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Bacteriophage biology, genomics, and genome evolution

Project Full Title:

Bacteriophage biology, genomics, and the evolution of phage genomes

Project Mentor(s):

Stukey,Joseph

Project Mentor(s) EMail:

stukey@hope.edu

Project Start Date:

5/14/2020

Project End Date:

7/20/2020

Project Description:

A phage is a virus that infects bacterial cells. Initiation of phage infection starts with recognition and attachment to a receptive host cell. Phage genomic DNA is then transferred into the cell where phage genes are expressed that can lead to lysis with release of new phage particles or lysogeny (cell survival with integration of phage genome into host genome). Both developmental processes require multiple molecular interactions between specific phage and host cell components. Research in my lab is focused on understanding basic mycobacteriophage biology and more broadly, phage genome evolution. Mycobacteriophages are phages that infect the bacterial genus, Mycobacterium. I have several projects in various state of completion and several others on my future project list: 1) Identify and characterize phage-host intracellular interactions at the molecular level. We have identified multiple genes in two different mycobacteriophages that impair growth of M. smegmatis when expressed as individual genes. We have preliminary data indicating that for many, the expression of the phage gene results in enlarged cell growth, suggesting the phage protein may interfere with cell division processes. Future research goals include further examining the impact of cytotoxic phage gene expression on host cell growth using a variety of methods including cell staining and microscopic visualization, and testing whether the identified cytotoxic phage gene is essential to the phage during infection. 2) Investigate the growth biology of ‘Cluster K’ mycobacteriophages. Mycobacteriophage members of this cluster are particularly noteworthy because of their general ability to infect a broad range of mycobacterial hosts, often including the noted pathogen, M. tuberculosis. We are investigating growth features of several distinct subgroups of Cluster K1 phages, which may relate to differences in host preference and usage in the environment. Our current findings suggest a subset of K1 mycobacteriophage are optimized for growth at lower temperatures and are well-adapted to an environment with a low host density. We believe there is a link between these growth features and the ability of cluster K mycobacteriophages to recognize a broader range of hosts. This project is near completion. 3) Investigate phage genome evolution. This project seeks to better understand the similarities and differences in genome structure and gene content across known mycobacteriophages, and to address questions on the nature and function of the evolutionary mechanisms that generate the observed genome architecture and genetic diversity. To address these questions, we have designed and constructed pairs of modified phage genomes, that differ in the presence/absence of specific coding information. We have just started testing the specific pairs for impacts on phage growth using a variety of different assays. This work may help us understand how genetic diversity, prevalent in phage genomes, is generated, as well as better understand the modular nature of phage genomes. Future projects of interest: a) investigate how mycobacteriophages recognize and “irreversibly” adsorb onto host cells, including identification of host receptor components of both phage and host, and then transfer their DNA into host cells at initiation of infection, b) investigate mycobacteriophage and/or host properties that contribute to differences in “efficiency of plating” on different mycobacterial host strains or species. All research projects employ a combination of microbiological, molecular, biochemical and bioinformatic methods of analyses. Our findings will provide new and important information on the molecular biology of phage-host cell interactions from mycobacterial host selection through mycobacteriophage infection and a better understanding of the evolution of mycobacteriophage genomes. These opportunities are open to Hope College students only.

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