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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #382660

Research Project: Identification of Novel Management Strategies for Key Pests and Pathogens of Grapevine with Emphasis on the Xylella Fastidiosa Pathosystem

Location: Crop Diseases, Pests and Genetics Research

Title: Assessing strain-level variation among type I restriction-modification systems and methylation patterns in Xylella fastidiosa

item O'Leary, Michael
item Burbank, Lindsey
item Stenger, Drake

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/7/2021
Publication Date: 4/28/2021
Citation: O'Leary, M.L., Burbank, L.P., Stenger, D.C. 2021. Assessing strain-level variation among type I restriction-modification systems and methylation patterns in Xylella fastidiosa. Meeting Abstract.

Interpretive Summary:

Technical Abstract: Xylella fastidiosa is a bacterial plant pathogen with five genetically distinct subspecies that collectively cause disease on a diverse set of host plants. Genomes of X. fastidiosa strains are enriched in genes encoding Restriction-Modification systems, which methylate native DNA and cut unmethylated DNA at specific sequence motifs. Type I Restriction-Modification systems function as a protein complex composed of modification (HsdM), restriction (HsdR), and specificity (HsdS) subunits. Sequence recognition of Type I Restriction-Modification systems depends on HsdS, which contains two target recognition domains (TRDs) that each recognize a 3-5 bp sequence on either side of a 4-7 bp nonspecific spacer. TRD sequences are extraordinarily variable; nucleotide and amino acid sequences of TRDs with different sequence specificities typically share little to no homology. Recombination between hsdS genes can generate new TRD domains combinations, resulting in hsdS alleles with novel sequence specificities. Analysis of genome assemblies of 117 X. fastidiosa strains reveals each strain contains three conserved Type I Restriction-Modification systems, while strains of subspecies multiplex and pauca contain a fourth system absent from other subspecies. Three to twenty-two unique hsdS alleles and two to fourteen unique TRD domains were identified per system. In total, at least 30 combined hsdS allele profiles were identified across X. fastidiosa strains. Distribution of hsdS alleles is associated with MLST classification, but does not correlate with geographic origin or host of isolation. Genomic methylation profiles of twelve X. fastidiosa strains were derived using nanopore sequencing. Two to four methylated motifs characteristic of Type I Restriction-Modification recognition sites (e.g., bipartite) were identified per strain, suggesting some of these systems are active. Variation among bipartite motif sequences was identified within and between X. fastidiosa subspecies and correlates with variation among hsdS alleles, allowing for identified motifs to be tentatively assigned to specific Type I Restriction-Modification systems and hsdS alleles.