Université de Toulouse, ENVT, UMR 1225 Interactions Hôtes - Agents Pathogènes, 31076 Toulouse, France.
BMC Genomics. 2010 Feb 2;11:86. doi: 10.1186/1471-2164-11-86.
While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study.
The two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms.
Overall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.
虽然基因组时代积累了大量的数据，但如何用基因组学来描述一个细菌仍然没有得到充分解决。最近对牛支原体标准株基因组的测序挑战了我们对支原体的一般看法，表明这些简单的细菌能够通过水平基因转移交换大量的遗传物质。然而，塑造支原体基因组并强调该物种内多样性的事件仍需全面评估。为此，我们比较了两种代表该物种遗传谱的菌株：已经有基因组可用的标准株 PG2 和本研究中完全测序和注释的田间分离株 5632。
两个基因组相差约 130 kbp，5632 的基因组最大（1006 kbp）。这部分额外遗传物质的组成主要对应（i）可移动遗传元件和（ii）扩展的基因家族 repertoire，这些基因家族编码推测的表面蛋白，并具有高度可变系统的特征。更具体地说，在 5632 中发现了三个完整的先前描述的整合共轭元件拷贝，约占 80 kbp。在 5632 中发现但在 PG2 中未发现的其他可移动遗传元件是更经典的插入序列，这些序列与另外两种反刍动物病原体 M. bovis 和 M. mycoides subsp. mycoides SC 中的插入序列有关。在 5632 中，由于基因重复，编码表面蛋白的基因家族 repertoire 更大。对两种菌株的比较蛋白质组学分析表明，5632 的额外编码能力影响了表面的整体结构，并表明基于单核苷酸多态性的新的相变异系统的发生。
总之，对两种牛支原体菌株的比较分析揭示了一个非常动态的基因组，其结构受到反刍动物支原体之间的基因流动和编码表面蛋白的基因 repertoire 扩张-减少的影响，而这些基因的表达则由局部遗传微事件驱动。
