Watanabe Takayasu, Shibasaki Masaki, Maruyama Fumito, Sekizaki Tsutomu, Nakagawa Ichiro
Laboratory of Food-borne Pathogenic Microbiology, Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.
Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
PLoS One. 2017 Aug 24;12(8):e0183752. doi: 10.1371/journal.pone.0183752. eCollection 2017.
The oral bacterial species Porphyromonas gingivalis, a periodontal pathogen, has plastic genomes that may be driven by homologous recombination with exogenous deoxyribonucleic acid (DNA) that is incorporated by natural transformation and conjugation. However, bacteriophages and plasmids, both of which are main resources of exogenous DNA, do not exist in the known P. gingivalis genomes. This could be associated with an adaptive immunity system conferred by clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes in P. gingivalis as well as innate immune systems such as a restriction-modification system. In a previous study, few immune targets were predicted for P. gingivalis CRISPR/Cas. In this paper, we analyzed 51 P. gingivalis genomes, which were newly sequenced, and publicly available genomes of 13 P. gingivalis and 46 other Porphyromonas species. We detected 6 CRISPR/Cas types (classified by sequence similarity of repeat) in P. gingivalis and 12 other types in the remaining species. The Porphyromonas CRISPR spacers with potential targets in the genus Porphyromonas were approximately 23 times more abundant than those with potential targets in other genus taxa (1,720/6,896 spacers vs. 74/6,896 spacers). Porphyromonas CRISPR/Cas may be involved in genome plasticity by exhibiting selective interference against intra- and interspecies nucleic acids.
口腔细菌牙龈卟啉单胞菌是一种牙周病原体，其基因组具有可塑性，可能是由与通过自然转化和接合作用整合的外源脱氧核糖核酸（DNA）发生同源重组所驱动。然而，已知的牙龈卟啉单胞菌基因组中不存在噬菌体和质粒，而它们都是外源DNA的主要来源。这可能与牙龈卟啉单胞菌中由成簇规律间隔短回文重复序列（CRISPR）和CRISPR相关（cas）基因赋予的适应性免疫系统以及诸如限制修饰系统等固有免疫系统有关。在先前的一项研究中，预测牙龈卟啉单胞菌CRISPR/Cas的免疫靶标很少。在本文中，我们分析了51个新测序的牙龈卟啉单胞菌基因组以及公开可得的13个牙龈卟啉单胞菌基因组和46个其他卟啉单胞菌属物种的基因组。我们在牙龈卟啉单胞菌中检测到6种CRISPR/Cas类型（根据重复序列的序列相似性分类），在其余物种中检测到12种其他类型。在卟啉单胞菌属中具有潜在靶标的卟啉单胞菌CRISPR间隔序列比在其他属分类群中具有潜在靶标的间隔序列丰富约23倍（1720/6896个间隔序列对74/6896个间隔序列）。卟啉单胞菌CRISPR/Cas可能通过对种内和种间核酸表现出选择性干扰而参与基因组可塑性。
