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

By: Steinrück, Magdalena
Material type: TextTextPublisher: IST Austria 2018Online resources: Click here to access online
Contents:
Abstract
Acknowledgements
List of Symbols/Abbreviations
Preface
1 Introduction
2 Complex Chromosome Neighborhood effects Determine the Adaptive Potential of a Gene under Selection
3 Context-Specific Effects of Promoter Mutations
4 The Distribution and Prediction of Promoter Function in a Random Sample of a Full Sequence Space
5 Conclusions
References
6 Appendix
Summary: 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.
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Thesis

Abstract

Acknowledgements

List of Symbols/Abbreviations

Preface

1 Introduction

2 Complex Chromosome Neighborhood effects Determine the Adaptive Potential of a Gene under Selection

3 Context-Specific Effects of Promoter Mutations

4 The Distribution and Prediction of Promoter Function in a Random Sample of a Full Sequence Space

5 Conclusions

References

6 Appendix

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.

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