USDA Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, California, USA.
Appl Environ Microbiol. 2023 Jan 31;89(1):e0187322. doi: 10.1128/aem.01873-22. Epub 2023 Jan 4.
Xylella fastidiosa is an important bacterial plant pathogen causing high-consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect many host plants, there is significant variability between strains regarding virulence on specific host plant species and other traits. Natural competence and horizontal gene transfer are believed to occur frequently in X. fastidiosa and likely influence the evolution of this pathogen. However, some X. fastidiosa strains are difficult to manipulate genetically using standard transformation techniques. Several type I restriction-modification (R-M) systems are encoded in the X. fastidiosa genome, which may influence horizontal gene transfer and recombination. Type I R-M systems themselves may undergo recombination, exchanging target recognition domains (TRDs) between specificity subunits () to generate novel alleles with new target specificities. 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. Forty-four unique TRDs were identified among 50 alleles, which are arrayed in 31 allele profiles that are 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 complements 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, these data suggest genes recombine among strains and/or unknown donors, and the resulting TRD reassortment establishes differential epigenetic modifications across lineages. Economic 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 more insight into X. fastidiosa genetic diversity and horizontal gene transfer, but the mechanics of genomic recombination in natural settings and the 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.
韧皮部坏死无枝菌是一种重要的细菌性植物病原体，可导致全球农业作物发生高后果疾病。尽管作为一个物种，韧皮部坏死无枝菌可以感染许多宿主植物，但不同菌株在特定宿主植物物种上的毒力和其他特性方面存在显著差异。天然感受态和水平基因转移被认为在韧皮部坏死无枝菌中经常发生，并且可能影响该病原体的进化。然而，一些韧皮部坏死无枝菌菌株使用标准转化技术进行遗传操作较为困难。几种 I 型限制修饰（R-M）系统编码在韧皮部坏死无枝菌基因组中，这可能影响水平基因转移和重组。I 型 R-M 系统本身可能会发生重组，在特异性亚基之间交换靶标识别结构域（TRD），以产生具有新靶特异性的新等位基因。在这项研究中，比较了代表所有已知亚种和 32 个序列类型的 129 个韧皮部坏死无枝菌基因组组装中的几个保守的 I 型 R-M 系统。在 50 个等位基因中鉴定出 44 个独特的 TRD，这些 TRD 排列在 31 个等位基因谱中，通常在菌株的单系聚类中保守。在特定菌株的 I 型 R-M 系统中鉴定出失活突变，表明在韧皮部坏死无枝菌中功能性 I 型 R-M 系统的互补具有异质性。在 20 个韧皮部坏死无枝菌菌株中表征了基因组 DNA 甲基化模式，并与 I 型 R-M 系统等位基因谱相关。总体而言，这些数据表明基因在菌株之间和/或未知供体中重组，并且由此产生的 TRD 重排在谱系中建立了不同的表观遗传修饰。由于韧皮部坏死无枝菌，对农业生产的经济影响在美洲、欧洲和亚洲部分地区非常严重。尽管对这种病原体进行了长期研究，但关于韧皮部坏死无枝菌的生物学、致病性和进化的某些基本问题仍未得到解答。全基因组测序的广泛开展开始提供更多关于韧皮部坏死无枝菌遗传多样性和水平基因转移的信息，但自然环境中基因组重组的机制以及这在多大程度上直接影响细菌表型（如植物宿主范围）尚不清楚。基因组甲基化是水平基因转移和细菌重组的一个重要因素，但在韧皮部坏死无枝菌中尚未得到全面研究。本研究描述了广泛的韧皮部坏死无枝菌菌株中与 I 型限制修饰系统相关的甲基化，为通过表观遗传学更好地理解韧皮部坏死无枝菌的生物学和进化奠定了基础。
