Bioinformatička analiza alkan 1-monooksigenaza otkrivenih u metagenomu sedimenta sjevernog Jadrana

master's thesis

• Title (english): Bioinformatics analysis of alkane 1-monooxygenases discovered in metagenomic samples of sediment from the Adriatic sea
• Author: Domagoj Kolesarić
• Mentor: Jurica Žučko (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2015-09-21, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Istraživanje je provedeno s ciljem funkcionalne karakterizacije dviju vjerojatnih AlkB monooksigenaza otkrivenih u metagenomskom uzorku morskog sedimenta prikupljenog iz pristaništa za tankere u Puli gdje postoji selektivni pritisak alkana iz nafte na mikroorganizme tog staništa. Filogenetska analiza vjerojatnih AlkB monooksigenaza je provedena u programu MEGA 6 kojom se utvrdio evolucijski međuodnos potencijalnih AlkB monooksigenaza iz metagenomskog uzorka i već opisanih AlkB enzima dostupnih u bazama podataka. Funkcionalna karakterizacija je provedena pomoću resursa: CDD, InterPro i UniProt. Funkcionalnom analizom je potvrđeno pripadanje enzima alkan 1-monooksigenazama i određena su aktivna mjesta. Strukturno modeliranje je izvršeno pomoću SWISS-MODEL i I-TASSER web servisa za 3D modeliranje. Neuspješno 3D modeliranje pripisuje se nedostatku homolognih proteina kojima je eksperimentalno određena struktura.

Abstract (english)

This study has been aimed at the functional characterization of two putative alkane 1-monooxygenase discovered in a metagenomic sample of sea sediment collected in the docking bay in Pula where alkanes from oil are present in a higher concentration than in other environments. The phylogenetic analysis of putative alkane 1-monooxygenases has been conducted using MEGA 6 with the goal of determining the evolutionary connection between the putative alkane 1-monooxygenases and the well known AlkB enzymes. The web services CDD, InterPro and UniProt have been used for the functional characterization of the enzymes which determined similarities between the putative proteins and alkane 1-monooxygenases. For the structural modeling the web services SWISS-MODEL and I-TASSER have been used but with little success. This is explained by the lack of homologous proteins with experimentally determined structures.

• Keywords: alkB; alkani; karakterizacija; filogenija
• Keywords (english): alkB; alkanes; characterization; phylogeny
• Language: croatian
• URN:NBN: urn:nbn:hr:159:817190
• Study programme: Title: Molecular Biotechnology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka molekularne biotehnologije (magistar/magistra inženjer/inženjerka molekularne biotehnologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2017-05-05 09:46:27