Molecular evolution in plant pathogens and mutualistic bacteria

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All organisms exist within a complex network of interdependencies between species, including predator-prey, parasitic, mutualistic and symbiotic relationships. These interactions in turn shape ecological communities for both natural systems and crop species. In addition to pathogen-host interactions, plants have developed mutually beneficial interactions with soil microbes, through which they can gain improved access to nutrients and potentially lessen the impact of microbial pathogens. An understanding of the mechanisms facilitating interactions with both pathogenic and beneficial microbes can have a direct impact on crop management strategies and agricultural practices. The proposal research will investigate plant-microbial interactions using a comparative genomics approach, augmented by RNA sequencing and proteomics analysis. Both beneficial and pathogenic bacteria will be investigated, and links between symbiosis and pathogenicity will be explored. The proposed research builds directly upon previous work in the McConkey lab, which has combined computational and wet-lab techniques to investigate protein function, structure, evolution, and interaction. Loss of agricultural crops due to pathogens is an ongoing problem worldwide, and has broad impacts on health, society, and local and national economies. Conversely, beneficial bacteria have been shown to enhance plant growth and production, and can markedly reduce the impact of plant pathogens. Better understanding the interactions of pathogenic and beneficial bacteria with plants will have direct impacts on crop management and pathogen control strategies. In particular, pathogen control strategies can be targeted to have maximum impact on specific pathogens, while having a reduced impact on beneficial soil bacteria. To do this effectively, we require an in-depth understanding on the interactions between plants, pathogens, and beneficial bacteria. The research proposed in this grant will help provide this knowledge, and importantly may identify new molecular targets for controlling plant pathogens. Identification of novel mechanisms of pathogenicity can in turn lead to novel, targeted strategies for pathogen management. As our recent study on human pathogens has shown (Doxey and McConkey, 2013), there are numerous highly specific mechanisms of pathogenicity that can be uncovered using comparative genomics strategies. We will apply similar methodology to plant pathogens and beneficial bacteria to identify proteins that mediate plant-bacterial interactions. To complement genomics based analyses, high-throughput proteomics and RNA-sequencing will also be used to identify bacterial effector proteins for both pathogens and beneficial bacteria.