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

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. ImportanceEconomic impacts on agricultural production due to X. fastidiosa have been severe in the Americas, Europe, and parts of Asia. Despite a long history of research on this pathogen, certain fundamental questions regarding the biology, pathogenicity, and evolution of X. fastidiosa have still not been answered. Wide scale whole genome sequencing has begun to provide a more insight into X. fastidiosa genetic diversity and horizontal gene transfer but the mechanics of genomic recombination in natural settings and extent to which this directly influences bacterial phenotypes such as plant host range are not well understood. Genome methylation is an important factor in horizontal gene transfer and bacterial recombination that has not been comprehensively studied in X. fastidiosa. This study characterizes methylation associated with Type I restriction-modification systems across a wide range of X. fastidiosa strains and lays the groundwork for a better understanding of X. fastidiosa biology and evolution through epigenetics.