Abstract
The majority of retroviral envelope glycoproteins characterized to date are typical of type I viral fusion proteins, having a receptor binding subunit associated with a fusion subunit. The fusion subunits of lentiviruses and alpha-, beta-, delta- and gammaretroviruses have a very conserved domain organization and conserved features of secondary structure, making them suitable for phylogenetic analyses. Such analyses, along with sequence comparisons, reveal evidence of numerous recombination events in which retroviruses have acquired envelope glycoproteins from heterologous sequences. Thus, the envelope gene (env) can have a history separate from that of the polymerase gene (pol), which is the most commonly used gene in phylogenetic analyses of retroviruses. Focusing on the fusion subunits of the genera listed above, we describe three distinct types of retroviral envelope glycoproteins, which we refer to as gamma-type, avian gamma-type and beta-type. By tracing these types within the ‘fossil record’ provided by endogenous retroviruses, we show that they have surprisingly distinct evolutionary histories and dynamics, with important implications for cross-species transmissions and the generation of novel lineages. These findings validate the utility of env sequences in contributing phylogenetic signal that enlarges our understanding of retrovirus evolution.
Highlights
Much of the reconstruction of retroviral lineages has centred on the wellconserved reverse transcriptase (RT) motif of the polymerase gene [1,2,3,4,5]
Phylogenetic trees combining RT sequences from both endogenous and exogenous retroviruses suggest that all known retroviruses can be grouped into three broad classes [4,15]: class I consists of gammaretroviruses, epsilonretroviruses and the ERVs that cluster along with them
While no endogenous deltaretrovirus-like element has yet been discovered, an argument to include deltaretroviruses under the class II umbrella can be made based upon the catalytic site (YMDD) in RT, which matches that of the other class II members
Summary
Much of the reconstruction of retroviral lineages has centred on the wellconserved reverse transcriptase (RT) motif of the polymerase gene ( pol) [1,2,3,4,5]. RT-based analyses revealed the surprising fact that proviruses representing retroviruses estimated to have infected their hosts tens of millions of years ago or more harbour recognizable features of extant retroviruses, despite their notoriously high substitution rate [11,12,13]. While this situation leads evolutionists to ponder the ‘molecular clock’ conundrum [14], the fidelity of features over deep evolutionary time gives us a set of data that can be analysed using phylogenetic methods, revealing evolutionary dynamics of retrovirus–host interactions. When we allow env to tell its own story, new insights into retroviral evolution emerge, involving evidence and likelihood of cross-species transmissions, the evolution of new lineages and possibly genera, and even recombination between virus families that could generate new types of viruses
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