Abstract
BackgroundViruses are the most abundant and genetically diverse biological entities on earth, yet the repertoire of viral proteins remains poorly explored. As the number of sequenced virus genomes grows into the thousands, and the number of viral proteins into the hundreds of thousands, we report a systematic computational analysis of the point of first-contact between viruses and their hosts, namely viral transmembrane (TM) proteins.ResultsThe complement of α-helical TM proteins in double-stranded DNA viruses infecting bacteria and archaea reveals large-scale trends that differ from those of their hosts. Viruses typically encode a substantially lower fraction of TM proteins than archaea or bacteria, with the notable exception of viruses with virions containing a lipid component such as a lipid envelope, internal lipid core, or inner membrane vesicle. Compared to bacteriophages, archaeal viruses are substantially enriched in membrane proteins. However, this feature is not always stable throughout the evolution of a viral lineage; for example, TM proteins are not part of the common heritage shared between Lipothrixviridae and Rudiviridae. In contrast to bacteria and archaea, viruses almost completely lack proteins with complicated membrane topologies composed of more than 4 TM segments, with the few detected exceptions being obvious cases of relatively recent horizontal transfer from the host.ConclusionsThe dramatic differences between the membrane proteomes of cells and viruses stem from the fact that viruses do not depend on essential membranes for energy transformation, ion homeostasis, nutrient transport and signaling.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0817-4) contains supplementary material, which is available to authorized users.
Highlights
Viruses are the most abundant and genetically diverse biological entities on earth, yet the repertoire of viral proteins remains poorly explored
Overall TM complement of double-stranded DNA (dsDNA) prokaryotic viruses Focusing on the >900 genomes available for the extensively studied class of dsDNA viruses that infect bacteria and archaea, Prokaryotic virus Orthologous Groups (POG) were constructed and TM predictions were made as described in the Methods
The proportion of proteins per genome that are conserved in POG gene families is highly variable, from none of the 5 proteins in Leuconostoc phage L5 or other poorly characterized viruses, up to 100 % in several well-characterized Staphylococcus and Mycobacterium phages
Summary
Viruses are the most abundant and genetically diverse biological entities on earth, yet the repertoire of viral proteins remains poorly explored. The number of TM proteins scales linearly with the total number of genes (and, for bacteria and archaea, with the genome size) and fits together with metabolic enzymes in the framework of universal scaling laws of functional classes of genes [11,12,13]. These findings conform to the model of genome evolution that postulates coupling between the evolutionary trajectories of different gene classes [14] and imply that evolution of membranes is coupled with the evolution of metabolic networks
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