Unité d'Epidémiologie Animale, UR356, INRA centre de Clermont-Ferrand Theix, Route de Theix, 63122 Saint Genès Champanelle, France.
Res Microbiol. 2011 Feb-Mar;162(2):132-43. doi: 10.1016/j.resmic.2010.11.003. Epub 2010 Dec 7.
A novel extrachromosomal element that we called pAMT11 was discovered in a deep-sea vent isolate belonging to the hyperthermophilic euryarchaeal order Thermococcales. It consists of a double-stranded DNA of 20,534bp which encodes 30 putative open reading frames (ORFs) of which six could be assigned to a putative function on the basis of sequence similarity to known genes or to protein domain families. Most of the ORFs of pAMT1 showed homology and synteny with a genomic island of Thermococcus kodakaraensis KOD1. This region, named TKV1, was previously described as a "virus-like integrated element" and assumed to integrate into the host chromosome by a site-specific recombination mechanism similar to that of Sulfolobus solfataricus virus 1. While most of the genes shared by pAMT11 and TKV1 encode putative membrane proteins presumably involved in virus particle formation, attempts to induce production of virus particles by mitomycin treatment of AMT11 cultures failed, suggesting that pAMT11 may represent the genome of a defective virus or a plasmid. Genomes of mobile elements usually contain two regions: a core of conserved genes mainly involved in replication, maintenance or spreading of the genetic element, and a variable set of accessory genes. Surprisingly, genes presumably implied in the replication process are quite divergent between TKV1 and pAMT11. Indeed, TKV1 possesses a MCM-like protein that may function as a replication initiator, while pAMT11 encodes a putative non-conventional protein distantly related to the Rep protein previously described in a small plasmid of Pyrococcus sp. strain JT1, assumed to replicate by a rolling-circle (RC) mechanism. However, in the case of pAMT11, this mode of plasmid replication could not be experimentally proven and is questionable given the lack of significant similarities with any other members of the RC-Rep superfamily and its unusual large size compared to other RC plasmids.
我们在一个属于高温古菌目的Thermococcales 的深海喷口分离株中发现了一个新型的染色体外元件，我们称之为 pAMT11。它由一条 20534bp 的双链 DNA 组成，编码 30 个假定的开放阅读框（ORF），其中 6 个可以根据与已知基因或蛋白结构域家族的序列相似性来确定假定的功能。pAMT11 的大多数 ORF 与 Thermococcus kodakaraensis KOD1 的一个基因组岛显示出同源性和基因排列顺序。这个区域，命名为 TKV1，以前被描述为一个“类似病毒的整合元件”，并假设通过类似于 Sulfolobus solfataricus virus 1 的位点特异性重组机制整合到宿主染色体中。虽然 pAMT11 和 TKV1 共享的大多数基因编码假定的膜蛋白，可能参与病毒颗粒的形成，但用丝裂霉素处理 AMT11 培养物诱导病毒颗粒产生的尝试失败了，这表明 pAMT11 可能代表一个缺陷病毒或质粒的基因组。移动元件的基因组通常包含两个区域：一个核心保守基因，主要涉及遗传元件的复制、维持或传播，和一个可变的辅助基因集。令人惊讶的是，TKV1 和 pAMT11 之间复制过程中假定涉及的基因相当不同。事实上，TKV1 拥有一个可能作为复制起始子的 MCM 样蛋白，而 pAMT11 编码一个假定的非传统蛋白，与以前在 Pyrococcus sp. strain JT1 的一个小质粒中描述的 Rep 蛋白有较远的关系，假定通过滚环（RC）机制复制。然而，在 pAMT11 的情况下，这种质粒复制模式不能通过实验证明，并且考虑到它与 RC-Rep 超家族的其他成员缺乏显著的相似性以及与其他 RC 质粒相比其异常的大尺寸，这是值得怀疑的。
