Raznolikost, evolucijski odnosi i uloga proteina SSB, DnaB i DnaG u bakterijama roda 'Candidatus Phytoplasma'

master's thesis

• Title (english): Diversity, evolutionary relationships and role of SSB, DnaB and DnaG proteins in 'Candidatus Phytoplasma' bacteria
• Author: Doris Brkić
• Mentor: Martina Šeruga Musić (mentor)
• Committee member: Martina Šeruga Musić (predsjednik povjerenstva)
• Committee member: Dunja Leljak-Levanić (član povjerenstva)
• Committee member: Rosa Karlić (član povjerenstva)
• Committee member: Julija Erhardt (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2021-09-27, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Bakterije roda 'Candidatus Phytoplasma' su bakterije bez stanične stijenke koji nastanjuju floem biljaka i kukce-vektore, a nije ih moguće uzgajati u čistoj kulturi in vitro. Njihovi genomi su mali i reducirani, no često bogati ponavljajućim sljedovima koji mogu biti organizirani u potencijalne mobilne jedinice (potential mobile unit; PMU). Geni koje ovi elementi nose mogu biti prisutni u više kopija u genomu, a neki od njih su geni ssb, dnaB i dnaG koji kodiraju za proteine replisoma. Napravljena je filogenetska analiza nukleotidnih i proteinskih sekvenci gena ssb, dnaB i dnaG iz uzoraka sekvenciranih u ovom radu preuzetih iz sekvenciranih i anotiranih genoma bakterija roda 'Ca. Phytoplasma', Acholeplasma i Spiroplasma iz NCBI baze podataka. Analiza je pokazala da su se u slučaju sva tri istraživana gena sekvence koje pripadaju PMU dijelovima genoma izdvojile od drugih sekvenci što upućuje na njihovu neovisnu evoluciju tijekom horizontalnog prijenosa kroz različite vrste fitoplazmi. Gen ssb kod fitoplazmi nalazi se kao izvorna kopija u genomu te kao geni s drugačijim evolucijskim porijeklom na PMU elementima, dok su kod gena dnaB i dnaG sekvence na PMU nastale kao kopije gena iz stabilnog dijela genoma. Gen dnaB razdvojio se na dvije velike skupine koje odgovaraju varijantama gena dnaB1 i dnaB2, a samo varijanta gena dnaB1 sadržava sekvence koje pripadaju PMU elementima. Iz svega navedenog proizlazi da je uloga višestrukih kopija ovih gena u genomima fitoplazmi u povećanju plastičnosti njihovog genoma kako bi bile sposobne za nastanjivanje različitih domaćina i životnih uvjeta.

Abstract (english)

Bacteria of the genus 'Candidatus Phytoplasma' are bacteria without a cell wall that inhabit the phloem of plants and insect vectors, and they cannot be grown in pure culture in vitro. Their genomes are small and reduced, but often rich in repetitive sequences that can be organized into potential mobile units (PMUs). The genes carried by these elements may be present in multiple copies in the genome, such as ssb, dnaB, and dnaG genes encoding replisome proteins. A phylogenetic analysis of the nucleotide and protein sequences of the ssb, dnaB and dnaG genes was performed on sequences obtained within this study as well as on samples taken from sequenced and annotated genomes of bacteria of the genus 'Ca. Phytoplasma ', Acholeplasma and Spiroplasma from the NCBI database. The analysis showed that in the case of all three investigated genes, the sequences belonging to the PMU parts of the genome were separated from other sequences suggesting their independent evolution during horizontal transfer through different strains of phytoplasmas. The ssb gene in phytoplasmas is found as the original copy in the genome as well as sequences with a different evolutionary origin on PMU elements, while dnaB and dnaG sequences on PMU elements were copied from the gene from a stable part of the genome. The dnaB gene has split into two large groups corresponding to the dnaB1 and dnaB2 gene variants, and only the dnaB1 gene variant contains sequences belonging to the PMU elements. All the above suggests that the role of multiple copies of these genes on PMU elements is to increase genome plasticity to make phytoplasmas capable of inhabiting different hosts and living conditions.

• Keywords: evolucija; replisom; nestabilnost genoma; horizontalni prijenos gena; potencijalna mobilna jedinica; biljni patogen; sekvenciranje
• Keywords (english): evolution; replisome; genome instability; horizontal gene transfer; potential mobilne unit; plant pathogen; sequencing
• Language: croatian
• URN:NBN: urn:nbn:hr:217:592564
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2021-10-05 12:41:55