Data from: Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides

Background: Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results: We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters and share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or the secretion of peptides. In silico prediction of peptide structures according to NRPS architecture suggests eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas translucens and X. oryzae pv. oryzicola. Further genome mining revealed other novel NRPS genes specific to X. oryzae pv. oryzicola or Xanthomonas sacchari. Conclusions: This study revealed the significant potential of the genus Xanthomonas to produce new non-ribosomally synthesized peptides. Interestingly, this biosynthetic potential seems to be specific to strains of Xanthomonas associated with monocotyledonous plants, suggesting a putative involvement of non-ribosomally synthesized peptides in plant-bacteria interactions.

背景：多种细菌可通过非核糖体肽合成（non-ribosomal peptide synthesis, NRPS）途径合成肽类或其他小分子化合物。NRPS合成机器的保守特征可用于预测所合成多肽的类型，有时甚至可预测其结构。因此，通过对NRPS基因开展计算机模拟分析（in silico）进行细菌基因组挖掘，为发现新的活性非核糖体肽类化合物提供了极具吸引力的途径。黄单胞菌属（Xanthomonas）是一类大型革兰氏阴性菌，可侵染数百种植物并引发病害。迄今为止，该属中已知唯一由NRPS合成的小分子化合物是甘蔗白叶病黄单胞菌（Xanthomonas albilineans）产生的albicidin。本研究旨在通过对近期在已测序的X. albilineans及相关黄单胞菌物种基因组中发现的功能未知的NRPS基因开展计算机模拟分析，评估黄单胞菌属菌株的生物合成潜力。
结果：本研究对所有已公开的黄单胞菌属物种基因组序列中的NRPS基因，以及未公开的水稻白叶枯病菌（Xanthomonas oryzae pv. oryzae）菌株BAI3和黄单胞菌属菌株XaS3的草图基因组序列中的NRPS基因进行了分析。上述两株菌株与甘蔗白叶病黄单胞菌菌株GPE PC73、水稻白叶枯病菌菌株X8-1A及X11-5A均携带新型NRPS基因簇，且共享与NRPS相关的功能基因，包括非蛋白源性氨基酸生物合成所需基因以及肽类分泌相关基因。基于NRPS结构域架构进行的计算机模拟肽结构预测结果显示，共存在8种不同的肽类，每种均由对应的菌株特异性合成。值得注意的是，这8种肽类均无法对应到任何已知基因簇，也与天然产物数据库中的已知化合物无关联。对94株植物病原细菌集合的PCR筛选结果显示，这些新型NRPS基因簇为黄单胞菌属所特有，且在半透明黄单胞菌（Xanthomonas translucens）以及稻黄单胞菌致病变种（X. oryzae pv. oryzicola）中也存在。进一步的基因组挖掘还发现了其他分别特异性存在于稻黄单胞菌致病变种（X. oryzae pv. oryzicola）以及糖黄单胞菌（Xanthomonas sacchari）中的新型NRPS基因。
结论：本研究揭示了黄单胞菌属合成新型非核糖体肽类化合物的巨大潜力。值得注意的是，这类生物合成潜力似乎仅存在于侵染单子叶植物的黄单胞菌菌株中，这提示非核糖体肽类可能参与了植物与细菌的互作过程。