EAGER: Identifying the genetic determinants of plasmid-dependent phage host range

Harvard University, Cambridge MA

Investigators

Abstract

Many functional genes, including genes involved in antibiotic resistance, are found on plasmids in bacteria. These plasmids are able to move from one bacterium to another, through horizontal gene transfer. Certain viruses, bacteriophages, exploit these plasmids to infect bacteria. A recent discovery suggests that these plasmid-dependent phages are common and readily discoverable from the environment. This project aims to leverage a unique collection of novel plasmid-dependent phages to answer outstanding questions related to the biology and evolution of this unusual group of viruses. In particular, this project concerns the identification of genetic factors that determine host range of plasmid-dependent phages. Broader impacts of the project include toolsets for high-throughput characterization of phages, as well as protocols and software that will aid the community more broadly. Students will be trained in bioinformatic analysis and will be involved in the phage discovery part of the research project. The enhanced understanding of the molecular biology of these phages and host range may eventually provide novel solutions to the problem of antibiotic resistance. Many functional genes, including determinants of antibiotic resistance, are readily transferred on conjugative plasmids. Plasmid-dependent phages appear to target these vectors of gene transfer, possibly exerting a negative frequency dependent selective pressure on traits such as antibiotic resistance. The investigators aim to leverage their unique collection of novel plasmid-dependent phages to answer outstanding questions related to the biology and evolution of this unusual group of viruses. Employing a receptor-guided discovery platform using engineered target bacteria for high-throughput discovery, the investigators have identified 51 new plasmid-dependent phages that are dependent on IncP conjugative plasmids, share between 82.5% - 99% average nucleotide identity, and contain no accessory genes. However, despite their close genetic identity, the phages demonstrate large differences in host range that is independent of plasmid presence. One aim of the research project is to interrogate how small genetic differences can manifest as large changes in host specificity using bioinformatics and engineering and testing mutations that result in changes in host range. Another aim is to determine the genetic mechanisms of the variation within host range and shed light on how the IncP conjugative plasmid phages are able to adapt to the diverse biology and physiology, and perhaps evade the defenses, of a wide range of bacterial hosts. More broadly, these experiments will illuminate the genetic mechanisms by which phages adapt to new hosts via allelic variation, and how the hosts, in turn, evade and defend against phages. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.