The variation in Mycoplasma lipoproteins attributed to genome rearrangements and genetic insertions leads to phenotypic plasticity that allows for the evasion of the host's defence system and pathogenesis. This paper compared for the first time the genomes of four human urogenital Mycoplasma species (M. penetrans HF-2, M. fermentans JER, M. genitalium G37 and M. hominis PG21) to categorise the metabolic functions of the core genes and to assess the effects of tandem repeats, phage-like genetic elements and prophages on the virulence genes. The results of this comparative in silico genomic analysis revealed that the genes constituting their core genomes can be separated into three distinct categories: nuclear metabolism, protein metabolism and energy generation each making up 52%, 31% and 23%, respectively. The genomes have repeat sequences ranging from 3.7% in M. hominis PG21 to 9.5% in M. fermentans JER. Tandem repeats (mostly minisatellites) and phage-like proteins (including DNA gyrases/topoisomerases) were randomly distributed in the Mycoplasma genomes. Here, we identified a coiled-coil structure containing protein in M. penetrans HF-2 which is significantly similar to the Mem protein of M. fermentans ɸMFV1. Therefore, a Mycoplasma prophage seems to be embedded within M. penetrans HF-2 unannotated genome. To the best of our knowledge, no Mycoplasma phages or prophages have been detected in M. penetrans. This study is important not only in understanding the complex genetic factors involved in phenotypic plasticity and virulence in the relatively understudied Mycoplasma species but also in elucidating the effective arrangement of their redundant minimal genomes.

中文翻译：

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人类泌尿生殖道的四种支原体物种的比较基因组学：其核心基因组和毒力基因的分析。

支原体脂蛋白的变异归因于基因组重排和基因插入，导致表型可塑性，从而可以逃避宿主的防御系统和发病机理。本文首次比较了四种人类泌尿生殖道支原体物种（M. penetrans HF-2，M。fermentans JER，M。genitalium G37和M. hominis PG21）的基因组，以对核心基因的代谢功能进行分类并评估串联重复序列，噬菌体样遗传元件和噬菌体对毒力基因的影响。这种比较计算机模拟基因组分析的结果表明，构成其核心基因组的基因可以分为三类：核代谢，蛋白质代谢和能量生成，分别分别占52％，31％和23％。基因组的重复序列范围从人型支原体PG21中的3.7％到发酵性支原体JER中的9.5％。串联重复序列（主要是小卫星）和噬菌样蛋白（包括DNA陀螺/拓扑异构酶）随机分布在支原体基因组中。在这里，我们鉴定出了一种螺旋状螺旋结构，其在戊型支原体HF-2中含有与发酵乳杆菌MFF1的Mem蛋白明显相似的蛋白。因此，支原体噬菌体似乎被嵌入到戊型支原体HF-2未注释的基因组中。据我们所知，未在Penetrans支原体中检测到支原体噬菌体或噬菌体。