M. Sc. thesis
Abstract
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
Keywords
actinomycetes;biosynthetic gene cluster;biotechnology;type II polyketide synthase;
Data
Language: |
English |
Year of publishing: |
2021 |
Typology: |
2.09 - Master's Thesis |
Organization: |
UL BF - Biotechnical Faculty |
Publisher: |
[V. Grujić] |
UDC: |
602.3:579.873.7:602.1:681.5:604.4:615.33(043.2) |
COBISS: |
67559427
|
Views: |
392 |
Downloads: |
90 |
Average score: |
0 (0 votes) |
Metadata: |
|
Other data
Secondary language: |
Slovenian |
Secondary title: |
Uporaba programskega orodja antiSMASH pri določanju in analizi genskih skupin poliketidov tipa II |
Secondary 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. |
Secondary keywords: |
Aktinomicete;antiSMASH;biosintezna genska skupina;biotehnologija;poliketid sintaza tipa II; |
Type (COBISS): |
Master's thesis/paper |
Study programme: |
0 |
Thesis comment: |
Univ. v Ljubljani, Biotehniška fak., Študij biotehnologije |
Pages: |
XVII, 131 f. |
ID: |
13040668 |