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2.
PLoS One ; 15(4): e0231864, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32302368

RESUMO

Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydrocarbon pollution in environmental (soil and water) samples. It was highly abundant in Hungarian hydrocarbon polluted samples and its genome was also present in the NCBI SRA database containing reads from hydrocarbon polluted samples collected in Canada, indicating the stability of its niche and the marker feature of this virus. MetMV, as the only currently identified marker virus for pollution in environmental samples, could contribute to the understanding of the complicated network of prokaryotes and their viruses driving the decomposition of environmental pollutants.


Assuntos
Archaea/virologia , Vírus de Archaea/isolamento & purificação , Poluição Ambiental/análise , Hidrocarbonetos/análise , Archaea/isolamento & purificação , Vírus de Archaea/genética , Canadá , DNA Viral/química , DNA Viral/metabolismo , Genoma Viral , Hungria , Microbiologia do Solo , Microbiologia da Água
4.
Nat Commun ; 10(1): 5442, 2019 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-31784519

RESUMO

Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and was proposed to protect phage DNA from a wide variety of restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, which are all intermediates of the same pathway, in viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine (dPreQ0) and 2'-deoxy-7- aminomethyl-7-deazaguanine (dPreQ1). We identify 180 phages or archaeal viruses that encode at least one of the enzymes of this pathway with an overrepresentation (60%) of viruses potentially infecting pathogenic microbial hosts. Genetic studies with the Escherichia phage CAjan show that DpdA is essential to insert the 7-deazaguanine base in phage genomic DNA and that 2'-deoxy-7-deazaguanine modifications protect phage DNA from host restriction enzymes.


Assuntos
Vírus de Archaea/genética , Bacteriófagos/genética , Enzimas de Restrição do DNA/metabolismo , DNA/metabolismo , Guanina/análogos & derivados , Bacteriófagos/metabolismo , Guanina/metabolismo , Pirimidinonas/metabolismo , Pirróis/metabolismo
5.
Nat Commun ; 10(1): 5204, 2019 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-31729390

RESUMO

CRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome-all spacers contained in a microbiome-associated with hyperthermophilic archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some archaeal viruses carry mini-CRISPR arrays with 1-2 spacers and preceded by leader sequences but devoid of cas genes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote archaeal virus speciation.


Assuntos
Vírus de Archaea/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Archaea/virologia , Vírus de Archaea/classificação , Vírus de Archaea/isolamento & purificação , Sequência de Bases , Evolução Molecular , Genoma Viral , Filogenia
6.
Proc Natl Acad Sci U S A ; 116(45): 22591-22597, 2019 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-31636205

RESUMO

Studies on viruses infecting archaea living in the most extreme environments continue to show a remarkable diversity of structures, suggesting that the sampling continues to be very sparse. We have used electron cryo-microscopy to study at 3.7-Å resolution the structure of the Sulfolobus polyhedral virus 1 (SPV1), which was originally isolated from a hot, acidic spring in Beppu, Japan. The 2 capsid proteins with variant single jelly-roll folds form pentamers and hexamers which assemble into a T = 43 icosahedral shell. In contrast to tailed icosahedral double-stranded DNA (dsDNA) viruses infecting bacteria and archaea, and herpesviruses infecting animals and humans, where naked DNA is packed under very high pressure due to the repulsion between adjacent layers of DNA, the circular dsDNA in SPV1 is fully covered with a viral protein forming a nucleoprotein filament with attractive interactions between layers. Most strikingly, we have been able to show that the DNA is in an A-form, as it is in the filamentous viruses infecting hyperthermophilic acidophiles. Previous studies have suggested that DNA is in the B-form in bacteriophages, and our study is a direct visualization of the structure of DNA in an icosahedral virus.


Assuntos
Vírus de Archaea/fisiologia , Vírus de DNA/fisiologia , DNA Forma A/genética , DNA Viral/genética , Montagem de Vírus , Vírus de Archaea/genética , Vírus de Archaea/ultraestrutura , Capsídeo/metabolismo , Capsídeo/ultraestrutura , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/metabolismo , Microscopia Crioeletrônica , Vírus de DNA/genética , Vírus de DNA/ultraestrutura , DNA Forma A/metabolismo , DNA Viral/metabolismo , Sulfolobus/virologia
7.
Nat Microbiol ; 4(11): 1895-1906, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31332386

RESUMO

Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin-antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.


Assuntos
Archaea/virologia , Bactérias/virologia , Biologia Computacional/métodos , Inoviridae/classificação , Vírus de Archaea/classificação , Vírus de Archaea/genética , Bacteriófagos/classificação , Bacteriófagos/genética , Genoma Viral , Inoviridae/genética , Aprendizado de Máquina , Filogenia
8.
J Bacteriol ; 201(12)2019 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-30936372

RESUMO

Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems incorporate short DNA fragments from invasive genetic elements into host CRISPR arrays in order to generate host immunity. Recently, we demonstrated that the Csa3a regulator protein triggers CCN protospacer-adjacent motif (PAM)-dependent CRISPR spacer acquisition in the subtype I-A CRISPR-Cas system of Sulfolobus islandicus However, the mechanisms underlying specific protospacer selection and spacer insertion remained unclear. Here, we demonstrate that two Cas4 family proteins (Cas4 and Csa1) have essential roles (i) in recognizing the 5' PAM and 3' nucleotide motif of protospacers and (ii) in determining both the spacer length and its orientation. Furthermore, we identify amino acid residues of the Cas4 proteins that facilitate these functions. Overexpression of the Cas4 and Csa1 proteins, and also that of an archaeal virus-encoded Cas4 protein, resulted in strongly reduced adaptation efficiency, and the former proteins yielded a high incidence of PAM-dependent atypical spacer integration or of PAM-independent spacer integration. We further demonstrated that in plasmid challenge experiments, overexpressed Cas4-mediated defective spacer acquisition in turn potentially enabled targeted DNA to escape subtype I-A CRISPR-Cas interference. In summary, these results define the specific involvement of diverse Cas4 proteins in in vivo CRISPR spacer acquisition. Furthermore, we provide support for an anti-CRISPR role for virus-encoded Cas4 proteins that involves compromising CRISPR-Cas interference activity by hindering spacer acquisition.IMPORTANCE The Cas4 family endonuclease is an essential component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. The Crenarchaeota Sulfolobus islandicus REY15A carries two cas4 genes (cas4 and csa1) linked to the CRISPR arrays. Here, we demonstrate that Cas4 and Csa1 are essential to CRISPR spacer acquisition in this organism. Both proteins specify the upstream and downstream conserved nucleotide motifs of the protospacers and define the spacer length and orientation in the acquisition process. Conserved amino acid residues, in addition to those recently reported, were identified to be important for these functions. More importantly, overexpression of the Sulfolobus viral Cas4 abolished spacer acquisition, providing support for an anti-CRISPR role for virus-encoded Cas4 proteins that inhibit spacer acquisition.


Assuntos
Proteínas Associadas a CRISPR/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Endonucleases/genética , Sulfolobus/enzimologia , Sulfolobus/genética , Vírus de Archaea , DNA Bacteriano/genética , Endonucleases/metabolismo , Proteínas Virais
9.
Nat Commun ; 10(1): 1688, 2019 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-30975999

RESUMO

Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.


Assuntos
Archaea/fisiologia , Proteínas Arqueais/metabolismo , Vírus de Archaea/genética , DNA Viral/metabolismo , Interações entre Hospedeiro e Microrganismos/genética , Archaea/virologia , Proteínas Arqueais/genética , Proteínas Arqueais/imunologia , Vírus de Archaea/patogenicidade , Replicação do DNA/imunologia , Transferência Genética Horizontal/imunologia , Imunidade Inata/genética , Imunidade Inata/imunologia , Oligonucleotídeos Fosforotioatos/metabolismo , RNA Arqueal/genética , RNA Arqueal/isolamento & purificação , Análise de Sequência de DNA
10.
Nat Commun ; 10(1): 1456, 2019 03 29.
Artigo em Inglês | MEDLINE | ID: mdl-30926810

RESUMO

Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). Here, by high-resolution cryo-EM analysis, we show that a class of archaeal viruses possess hetero-hexameric MCPs which mimic the PRD1-adeno lineage trimer. These hetero-hexamers are built from heterodimers and utilise a jigsaw-puzzle system of pegs and holes, and underlying minor capsid proteins, to assemble the capsid laterally from the 5-fold vertices. At these vertices proteins engage inwards with the internal membrane vesicle whilst 2-fold symmetric horn-like structures protrude outwards. The horns are assembled from repeated globular domains attached to a central spine, presumably facilitating multimeric attachment to the cell receptor. Such viruses may represent precursors of the main PRD1-adeno lineage, similarly engaging cell-receptors via 5-fold spikes and using minor proteins to define particle size.


Assuntos
Vírus de Archaea/fisiologia , Montagem de Vírus/fisiologia , Vírus de Archaea/química , Vírus de Archaea/ultraestrutura , Proteínas do Capsídeo/química , Proteínas do Capsídeo/ultraestrutura , Modelos Moleculares
11.
Environ Microbiol ; 21(6): 2129-2147, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30920125

RESUMO

The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.


Assuntos
Vírus de Archaea/isolamento & purificação , Haloferax/virologia , Halorubrum/virologia , Lagos/virologia , Vírus de Archaea/classificação , Vírus de Archaea/genética , Metagenoma , Filogenia , Senegal , Vírion/classificação , Vírion/genética , Vírion/isolamento & purificação
12.
Nat Commun ; 10(1): 1184, 2019 03 12.
Artigo em Inglês | MEDLINE | ID: mdl-30862777

RESUMO

The vertical double ß-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single ß-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double ß-barrel MCPs.


Assuntos
Vírus de Archaea/fisiologia , Proteínas do Capsídeo/ultraestrutura , Vírus de DNA/fisiologia , Haloarcula/virologia , Montagem de Vírus , Proteínas do Capsídeo/química , Proteínas do Capsídeo/metabolismo , Microscopia Crioeletrônica , Modelos Moleculares , Conformação Proteica em Folha beta , Multimerização Proteica , Vírion/ultraestrutura
13.
Nat Commun ; 10(1): 846, 2019 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-30783086

RESUMO

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.


Assuntos
Vírus de Archaea/química , Proteínas de Fusão de Membrana/química , Proteínas do Envelope Viral/química , Microscopia Crioeletrônica , Cristalografia por Raios X , Tomografia com Microscopia Eletrônica , Halorubrum/virologia , Fusão de Membrana , Proteínas de Fusão de Membrana/genética , Proteínas de Fusão de Membrana/metabolismo , Domínios Proteicos , Dobramento de Proteína , Proteínas do Envelope Viral/genética , Proteínas do Envelope Viral/metabolismo , Vírion/química
14.
Viruses ; 11(1)2019 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-30669250

RESUMO

Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of "viral lineages", postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 1031) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.


Assuntos
Bacteriófagos/fisiologia , Evolução Molecular , Membranas/metabolismo , Vírus de Archaea/genética , Bacteriófago PRD1/fisiologia , Bacteriófagos/genética , Proteínas do Capsídeo/genética , DNA Viral/genética , Modelos Moleculares , Vírion/metabolismo , Montagem de Vírus
15.
Environ Microbiol ; 21(6): 2002-2014, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30451355

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 Viral
16.
Environ Microbiol ; 21(6): 1980-1988, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30370610

RESUMO

Marine Group I (MGI) Thaumarchaeota are some of the most abundant microorganisms in the deep ocean and responsible for much of the ammonia oxidation occurring in this environment. In this work, we present 35 sequences assembled from metagenomic samples of the first uncultivated Caudovirales viruses associated with Thaumarchaeota, which we designated marthavirus. Most of the sequences were obtained from cellular metagenomes confirming that they represent an important tool to study environmental viral communities due to cells retrieved while undergoing viral lysis. Metagenomic recruitment showed that this viral population is formed by very divergent entities with high intrapopulation homogeneity. However, metatranscriptomic analyses revealed the same differential expression profile with the capsid as major transcript, indicative of viruses during the lytic cycle. The cobalamine biosynthesis gene cobS, an auxiliary metabolic gene, was also highly expressed during the infection. These analyses expand our understanding of the global diversity of archaeal viruses.


Assuntos
Archaea/virologia , Vírus de Archaea/isolamento & purificação , Caudovirales/isolamento & purificação , Archaea/genética , Vírus de Archaea/classificação , Vírus de Archaea/genética , Caudovirales/classificação , Caudovirales/genética , Genoma Viral , Metagenoma , Filogenia
17.
Arch Virol ; 164(3): 667-674, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30523430

RESUMO

Viruses are ubiquitous in the biosphere and greatly affect the hosts they infect. It is generally accepted that members of every microbial taxon are susceptible to at least one virus, and a plethora of bacterial viruses are known. In contrast, knowledge of the archaeal virosphere is still limited. Here, a novel lytic archaeal virus is described, designated "Drs3", as well as its host, Methanobacterium formicicum strain Khl10. This hydrogenotrophic methanogenic archaeon and its virus were isolated from the anaerobic digester of an experimental biogas plant in Germany. The tailed virus has an icosahedral head with a diameter of approximately 60 nm and a long non-contractile tail of approximately 230 nm. These structural observations suggest that the new isolate belongs to the family Siphoviridae, but it could not be assigned to an existing genus. Lysis of the host Khl10 was observed 40-44 h after infection. Lysis of the type strain Methanobacterium formicicum DSMZ 1535 was not observed in the presence of Drs3, pointing towards resistance in the type strain or a rather narrow host range of this newly isolated archaeal virus. The complete 37-kb linear dsDNA genome of Drs3 contains 39 open reading frames, only 12 of which show similarity to genes with predicted functions.


Assuntos
Vírus de Archaea/isolamento & purificação , Methanobacterium/virologia , Siphoviridae/isolamento & purificação , Vírus de Archaea/classificação , Vírus de Archaea/genética , Vírus de Archaea/fisiologia , Alemanha , Especificidade de Hospedeiro , Fases de Leitura Aberta , Filogenia , Siphoviridae/classificação , Siphoviridae/genética , Siphoviridae/fisiologia , Proteínas Virais/genética
18.
RNA Biol ; 16(4): 549-556, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-29629622

RESUMO

Sulfolobus islandicus Rey15A encodes one Type I-A and two Type III-B systems, all of which are active in mediating nucleic acids interference. However, the effectiveness of each CRISPR system against virus infection was not tested in this archaeon. Here we constructed S. islandicus strains that constitutively express the antiviral immunity from either I-A, or III-B, or I-A plus III-B systems against SMV1 and tested the response of each host to SMV1 infection. We found that, although both CRISPR immunities showed a strong inhibition to viral DNA replication at an early stage of incubation, the host I-A CRISPR immunity gradually lost the control on virus proliferation, allowing accumulation of cellular viral DNA and release of a large number of viral particles. In contrast, the III-B CRISPR immunity showed a tight control on both viral DNA replication and virus particle formation. Furthermore, the SMV1 tolerance to the I-A CRISPR immunity did not result from the occurrence of escape mutations, suggesting the virus probably encodes an anti-CRISPR protein (Acr) to compromise the host I-A CRISPR immunity. Together, this suggests that the interplay between viral Acrs and CRISPR-Cas systems in thermophilic archaea could have shaped the stable virus-host relationship that is observed for many archaeal viruses.


Assuntos
Vírus de Archaea/fisiologia , Sistemas CRISPR-Cas/genética , Imunidade , Sulfolobus/imunologia , Sulfolobus/virologia , Replicação do DNA/genética , Genoma Viral , Sulfolobus/genética , Vírion/metabolismo
19.
J Gen Virol ; 99(9): 1331-1343, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-30016225

RESUMO

Genome Relationship Applied to Virus Taxonomy (GRAViTy) is a genetics-based tool that computes sequence relatedness between viruses. Composite generalized Jaccard (CGJ) distances combine measures of homology between encoded viral genes and similarities in genome organizational features (gene orders and orientations). This scoring framework effectively recapitulates the current, largely morphology and phenotypic-based, family-level classification of eukaryotic viruses. Eukaryotic virus families typically formed monophyletic groups with consistent CGJ distance cut-off dividing between and within family divergence ranges. In the current study, a parallel analysis of prokaryotic virus families revealed quite different sequence relationships, particularly those of tailed phage families (Siphoviridae, Myoviridae and Podoviridae), where members of the same family were generally far more divergent and often not detectably homologous to each other. Analysis of the 20 currently classified prokaryotic virus families indeed split them into 70 separate clusters of tailed phages genetically equivalent to family-level assignments of eukaryotic viruses. It further divided several bacterial (Sphaerolipoviridae, Tectiviridae) and archaeal (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of eukaryotic viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1virus taxa as new virus families. The current study applied a common benchmark with which to compare taxonomies of eukaryotic and prokaryotic viruses. The findings support the planned shift away from traditional morphology-based classifications of prokaryotic viruses towards a genome-based taxonomy. They demonstrate the feasibility of a unified taxonomy of viruses into which the vast body of metagenomic viral sequences may be consistently assigned.


Assuntos
Vírus de Archaea/genética , Bacteriófagos/genética , Biologia Computacional/métodos , Variação Genética , Genoma Viral , Archaea/virologia , Bactérias/virologia , Eucariotos/virologia , Genes Virais , Genômica , Metagenômica , Filogenia , Vírus/genética
20.
Microbiome ; 6(1): 113, 2018 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-29925429

RESUMO

BACKGROUND: The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised. RESULTS: The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica. CONCLUSION: The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea.


Assuntos
Vírus de Archaea/genética , Genoma Arqueal/genética , Halorubrum/genética , Microbiota/genética , Regiões Antárticas , Vírus de Archaea/isolamento & purificação , Sequência de Bases , Variação Genética/genética , Ilhas Genômicas/genética , Geografia , Halorubrum/classificação , Halorubrum/isolamento & purificação , Lagos/microbiologia , Metagenoma/genética , Análise de Sequência de DNA
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