Natural recombination among Type I restriction-modification systems creates diverse genomic methylation patterns among Xylella fastidiosa strains

Authors: O'Leary, Michael; Burbank, Lindsey

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2022
Publication Date: 1/4/2023
Citation: O'Leary, M.L., Burbank, L.P. 2023. Natural recombination among Type I restriction-modification systems creates diverse genomic methylation patterns among Xylella fastidiosa strains. Applied and Environmental Microbiology. 89(1). https://doi.org/10.1128/aem.01873-22.
DOI: https://doi.org/10.1128/aem.01873-22

Interpretive Summary: Xylella fastidiosa is an important bacterial pathogen of plants causing high consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect an extremely broad range of host plants, significant variability exists between strains regarding which host plants are most impacted. Some of this variability is thought to be due to recombination between X. fastidiosa strains. Bacterial genomic DNA often contains chemical modifications such as the addition of methyl groups at specific sequences, and the pattern of modification may be specific to a species or strain of bacteria. For recombination to occur between different bacterial strains, patterns of DNA modification need to be similar between the two strains or else the incoming DNA may be recognized as foreign material and degraded by the cell. DNA modification patterns were compared across 129 strains of X. fastidiosa to better understand the potential for recombination between strains. Specific patterns of DNA modification were identified and associated with related groups of strains. Many of the genes responsible for DNA modification systems were also found to be inactivated in certain X. fastidiosa strains but not others. This information adds to our understanding of how different strains of X. fastidiosa might be able to recombine with each other based on how closely related they are.

Technical Abstract: Xylella fastidiosa is an important bacterial pathogen of plants causing high consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect an extremely broad range of host plants, significant variability exists between strains and subspecies groups in virulence on specific host plant species, and other traits such as growth habits. Natural competence and horizontal gene transfer are believed to occur frequently in X. fastidiosa, and likely influences the evolution of this pathogen. However, some X. fastidiosa strains are extremely difficult or impossible to manipulate genetically using standard transformation techniques. Several restriction-modification systems are encoded in the X. fastidiosa genome, including multiple Type I R-M systems that may influence horizontal gene transfer and recombination. In this study, several conserved Type I R-M systems were compared across 129 X. fastidiosa genome assemblies representing all known subspecies and 32 sequence types. Considerable allelic variation among strains was identified among the single specificity subunit (hsdS) of each Type I R-M system, with a unique hsdS allele profile generally conserved within a monophyletic cluster of strains. Inactivating mutations were identified in Type I R-M systems of specific strains, showing heterogeneity in the complement of functional Type I R-M systems across X. fastidiosa. Genomic DNA methylation patterns were characterized in 20 X. fastidiosa strains and associated with Type I R-M system allele profiles. Overall, this study describes epigenetic modifications in X. fastidiosa associated with functional Type I R-M systems and characterizes the diversity in these systems across X. fastidiosa lineages.