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A survey of protein structures from archaeal viruses. Life (Basel) 2013; 3:118-30. [PMID: 25371334 PMCID: PMC4187194 DOI: 10.3390/life3010118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 01/18/2013] [Accepted: 01/21/2013] [Indexed: 11/17/2022] Open
Abstract
Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating in extreme environments, contain highly mosaic genomes with open reading frames (ORFs) whose sequences are often dissimilar to all other known ORFs. It has been estimated that approximately 85% of virally encoded ORFs do not match known sequences in the nucleic acid databases, and this percentage is even higher for archaeal viruses (typically 90%–100%). This statistic suggests that either virus genomes represent a larger segment of sequence space and/or that viruses encode genes of novel fold and/or function. Because the overall three-dimensional fold of a protein evolves more slowly than its sequence, efforts have been geared toward structural characterization of proteins encoded by archaeal viruses in order to gain insight into their potential functions. In this short review, we provide multiple examples where structural characterization of archaeal viral proteins has indeed provided significant functional and evolutionary insight.
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ORF157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease. J Virol 2010; 84:5025-31. [PMID: 20200253 DOI: 10.1128/jvi.01664-09] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acidianus filamentous virus 1 (AFV1) (Lipothrixviridae) is an enveloped filamentous virus that was characterized from a crenarchaeal host. It infects Acidianus species that thrive in the acidic hot springs (>85 degrees C and pH <3) of Yellowstone National Park, WY. The AFV1 20.8-kb, linear, double-stranded DNA genome encodes 40 putative open reading frames whose sequences generally show little similarity to other genes in the sequence databases. Because three-dimensional structures are more conserved than sequences and hence are more effective at revealing function, we set out to determine protein structures from putative AFV1 open reading frames (ORF). The crystal structure of ORF157 reveals an alpha+beta protein with a novel fold that remotely resembles the nucleotidyltransferase topology. In vitro, AFV1-157 displays a nuclease activity on linear double-stranded DNA. Alanine substitution mutations demonstrated that E86 is essential to catalysis. AFV1-157 represents a novel class of nuclease, but its exact role in vivo remains to be determined.
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Goulet A, Blangy S, Redder P, Prangishvili D, Felisberto-Rodrigues C, Forterre P, Campanacci V, Cambillau C. Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Proc Natl Acad Sci U S A 2009; 106:21155-60. [PMID: 19934032 PMCID: PMC2795548 DOI: 10.1073/pnas.0909893106] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Indexed: 11/18/2022] Open
Abstract
Acidianus filamentous virus 1 (AFV1), a member of the Lipothrixviridae family, infects the hyperthermophilic, acidophilic crenarchaeaon Acidianus hospitalis. The virion, covered with a lipidic outer shell, is 9,100-A long and contains a 20.8-kb linear dsDNA genome. We have identified the two major coat proteins of the virion (MCPs; 132 and 140 amino acids). They bind DNA and form filaments when incubated with linear dsDNA. A C-terminal domain is identified in their crystal structure with a four-helix-bundle fold. In the topological model of the virion filament core, the genomic dsDNA superhelix wraps around the AFV1-132 basic protein, and the AFV1-140 basic N terminus binds genomic DNA, while its lipophilic C-terminal domain is imbedded in the lipidic outer shell. The four-helix bundle fold of the MCPs from AFV1 is identical to that of the coat protein (CP) of Sulfolobus islandicus rod-shaped virus (SIRV), a member of the Rudiviridae family. Despite low sequence identity between these proteins, their high degree of structural similarity suggests that they could have derived from a common ancestor and could thus define an yet undescribed viral lineage.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Peter Redder
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
| | - Catarina Felisberto-Rodrigues
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Patrick Forterre
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
- Institut de Génétique et Microbiologie, Université Paris-Sud and Centre national de la recherche scientifique, Unité Mixte de Recherche 8621, 91405 Orsay Cedex, France
| | - Valérie Campanacci
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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