Castillo José A, Secaira-Morocho Henry, Maldonado Stephanie, Sarmiento Katlheen N
School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Ecuador.
Front Microbiol. 2020 May 20;11:961. doi: 10.3389/fmicb.2020.00961. eCollection 2020.
Over the years, many researchers have reported a great diversity of bacteriophages infecting members of the species complex (RSSC). This diversity has driven bacterial evolution by leading the emergence and maintenance of bacterial defense systems to combat phage infection. In this work, we present an study of the arsenal of defense systems that RSSC harbors and their evolutionary history. For this purpose, we used a combination of genomic, phylogenetic and associative methods. We found that in addition to the CRISPR-Cas system already reported, there are eight other antiphage defense systems including the well-known Restriction-Modification and Toxin-Antitoxin systems. Furthermore, we found a tenth defense system, which is dedicated to reducing the incidence of plasmid transformation in bacteria. We undertook an analysis of the gene gain and loss patterns of the defense systems in 15 genomes of RSSC. Results indicate that the dynamics are inclined toward the gain of defense genes as opposed to the rest of the genes that were preferably lost throughout evolution. This was confirmed by evidence on independent gene acquisition that has occurred by profuse horizontal transfer. The mutation and recombination rates were calculated as a proxy of evolutionary rates. Again, genes encoding the defense systems follow different rates of evolution respect to the rest of the genes. These results lead us to conclude that the evolution of RSSC defense systems is highly dynamic and responds to a different evolutionary regime than the rest of the genes in the genomes of RSSC.
多年来，许多研究人员报告了感染该种系复合体（RSSC）成员的噬菌体具有巨大多样性。这种多样性通过促使细菌防御系统的出现和维持以对抗噬菌体感染，推动了细菌的进化。在这项工作中，我们展示了对RSSC所拥有的防御系统库及其进化历史的研究。为此，我们结合使用了基因组学、系统发育学和关联方法。我们发现，除了已报道的CRISPR-Cas系统外，还有其他八种抗噬菌体防御系统，包括著名的限制修饰系统和毒素-抗毒素系统。此外，我们还发现了第十种防御系统，它专门用于降低细菌中质粒转化的发生率。我们对RSSC的15个基因组中的防御系统的基因得失模式进行了分析。结果表明，与在整个进化过程中更倾向于丢失的其他基因相比，其动态变化倾向于获得防御基因。通过大量水平转移发生的独立基因获取的证据证实了这一点。计算突变率和重组率作为进化速率的代表。同样，编码防御系统的基因相对于RSSC基因组中的其他基因遵循不同的进化速率。这些结果使我们得出结论，RSSC防御系统的进化具有高度动态性，并且与RSSC基因组中的其他基因相比，对不同的进化机制做出反应。
