Application of antiSMASH tool for identification and analysis of type II polyketide gene clusters

Grujić, Vladimir (author), Petković, Hrvoje (mentor), Starcevic, Antonio (co-mentor)

Actinomycetes are one of the most economically and biotechnologically valuable prokaryotes considering that they produce wide range of bioactive secondary metabolites, such as antibacterials, antitumor agents and immunosuppressive agents. Aromatic polyketides are produced by type II polyketide synthases (type II PKSs). In recent years, genome mining has seen broad applications in identifying and characterizing new compounds, and metabolic engineering approaches have been applied to generate new analogues. The secondary metabolite analysis shell-antiSMASH has assisted researchers in this search for new potential bioactive compounds. Using the antiSMASH, we minned and analyzed 34 Acintomycetes genomes which contained type II PKS identified. We identified potentially new metabolites encoded BGCs from 9 Actinomycetes strains, for which we propose to produce novel structures. We observed that for predicting the structure of metabolite encoded by analysed BGC, the most important roles have the enzymes involved in tailoring modifications, especially oxygenases. We have demonstrated that antiSMASH represents the reliable in silico method for the analysis of Type II PKS BGC in case when good quality of genomes are available. Wet laboratory experiments would have to be carried out to confirm in silico predictions, which were generated in the scope of this work

• Language: English
• Keywords: Actinomycetes, antiSMASH, biosynthetic gene cluster, biotechnology, type II polyketide synthase
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: BF - Biotechnical Faculty
• Place of publishing: Ljubljana
• Publisher: [V. Grujić]
• Year: 2021
• PID: 20.500.12556/RUL-127647
• UDC: 602.3:579.873.7:602.1:681.5:604.4:615.33(043.2)
• COBISS.SI-ID: 67559427
• Publication date in RUL: 18.06.2021

Secondary language

• Language: Slovenian
• Title: Uporaba programskega orodja antiSMASH pri določanju in analizi genskih skupin poliketidov tipa II

Abstract

Aktinomicete so ekonomsko in biotehnološko ene najbolj uporabnih prokariontov, saj so sposobni proizvajati sirok nabor biolosko aktivnih sekundarnih metabolitov, kot so antibiotiki, protirakaste ucinkovine, imunosupresivne ucinkovine in encime. Aromatski poliketidi nastajajo na poliketid sintazah tipa II (PKS tipa II). V zadnjih letih se je na področju odkrivanja in karakterizacije novih spojin, kot tudi na področju metabolnega inzenirstva mocno razsirila uporaba genomskega rudarjenja. Pri tem si raziskovalci pomagajo s programsko opremo antiSMASH (angl. antibiotics and secondary metabolite analysis shell), ki pomaga raziskovalcem v iskanju novih bioaktivnih spojin. S programom antiSMASH smo pregledali in analizirali 34 genomov aktinomicet kje smo identificirali PKS tipa II biosintezne genske skupine. Izbrali smo biosintezne genske skupin devetih aktinomicet, za katere predvidevamo, da so odgovorni za sintezo potencialno novih metabolitov z novo strukturo. Spoznali smo, da imajo pri napovedovanju strukture neznanih metabolitov najpomembnejšo vlogo encimi vključeni v pozne stopnje modifikacij, med katerimi so najpomembnejse oksigenaze. Dokazali smo, da anti-SMASH predstavlja zanesljivo in silico metodo za analizo BGC (biosinteznih genskih skupin) PKS tipa II, ko so nam na voljo genomi z visoko kakovostjo, in ce je podobnost genov in homologov iz podobnih BGC na nivoju aminokislin dovolj visoka. Za potrditev rezultatov pridobljenih z metodami, ki smo jih uporabljali v tej magistrski nalogi, je potrebno izvesti praktične eksperimente.

• Keywords: Aktinomicete, antiSMASH, biosintezna genska skupina, biotehnologija, poliketid sintaza tipa II