A Single Molecule Study of Two Bacteriophage Epigenetic Switches Open Access

Abstract

Epigenetic switches allow organisms to evolve into different states by activating/repressing different sets of genes without mutations of the underlying DNA sequence. The study of epigenetic switches is very important to understand the mechanism of human development, the origin of cancer, mental illness and fundamental processes such as gene regulation.
The coliphage λ epigenetic switch, which allows switching from lysogeny to lysis, has been studied for more than 50 years as a paradigm, and has recently received renewed attention. Atomic force microscopy (AFM) was used here to show that the λ repressor oligomerizes on DNA, primarily as a dodecamer, to secure a DNA loop, which is the basis of the λ switch. This study also provides support for the idea that specifically bound repressor stabilizes adjacent, non-specifically bound repressor molecules, which confers robustness to the switch.
186 is a member of a different coliphage family. One of the major differences between the two coliphage families is that lambda phages can be induced to switch from the lysogenic to the lytic state by UV radiation, but most coliphages of P2 family, to which 186 belongs, cannot. Interaction between coliphage 186 repressor and DNA is characterized by AFM and tethered particle microscopy (TPM). To expedite analysis of the AFM data, MatLab codes were written to automate the laborious, manual tracing procedures. The programs automatically recognize DNA segments and protein particles in an image, in order to measure the DNA length and position of bound particles as well as their height, diameter and volume. Application of these algorithms greatly improved the efficiency of AFM analysis. It was showed that 186 CI dimers form heptameric wheels, which induce DNA wrapping and different kinds of DNA looping producing various conformations of nucleoprotein complexes. Information about the dynamics of DNA wrapping and looping on 186 CI particles was also obtained by TPM.

Table of Contents

Table of Contents

Chapter 1

Introduction ................................................................................................1
§1.1 Epigenetic switches ...............................................................................1
§1.2 Prophage and the λ epigenetic switch .......................................................3
§1.3 The 186 prophage .................................................................................6
§1.3.1 Transcriptional interference ..................................................................6
§1.3.2 Coliphage 186 ....................................................................................8
§1.3.3 Chromatin and DNA wrapping ...............................................................10

Chapter 2 AFM Studies of λ Repressor Oligomers Securing DNA Loops
§2.1 Background .........................................................................................12
§2.2 Material and method .............................................................................15
§2.2.1 Material ...........................................................................................15
§2.2.2 DNA contour length on mica surface ......................................................17
§2.3 Result and discussion ............................................................................19
§2.3.1 DNA contour length measured by AFM ...................................................19
§2.3.2 Specific binding to operator sites ..........................................................21
§2.3.3 Weak affinity for the OR3 operator site ..................................................23
§2.3.4 Multiple operators may recruit dimers .....................................................24
§2.3.5 Loop equilibrium .................................................................................26
§2.3.6 Volume calibration ..............................................................................27
§2.3.7 Loop closures are prevalently dodecamers ..............................................30
§2.3.8 Alternative loop closures .....................................................................33
§2.3.9 Conclusion ........................................................................................35

Chapter 3 AFM and TPM Studies of DNA wrapping and looping of phage 186
§3.1 Background and introduction ...................................................................37
§3.2 Material and method ..............................................................................39
§3.2.1 AFM sample preparation .......................................................................39

§3.2.2 TPM sample preparation .......................................................................40
§3.2.3 Measurement of wheel diameter ............................................................41
§3.3 Result and discussion .............................................................................45
§3.3.1 Conformation of basic model .................................................................45
§3.3.1.1 The 186 repressor and its assembling ...................................................45
§3.3.1.2 CI regulated mechanism ....................................................................50
§3.3.2 Pseudo site on FL ...............................................................................55
§3.3.3 Asymmetric DNA wrapping on pR region ...................................................57
§3.3.4 DNA wrapping/unwrapping ....................................................................58
§3.3.5 TPM study of DNA wrapping and looping ..................................................58
§3.3.6 DNA looping .......................................................................................62
§3.3.7 Other CI binding forms and non-specific binding ........................................70

Chapter 4 Automated DNA segmentation and protein recognition from AFM images
§4.1 Background.…………………………………………....................................……….……………71
§4.2 Method and algorithm……………………………………………………..................................73
§4.2.1 Filtering…………………………………………………………........................................…..73
§4.2.2 Threshold and segmentation……………………………………….................................74
§4.2.3 Thinning and selection of DNA skeleton…………………………..............................77
§4.2.4 DNA length estimation ………………………..................................………………...….80
§4.3 Application and programming………………………….............................………………..…82
§4.3.1 DNA tracing …………………………………………..….......................................………..82
§4.3.2 Masking and interactive modifying …………..…………...........................…………...83
§4.3.3 DNA contour length measuring……………………..………………...............................87
§4.3.4 Automatic particle analysis on DNA or surface …..………….......................………90
§4.3.5 Auto-analysis of DNA protein interaction ……………...…………….........................94
§4.3.6 Data conversion…………………………………………………........................................ 96
§4.4 Discussion ………………………………………….........................................…………………96

References ………………………………………………...……………………..................................…97

Apendices …………………......................................………………………………………………….110
Appendix A AFM studies of λ repressor oligomers securing DNA loops .....................111
Appendix B The lambda bacteriophage epigenetic switch: new insight from

single-molecule microscopy ................……………………………………….....................…...119
Appendix C A missing link between transcription factors and nucleosomes:

the bacteriophage 186 CI repressor wraps and loops DNA ……….............................139
Appendix D Matlab code for protein particle measurement and simulation ................148
Appendix E Matlab code for automated tracing and DNA protein analysis programs
155

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School	Laney Graduate School
Department	Physics
Degree	PhD
Submission	Dissertation
Language	English
Research Field	Physics, General Biology, Molecular Biophysics, General
Keyword	lysogenetic DNA coliphage epigenetics TPM lambda repressor 186 DNA tracing AFM
Committee Chair / Thesis Advisor	Finzi, Laura, Emory University
Committee Members	Warncke, Kurt, Emory University Dunlap, David, Emory University Rasnik, Ivan, Emory University Berland, Keith, Emory University

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