title: A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea.
abstract: BACKGROUND
  Viruses 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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. david-kristensen@uiowa.edu.|Current address: Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA. david-kristensen@uiowa.edu.
authors.forename: David M
authors.initials: DM
authors.lastname: Kristensen
authors.affiliation: Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354, Freising, Germany. usman.saeed08@gmail.com.|Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany. usman.saeed08@gmail.com.
authors.forename: Usman
authors.initials: U
authors.lastname: Saeed
authors.affiliation: Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354, Freising, Germany. d.frishman@wzw.tum.de.|Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany. d.frishman@wzw.tum.de.
authors.forename: Dmitrij
authors.initials: D
authors.lastname: Frishman
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. koonin@ncbi.nlm.nih.gov.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D001105:Archaea / Q000378:metabolism* / Q000821:virology; D023641:Archaeal Viruses / Q000302:isolation & purification / Q000378:metabolism*; D001419:Bacteria / Q000378:metabolism* / Q000821:virology; D004267:DNA Viruses / Q000302:isolation & purification / Q000378:metabolism*; D054884:Host-Pathogen Interactions; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism*; D014764:Viral Proteins / Q000378:metabolism*; D014771:Virion / Q000502:physiology*; D016662:Virus Integration
chemical_list: D008565:Membrane Proteins; D014764:Viral Proteins