The influence of sequence context on the evolution of bacterial gene expression Dissertation Thesis

Author(s): Steinrück, Magdalena
Advisor(s): Guet, Calin
Committee Chair(s): Siekhaus, Daria
Committee Member(s): Barton, Nicholas; Ackermann, Martin
Title: The influence of sequence context on the evolution of bacterial gene expression
Affiliation IST Austria
Abstract: Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer.
Publication Title: IST Dissertation
Degree Granting Institution: IST Austria  
Degree: PhD
Degree Date: 2018-10-30
Start Page: 1
Total Pages: 109
DOI: 10.15479/AT:ISTA:th1059
Notes: I am very grateful to my advisor Călin Guet. From the very beginning, he gave me trust and freedom, much more than I could have asked for. He always nurtured my own trust in my capabilities and encouraged me to push my boundaries. Whenever it was important, he was available. When I became a mother, he motivated me to protect the scientist in me, in the light of my new role. To me, Calin s an extraordinary role model as freethinker, intrepid of doing things differently, and nurturing the freshness of the beginner’s mind. I thank my committee members: Martin Ackermann for his inspiring joy in doing science and for moral support; Nick Barton for the rotation in his group, and for his fast and helpful feedback on manuscripts; Jon Bollback for bringing microbial evolutionary biology to IST and for advice on statistics. I thank Daria Siekhaus for her charming way of chairing my defense, and for being an important female role model. I thank all Guet group members for their peer support, for their constructive criticism in our lab meetings, and for many fun hours in the lab. In particular, I thank Maroš Pleška for his critical comments on many versions of the eLife manuscript; Remy Chait for building the macroscopes and for all his little tinkering, making me laugh so often; Kathrin Tomašek for keeping the lab in an organized state; Bella Tomanek for taking the amplification reporter idea to the next level; Tobi Bergmiller for bringing solid molecular microbiology experience to the young lab. I thank Kirti, Bor, Dora, Michael, Allen, Anna, Anna, Moritz, Karin, Marta, Marjon, Guillaume, Bella, Kathrin and many others for engaging and relaxing lunch and coffee breaks. Special thanks go to my collaborators, to Murat Tuğrul for his persistent genuine interest in the experiments, to our data magician Srdjan Sarikas for finding those project hours while being on paternity leave, to Mato Lagator for his efforts in pulling it all together, and to Gašper Tkačik for his sharp and instructive analyses and for his positive attitude. Many thanks to everyone dedicated to building IST Austria. It was a unique experience to be part of it as it was growing from infancy to adolescence. In particular, I thank everyone involved in making it a family-friendly place. I am grateful for the friends I made here, and for the kindergarten community.
Open access: no