magistrsko delo
Anže Lovše (Author), Jernej Jakše (Reviewer), Matej Butala (Mentor), Janez Kokošar (Co-mentor)

Abstract

Bakterija B. thuringiensis serotip israelensis je pomemben biopesticid, ki se uporablja za biološki nadzor komarjev. Izolati te bakterije vključujejo več zunajkromosomskih elementov. Linearni element GIL01 in krožni plazmid pBtic235 nosita zapis za bakteriofaga, ki ob poškodbah DNA preideta iz lizogenega v litični cikel. V magistrskem delu smo s sekvenciranjem RNA raziskali dinamiko transkriptoma med indukcijo litičnega cikla bakteriofaga GIL01 in vpliv na plazmid pBtic235. Za ta namen smo razvili cevovod, ki omogoča jasno in ponovljivo analizo podatkov sekvenciranja RNA. Dokažemo zvečanje izražanja gostiteljevih genov, vključenih v odgovor SOS in popravilo poškodb DNA, ki kažejo vrh izražanja po 30 minutah od indukcije. Podoben vzorec izražanja smo odkrili tudi na plazmidu GIL01, kjer se poviša izražanje regulatornih genov pod promotorjem P1 in na plazmidu pBtic235. Poleg tega smo pokazali, da je nivo izražanja genov za strukturne in litične proteine GIL01 konstanten in se ne spreminja v odvisnosti od časa ali indukcije, kar nakazuje na specifično uravnavanje prepisa slednjih genov. Vzorec izražanja na plazmidu GIL01 nakazuje na dva funkcionalna modula, ki sta najverjetneje ločena transkripta. Kot prvi smo opisali dinamiko transkriptoma po sprožitvi poškodbe DNA v entomopatogenu B. thuringiensis, ki vključuje plazmida GIL01 in pBtic235.

Keywords

Bacillus thuringiensis;temperatni fag GIL01;plazmid pBtic235;dinamika transkriptoma;bioinformatski cevovod;

Data

Language: Slovenian
Year of publishing:
Typology: 2.09 - Master's Thesis
Organization: UL BF - Biotechnical Faculty
Publisher: [A. Lovše]
UDC: 602.3:579.852.11:578.347:601.4:577.21(043.2)
COBISS: 84580867 Link will open in a new window
Views: 287
Downloads: 101
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Other data

Secondary language: English
Secondary title: Analysis of transcriptomic data and visualisation of gene expression dynamics during the lytic life cycle induction of bacteriophage GIL01 in the Bacillus thuringiensis bacterium
Secondary abstract: Bacillus thuringiensis serovar israelensis, an important agent for biological control of mosquitoes, carries many extrachromosomal elements. A linear molecule GIL01 and a circular plasmid pBtic235 correspond to bacteriophages that switch from the lysogenic to the lytic cycle in response to DNA damage. In this master's thesis, we used RNA sequencing to investigate the transcriptome dynamics during the induction of the lytic cycle of bacteriophage GIL01 and the effect on the pBtic235 plasmid. To this end, we developed a pipeline for reproducible and transparent analysis of RNA sequencing data. We detected an upregulation of host SOS response and genes involved in genome maintenance over time, peaking 30 minutes after induction. We observed a similar expression pattern for regulatory genes under the control of the P1 promoter on the GIL01 plasmid and genes on the pBtic235 plasmid. In addition, we detected time- and induction-independent expression of structural and lytic genes of the GIL01 plasmid, suggesting additional regulatory mechanisms. The transcriptional patterns on the GIL01 indicate two functional modules that likely correspond to individual transcripts. Overall, this work provides the first characterisation transcriptome dynamics in an important entomopathogenic strain B. thuringiensis carrying GIL01 and pBtic235 plasmids.
Secondary keywords: temperate phage GIL01;pBtic235 plasmid;transcriptome dynamics;bioinformatics pipeline;
Type (COBISS): Master's thesis/paper
Study programme: 0
Thesis comment: Univ. v Ljubljani, Biotehniška fak., Študij biotehnologije
Pages: XI, 54 f., [27] f.pril.
ID: 13870668