktinoporine. Vzroki in mehanizmi za takšno povečanje števila genov, njihova evolucija in raznolikost še niso znani. Z uporabo različnih bioinformacijskih orodij in filogenomske analize sem zbrala aminokislinska zaporedja aerolizinov in aktinoporinov pri piškurjih in sorodnih organizmih. Tako za aerolizine, kot aktinoporine velja, da je prišlo do obsežnega povečanja števila genov le pri piškurjih. Glenavice, ki so najbolj sorodne piškurjem, nimajo genov za aerolizine in aktinoporine, torej je pri njih prišlo do izgube teh genov. Aerolizinski geni so izjemno ohranjeni pri piškurjih (>90 % nukleotidna identičnost), ter so dokaj podobni aerolizinu Dln1 ribe cebrice. Do njihovega tandemskega podvojevanja je prišlo po genskih duplikacijah s hkratno evolucijo in gensko konverzijo. Posledica povečanega števila kopij genov za aerolizine pri piškurjih je povečano izražanje teh toksinov, ki sodelujejo v imunski obrambi in delujejo citolitično. Analizirala sem tudi možen vpliv retroelementov penelope na tandemske duplikacije aerolizinov in ugotovila, da niso imeli vpliva, saj ne ležijo v bližini aerolizinskih genov. Za razliko od aerolizinov so aktinoporini pri piškurjih divergentni in so nastali po genskih duplikacijah s funkcionalno diverzifikacijo. Zaradi njihove raznolikosti verjetno delujejo na različne tarče. S homolognim modeliranjem 3D proteinskih struktur sem ugotovila, da so aerolizini piškurja strukturno zelo podobni aerolizinu Dln1 ribe cebrice in imajo verjetno podoben mehanizem delovanja. Modeli 3D-struktur za aktinoporine iz piškurja in morske vetrnice, pri kateri so najprej odkrili aktinoporine, se zelo razlikujejo, prav tako pa imajo spremenjeno za njih značilno vezavno mesto na membrane P-[WYF]-D. Analiza genskih družin, ki kodirajo aerolizine in aktinoporine pri piškurjih, je dala nov vpogled v nastanek, raznolikost in pomen povečanega števila genov, ki kodirajo te toksine pri najstarejši skupini vretenčarjev.

• Language: Slovenian
• Keywords: piškur, aerolizini, aktinoporini
• 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-111171
• COBISS.SI-ID: 1538444739
• Publication date in RUL: 25.09.2019

Secondary language

• Language: English
• Title: Genomic and evolutionary analysis of aerolysins and actinoporins in the most ancient vertebrates

Abstract

Aerolysins and actinoporins are interesting representatives of toxins that form membrane pores. They are most prevalent in bacteria but are also found in vertebrates. A large increase in the number of genes that encode aerolysins and actinoporins has occurred in lampreys. The causes and mechanisms for such gene expansion, their evolution and diversity are not yet known. Using a variety of bioinformatics tools and phylogenomic analysis, I have obtained gene and protein sequences of aerolysins and actinoporins in lampreys and related organisms. Aerolysins and actinoporins underwent a large increase in the number of genes only in lampreys. Hagfishes, the closest relatives of lampreys have lost genes for aerolysins and actinoporins. Aerolysin genes are extremely conserved in lampreys (> 90\% nucleotide identity) and are quite similar to the zebrafish aerolysin Dln1. The mechanisms of their tandem duplications was gene duplication followed by concerted evolution and gene conversion. Increased number of aerosolysin genes in lampreys results in increased production of encoded proteins, which participate in the immune response and are cytolytic. I also analyzed the possible role of penelope retroelements on tandem duplications of aerolysins and found that they had no effect since they are not present in the vicinity of the aerolysin genes. In contrast to aerolysins, actinoporins are very divergent in lampreys and originated by numerous gene duplications followed by functional diversification. Due to their diversity, they are likely to act on different targets. By homologous modeling of 3D protein structures, I found that the lamprey aerolysins are structurally very similar to the zebrafish aerolysin Dln1 and probably have a similar mechanism of action. 3D structural models of actinoporins from lampreys and sea anemones, where actinoporines were first found, are very different, and also have a modified P-[WYF]-D membrane binding site. Analysis of aerolysin and actinoporin gene families in lampreys has provided a new insight on the origin, diversity and the biological role of the increased number of genes encoding these toxins in the oldest vertebrate lineage.

• Keywords: Lamprey, Aerolysins, Actinoporins