Identification and characterization of BPM2 splice variants in Arabidopsis thaliana

master's thesis

• Title (croatian): Identifikacija i karakterizacija varijanti alternativnog prekrajanja uročnjakova gena BPM2
• Author: Gaj Keresteš
• Mentor: Dunja Leljak-Levanić (mentor)
• Mentor: Paula Štancl (komentor)
• Committee member: Dunja Leljak-Levanić (predsjednik povjerenstva)
• Committee member: Rosa Karlić (član povjerenstva)
• Committee member: Nataša Bauer (član povjerenstva)
• Committee member: Mirjana Pavlica (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2024-07-17, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

IMATH-BTB proteins mediate turnover of specific proteins by acting as substrate adaptors of E3 ubiquitin ligases. The MATH-BTB gene family has undergone a significant expansion in grasses, with genomes of different grass species having dozens of MATH-BTB genes, some of which have roles in fundamental developmental processes. In contrast, the genome of Arabidopsis thaliana only contains six MATH-BTB genes: BPM1-6. In this thesis, alternative splicing was explored as a potential mechanism for A. thaliana to achieve the number and diversity of MATH-BTB proteins similar to grasses. A bioinformatic analysis of the newest A. thaliana transcriptome, AtRTD3, revealed 56 transcript isoforms encoded by BPM genes, 16 of which are encoded by BPM2. While proteins encoded by the 16 BPM2 transcripts differed in domain composition, they lacked the diversity in MATH domains that's present in grass-specific MATH-BTB proteins. Expressions of splice variants BPM2.3, BPM2.8, BPM2.9 and BPM2.15 were analyzed in some vegetative, reproductive and embryonic tissues with standard and quantitative PCR. Splice variants BPM2.3 and BPM2.15 had significant differences in expression levels across different tissues, indicating a possible role in developmental transitions. Theoretically unexpected amplicons represent potentially novel splice variants.

Abstract (croatian)

Proteini MATH-BTB sudjeluju u prometu specifičnih proteina djelujući kao adapteri supstrata E3 ubikvitinskih ligaza. Porodica gena MATH-BTB je prošla značajnu ekspanziju u travama, pri čemu genomi različitih vrsta trava imaju desetke gena MATH-BTB, od kojih neki imaju uloge u temeljnim razvojnim procesima. Nasuprot tome, genom uročnjaka Arabidopsis thaliana ima samo šest MATH-BTB gena: BPM1-6. U ovom radu, alternativno prekrajanje transkripata je istraženo kao potencijalni mehanizam kojim A. thaliana postiže broj i raznolikost proteina MATH-BTB sličan travama. Bioinformatička analiza najnovijeg transkriptoma A. thaliana, AtRTD3, otkrila je 56 izoformi transkripta kodiranih genima BPM, od kojih je 16 kodirano genom BPM2. Iako su se proteini kodirani sa 16 transkripata gena BPM2 razlikovali u sadržaju domena, nedostajala im je raznolikost u MATH domenama koja je prisutna u MATH-BTB proteinima specifičnima za trave. Ekspresije varijanata prekrajanja BPM2.3, BPM2.8, BPM2.9 i BPM2.15 analizirane su u nekim vegetativnim, reproduktivnim i embrionalnim tkivima standardnim i kvantitativnim reakcijama PCR-a. Varijante BPM2.3 i BPM2.15 imale su značajne razlike u razinama ekspresije u različitim tkivima, što ukazuje na moguću ulogu u razvojnim prijelazima. Standardni PCR je proizveo teoretski neočekivane amplikone koji predstavljaju potencijalno nove varijante prekrajanja

• Keywords: MATH-BTB; AtRTD3; alternative splicing; plant development
• Keywords (croatian): MATH-BTB; AtRTD3; alternativno prekrajanje transkripata; biljni razvitak
• Language: english
• URN:NBN: urn:nbn:hr:217:156156
• Project: Number: IP-2022-10-7874; Title: Alternativno prekrajanje gena BPM2 kao mehanizam uspostave funkcionalne raznolikosti porodice proteina MATH-BTB u uročnjaku Arabidopsis thaliana; Title: Alternative splicing of BPM2 as a mechanism for establishing a functional diversity of MATH-BTB protein family in Arabidopsis thaliana; Acronym: SpliceFun; Leader: Nataša Bauer; Jurisdiction: Croatia; Funder: Hrvatska zaklada za znanost; Funding stream: Research Projects
• Study programme: Title: Molecular Biology-University graduate programme; Study programme type: university; Study level: graduate; Academic / professional title: sveučilišni/a magistar/magistra molekularne biologije (sveučilišni/a magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-08-26 12:51:31