Kinetične simulacije izbranih modulov toksin-antitoksin

Urbič, Zala (author), Hadži, San (mentor)

Moduli toksin-antitoksin so manjši genetski sistemi, ki so množično prisotni v genomih bakterij in arhej. Najpogosteje zaporedje vsebuje zapis za proteina toksin in antitoksin, ter operatorsko regijo, preko katere se uravnava nivo izražanja obeh proteinov. Toksin ustavi celično rast, antitoksin pa tvori kompleks s toksinom in ga inhibira. Antitoksin in kompleksi toksin-antitoksin z različnimi stehiometrijami se vežejo na operatorsko regijo in tako regulirajo nivo izražanja obeh proteinov. V diplomskem delu bomo izvedli stohastično kinetično simulacijo delovanja modelnega sistema toksin-antitoksin tako, da bomo regulacijo delovanja modula opisali kot logično vezje in proučili vpliv parametrov na delovanje sistema. Pri številnih modulih je vezje zasnovano tako, da je regulacija odvisna od molskega razmerja toksin/antitoksin, zato bomo delovanje sistema primerjali s formalnimi vezji z bolj preprosto zasnovo, kjer izražanje ni odvisno od molskega razmerja.

• Language: Slovenian
• Keywords: moduli toksin-antitoksin, regulacija izražanja genov, kinetične simulacije, Gillespie algoritem
• Work type: Bachelor thesis/paper
• Typology: 2.11 - Undergraduate Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2024
• PID: 20.500.12556/RUL-160897-7db3acac-a8cd-8606-16b8-4424034b762e
• COBISS.SI-ID: 206653443
• Publication date in RUL: 05.09.2024

URBIČ, Zala, 2024, Kinetične simulacije izbranih modulov toksin-antitoksin [online]. Bachelor’s thesis. [Accessed 14 April 2025]. Retrieved from: https://repozitorij.uni-lj.si/IzpisGradiva.php?lang=eng&id=160897

Secondary language

• Language: English
• Title: Kinetic simulations of selected toxin-antitoxin modules

Abstract

Toxin-antitoxin modules are small genetic systems that are widely present in the genomes of bacteria and archaea. Most often, the sequence contains a code for a toxin and an antitoxin protein, along with an operator region through which the expression levels of both proteins are regulated. The toxin halts cell growth, while the antitoxin forms a complex with the toxin and inhibits it. Antitoxin and toxin-antitoxin complexes with various stoichiometries bind to the operator region, thereby regulating the expression levels of both proteins. In this thesis, we will conduct a stochastic kinetic simulation of the functioning of a model toxin-antitoxin system by describing the regulation of the module's operation as a logic circuit and then study the impact of parameters on the system's functioning. In many modules, the circuit is designed so that regulation depends on the molar ratio of toxin/antitoxin, so we will compare the operation of the sistem with formal circuits with a simpler design, where expression is not dependent on the molar ratio.

• Keywords: toxin-antitoxin modules, regulation of gene expression, kinetic simulations, Gillespie algorithm