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Chen S, Tu D, Hong T, Luo Y, Shen L, Ren P, Lu P, Chen X. Genomic features of a new head-tail halovirus VOLN27B infecting a Halorubrum strain. Gene 2022; 841:146766. [PMID: 35908623 DOI: 10.1016/j.gene.2022.146766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/26/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Relatively few viruses infecting haloarchaea (haloviruses) have been reported. In this study, the genome sequence of VOLN27B, a recently described archaeal tailed virus (arTV) with a myovirus morphotype was described, along with the sequence of its host, Halorubrum spp. LN27. Halovirus VOLN27B contains a linear, dsDNA genome of 76,891 bp which is predicted to encode 109 proteins and four tRNAs (tRNAThr, tRNAArg, tRNAGly and tRNAAsn). The DNA G+C content of VOLN27B genome is 56.1 mol%, nearly 10% lower than that of its host strain. A 315 bp LTR (long terminal repeat) was detected in the genome. The genome of its host strain LN27 was 3,301,211 bp (chromosome and 1 plasmid) with a DNA G+C content of 68.3 mol% and 3,142 annotated protein coding genes. At least two hypothetical proviruses were detected in the genome. It lacked a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus. Sequence similarity and phylogenetic tree reconstructions placed it within the genus Halorubrum as a potential new species. VOLN27B exhibits a distinct difference in the frequency of codon usage against its host strain Halorubrum sp. LN27. The organization of VOLN27B genome shows remarkable synteny and amino acid sequence similarity to the genomes and predicted proteins of HF1-like haloviruses (genus Haloferacalesvirus) and a provirus in the genome of Halorubrum depositum Y78. VOLN27B and its host Halorubrum sp. LN27 comprise a new virus-host system from a hypersaline ecosystem and can be used to further understand the novel biology at extreme salt concentration.
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Affiliation(s)
- Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
| | - Demei Tu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuqing Luo
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Peng Lu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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2
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VOLN27B: A New Head-Tailed Halovirus Isolated from an Underground Salt Crystal and Infecting Halorubrum. ARCHAEA (VANCOUVER, B.C.) 2022; 2021:8271899. [PMID: 34992502 PMCID: PMC8727067 DOI: 10.1155/2021/8271899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023]
Abstract
A novel halovirus, VOLN27B, was isolated from a drill core sample taken at a depth of approximately 430 m, from a layer formed during the Cretaceous period (Anhui, China). VOLN27B infects the halophilic archaeon Halorubrum sp. LN27 and has a head-tailed morphotype with a contractile tail, typical of myoviruses. The average head diameter is 64 ± 2.0 nm, and uncontracted tails are 15 ± 1.0 × 65 ± 2.0 nm. The latent period is about 10 h. The maturing time of VOLN27B in cells of Halorubrum sp. LN27 was nearly 8 h. The adsorption time of VOLN27B on cells of Halorubrum sp. LN27 was less than 1 min. Virus particles are unstable at pH values less than 5 or when the NaCl concentration is below 12% (w/v). VOLN27B and Halorubrum sp. LN27 were recovered from the same hypersaline environment and provide a new virus-host system in haloarchaea.
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3
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Halorubrum pleomorphic virus-6 Membrane Fusion Is Triggered by an S-Layer Component of Its Haloarchaeal Host. Viruses 2022; 14:v14020254. [PMID: 35215847 PMCID: PMC8875312 DOI: 10.3390/v14020254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 01/27/2023] Open
Abstract
(1) Background: Haloarchaea comprise extremely halophilic organisms of the Archaea domain. They are single-cell organisms with distinctive membrane lipids and a protein-based cell wall or surface layer (S-layer) formed by a glycoprotein array. Pleolipoviruses, which infect haloarchaeal cells, have an envelope analogous to eukaryotic enveloped viruses. One such member, Halorubrum pleomorphic virus 6 (HRPV-6), has been shown to enter host cells through virus-cell membrane fusion. The HRPV-6 fusion activity was attributed to its VP4-like spike protein, but the physiological trigger required to induce membrane fusion remains yet unknown. (2) Methods: We used SDS-PAGE mass spectroscopy to characterize the S-layer extract, established a proteoliposome system, and used R18-fluorescence dequenching to measure membrane fusion. (3) Results: We show that the S-layer extraction by Mg2+ chelating from the HRPV-6 host, Halorubrum sp. SS7-4, abrogates HRPV-6 membrane fusion. When we in turn reconstituted the S-layer extract from Hrr. sp. SS7-4 onto liposomes in the presence of Mg2+, HRPV-6 membrane fusion with the proteoliposomes could be readily observed. This was not the case with liposomes alone or with proteoliposomes carrying the S-layer extract from other haloarchaea, such as Haloferax volcanii. (4) Conclusions: The S-layer extract from the host, Hrr. sp. SS7-4, corresponds to the physiological fusion trigger of HRPV-6.
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4
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Baquero DP, Liu J, Prangishvili D. Egress of archaeal viruses. Cell Microbiol 2021; 23:e13394. [PMID: 34515400 DOI: 10.1111/cmi.13394] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/15/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022]
Abstract
Viruses of Archaea, arguably the most mysterious part of the virosphere due to their unique morphotypes and genome contents, exploit diverse mechanisms for releasing virus progeny from the host cell. These include virus release as a result of the enzymatic degradation of the cell wall or budding through it, common for viruses of Bacteria and Eukarya, as well as a unique mechanism of virus egress through small polygonal perforations on the cell surface. The process of the formation of these perforations includes the development of pyramidal structures on the membrane of the infected cell, which gradually grow by the expansion of their faces and eventually open like flower petals. This mechanism of virion release is operating exclusively in cells of hyperthermophilic hosts from the phylum Crenarchaeota, which are encased solely by a layer of surface proteins, S-layer. The review focuses on recent developments in understanding structural and biochemical details of all three types of egress mechanisms of archaeal viruses. TAKE AWAYS: Many archaeal viruses exit the host via polygonal perforations on the cell membrane. The molecular mechanism of exit via specific apertures is unique for archaeal viruses. Some enveloped archaeal viruses exploit the budding mechanism for egress.
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Affiliation(s)
- Diana P Baquero
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, Paris, France
| | - Junfeng Liu
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, Paris, France
| | - David Prangishvili
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, Paris, France.,Faculty of Medicine, Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
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5
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Naureen Z, Dautaj A, Anpilogov K, Camilleri G, Dhuli K, Tanzi B, Maltese PE, Cristofoli F, De Antoni L, Beccari T, Dundar M, Bertelli M. Bacteriophages presence in nature and their role in the natural selection of bacterial populations. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:e2020024. [PMID: 33170167 PMCID: PMC8023132 DOI: 10.23750/abm.v91i13-s.10819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 01/21/2023]
Abstract
Phages are the obligate parasite of bacteria and have complex interactions with their hosts. Phages can live in, modify, and shape bacterial communities by bringing about changes in their abundance, diversity, physiology, and virulence. In addition, phages mediate lateral gene transfer, modify host metabolism and reallocate bacterially-derived biochemical compounds through cell lysis, thus playing an important role in ecosystem. Phages coexist and coevolve with bacteria and have developed several antidefense mechanisms in response to bacterial defense strategies against them. Phages owe their existence to their bacterial hosts, therefore they bring about alterations in their host genomes by transferring resistance genes and genes encoding toxins in order to improve the fitness of the hosts. Application of phages in biotechnology, environment, agriculture and medicines demands a deep insight into the myriad of phage-bacteria interactions. However, to understand their complex interactions, we need to know how unique phages are to their bacterial hosts and how they exert a selective pressure on the microbial communities in nature. Consequently, the present review focuses on phage biology with respect to natural selection of bacterial populations.
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Affiliation(s)
- Zakira Naureen
- Department of Biological Sciences and Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Oman.
| | | | | | | | | | | | | | | | | | - Tommaso Beccari
- Department of Pharmaceutical Science, University of Perugia, Perugia, Italy.
| | - Munis Dundar
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey.
| | - Matteo Bertelli
- EBTNA-LAB, Rovereto (TN), Italy; MAGI EUREGIO, Bolzano, Italy; MAGI'S LAB, Rovereto (TN), Italy.
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6
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Abstract
Established in 2016, the family Pleolipoviridae comprises globally distributed archaeal viruses that produce pleomorphic particles. Pseudo-spherical enveloped virions of pleolipoviruses are membrane vesicles carrying a nucleic acid cargo. The cargo can be either a single-stranded or double-stranded DNA molecule, making this group the first family introduced in the 10th Report on Virus Taxonomy including both single-stranded and double-stranded DNA viruses. The length of the genomes is approximately 7–17 kilobase pairs, or kilonucleotides in the case of single-stranded molecules. The genomes are circular single-stranded DNA, circular double-stranded DNA, or linear double-stranded DNA molecules. Currently, eight virus species and seven proposed species are classified in three genera: Alphapleolipovirus (five species), Betapleolipovirus (nine species), and Gammapleolipovirus (one species). Here, we summarize the updated taxonomy of the family Pleolipoviridae to reflect recent advances in this field, with the focus on seven newly proposed species in the genus Betapleolipovirus: Betapleolipovirus HHPV3, HHPV4, HRPV9, HRPV10, HRPV11, HRPV12, and SNJ2.
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Affiliation(s)
- Tatiana A Demina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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7
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Singh AR, Košmrlj A, Bruinsma R. Finite Temperature Phase Behavior of Viral Capsids as Oriented Particle Shells. PHYSICAL REVIEW LETTERS 2020; 124:158101. [PMID: 32357054 PMCID: PMC7219451 DOI: 10.1103/physrevlett.124.158101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/16/2020] [Indexed: 05/02/2023]
Abstract
A general phase plot is proposed for discrete particle shells that allows for thermal fluctuations of the shell geometry and of the inter-particle connectivities. The phase plot contains a first-order melting transition, a buckling transition, and a collapse transition and is used to interpret the thermodynamics of microbiological shells.
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Affiliation(s)
- Amit R Singh
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Currently at Department of Mechanical Engineering, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, India
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08540, USA
- Princeton Institute for the Science and Technology of Materials (PRISM), Princeton University, Princeton, New Jersey 08544, USA
| | - Robijn Bruinsma
- Departments of Physics and Astronomy, and Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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8
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Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, Sánchez-Carbente MDR, Peralta R, Hernández-Mendoza A, Dobson ADW, Gonzalez RA, Pastor N, Batista-García RA. A Review on Viral Metagenomics in Extreme Environments. Front Microbiol 2019; 10:2403. [PMID: 31749771 PMCID: PMC6842933 DOI: 10.3389/fmicb.2019.02403] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives.
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Affiliation(s)
- Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Hugo G. Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | | | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Ramón A. Gonzalez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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9
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Maestre‐Carballa L, Lluesma Gomez M, Angla Navarro A, Garcia‐Heredia I, Martinez‐Hernandez F, Martinez‐Garcia M. Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter. Environ Microbiol 2019; 21:4582-4596. [DOI: 10.1111/1462-2920.14758] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/21/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Lucia Maestre‐Carballa
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Andrea Angla Navarro
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Inmaculada Garcia‐Heredia
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Francisco Martinez‐Hernandez
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
| | - Manuel Martinez‐Garcia
- Department of Physiology, Genetics, and MicrobiologyUniversity of Alicante C/San Vicente s/n 03080 Alicante Spain
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10
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Martin‐Cuadrado A, Senel E, Martínez‐García M, Cifuentes A, Santos F, Almansa C, Moreno‐Paz M, Blanco Y, García‐Villadangos M, Cura MÁG, Sanz‐Montero ME, Rodríguez‐Aranda JP, Rosselló‐Móra R, Antón J, Parro V. Prokaryotic and viral community of the sulfate‐rich crust from Peñahueca ephemeral lake, an astrobiology analogue. Environ Microbiol 2019; 21:3577-3600. [DOI: 10.1111/1462-2920.14680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ece Senel
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
- Department of BiologyGraduate School of Sciences, Eskisehir Technical University Yunusemre Campus, Eskisehir 26470 Turkey
| | - Manuel Martínez‐García
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Ana Cifuentes
- Department of Ecology and Marine Resources, Marine Microbiology GroupMediterranean Institute for Advanced Studies (IMEDEA, CSIC‐UIB) Esporles Spain
| | - Fernando Santos
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Cristina Almansa
- Research Technical Services (SSTTI), Microscopy UnitUniversity of Alicante Alicante Spain
| | - Mercedes Moreno‐Paz
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
| | - Yolanda Blanco
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
| | | | | | | | | | - Ramon Rosselló‐Móra
- Department of BiologyGraduate School of Sciences, Eskisehir Technical University Yunusemre Campus, Eskisehir 26470 Turkey
| | - Josefa Antón
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Víctor Parro
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
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11
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Rodela ML, Sabet S, Peterson A, Dillon JG. Broad Environmental Tolerance for a Salicola Host-Phage Pair Isolated from the Cargill Solar Saltworks, Newark, CA, USA. Microorganisms 2019; 7:E106. [PMID: 31010175 PMCID: PMC6518143 DOI: 10.3390/microorganisms7040106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/13/2019] [Accepted: 04/17/2019] [Indexed: 11/29/2022] Open
Abstract
Phages greatly influence the ecology and evolution of their bacterial hosts; however, compared to hosts, a relatively low number of phages, especially halophilic phages, have been studied. This study describes a comparative investigation of physicochemical tolerance between a strain of the halophilic bacterium, Salicola, isolated from the Cargill Saltworks (Newark, CA, USA) and its associated phage. The host grew in media between pH 6-8.5, had a salinity growth optimum of 20% total salts (ranging from 10%-30%) and an upper temperature growth limit of 48 °C. The host utilized 61 of 190 substrates tested using BIOLOG Phenotype MicroArrays. The CGφ29 phage, one of only four reported Salicola phages, is a DNA virus of the Siphoviridae family. Overall, the phage tolerated a broader range of environmental conditions than its host (salinity 0-30% total salts; pH 3-9; upper thermal limit 80 °C) and is the most thermotolerant halophilic phage ever reported. This study is the most comprehensive investigation to date of a Salicola host-phage pair and provides novel insights into extreme environmental tolerances among bacteriophages.
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Affiliation(s)
- Meghan L Rodela
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA.
| | - Shereen Sabet
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA.
| | - Allison Peterson
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA.
| | - Jesse G Dillon
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA.
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12
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Mizuno CM, Prajapati B, Lucas‐Staat S, Sime‐Ngando T, Forterre P, Bamford DH, Prangishvili D, Krupovic M, Oksanen HM. Novel haloarchaeal viruses from Lake Retba infecting
Haloferax
and
Halorubrum
species. Environ Microbiol 2019; 21:2129-2147. [DOI: 10.1111/1462-2920.14604] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Carolina M. Mizuno
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Bina Prajapati
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - Soizick Lucas‐Staat
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Telesphore Sime‐Ngando
- CNRS UMR 6023, Université Clermont‐AuvergneLaboratoire "Microorganismes: Génome et Environnement" (LMGE) F‐63000, Clermont‐Ferrand France
| | - Patrick Forterre
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Dennis H. Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - David Prangishvili
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
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13
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El Omari K, Li S, Kotecha A, Walter TS, Bignon EA, Harlos K, Somerharju P, De Haas F, Clare DK, Molin M, Hurtado F, Li M, Grimes JM, Bamford DH, Tischler ND, Huiskonen JT, Stuart DI, Roine E. The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins. Nat Commun 2019; 10:846. [PMID: 30783086 PMCID: PMC6381117 DOI: 10.1038/s41467-019-08728-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022] Open
Abstract
Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion.
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Affiliation(s)
- Kamel El Omari
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Sai Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Thomas S Walter
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Eduardo A Bignon
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Pentti Somerharju
- Department of Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Felix De Haas
- Thermo Fisher Scientific, Achtseweg Noorg 5, 5651 GG, Eindhoven, The Netherlands
| | - Daniel K Clare
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Mika Molin
- Helsinki Institute of Life Science HiLIFE, Institute of Biotechnology, University of Helsinki, Viikinkaari 5, 00014, Helsinki, Finland
| | - Felipe Hurtado
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Mengqiu Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Nicole D Tischler
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile.
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Helsinki Institute of Life Science HiLIFE and Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
| | - David I Stuart
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Elina Roine
- Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
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14
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Zaretsky M, Roine E, Eichler J. Sialic Acid-Like Sugars in Archaea: Legionaminic Acid Biosynthesis in the Halophile Halorubrum sp. PV6. Front Microbiol 2018; 9:2133. [PMID: 30245679 PMCID: PMC6137143 DOI: 10.3389/fmicb.2018.02133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/20/2018] [Indexed: 11/25/2022] Open
Abstract
N-glycosylation is a post-translational modification that occurs in all three domains. In Archaea, however, N-linked glycans present a degree of compositional diversity not observed in either Eukarya or Bacteria. As such, it is surprising that nonulosonic acids (NulOs), nine-carbon sugars that include sialic acids, pseudaminic acids, and legionaminic acids, are routinely detected as components of protein-linked glycans in Eukarya and Bacteria but not in Archaea. In the following, we report that the N-linked glycan attached to the S-layer glycoprotein of the haloarchaea Halorubrum sp. PV6 includes an N-formylated legionaminic acid. Analysis of the Halorubrum sp. PV6 genome led to the identification of sequences predicted to comprise the legionaminic acid biosynthesis pathway. The transcription of pathway genes was confirmed, as was the co-transcription of several of these genes. In addition, the activities of LegI, which catalyzes the condensation of 2,4-di-N-acetyl-6-deoxymannose and phosphoenolpyruvate to generate legionaminic acid, and LegF, which catalyzes the addition of cytidine monophosphate (CMP) to legionaminic acid, both heterologously expressed in Haloferax volcanii, were demonstrated. Further genome analysis predicts that the genes encoding enzymes of the legionaminic acid biosynthetic pathway are clustered together with sequences seemingly encoding components of the N-glycosylation pathway in this organism. In defining the first example of a legionaminic acid biosynthesis pathway in Archaea, the findings reported here expand our insight into archaeal N-glycosylation, an almost universal post-translational modification in this domain of life.
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Affiliation(s)
- Marianna Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Elina Roine
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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15
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Atanasova NS, Heiniö CH, Demina TA, Bamford DH, Oksanen HM. The Unexplored Diversity of Pleolipoviruses: The Surprising Case of Two Viruses with Identical Major Structural Modules. Genes (Basel) 2018; 9:genes9030131. [PMID: 29495629 PMCID: PMC5867852 DOI: 10.3390/genes9030131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 01/01/2023] Open
Abstract
Extremely halophilic Archaea are the only known hosts for pleolipoviruses which are pleomorphic non-lytic viruses resembling cellular membrane vesicles. Recently, pleolipoviruses have been acknowledged by the International Committee on Taxonomy of Viruses (ICTV) as the first virus family that contains related viruses with different DNA genomes. Genomic diversity of pleolipoviruses includes single-stranded and double-stranded DNA molecules and their combinations as linear or circular molecules. To date, only eight viruses belong to the family Pleolipoviridae. In order to obtain more information about the diversity of pleolipoviruses, further isolates are needed. Here we describe the characterization of a new halophilic virus isolate, Haloarcula hispanica pleomorphic virus 4 (HHPV4). All pleolipoviruses and related proviruses contain a conserved core of approximately five genes designating this virus family, but the sequence similarity among different isolates is low. We demonstrate that over half of HHPV4 genome is identical to the genome of pleomorphic virus HHPV3. The genomic regions encoding known virion components are identical between the two viruses, but HHPV4 includes unique genetic elements, e.g., a putative integrase gene. The co-evolution of these two viruses demonstrates the presence of high recombination frequency in halophilic microbiota and can provide new insights considering links between viruses, membrane vesicles, and plasmids.
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Affiliation(s)
- Nina S Atanasova
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
- Finnish Meteorological Institute; Erik Palménin aukio 1, FI-00101 Helsinki, Finland.
| | - Camilla H Heiniö
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Tatiana A Demina
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Dennis H Bamford
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Hanna M Oksanen
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
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16
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Abstract
One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus-host interactions, including interactions with archaeal CRISPR-Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.
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17
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Bamford DH, Pietilä MK, Roine E, Atanasova NS, Dienstbier A, Oksanen HM, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Pleolipoviridae. J Gen Virol 2017; 98:2916-2917. [PMID: 29125455 PMCID: PMC5882103 DOI: 10.1099/jgv.0.000972] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Members of the family Pleolipoviridae (termed pleolipoviruses) are pseudo-spherical and pleomorphic archaeal viruses. The enveloped virion is a simple membrane vesicle, which encloses different types of DNA genomes of approximately 7–16 kbp (or kilonucleotides). Typically, virions contain a single type of transmembrane (spike) protein at the envelope and a single type of membrane protein, which is embedded in the envelope and located in the internal side of the membrane. All viruses infect extremely halophilic archaea in the class Halobacteria (phylum Euryarchaeota). Pleolipoviruses have a narrow host range and a persistent, non-lytic life cycle. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Pleolipoviridae which is available at www.ictv.global/report/pleolipoviridae.
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Affiliation(s)
- Dennis H Bamford
- Department of Biosciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland
| | - Maija K Pietilä
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI00014, Helsinki, Finland
| | - Elina Roine
- Department of Biosciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland
| | - Nina S Atanasova
- Department of Biosciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland
| | - Ana Dienstbier
- Institute of Microbiology of the CAS, v.v.i., Videnska 1083, Prague, Czech Republic
| | - Hanna M Oksanen
- Department of Biosciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland
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18
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Eskelin K, Lampi M, Meier F, Moldenhauer E, Bamford DH, Oksanen HM. Halophilic viruses with varying biochemical and biophysical properties are amenable to purification with asymmetrical flow field-flow fractionation. Extremophiles 2017; 21:1119-1132. [PMID: 29019077 DOI: 10.1007/s00792-017-0963-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023]
Abstract
Viruses come in various shapes and sizes, and a number of viruses originate from extremities, e.g. high salinity or elevated temperature. One challenge for studying extreme viruses is to find efficient purification conditions where viruses maintain their infectivity. Asymmetrical flow field-flow fractionation (AF4) is a gentle native chromatography-like technique for size-based separation. It does not have solid stationary phase and the mobile phase composition is readily adjustable according to the sample needs. Due to the high separation power of specimens up to 50 µm, AF4 is suitable for virus purification. Here, we applied AF4 for extremophilic viruses representing four morphotypes: lemon-shaped, tailed and tailless icosahedral, as well as pleomorphic enveloped. AF4 was applied to input samples of different purity: crude supernatants of infected cultures, polyethylene glycol-precipitated viruses and viruses purified by ultracentrifugation. All four virus morphotypes were successfully purified by AF4. AF4 purification of culture supernatants or polyethylene glycol-precipitated viruses yielded high recoveries, and the purities were comparable to those obtained by the multistep ultracentrifugation purification methods. In addition, we also demonstrate that AF4 is a rapid monitoring tool for virus production in slowly growing host cells living in extreme conditions.
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Affiliation(s)
- Katri Eskelin
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Mirka Lampi
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Florian Meier
- Postnova Analytics, Max-Planck-Str. 14, 86899, Landsberg, Germany
| | | | - Dennis H Bamford
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland.
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19
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Demina TA, Atanasova NS, Pietilä MK, Oksanen HM, Bamford DH. Vesicle-like virion of Haloarcula hispanica pleomorphic virus 3 preserves high infectivity in saturated salt. Virology 2016; 499:40-51. [DOI: 10.1016/j.virol.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 12/26/2022]
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20
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Ruiz-Guillen M, Gabev E, Quetglas JI, Casales E, Ballesteros-Briones MC, Poutou J, Aranda A, Martisova E, Bezunartea J, Ondiviela M, Prieto J, Hernandez-Alcoceba R, Abrescia NGA, Smerdou C. Capsid-deficient alphaviruses generate propagative infectious microvesicles at the plasma membrane. Cell Mol Life Sci 2016; 73:3897-916. [PMID: 27117550 PMCID: PMC7079800 DOI: 10.1007/s00018-016-2230-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/04/2016] [Accepted: 04/14/2016] [Indexed: 12/25/2022]
Abstract
Alphavirus budding is driven by interactions between nucleocapsids assembled in the cytoplasm and envelope proteins present at the plasma membrane. So far, the expression of capsid and envelope proteins in infected cells has been considered an absolute requirement for alphavirus budding and propagation. In the present study, we show that Semliki Forest virus and Sindbis virus lacking the capsid gene can propagate in mammalian and insect cells. This propagation is mediated by the release of infectious microvesicles (iMVs), which are pleomorphic and have a larger size and density than wild-type virus. iMVs, which contain viral RNA inside and viral envelope proteins on their surface, are released at the plasma membrane and infect cells using the endocytic pathway in a similar way to wild-type virus. iMVs are not pathogenic in immunocompetent mice when injected intravenously, but can infect different organs like lungs and heart. Finally, we also show that alphavirus genomes without capsid can mediate the propagation of heterologous genes, making these vectors potentially interesting for gene therapy or vaccination studies. The minimalist infectious system described in this study shows that a self-replicating RNA able to express membrane proteins with binding and fusion properties is able to propagate, providing some insights into virus evolution.
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Affiliation(s)
- Marta Ruiz-Guillen
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- 3P Biopharmaceuticals S.L., Noain, Spain
| | - Evgeni Gabev
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Jose I Quetglas
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Erkuden Casales
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | | | - Joanna Poutou
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Alejandro Aranda
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- UFR des Sciences de la Santé Simone Veil, 2 avenue de la Source de la Bievre, 78180, Montugny-le-Bretonneux, France
| | - Eva Martisova
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Jaione Bezunartea
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Experimental Ophthalmology Laboratory, School of Medicine, University of Navarra, Pamplona, Spain
| | - Marina Ondiviela
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain
| | - Jesus Prieto
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Liver Unit, Clinica Universitaria de Navarra, CIBERehd, Pamplona, Spain
| | - Ruben Hernandez-Alcoceba
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Nicola G A Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Cristian Smerdou
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain.
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
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21
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Atanasova NS, Bamford DH, Oksanen HM. Virus-host interplay in high salt environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:431-444. [PMID: 26929102 DOI: 10.1111/1758-2229.12385] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
Interaction of viruses and cells has tremendous impact on cellular and viral evolution, nutrient cycling and decay of organic matter. Thus, viruses can indirectly affect complex processes such as climate change and microbial pathogenicity. During recent decades, studies on extreme environments have introduced us to archaeal viruses and viruses infecting extremophilic bacteria or eukaryotes. Hypersaline environments are known to contain strikingly high numbers of viruses (∼10(9) particles per ml). Halophilic archaea, bacteria and eukaryotes inhabiting hypersaline environments have only a few cellular predators, indicating that the role of viruses is highly important in these ecosystems. Viruses thriving in high salt are called haloviruses and to date more than 100 such viruses have been described. Virulent, temperate, and persistent halovirus life cycles have been observed among the known isolates including the recently described SNJ1-SNJ2 temperate virus pair which is the first example of an interplay between two haloviruses in one host cell. In addition to direct virus and cell isolations, metagenomics have provided a wealth of information about virus-host dynamics in hypersaline environments suggesting that halovirus populations and halophilic microorganisms are dynamic over time and spatially distributed around the highly saline environments on the Earth.
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Affiliation(s)
- Nina S Atanasova
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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22
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Perotti LE, Dharmavaram S, Klug WS, Marian J, Rudnick J, Bruinsma RF. Useful scars: Physics of the capsids of archaeal viruses. Phys Rev E 2016; 94:012404. [PMID: 27575161 DOI: 10.1103/physreve.94.012404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Indexed: 11/07/2022]
Abstract
We propose a physical model for the capsids of tailed archaeal viruses as viscoelastic membranes under tension. The fluidity is generated by thermal motion of scarlike structures that are an intrinsic feature of the ground state of large particle arrays covering surfaces with nonzero Gauss curvature. The tension is generated by a combination of the osmotic pressure of the enclosed genome and an extension force generated by filamentous structure formation that drives the formation of the tails. In continuum theory, the capsid has the shape of a surface of constant mean curvature: an unduloid. Particle arrays covering unduloids are shown to exhibit pronounced subdiffusive and diffusive single-particle transport at temperatures that are well below the melting temperature of defect-free particle arrays on a surface with zero Gauss curvature.
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Affiliation(s)
- L E Perotti
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| | - S Dharmavaram
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| | - W S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| | - J Marian
- Department of Materials Science and Engineering, University of California, Los Angeles, California 90095, USA
| | - J Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| | - R F Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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23
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Crits-Christoph A, Gelsinger DR, Ma B, Wierzchos J, Ravel J, Davila A, Casero MC, DiRuggiero J. Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community. Environ Microbiol 2016; 18:2064-77. [DOI: 10.1111/1462-2920.13259] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/08/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine; Baltimore MD USA
| | - Jacek Wierzchos
- Department of Biochemistry and Microbial Ecology; Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas; Madrid Spain
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine; Baltimore MD USA
| | | | - M. Cristina Casero
- Department of Biochemistry and Microbial Ecology; Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas; Madrid Spain
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24
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Abstract
Many plasmids have been described in Euryarchaeota, one of the three major archaeal phyla, most of them in salt-loving haloarchaea and hyperthermophilic Thermococcales. These plasmids resemble bacterial plasmids in terms of size (from small plasmids encoding only one gene up to large megaplasmids) and replication mechanisms (rolling circle or theta). Some of them are related to viral genomes and form a more or less continuous sequence space including many integrated elements. Plasmids from Euryarchaeota have been useful for designing efficient genetic tools for these microorganisms. In addition, they have also been used to probe the topological state of plasmids in species with or without DNA gyrase and/or reverse gyrase. Plasmids from Euryarchaeota encode both DNA replication proteins recruited from their hosts and novel families of DNA replication proteins. Euryarchaeota form an interesting playground to test evolutionary hypotheses on the origin and evolution of viruses and plasmids, since a robust phylogeny is available for this phylum. Preliminary studies have shown that for different plasmid families, plasmids share a common gene pool and coevolve with their hosts. They are involved in gene transfer, mostly between plasmids and viruses present in closely related species, but rarely between cells from distantly related archaeal lineages. With few exceptions (e.g., plasmids carrying gas vesicle genes), most archaeal plasmids seem to be cryptic. Interestingly, plasmids and viral genomes have been detected in extracellular membrane vesicles produced by Thermococcales, suggesting that these vesicles could be involved in the transfer of viruses and plasmids between cells.
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25
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Pietilä MK, Roine E, Sencilo A, Bamford DH, Oksanen HM. Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes. Arch Virol 2015; 161:249-56. [PMID: 26459284 DOI: 10.1007/s00705-015-2613-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/13/2015] [Indexed: 11/24/2022]
Abstract
Viruses infecting archaea show a variety of virion morphotypes, and they are currently classified into more than ten viral families or corresponding groups. A pleomorphic virus morphotype is very common among haloarchaeal viruses, and to date, several such viruses have been isolated. Here, we propose the classification of eight such viruses and formation of a new family, Pleolipoviridae (from the Greek pleo for more or many and lipos for lipid), containing three genera, Alpha-, Beta-, and Gammapleolipovirus. The proposal is currently under review by the International Committee on Taxonomy of Viruses (ICTV). The members of the proposed family Pleolipoviridae infect halophilic archaea and are nonlytic. They share structural and genomic features and differ from any other classified virus. The virion of pleolipoviruses is composed of a pleomorphic membrane vesicle enclosing the genome. All pleolipoviruses have two major structural protein species, internal membrane and spike proteins. Although the genomes of the pleolipoviruses are single- or double-stranded, linear or circular DNA molecules, they share the same genome organization and gene synteny and show significant similarity at the amino acid level. The canonical features common to all members of the proposed family Pleolipoviridae show that they are closely related and thus form a new viral family.
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Affiliation(s)
- Maija K Pietilä
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Elina Roine
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Ana Sencilo
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the ASCR, v.v.i., Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland.
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26
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Liu Y, Wang J, Liu Y, Wang Y, Zhang Z, Oksanen HM, Bamford DH, Chen X. Identification and characterization of SNJ2, the first temperate pleolipovirus integrating into the genome of the SNJ1-lysogenic archaeal strain. Mol Microbiol 2015; 98:1002-20. [PMID: 26331239 DOI: 10.1111/mmi.13204] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2015] [Indexed: 11/29/2022]
Abstract
Proviral regions have been identified in the genomes of many haloarchaea, but only a few archaeal halophilic temperate viruses have been studied. Here, we report a new virus, SNJ2, originating from archaeal strain Natrinema sp. J7-1. We demonstrate that this temperate virus coexists with SNJ1 virus and is dependent on SNJ1 for efficient production. Here, we show that SNJ1 is an icosahedral membrane-containing virus, whereas SNJ2 is a pleomorphic one. Instead of producing progeny virions and forming plaques, SNJ2 integrates into the host tRNA(Met) gene. The virion contains a discontinuous, circular, double-stranded DNA genome of 16 992 bp, in which both nicks and single-stranded regions are present preceded by a 'GCCCA' motif. Among 25 putative SNJ2 open reading frames (ORFs), five of them form a cluster of conserved ORFs homologous to archaeal pleolipoviruses isolated from hypersaline environments. Two structural protein encoding genes in the conserved cluster were verified in SNJ2. Furthermore, SNJ2-like proviruses containing the conserved gene cluster were identified in the chromosomes of archaea belonging to 10 different genera. Comparison of SNJ2 and these proviruses suggests that they employ a similar integration strategy into a tRNA gene.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yang Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuchen Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ziqian Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hanna M Oksanen
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, 00014, Helsinki, Finland
| | - Dennis H Bamford
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, 00014, Helsinki, Finland
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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27
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Abstract
Hypersaline waters and salt crystals are known to contain high numbers of haloarchaeal cells and their viruses. Both culture-dependent and culture-independent studies indicate that these viruses represent a world-wide distributed reservoir of orphan genes and possibly novel virion morphotypes. To date, 90 viruses have been described for halophilic archaeal hosts, all belonging to the Halobacteriaceae family. This number is higher than that described for the members of any other archaeal family, but still very low compared to the viruses of bacteria and eukaryotes. The known haloarchaeal viruses represent icosahedral tailed, icosahedral internal membrane-containing, pleomorphic, and spindle-shaped virion morphotypes. This morphotype distribution is low, especially when compared to the astronomical number (>10(31)) of viruses on Earth. This strongly suggests that only certain protein folds are capable of making a functional virion. Viruses infecting cells belonging to any of the three domains of life are known to share similar major capsid protein folds which can be used to classify viruses into structure-based lineages. The latest observation supporting this proposal comes from the studies of icosahedral tailed haloarchaeal viruses which are the most abundant virus isolates from hypersaline environments. These viruses were shown to have the same major capsid protein fold (HK97-fold) with tailed bacteriophages belonging to the order Caudovirales and with eukaryotic herpes viruses. This proposes that these viruses have a common origin dating back to ancient times. Here we summarize the current knowledge of haloarchaeal viruses from the perspective of virus morphotypes.
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Haloviruses of archaea, bacteria, and eukaryotes. Curr Opin Microbiol 2015; 25:40-8. [DOI: 10.1016/j.mib.2015.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/06/2015] [Indexed: 02/04/2023]
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29
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Atanasova NS, Senčilo A, Pietilä MK, Roine E, Oksanen HM, Bamford DH. Comparison of lipid-containing bacterial and archaeal viruses. Adv Virus Res 2015; 92:1-61. [PMID: 25701885 DOI: 10.1016/bs.aivir.2014.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Lipid-containing bacteriophages were discovered late and considered to be rare. After further phage isolations and the establishment of the domain Archaea, several new prokaryotic viruses with lipids were observed. Consequently, the presence of lipids in prokaryotic viruses is reasonably common. The wealth of information about how prokaryotic viruses use their lipids comes from a few well-studied model viruses (PM2, PRD1, and ϕ6). These bacteriophages derive their lipid membranes selectively from the host during the virion assembly process which, in the case of PM2 and PRD1, culminates in the formation of protein capsid with an inner membrane, and for ϕ6 an outer envelope. Several inner membrane-containing viruses have been described for archaea, and their lipid acquisition models are reminiscent to those of PM2 and PRD1. Unselective acquisition of lipids has been observed for bacterial mycoplasmaviruses and archaeal pleolipoviruses, which resemble each other by size, morphology, and life style. In addition to these shared morphotypes of bacterial and archaeal viruses, archaea are infected by viruses with unique morphotypes, such as lemon-shaped, helical, and globular ones. It appears that structurally related viruses may or may not have a lipid component in the virion, suggesting that the significance of viral lipids might be to provide viruses extended means to interact with the host cell.
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Affiliation(s)
- Nina S Atanasova
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ana Senčilo
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maija K Pietilä
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Elina Roine
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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30
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Luk AWS, Williams TJ, Erdmann S, Papke RT, Cavicchioli R. Viruses of haloarchaea. Life (Basel) 2014; 4:681-715. [PMID: 25402735 PMCID: PMC4284463 DOI: 10.3390/life4040681] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 12/26/2022] Open
Abstract
In hypersaline environments, haloarchaea (halophilic members of the Archaea) are the dominant organisms, and the viruses that infect them, haloarchaeoviruses are at least ten times more abundant. Since their discovery in 1974, described haloarchaeoviruses include head-tailed, pleomorphic, spherical and spindle-shaped morphologies, representing Myoviridae, Siphoviridae, Podoviridae, Pleolipoviridae, Sphaerolipoviridae and Fuselloviridae families. This review overviews current knowledge of haloarchaeoviruses, providing information about classification, morphotypes, macromolecules, life cycles, genetic manipulation and gene regulation, and host-virus responses. In so doing, the review incorporates knowledge from laboratory studies of isolated viruses, field-based studies of environmental samples, and both genomic and metagenomic analyses of haloarchaeoviruses. What emerges is that some haloarchaeoviruses possess unique morphological and life cycle properties, while others share features with other viruses (e.g., bacteriophages). Their interactions with hosts influence community structure and evolution of populations that exist in hypersaline environments as diverse as seawater evaporation ponds, to hot desert or Antarctic lakes. The discoveries of their wide-ranging and important roles in the ecology and evolution of hypersaline communities serves as a strong motivator for future investigations of both laboratory-model and environmental systems.
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Affiliation(s)
- Alison W S Luk
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Susanne Erdmann
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA.
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
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31
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Clokie MR, Millard AD, Letarov AV, Heaphy S. Phages in nature. BACTERIOPHAGE 2014; 1:31-45. [PMID: 21687533 DOI: 10.4161/bact.1.1.14942] [Citation(s) in RCA: 646] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 12/28/2022]
Abstract
Bacteriophages or phages are the most abundant organisms in the biosphere and they are a ubiquitous feature of prokaryotic existence. A bacteriophage is a virus which infects a bacterium. Archaea are also infected by viruses, whether these should be referred to as 'phages' is debatable, but they are included as such in the scope this article. Phages have been of interest to scientists as tools to understand fundamental molecular biology, as vectors of horizontal gene transfer and drivers of bacterial evolution, as sources of diagnostic and genetic tools and as novel therapeutic agents. Unraveling the biology of phages and their relationship with their hosts is key to understanding microbial systems and their exploitation. In this article we describe the roles of phages in different host systems and show how modeling, microscopy, isolation, genomic and metagenomic based approaches have come together to provide unparalleled insights into these small but vital constituents of the microbial world.
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Affiliation(s)
- Martha Rj Clokie
- Department of Infection, Immunity and Inflammation; Medical Sciences Building; University of Leicester; Leicester, UK
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32
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Abstract
The Archaea-and their viruses-remain the most enigmatic of life's three domains. Once thought to inhabit only extreme environments, archaea are now known to inhabit diverse environments. Even though the first archaeal virus was described over 40 years ago, only 117 archaeal viruses have been discovered to date. Despite this small number, these viruses have painted a portrait of enormous morphological and genetic diversity. For example, research centered around the various steps of the archaeal virus life cycle has led to the discovery of unique mechanisms employed by archaeal viruses during replication, maturation, and virion release. In many instances, archaeal virus proteins display very low levels of sequence homology to other proteins listed in the public database, and therefore, structural characterization of these proteins has played an integral role in functional assignment. These structural studies have not only provided insights into structure-function relationships but have also identified links between viruses across all three domains of life.
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Affiliation(s)
- Nikki Dellas
- Thermal Biology Institute and Departments of.,Plant Sciences and
| | - Jamie C Snyder
- Thermal Biology Institute and Departments of.,Plant Sciences and
| | - Benjamin Bolduc
- Thermal Biology Institute and Departments of.,Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717;
| | - Mark J Young
- Thermal Biology Institute and Departments of.,Plant Sciences and
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33
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Pietilä MK, Demina TA, Atanasova NS, Oksanen HM, Bamford DH. Archaeal viruses and bacteriophages: comparisons and contrasts. Trends Microbiol 2014; 22:334-44. [PMID: 24647075 DOI: 10.1016/j.tim.2014.02.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/14/2014] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
Abstract
Isolated archaeal viruses comprise only a few percent of all known prokaryotic viruses. Thus, the study of viruses infecting archaea is still in its early stages. Here we summarize the most recent discoveries of archaeal viruses utilizing a virion-centered view. We describe the known archaeal virion morphotypes and compare them to the bacterial counterparts, if such exist. Viruses infecting archaea are morphologically diverse and present some unique morphotypes. Although limited in isolate number, archaeal viruses reveal new insights into the viral world, such as deep evolutionary relationships between viruses that infect hosts from all three domains of life.
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Affiliation(s)
- Maija K Pietilä
- Institute of Biotechnology and Department of Biosciences, P.O. Box 56, Viikinkaari 5, 00014 University of Helsinki, Helsinki, Finland
| | - Tatiana A Demina
- Institute of Biotechnology and Department of Biosciences, P.O. Box 56, Viikinkaari 5, 00014 University of Helsinki, Helsinki, Finland
| | - Nina S Atanasova
- Institute of Biotechnology and Department of Biosciences, P.O. Box 56, Viikinkaari 5, 00014 University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Institute of Biotechnology and Department of Biosciences, P.O. Box 56, Viikinkaari 5, 00014 University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Institute of Biotechnology and Department of Biosciences, P.O. Box 56, Viikinkaari 5, 00014 University of Helsinki, Helsinki, Finland.
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34
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Pawlowski A, Rissanen I, Bamford JKH, Krupovic M, Jalasvuori M. Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae. Arch Virol 2014; 159:1541-54. [PMID: 24395078 DOI: 10.1007/s00705-013-1970-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/20/2013] [Indexed: 11/30/2022]
Abstract
A new family of viruses named Sphaerolipoviridae has been proposed recently. It comprises icosahedral, tailless haloarchaeal viruses with an internal lipid membrane located between the protein capsid and the dsDNA genome. The proposed family Sphaerolipoviridae was divided into two genera: Alphasphaerolipovirus, including Haloarcula hispanica viruses SH1, PH1 and HHIV-2, and Betasphaerolipovirus, including Natrinema virus SNJ1. Here, we propose to expand the family Sphaerolipoviridae to include a group of bacteriophages infecting extreme thermophilic Thermus thermophilus and sharing a number of structural and genomic properties with archaeal sphaerolipoviruses. This new group comprises two members, lytic phage P23-77 and temperate phage IN93, as well as putative members P23-72 and P23-65H. In addition, several related proviruses have been discovered as integrated elements in bacterial genomes of the families Thermus and Meiothermus. Morphology of the virus particles and the overall capsid architecture of these bacteriophages resembles that of archaeal members of the Sphaerolipoviridae, including an unusual capsid arrangement in a T = 28 dextro lattice. Alpha- and betasphaerolipoviruses share with P23-77-like bacteriophages a conserved block of core genes that encode a putative genome-packaging ATPase and the two major capsid proteins (MCPs). The recently determined X-ray structure of the small and large MCPs of P23-77 revealed a single beta-barrel (jelly-roll) fold that is superimposable with the cryo-EM density maps of the SH1 capsomers. Given the common features of these viruses, we propose to include the so far unclassified P23-77-like bacteriophages into a new genus, "Gammasphaerolipovirus", within the family Sphaerolipoviridae.
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Affiliation(s)
- Alice Pawlowski
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, 40014, Jyväskylä, Finland
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35
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Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol 2013; 3:578-86. [PMID: 23850154 DOI: 10.1016/j.coviro.2013.06.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 06/13/2013] [Accepted: 06/17/2013] [Indexed: 11/22/2022]
Abstract
Viruses with single-stranded (ss) DNA genomes infect hosts from all three domains of life and are present in all imaginable environments. Many new ssDNA viruses have been recently isolated, including those infecting algae, fungi, insects and even archaea. In parallel, culture-independent metagenomic approaches have illuminated the tremendous genetic diversity of these viruses, yielding valuable insights into their evolution. Here, I integrate this knowledge to propose a scenario in which certain groups of ssDNA viruses (including Geminiviridae, Circoviridae, Parvoviridae and Microviridae) have originated from plasmids via acquisition of jelly-roll capsid protein genes from ssRNA viruses. This scenario places structurally related viruses with DNA and RNA genomes into an evolutionary continuum and highlights general evolutionary trends in the virosphere.
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36
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Krupovic M, White MF, Forterre P, Prangishvili D. Postcards from the edge: structural genomics of archaeal viruses. Adv Virus Res 2013; 82:33-62. [PMID: 22420850 DOI: 10.1016/b978-0-12-394621-8.00012-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ever since their discovery, archaeal viruses have fascinated biologists with their unusual virion morphotypes and their ability to thrive in extreme environments. Attempts to understand the biology of these viruses through genome sequence analysis were not efficient. Genomes of archaeoviruses proved to be terra incognita with only a few genes with predictable functions but uncertain provenance. In order to facilitate functional characterization of archaeal virus proteins, several research groups undertook a structural genomics approach. This chapter summarizes the outcome of these efforts. High-resolution structures of 30 proteins encoded by archaeal viruses have been solved so far. Some of these proteins possess new structural folds, whereas others display previously known topologies, albeit without detectable sequence similarity to their structural homologues. Structures of the major capsid proteins have illuminated intriguing evolutionary connections between viruses infecting hosts from different domains of life and also revealed new structural folds not yet observed in currently known bacterial and eukaryotic viruses. Structural studies, discussed here, have advanced our understanding of the archaeal virosphere and provided precious information on different aspects of biology of archaeal viruses and evolution of viruses in general.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Paris, France
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37
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Abstract
Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice.
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38
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Pietilä MK, Atanasova NS, Oksanen HM, Bamford DH. Modified coat protein forms the flexible spindle-shaped virion of haloarchaeal virus His1. Environ Microbiol 2012; 15:1674-86. [PMID: 23163639 DOI: 10.1111/1462-2920.12030] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 10/12/2012] [Indexed: 11/28/2022]
Abstract
Extremophiles are found in all three domains of cellular life. However, hyperthermic and hypersaline environments are typically dominated by archaeal cells which also hold the records for the highest growth temperature and are able to grow even at saturated salinity. Hypersaline environments are rich of virus-like particles, and spindle-shaped virions resembling lemons are one of the most abundant virus morphotypes. Spindle-shaped viruses are archaea-specific as all the about 15 such virus isolates infect either hyperthermophilic or halophilic archaea. In the present work, we studied spindle-shaped virus His1 infecting an extremely halophilic euryarchaeon, Haloarcula hispanica. We demonstrate that His1 tolerates a variety of salinities, even lower than that of seawater. The detailed analysis of the structural constituents showed that the His1 virion is composed of only one major and a few minor structural proteins. There is no lipid bilayer in the His1 virion but the major structural protein VP21 is most likely lipid modified. VP21 forms the virion capsid, and the lipid modification probably enables hydrophobic interactions leading to the flexible nature of the virion. Furthermore, we propose that euryarchaeal virus His1 may be related to crenarchaeal fuselloviruses, and that the short-tailed spindle-shaped viruses could form a structure-based viral lineage.
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Affiliation(s)
- Maija K Pietilä
- Institute of Biotechnology, University of Helsinki, PO Box 56, Viikinkaari 5, Helsinki 00014, Finland
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39
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Lipids of archaeal viruses. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:384919. [PMID: 23049284 PMCID: PMC3461281 DOI: 10.1155/2012/384919] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 08/13/2012] [Indexed: 11/17/2022]
Abstract
Archaeal viruses represent one of the least known territory of the viral universe and even less is known about their lipids. Based on the current knowledge, however, it seems that, as in other viruses, archaeal viral lipids are mostly incorporated into membranes that reside either as outer envelopes or membranes inside an icosahedral capsid. Mechanisms for the membrane acquisition seem to be similar to those of viruses infecting other host organisms. There are indications that also some proteins of archaeal viruses are lipid modified. Further studies on the characterization of lipids in archaeal viruses as well as on their role in virion assembly and infectivity require not only highly purified viral material but also, for example, constant evaluation of the adaptability of emerging technologies for their analysis. Biological membranes contain proteins and membranes of archaeal viruses are not an exception. Archaeal viruses as relatively simple systems can be used as excellent tools for studying the lipid protein interactions in archaeal membranes.
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40
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Kandiba L, Aitio O, Helin J, Guan Z, Permi P, Bamford DH, Eichler J, Roine E. Diversity in prokaryotic glycosylation: an archaeal-derived N-linked glycan contains legionaminic acid. Mol Microbiol 2012; 84:578-93. [PMID: 22435790 DOI: 10.1111/j.1365-2958.2012.08045.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
VP4, the major structural protein of the haloarchaeal pleomorphic virus, HRPV-1, is glycosylated. To define the glycan structure attached to this protein, oligosaccharides released by β-elimination were analysed by mass spectrometry and nuclear magnetic resonance spectroscopy. Such analyses showed that the major VP4-derived glycan is a pentasaccharide comprising glucose, glucuronic acid, mannose, sulphated glucuronic acid and a terminal 5-N-formyl-legionaminic acid residue. This is the first observation of legionaminic acid, a sialic acid-like sugar, in an archaeal-derived glycan structure. The importance of this residue for viral infection was demonstrated upon incubation with N-acetylneuraminic acid, a similar monosaccharide. Such treatment reduced progeny virus production by half 4 h post infection. LC-ESI/MS analysis confirmed the presence of pentasaccharide precursors on two different VP4-derived peptides bearing the N-glycosylation signal, NTT. The same sites modified by the native host, Halorubrum sp. strain PV6, were also recognized by the Haloferax volcanii N-glycosylation apparatus, as determined by LC-ESI/MS of heterologously expressed VP4. Here, however, the N-linked pentasaccharide was the same as shown to decorate the S-layer glycoprotein in this species. Hence, N-glycosylation of the haloarchaeal viral protein, VP4, is host-specific. These results thus present additional examples of archaeal N-glycosylation diversity and show the ability of Archaea to modify heterologously expressed proteins.
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Affiliation(s)
- Lina Kandiba
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 84105, Israel
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41
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Sencilo A, Paulin L, Kellner S, Helm M, Roine E. Related haloarchaeal pleomorphic viruses contain different genome types. Nucleic Acids Res 2012; 40:5523-34. [PMID: 22396526 PMCID: PMC3384331 DOI: 10.1093/nar/gks215] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Archaeal viruses have been the subject of recent interest due to the diversity discovered in their virion architectures. Recently, a new group of haloarchaeal pleomorphic viruses has been discovered. It is distinctive in terms of the virion morphology and different genome types (ssDNA/dsDNA) harboured by rather closely related representatives. To date there are seven isolated viruses belonging to this group. Most of these share a cluster of five conserved genes, two of which encode major structural proteins. Putative proviruses and proviral remnants containing homologues of the conserved gene cluster were also identified suggesting a long-standing relationship of these viruses with their hosts. Comparative genomic analysis revealed three different ways of the genome organization, which possibly reflect different replication strategies employed by these viruses. The dsDNA genomes of two of these viruses were shown to contain single-strand interruptions. Further studies on one of the genomes suggested that the interruptions are located along the genome in a sequence-specific manner and exhibit polarity in distribution.
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Affiliation(s)
- Ana Sencilo
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, P.O. Box 56, FIN-00014 University of Helsinki, Finland
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42
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Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J Virol 2012; 86:5067-79. [PMID: 22357279 DOI: 10.1128/jvi.06915-11] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our understanding of the third domain of life, Archaea, has greatly increased since its establishment some 20 years ago. The increasing information on archaea has also brought their viruses into the limelight. Today, about 100 archaeal viruses are known, which is a low number compared to the numbers of characterized bacterial or eukaryotic viruses. Here, we have performed a comparative biological and structural study of seven pleomorphic viruses infecting extremely halophilic archaea. The pleomorphic nature of this novel virion type was established by sedimentation analysis and cryo-electron microscopy. These nonlytic viruses form virions characterized by a lipid vesicle enclosing the genome, without any nucleoproteins. The viral lipids are unselectively acquired from host cell membranes. The virions contain two to three major structural proteins, which either are embedded in the membrane or form spikes distributed randomly on the external membrane surface. Thus, the most important step during virion assembly is most likely the interaction of the membrane proteins with the genome. The interaction can be driven by single-stranded or double-stranded DNA, resulting in the virions having similar architectures but different genome types. Based on our comparative study, these viruses probably form a novel group, which we define as pleolipoviruses.
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43
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Atanasova NS, Roine E, Oren A, Bamford DH, Oksanen HM. Global network of specific virus-host interactions in hypersaline environments. Environ Microbiol 2011; 14:426-40. [PMID: 22003883 DOI: 10.1111/j.1462-2920.2011.02603.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hypersaline environments are dominated by archaea and bacteria and are almost entirely devoid of eukaryotic organisms. In addition, hypersaline environments contain considerable numbers of viruses. Currently, there is only a limited amount of information about these haloviruses. The ones described in detail mostly resemble head-tail bacteriophages, whereas observations based on direct microscopy of the hypersaline environmental samples highlight the abundance of non-tailed virus-like particles. Here we studied nine spatially distant hypersaline environments for the isolation of new halophilic archaea (61 isolates), halophilic bacteria (24 isolates) and their viruses (49 isolates) using a culture-dependent approach. The obtained virus isolates approximately double the number of currently described archaeal viruses. The new isolates could be divided into three tailed and two non-tailed virus morphotypes, suggesting that both types of viruses are widely distributed and characteristic for haloarchaeal viruses. We determined the sensitivity of the hosts against all isolated viruses. It appeared that the host ranges of numerous viruses extend to hosts in distant locations, supporting the idea that there is a global exchange of microbes and their viruses. It suggests that hypersaline environments worldwide function like a single habitat.
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Affiliation(s)
- Nina S Atanasova
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Viikinkaari 5, Helsinki, Finland
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44
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Abstract
Since their discovery in the early 1980s, viruses that infect the third domain of life, the Archaea, have captivated our attention because of their virions' unusual morphologies and proteins, which lack homologues in extant databases. Moreover, the life cycles of these viruses have unusual features, as revealed by the recent discovery of a novel virus egress mechanism that involves the formation of specific pyramidal structures on the host cell surface. The available data elucidate the particular nature of the archaeal virosphere and shed light on questions concerning the origin and evolution of viruses and cells. In this review, we summarize the current knowledge of archeoviruses, their interaction with hosts and plasmids and their role in the evolution of life.
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Affiliation(s)
- Mery Pina
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Paris, France
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45
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46
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Claverie JM, Abergel C. Mimivirus: the emerging paradox of quasi-autonomous viruses. Trends Genet 2010; 26:431-7. [PMID: 20696492 DOI: 10.1016/j.tig.2010.07.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 07/04/2010] [Accepted: 07/15/2010] [Indexed: 11/16/2022]
Abstract
What is a virus? Are viruses alive? Should they be classified among microorganisms? One would expect these simple questions to have been settled a century after the discovery of the first viral disease. For years, modern virology successfully unravelled the huge diversity of viruses in terms of genetic material, replication mechanism, pathogenicity, host infection, and more recently particle structure, planet-wide distribution and ecological significance. Yet, little progress was made in understanding their evolutionary origin(s), as well as the fundamental nature of their relationship with the cellular world. Thanks to the recent studies on Mimivirus and other large DNA viruses, we are now entering a new era where the most basic concepts about viruses are revisited, including their true nature, how fundamentally different they are from cellular microorganisms, and how essential they might have been in the major innovations that punctuated the evolution of life.
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Affiliation(s)
- Jean-Michel Claverie
- Structural and Genomic Information Laboratory, CNRS-UPR 2589, Aix-Marseille University, Mediterranean Institute of Microbiology, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France.
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New, closely related haloarchaeal viral elements with different nucleic Acid types. J Virol 2010; 84:3682-9. [PMID: 20089654 DOI: 10.1128/jvi.01879-09] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the search for haloarchaeal viruses, we isolated and characterized a new pleomorphic lipid-containing virus, Haloarcula hispanica pleomorphic virus 1 (HHPV-1), that infects the halophilic archaeon Haloarcula hispanica. The virus contains a circular double-stranded DNA genome of 8,082 bp in size. The organization of the genome shows remarkable synteny and amino acid sequence similarity to the genome and predicted proteins of the halovirus HRPV-1, a pleomorphic single-stranded DNA virus that infects a halophilic archaeon Halorubrum sp. Analysis of the two halovirus sequences, as well as the entire nucleotide sequence of the 10.8-kb pHK2-plasmid and a 12.6-kb chromosomal region in Haloferax volcanii, allows us to suggest a new group of closely related viruses with genomes of either single-stranded or double-stranded DNA. Currently, closely related viruses are considered to have the same genome type. Our observation clearly contradicts this categorization and indicates that we should reconsider the way we classify viruses. Our results also provide a new example of related viruses where the viral structural proteins have not diverged as much as the proteins associated with genome replication. This result further strengthens the proposal for higher-order classification to be based on virion architecture rather than on genome type or replication mechanism.
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