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VILNIAUS UNIVERSITETAS Darius Kazlauskas DVIGRANDĖS DNR VIRUSŲ DNR REPLIKACIJOS BALTYMŲ ANALIZĖ KOMPIUTERINIAIS METODAIS

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VILNIAUS UNIVERSITETAS Darius Kazlauskas DVIGRANDĖS DNR VIRUSŲ DNR REPLIKACIJOS BALTYMŲ ANALIZĖ KOMPIUTERINIAIS METODAIS VILNIAUS UNIVERSITETAS Darius Kazlauskas DVIGRAND ĖS DNR VIRUS Ų DNR REPLIKACIJOS BALTYM Ų ANALIZ Ė KOMPIUTERINIAIS METODAIS Daktaro disertacija Fiziniai mokslai, biochemija (04 P) Vilnius, 2014 Disertacija rengta 2010-2014 m. Vilniaus universiteto Biotechnologijos institute. Mokslinis vadovas: dr. Česlovas Venclovas (biomedicinos mokslai; biologija – 01 B ir fiziniai mokslai, biochemija – 04 P) 2 TURINYS SANTRUMPOS.................................................................................................. 6 ĮVADAS ............................................................................................................. 7 1. LITERAT ŪROS APŽVALGA .................................................................... 10 1.1. DNR replikacija ..................................................................................... 10 1.2. DNR replikacijos baltymai .................................................................... 12 1.2.1. DNR replikaz ės ............................................................................... 12 1.2.2. Helikaz ės ......................................................................................... 18 1.2.3. Praimaz ės ........................................................................................ 21 1.2.4. Viengrand ę DNR surišantys baltymai ............................................ 22 1.2.5. Pradmen į pašalinantys baltymai ..................................................... 23 1.2.6. Ligaz ės ............................................................................................ 24 1.2.7. Topoizomeraz ės .............................................................................. 25 2. METODAI .................................................................................................... 27 2.1. Pradiniai duomenys ir duomen ų baz ės .................................................. 27 2.2. Replikacijos baltym ų paieška ................................................................ 27 2.3. Baltym ų sek ų grupavimas ...................................................................... 29 2.4. Replikacini ų baltym ų identifikavimas ................................................... 30 2.5. Papildomos homolog ų paieškos ............................................................ 30 2.6. Sek ų palyginiai ...................................................................................... 31 2.7. Antrin ės strukt ūros ir nestrukt ūrizuot ų region ų nustatymas .................. 31 2.8. Genom ų lyginimas ir genomin ės aplinkos analiz ė ................................ 31 2.9. Genom ų grupavimas ir filtravimas ........................................................ 31 2.10. Homologinis modeliavimas ir strukt ūros analiz ė ................................ 32 2.11. Elektrostatini ų savybi ų analiz ė ............................................................ 32 3 3. REZULTATAI IR J Ų APTARIMAS ........................................................... 34 3.1. DNR replikazi ų analiz ė .......................................................................... 34 3.1.1. DNR replikaz ės komponentai ir genomo dydis .............................. 34 3.1.2. DNR polimeraz ės ............................................................................ 38 3.1.1. Procesyvumo veiksniai ................................................................... 43 3.1.2. Žiedo užk ėlimo kompleksai ............................................................ 49 3.1.3. DNR replikazi ų tyrimo rezultat ų apibendrinimas ir s ąsajos su ląsteliniais organizmais ............................................................................. 52 3.2. DNR replikacijos baltym ų ir viruso genomo dydžio bei šeimininko taksonomijos ryšys ........................................................................................ 56 3.3. Replikacini ų helikazi ų ir praimazi ų analiz ė .......................................... 59 3.3.1. Replikacini ų helikazi ų ir praimazi ų identifikavimas, įvairov ė ir domenin ė organizacija .............................................................................. 60 3.3.2. Replikacin ės helikaz ės – dažniausias dgDNR virus ų replikacijos baltymas .................................................................................................... 63 3.3.3. Herpes virus ų helikaz ės-praimaz ės UL8 subvienetas yra inaktyvuota B šeimos polimeraz ė ............................................................. 65 3.4. Viengrand ę DNR surišantys baltymai ................................................... 73 3.4.1. Keturiose NCLDV šeimose rasti OB-sanklodos SSB baltymai ..... 75 3.4.2. NCLDV SSB strukt ūra tinkama s ąveikai su vgDNR ..................... 77 3.4.3. Raup ų SSB baltymai (I3) negiminingi NCLDV SSB .................... 80 3.4.4. NCLDV vgDNR surišan čių baltym ų taksonominis pasiskirstymas ir evoliucija ................................................................................................... 83 3.5. Pradmens pašalinimo baltymai .............................................................. 84 3.6. Ligaz ės ................................................................................................... 85 3.7. Topoizomeraz ės ..................................................................................... 85 4 IŠVADOS ......................................................................................................... 86 MOKSLINI Ų DARB Ų S ĄRAŠAS .................................................................. 87 FINANSIN Ė PARAMA ................................................................................... 88 GYVENIMO APRAŠYMAS ........................................................................... 89 PAD ĖKA .......................................................................................................... 90 LITERAT ŪROS S ĄRAŠAS ............................................................................ 91 5 SANTRUMPOS AEP – arch ėjų-eukariot ų praimaz ė a-r. – aminor ūgštis bp – bazi ų pora; kbp – 10 3 bp; Mb – 10 6 bp DB – duomen ų baz ė dg – dvigrand ė DUF – nežinomos funkcijos domenas (domain of unknown function) NCBI – JAV nacionalinis biotechnologin ės informacijos centras (National Center for Biotechnology Information) NCLDV – Branduolyje ir citoplazmoje besidauginantys didelio genomo DNR virusai (Nuclear and Cytoplasmic Large DNA Viruses) NTP – nukleotid ų trifosfatas nr – NCBI nepasikartojan čių baltym ų sekų (non-redundant) duomen ų baz ė nr70 – „nr“ duomen ų baz ė nufiltruota iki 70% identiškumo OB – sąveikaujantis su oligonukleotidais (oligonucleotide-binding) Pfam – baltym ų šeim ų (protein families) duomen ų baz ė PCNA – besidauginan čių l ąsteli ų branduolio antigenas (Proliferating Cell Nuclear Antigen) PV – procesyvumo veiksnys RFC – replikacijos veiksnys C (Replication Factor C) RFCL – replikacijos veiksnio C didysis subvienetas (Replication Factor C, large) RFCS – replikacijos veiksnio C mažasis subvienetas (Replication Factor C, small) SF – superšeima (superfamily) SmpB – mažasis baltymas B (Small protein B) – bakterij ų baltymas, surišantis tmRNR SSB – viengrand ę DNR surišantis baltymas (single-stranded DNA-binding) Toprim – topoizomeraz ės-praimaz ės domenas UDG – uracil-DNR glikozilaz ė vg – viengrand ė ŽUK – žiedo užk ėlimo kompleksas 6 ĮVADAS Sugeb ėjimas daugintis ir evoliucionuoti yra pagrindin ės gyv ų esybi ų ypatyb ės. Genetin ės informacijos kopijavim ą atlieka replikacijos baltymai. Laisvai gyvenan čių l ąstelini ų organizm ų replikacijos aparato sandara yra vienoda. Skiriasi tik atskir ų šios sistemos komponent ų kilm ė. Pavyzdžiui, sek ų ir strukt ūrų analiz ės rodo, kad eukariot ų-arch ėjų ir bakterij ų DNR polimeraz ės yra negiminingos (Leipe, Aravind et al., 1999; Bailey, Wing et al., 2006). Tuo tarpu virus ų DNR replikacijos baltymai yra labai įvair ūs. Jie gerai ištirti T7, T4 faguose, herpes, poliomos ir papilomos virusuose, ta čiau šios grup ės sudaro tik maž ą dal į (~10%) visos tyrin ėtos jų įvairov ės. Kaip dauginasi mažiau žinomi dgDNR virusai? Ar jie naudoja jau žinom ų replikacijos sistem ų variacijas? O gal jiems b ūdingos specifin ės, dar nežinomos DNR replikacijos strategijos? DgDNR virusai stebina ne tik savo įvairove, bet ir genomo dydžio svyravimu. Pavyzdžiui, mažiausi ų šios grup ės virus ų (poliomos) genomai yra 500 kart ų mažesni už didžiausi ų Pandora virus ų (genomas – 2500 kbp). Laisvai gyvenan čių ląstelini ų organizm ų genomo dydis taip pat varijuoja. Pavyzdžiui, mažiausio eukarioto ( Ostreococcus tauri ) ir žmogaus genomo dydis skiriasi ~260 kart ų (Derelle, Ferraz et al., 2006). Nepaisant to, ši ų organizm ų DNR replikacijos aparatas turi tuos pa čius komponentus. Ar jie vienodi ir dgDNR virusuose? O galb ūt replikacijos baltym ų įvairov ė ir pasiskirstymas genomuose priklauso nuo viruso genomo dydžio? Siekiant atsakyti į aukš čiau pateiktus klausimus, buvo atlikta išsami dgDNR virusų DNR replikacijos baltym ų kompiuterin ė analiz ė. Naudojant pažangiausius bioinformatikos metodus, identifikuoti ir charakterizuoti virus ų replikacijos baltymai (DNR polimeraz ės, procesyvumo veiksniai, žiedo užk ėlimo kompleksai, DNR praimaz ės, helikaz ės, viengrandę DNR surišantys baltymai, pradmens pašalinime dalyvaujan čios nukleaz ės, DNR ligaz ės ir topoizomeraz ės) bei nustatyti j ų pasiskirstymo genomuose d ėsningumai. DgDNR virus ų replikacijos baltym ų tyrimas vyko dviem etapais. Iš pradži ų buvo tiriamos DNR replikaz ės (DNR polimeraz ės, procesyvumo 7 veiksniai, žiedo užk ėlimo kompleksai). Nustatyta, kad šios sistemos komponent ų buvimas
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