RESUMO
Viruses infecting hyperthermophilic archaea of the phylum Crenarchaeota display enormous morphological and genetic diversity, and are classified into 12 families. Eight of these families include only one or two species, indicating sparse sampling of the crenarchaeal virus diversity. In an attempt to expand the crenarchaeal virome, we explored virus diversity in the acidic, hot spring Umi Jigoku in Beppu, Japan. Environmental samples were used to establish enrichment cultures under conditions favouring virus replication. The host diversity in the enrichment cultures was restricted to members of the order Sulfolobales. Metagenomic sequencing of the viral communities yielded seven complete or near-complete double-stranded DNA virus genomes. Six of these genomes could be attributed to polyhedral and filamentous viruses that were observed by electron microscopy in the enrichment cultures. Two icosahedral viruses represented species in the family Portogloboviridae. Among the filamentous viruses, two were identified as new species in the families Rudiviridae and Lipothrixviridae, whereas two other formed a group seemingly distinct from the known virus genera. No particle morphotype could be unequivocally assigned to the seventh viral genome, which apparently represents a new virus type. Our results suggest that filamentous viruses are globally distributed and are prevalent virus types in extreme geothermal environments.
Assuntos
Archaea/virologia , Vírus de Archaea/isolamento & purificação , Bacteriófagos/isolamento & purificação , Fontes Termais/virologia , Rudiviridae/genética , Rudiviridae/isolamento & purificação , Archaea/genética , Archaea/isolamento & purificação , Vírus de Archaea/classificação , Vírus de Archaea/genética , Vírus de Archaea/fisiologia , Bacteriófagos/classificação , Bacteriófagos/genética , Bacteriófagos/fisiologia , Genoma Viral , Fontes Termais/química , Japão , Lipothrixviridae/classificação , Lipothrixviridae/genética , Lipothrixviridae/isolamento & purificação , Lipothrixviridae/fisiologia , Metagenoma , Filogenia , Rudiviridae/classificação , Replicação ViralRESUMO
Screening for viruses in samples taken from acidic hot springs of Kamchatka (Russia) revealed a collection of morphotypes, including linear, spherical and complex fusiform shapes, which show partial similarity to those found in acidic geothermal environments in other geographical locations. One of the viruses, Acidianus filamentous virus 9, AFV9, was isolated and its structure and genome were studied in detail.
Assuntos
Acidianus/virologia , Fontes Termais/virologia , Lipothrixviridae/isolamento & purificação , Acidianus/classificação , Acidianus/genética , Ácidos , Genoma Viral , Interações Hospedeiro-Patógeno , Lipothrixviridae/genética , Lipothrixviridae/ultraestrutura , Dados de Sequência Molecular , Filogenia , Federação Russa , Proteínas Virais/genética , Proteínas Virais/metabolismo , Vírion/classificação , Vírion/genética , Vírion/isolamento & purificação , Vírion/ultraestruturaRESUMO
Four novel filamentous viruses with double-stranded DNA genomes, namely, Acidianus filamentous virus 3 (AFV3), AFV6, AFV7, and AFV8, have been characterized from the hyperthermophilic archaeal genus Acidianus, and they are assigned to the Betalipothrixvirus genus of the family Lipothrixviridae. The structures of the approximately 2-mum-long virions are similar, and one of them, AFV3, was studied in detail. It consists of a cylindrical envelope containing globular subunits arranged in a helical formation that is unique for any known double-stranded DNA virus. The envelope is 3.1 nm thick and encases an inner core with two parallel rows of protein subunits arranged like a zipper. Each end of the virion is tapered and carries three short filaments. Two major structural proteins were identified as being common to all betalipothrixviruses. The viral genomes were sequenced and analyzed, and they reveal a high level of conservation in both gene content and gene order over large regions, with this similarity extending partly to the earlier described betalipothrixvirus Sulfolobus islandicus filamentous virus. A few predicted gene products of each virus, in addition to the structural proteins, could be assigned specific functions, including a putative helicase involved in Holliday junction branch migration, a nuclease, a protein phosphatase, transcriptional regulators, and glycosyltransferases. The AFV7 genome appears to have undergone intergenomic recombination with a large section of an AFV2-like viral genome, apparently resulting in phenotypic changes, as revealed by the presence of AFV2-like termini in the AFV7 virions. Shared features of the genomes include (i) large inverted terminal repeats exhibiting conserved, regularly spaced direct repeats; (ii) a highly conserved operon encoding the two major structural proteins; (iii) multiple overlapping open reading frames, which may be indicative of gene recoding; (iv) putative 12-bp genetic elements; and (v) partial gene sequences corresponding closely to spacer sequences of chromosomal repeat clusters.
Assuntos
Acidianus/virologia , Genoma Viral/genética , Lipothrixviridae/classificação , Lipothrixviridae/ultraestrutura , Sequência Conservada/genética , Microscopia Crioeletrônica , Ordem dos Genes , Lipothrixviridae/genética , Lipothrixviridae/isolamento & purificação , Microscopia Eletrônica de Transmissão , Dados de Sequência Molecular , Óperon , Análise de Sequência de DNA , Sequências Repetidas Terminais/genética , Proteínas não Estruturais Virais/genética , Proteínas Estruturais Virais/análise , Vírion/química , Vírion/ultraestruturaRESUMO
The crenarchaeote Sulfolobus spp. is a host for a remarkably large spectrum of viruses and plasmids. The genetic elements characterized so far indicate a large degree of novelty in terms of morphology (viruses) and in terms of genome content (plasmids and viruses). The viruses and conjugative plasmids encode a great number of conserved proteins of unknown function due to the lack of sequence similarity to functionally characterized proteins. These apparently essential proteins remain to be studied and should help to understand the physiology and genetics of the respective genetic elements as well as the host. Sulfolobus is one of the best-studied archaeons and could develop into an important model organism of the crenarchaea and the archaea.
Assuntos
Vírus de Archaea/genética , Plasmídeos/genética , Sulfolobus/genética , Sulfolobus/virologia , Sequência de Aminoácidos , Proteínas Arqueais/genética , Vírus de Archaea/classificação , Vírus de Archaea/isolamento & purificação , Sequência de Bases , Conjugação Genética , DNA Arqueal/genética , DNA Arqueal/isolamento & purificação , Fuselloviridae/genética , Fuselloviridae/isolamento & purificação , Genoma Viral , Guttaviridae/genética , Guttaviridae/isolamento & purificação , Lipothrixviridae/genética , Lipothrixviridae/isolamento & purificação , Dados de Sequência Molecular , Plasmídeos/isolamento & purificação , Rudiviridae/genética , Rudiviridae/isolamento & purificação , Homologia de Sequência de Aminoácidos , Homologia de Sequência do Ácido Nucleico , Sulfolobus/enzimologiaRESUMO
We describe a novel virus, AFV1, of the hyperthermophilic archaeal genus Acidianus. Filamentous virions are covered with a lipid envelope and contain at least five different proteins with molecular masses in the range of 23-130 kDa and a 20.8-kb-long linear double-stranded DNA. The virus has been assigned to the family Lipothrixviridae on the basis of morphotypic characteristics. Host range is confined to several strains of Acidianus and the virus persists in its hosts in a stable carrier state. The latent period of virus infection is about 4 h. Viral DNA was sequenced and sequence similarities were found to the lipothrixvirus SIFV, the rudiviruses SIRV1 and SIRV2, as well as to conjugative plasmids and chromosomes of the genus Sulfolobus. Exceptionally for the linear genomes of archaeal viruses, many short direct repeats, with the sequence TTGTT or close variants thereof, are closely clustered over 300 bp at each end of the genome. They are reminiscent of the telomeric ends of linear eukaryal chromosomes.
Assuntos
Acidianus/virologia , Temperatura Alta , Lipothrixviridae/classificação , Lipothrixviridae/isolamento & purificação , Acidianus/crescimento & desenvolvimento , Sequência de Bases , Genoma Viral , Lipothrixviridae/genética , Lipothrixviridae/ultraestrutura , Microscopia Eletrônica , Dados de Sequência Molecular , Fases de Leitura Aberta , Análise de Sequência de DNA , Proteínas Virais/química , Proteínas Virais/genética , Proteínas Virais/metabolismo , Vírion/ultraestruturaRESUMO
Electron microscopic studies of the viruses in two hot springs (85 degrees C, pH 1.5-2.0, and 75-93 degrees C, pH 6.5) in Yellowstone National Park revealed particles with twelve different morphotypes. This diversity encompassed known viruses of hyperthermophilic archaea, filamentous Lipothrixviridae, rod-shaped Rudiviridae, and spindle-shaped Fuselloviridae, and novel morphotypes previously not observed in nature. Two virus types resembled head-and-tail bacteriophages from the families Siphoviridae and Podoviridae, and constituted the first observation of these viruses in a hydrothermal environment. Viral hosts in the acidic spring were members of the hyperthermophilic archaeal genus Acidianus.