Unraveling the Mechanisms of Bacterial Transcription through A Multi-tiered Lens Restricted; Files Only

Abstract

Bacterial transcription, a fundamental process essential for cellular function and regulation, presents a complex interplay of mechanisms operating at various hierarchical levels. The significance of this field lies in its broad implications ranging from understanding basic cellular processes to developing targeted therapeutic interventions. This dissertation provides a comprehensive analysis of bacterial transcription dynamics from the base-pair level to the interactions within crowded cellular environments. Employing single-molecule biophysics and molecular biology techniques, I developed a model elucidating transcription kinetics at the base-pair level, informed by the thermal dynamics of transcription bubbles and nascent RNA structures. This model not only predicts transcriptional dynamics with high precision but also sheds light on the effects of transcriptional tension and regulatory proteins on transcription pauses. Further, the study explores the interaction of RNA polymerase with DNA-bound roadblocks, revealing mechanisms of navigational flexibility under genomic constraints. The mechanisms highlight two distinct mechanisms - passive waiting for obstacle dissociation, and active backtracking, recovery, and forceful passage. Additionally, the study reveals the mechanism of a non-canonical, post-termination fate of RNA polymerase, termed as transcriptional recycling. Lastly, the research extends to understanding DNA behavior in crowded cellular milieus, thereby providing insights into chromatin dynamics in vivo. The findings from this research enhance our understanding of transcription processes at a molecular level and provide valuable insights in the realms of genetic regulation.

Table of Contents

1 Introduction

2 Basis of Bacterial Transcription

3 A Model of the Kinetics of Pause-Interspersed Transcription

4 Single-molecule Insights into Transcriptional Trafficking and Regulation of Gene Expression

5 Magnetic Tweezers Experiments Revealed A Hybrid Mechanism for RNAP Transiting through Roadblocks

6 Transcription Recycling–An Overlooked Regulatory Mechanism

7 Transcription in Crowded Cellular Milieus

8 A Phenomenological Model of Crowding Effect on DNA under Tension

9 Conclusion

About this Dissertation

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School	Laney Graduate School
Department	Physics
Degree	Ph.D.
Submission	Dissertation
Language	English
Research Field	Biology, Cell Biology, Microbiology Biology, Molecular
关键词	Single-Molecule Techniques DNA-Protein Interaction Transcription
Committee Chair / Thesis Advisor	David Dunlap, Emory University Laura Finzi, Emory University
Committee Members	Shashank Shekhar, Emory University Daniel B. Weissman, Emory University Eric Weeks, Emory University Marco Cosentino Lagomarsino, University of Milan

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