Table_1_Genome Structure of the Opportunistic Pathogen Paracoccus yeei (Alphaproteobacteria) and Identification of Putative Virulence Factors.DOC

Bacteria of the genus Paracoccus are common components of the microbiomes of many naturally- and anthropogenically shaped environments. One species, Paracoccus yeei, is unique within the genus because it is associated with opportunistic human infections. Therefore, strains of P. yeei may serve as an interesting model to study the transition from a saprophytic to a pathogenic lifestyle in environmental bacteria. Unfortunately, knowledge concerning the biology, genetics and genomic content of P. yeei is fragmentary; also the mechanisms of pathogenicity of this bacterium remain unclear. In this study we provide the first insight into the genome composition and metabolic potential of a clinical isolate, P. yeei CCUG 32053. This strain has a multipartite genome (4,632,079 bp) composed of a circular chromosome plus eight extrachromosomal replicons pYEE1–8: 3 chromids and 5 plasmids, with a total size of 1,247,173 bp. The genome has been significantly shaped by the acquisition of genomic islands, prophages (Myoviridae and Siphoviridae phage families) and numerous insertion sequences (ISs) representing seven IS families. Detailed comparative analysis with other complete genomic sequences of Paracoccus spp. (including P. yeei FDAARGOS_252 and TT13, as well as non-pathogenic strains of other species in this genus) enabled us to identify P. yeei species-specific genes and to predict putative determinants of virulence. This is the first attempt to identify pathoadaptive genetic information of P. yeei and to estimate the role of the mobilome in the evolution of pathogenicity in this species.

副球菌属（Paracoccus）细菌是众多自然环境及人为活动影响环境的微生物组中常见的组成成分。该属中的耶氏副球菌（Paracoccus yeei）较为独特，其与人类机会性感染存在关联，为该属内唯一关联此类感染的物种。因此，耶氏副球菌菌株可作为研究环境细菌从腐生生活方式向致病生活方式转变的理想模型。遗憾的是，目前关于耶氏副球菌的生物学特性、遗传特征及基因组组成的相关认知仍较为零散，其致病机制仍未阐明。

本研究首次对临床分离株耶氏副球菌CCUG 32053的基因组组成与代谢潜力进行了揭示。该菌株拥有多分区基因组（总长度4,632,079 bp），由一条环状染色体与8个染色体外复制子pYEE1–8组成：其中3个为染色体粒（chromids）、5个为质粒（plasmids），总大小为1,247,173 bp。该基因组的演化显著受到基因组岛、前噬菌体（肌病毒科（Myoviridae）与长尾病毒科（Siphoviridae）噬菌体）以及涵盖7个家族的大量插入序列（ISs）的塑造。

通过与其他已完成全基因组测序的副球菌属各物种的完整基因组进行深入比较分析（包括耶氏副球菌FDAARGOS_252、TT13菌株，以及该属其他非致病性菌株），本研究成功鉴定出耶氏副球菌的物种特异性基因，并预测了其推定的毒力决定簇。本研究首次尝试解析耶氏副球菌的致病适应性遗传信息，并评估了可移动基因组（mobilome）在该物种致病性演化过程中的作用。