Hua, Jianfei
(2016)
Capsid Structure and DNA Packing in Jumbo Bacteriophages.
Doctoral Dissertation, University of Pittsburgh.
(Unpublished)
Abstract
Jumbo phages, the phages with genome length larger than 200 Kbp, are extreme examples of how the capsid and genome coordinate in evolution. To learn the mechanism of capsid size change during evolutionary time, the capsid and DNA of several jumbo phages were characterized.
The capsid structure and protein of a T=25 Sphingomonas paucimobilis phage PAU and a T=28 Escherichia coli phage 121Q were studied in detail. The high resolution cryo-EM structures show that the major capsid proteins (MCPs) of both phages adopt the HK97 fold which is conserved in all solved tailed phage MCP structures. The capsids contain decoration proteins with unprecedented shape and location. A pentameric protein structure is attached on the inner surface of the pentamer in both capsids. The PAU capsid has arcs of density located on hexamers surrounding the pentons, which may bend the conformation of the subunit it interacts with to improve capsid stability. 121Q capsid contains dimeric density near the local 2-fold symmetry axes and knob-like density at the middle of the hexamer, which may participate in forming the capsid shell because the 121Q MCP leaves holes at the two locations. Both capsids contain a number of internal proteins whose roles are not clear.
The study on the jumbo phage DNA started with showing that partial modification of the cytosine in PAU and phage G DNA significantly slowed the phage DNA in electrophoresis. A new technique was developed to quantify the effect of base modifications in large DNA in electrophoresis, with which reliable measurements of the chromosome size of our jumbo phage collection were made. Jumbo phages have larger terminal redundancy and lower DNA packing density compared to small and mid-sized phages. The result on the DNA packing density in different sizes of phages reveals a negative correlation between the capsid size and the DNA packing density. We explain this relationship by a model based on the strength limit between the capsomers of the capsid shell.
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| Item Type: |
University of Pittsburgh ETD
|
| Status: |
Unpublished |
| Creators/Authors: |
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| ETD Committee: |
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| Date: |
6 June 2016 |
| Date Type: |
Publication |
| Defense Date: |
30 March 2016 |
| Approval Date: |
6 June 2016 |
| Submission Date: |
12 April 2016 |
| Access Restriction: |
No restriction; Release the ETD for access worldwide immediately. |
| Number of Pages: |
197 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
Dietrich School of Arts and Sciences > Biological Sciences |
| Degree: |
PhD - Doctor of Philosophy |
| Thesis Type: |
Doctoral Dissertation |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
Bacteriophage, Jumbo phages, Capsid size, Triangulation Number, Capsid structure, Major capsid protein, Decoration protein, Internal protein, DNA packing density, Terminal redundancy, Capsid Evolution, PAU, 121Q, P1 |
| Date Deposited: |
06 Jun 2016 16:43 |
| Last Modified: |
15 Nov 2016 14:32 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/27666 |
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