Bénit L, Dessen P, Heidmann T
Unité des Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs, CNRS UMR 1573, Institut Gustave Roussy, 94805 Villejuif Cedex, France.
J Virol. 2001 Dec;75(23):11709-19. doi: 10.1128/JVI.75.23.11709-11719.2001.
Phylogenetic analyses of retroviral elements, including endogenous retroviruses, have relied essentially on the retroviral pol gene expressing the highly conserved reverse transcriptase. This enzyme is essential for the life cycle of all retroid elements, but other genes are also endowed with conserved essential functions. Among them, the transmembrane (TM) subunit of the envelope gene is involved in virus entry through membrane fusion. It has also been reported to contain a domain, named the immunosuppressive domain, that has immunosuppressive properties most probably essential for virus spread within the host. This domain is conserved among a large series of retroviral elements, and we have therefore attempted to generate phylogenetic links between retroviral elements identified from databases following tentative alignments of the immunosuppressive domain and adjacent sequences. This allowed us to unravel a conserved organization among TM domains, also found in the Ebola and Marburg filoviruses, and to identify a large number of human endogenous retroviruses (HERVs) from sequence databases. The latter elements are part of previously identified families of HERVs, and some of them define new families. A general phylogenetic analysis based on the TM proteins of retroelements, and including those with no clearly identified immunosuppressive domain, could then be derived and compared with pol-based phylogenetic trees, providing a comprehensive survey of retroelements and definitive evidence for recombination events in the generation of both the endogenous and the present-day infectious retroviruses.
对包括内源性逆转录病毒在内的逆转录病毒元件的系统发育分析，基本上依赖于表达高度保守逆转录酶的逆转录病毒 pol 基因。这种酶对于所有逆转录元件的生命周期至关重要，但其他基因也具有保守的基本功能。其中，包膜基因的跨膜（TM）亚基通过膜融合参与病毒进入。也有报道称它含有一个名为免疫抑制结构域的区域，该区域具有免疫抑制特性，很可能对病毒在宿主体内传播至关重要。这个结构域在大量逆转录病毒元件中是保守的，因此我们尝试在对免疫抑制结构域和相邻序列进行初步比对后，从数据库中鉴定出的逆转录病毒元件之间建立系统发育联系。这使我们能够揭示 TM 结构域之间的保守组织，这种组织在埃博拉病毒和马尔堡丝状病毒中也有发现，并从序列数据库中鉴定出大量人类内源性逆转录病毒（HERV）。后一类元件是先前鉴定的 HERV 家族的一部分，其中一些定义了新的家族。然后可以基于逆转录元件的 TM 蛋白进行全面的系统发育分析，包括那些没有明确鉴定出免疫抑制结构域的元件，并与基于 pol 的系统发育树进行比较，从而对逆转录元件进行全面调查，并为内源性和当今感染性逆转录病毒产生过程中的重组事件提供确凿证据。
