Bacteriophage-host interactions are influenced by genetic variation in genomic islands

Education Level

Undergraduate

Faculty Advisor(s)

Professor Marcia Marston

Academic Department(s)

Biology

Comments

This research was presented at the 2024 Rhode Island Summer Undergraduate Research Symposium, held on Friday, July 26, at the University of Rhode Island and supported by the National Science Foundation.

Symposium Date

2024

Abstract

T7-like bacteriophages that infect coastal cyanobacteria are ubiquitous in marine environments, where they impact the composition, evolution, and mortality of their hosts. Often these phages are very host-specific using tail-fibers, known as receptor binding proteins, to recognize and attach to lipopolysaccharide (LPS) features on the host's surface. Previous studies have described the T7-like phage genome as having three genomic islands where an abundance of horizontal gene transfer occurs. In particular, tail-fibers genes are observed to have the highest rate of transfer. We have isolated and sequenced 24 Synechococcus-infecting T7-like phages from Narragansett Bay, Rhode Island to identify genes that may be important in phage-host interactions. In this study we aimed to characterize a gene in the second genomic island that was extremely divergent among the sequenced isolates with only 14% to 47% predicted amino acid sequence identity. To explore possible functions of the gene, we utilized AlphaFold2 to make 3D models of single polypeptides and their corresponding homotrimers. Despite the amino acid variation, the predicted protein structures were all very similar, with the predicted shape suggesting that these proteins might serve as receptor binding proteins. Host range analysis was performed by setting up pairwise cross-infection assays using 6 Synechococcus cell types. A distinct infection pattern was seen; all the phages could infect a Synechococcus in clade I (MV1320), but only some could infect a Synechococcus in clade VI (WH8018). An infection kinetics experiment was then conducted to assess how the different gene variants may influence phage infection dynamics, such as attachment to cells and replication in host cells. For this assay, four T7-like phages were added to host cells (MV1320) and multiple samples were collected over a 48-hour period. At each time point the cells were removed via filtration and the extracellular DNA was quantified using a qPCR assay. We found the four phages showed different levels of both attachment to the cells and replication within the host cells. Further analysis of the function and content of genes located in the other islands will aid in the understanding of how the exchange of genetic material between phages impacts interactions with host cells.

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