Genske nakupine za proizvodnju sekundarnih metabolita u genomima bakterija iz roda Pseudomonas: identifikacija mehanizama inhibicije patogenih vodenih plijesni

master's thesis

• Title (english): Biosynthetic gene clusters for the production of secondary metabolites in the genomes of Pseudomonas bacteria: identification of inhibition mechanisms of pathogenic water molds
• Author: Karla Vasari
• Mentor: Jurica Žučko (mentor)
• Mentor: Ana Bielen (pomoć pri izradi, neposredni voditelj)
• Committee member: Marina Cvjetko Bubalo (predsjednik povjerenstva)
• Committee member: Ana Bielen (član povjerenstva)
• Committee member: Janko Diminić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2023-12-21, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Patogene vodene plijesni Aphanomyces astaci i Saprolegnia parasitica uzročnici su velikih šteta u akvakulturi pa je potrebno razviti ekološki prihvatljive metode njihove kontrole. Cilj ovog rada bio je in silico metodama identificirati biosintetske genske nakupine (engl. Biosynthetic Gene Clusters, BGC) za proizvodnju sekundarnih metabolita u genomima bakterija iz roda Pseudomonas. Sekvencirano je devet genoma okolišnih Pseudomonas izolata, od kojih je za šest ranije utvrđeno da inhibiraju A. astaci i/ili S. parasitica, a tri nisu pokazivala inhibicijski učinak. Nakon sastavljanja i analize genoma odabrana su dva filogenetski srodna izolata, inhibitor P. cerasi PL3-3 i ne-inhibitor P. syringae AT16-2, za identifikaciju BGC-a. U oba genoma je identificirano najviše BGC-a za proizvodnju siderofora (3) i lipopeptidnih biosurfaktanata (2). Kod inhibitora su pronađeni BGC za proizvodnju siringolina A, secimida, peptida FR901228, ektoina i neidentificiranog NRP-a, a kod neinhibitora nisu pa se može pretpostaviti da su ovi spojevi ključni za inhibicijsku aktivnost izolata P. cerasi PL3-3.

Abstract (english)

The pathogenic water moulds Aphanomyces astaci and Saprolegnia parasitica cause major losses in aquaculture, making it necessary to develop environmentally friendly control methods. The aim of this study was to identify in silico biosynthetic gene clusters (BGC) in the genomes of Pseudomonas bacteria that produce secondary metabolites. Nine genomes of Pseudomonas isolates were sequenced, six of which had previously shown an inhibitory effect on A. astaci and/or S. parasitica and three of which showed no inhibitory effect. After genome assembly and analysis, two phylogenetically related isolates, the inhibitor P. cerasi PL3-3 and the non-inhibitor P. syringae AT16- 2, were selected for the identification of BGCs. In both genomes, most BGCs were identified for the production of siderophores (3) and lipopeptide biosurfactants (2). BGCs producing syringolin A, secimide, peptide FR901228, ectoine and unidentified NRP were found in the inhibitor but not in the non-inhibitor, suggesting that these compounds may be crucial for the inhibitory activity of the P. cerasi PL3-3 isolate.

• Keywords: Aphanomyces astaci; Saprolegnia parasitica; antiSMASH; biosintetske genske nakupine (engl. Biosynthetic Gene Clusters; BGC); in silico analize genoma
• Keywords (english): Aphanomyces astaci; Saprolegnia parasitica; antiSMASH; biosynthetic gene clusters (BGC); in silico genome analysis
• Language: croatian
• URN:NBN: urn:nbn:hr:159:909094
• 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: Open access
• Created on: 2024-06-05 07:56:13