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  1. Article: New faces of prokaryotic mobile genetic elements: guide RNAs link transposition with host defense mechanisms.

    Koonin, Eugene V / Krupovic, Mart

    Current opinion in systems biology

    2023  Volume 36

    Abstract: Most life forms harbor multiple, diverse mobile genetic elements (MGE) that widely differ in their rates and mechanisms of mobility. Recent findings on two classes of MGE in prokaryotes revealed a novel mechanism, RNA-guided transposition, where a ... ...

    Abstract Most life forms harbor multiple, diverse mobile genetic elements (MGE) that widely differ in their rates and mechanisms of mobility. Recent findings on two classes of MGE in prokaryotes revealed a novel mechanism, RNA-guided transposition, where a transposon-encoded guide RNA directs the transposase to a unique site in the host genome. Tn7-like transposons, on multiple occasions, recruited CRISPR systems that lost the capacity to cleave target DNA and instead mediate RNA-guided transposition via CRISPR RNA. Conversely, the abundant transposon-associated, RNA-guided nucleases IscB and TnpB that appear to promote proliferation of IS
    Language English
    Publishing date 2023-08-29
    Publishing country England
    Document type Journal Article
    ISSN 2452-3100
    ISSN 2452-3100
    DOI 10.1016/j.coisb.2023.100473
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Mriyaviruses: Small Relatives of Giant Viruses.

    Yutin, Natalya / Mutz, Pascal / Krupovic, Mart / Koonin, Eugene V

    bioRxiv : the preprint server for biology

    2024  

    Abstract: ... The ... ...

    Abstract The phylum
    Language English
    Publishing date 2024-02-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.29.582850
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  3. Article ; Online: Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea.

    Baquero, Diana P / Bignon, Eduardo A / Krupovic, Mart

    The ISME journal

    2024  Volume 18, Issue 1

    Abstract: Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ... ...

    Abstract Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ecosystems remains largely unknown. Here, we show that evolutionarily-related viruses also infect hyperthermophilic archaea thriving in deep-sea hydrothermal vents. Archaeoglobus veneficus pleomorphic virus 1 (AvPV1), the first virus described for any member of the class Archaeoglobi, encodes a morphogenetic module typical of pleolipoviruses, including the characteristic VP4-like membrane fusion protein. We show that AvPV1 is a non-lytic virus chronically produced in liquid cultures without substantially affecting the growth dynamics of its host with a stable virus-to-host ratio of ~1. Mining of genomic and metagenomic databases revealed broad distribution of AvPV1-like viruses in geographically remote hydrothermal vents. Comparative genomics, coupled with phylogenetic analysis of VP4-like fusogens revealed deep divergence of pleomorphic viruses infecting halophilic, methanogenic, and hyperthermophilic archaea, signifying niche separation and coevolution of the corresponding virus-host pairs. Hence, we propose a new virus family, "Thalassapleoviridae," for classification of the marine hyperthermophilic virus AvPV1 and its relatives. Collectively, our results provide insights into the diversity and evolution of pleomorphic viruses beyond hypersaline environments.
    MeSH term(s) Archaea/genetics ; Phylogeny ; Ecosystem ; Viruses/genetics ; Virion ; Euryarchaeota ; Archaeal Viruses/genetics
    Language English
    Publishing date 2024-02-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406536-5
    ISSN 1751-7370 ; 1751-7362
    ISSN (online) 1751-7370
    ISSN 1751-7362
    DOI 10.1093/ismejo/wrae008
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  4. Article ; Online: A life LINE for large viruses.

    Koonin, Eugene V / Krupovic, Mart

    eLife

    2022  Volume 11

    Abstract: As long suspected, poxviruses capture host genes through a reverse-transcription process now shown to be mediated by retrotransposons. ...

    Abstract As long suspected, poxviruses capture host genes through a reverse-transcription process now shown to be mediated by retrotransposons.
    MeSH term(s) Retroelements ; Poxviridae/genetics ; Vaccinia virus/genetics ; Virus Replication
    Chemical Substances Retroelements
    Language English
    Publishing date 2022-10-25
    Publishing country England
    Document type Editorial
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.83488
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  5. Article ; Online: ICTV Virus Taxonomy Profile:

    Zhou, Yifan / Wang, Yongjie / Krupovic, Mart

    The Journal of general virology

    2023  Volume 104, Issue 11

    Abstract: ... The ... ...

    Abstract The family
    MeSH term(s) Virus Replication ; Genome, Viral ; Viruses/genetics ; Virion/genetics ; Phylogeny
    Language English
    Publishing date 2023-12-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 219316-4
    ISSN 1465-2099 ; 0022-1317
    ISSN (online) 1465-2099
    ISSN 0022-1317
    DOI 10.1099/jgv.0.001922
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  6. Article ; Online: Naryaviridae, Nenyaviridae, and Vilyaviridae: three new families of single-stranded DNA viruses in the phylum Cressdnaviricota.

    Krupovic, Mart / Varsani, Arvind

    Archives of virology

    2022  Volume 167, Issue 12, Page(s) 2907–2921

    Abstract: The phylum Cressdnaviricota includes viruses with circular single-stranded DNA (ssDNA) genomes and icosahedral capsids. These viruses display global environmental distribution and infect diverse eukaryotic hosts, including animals, plants, and fungi. ... ...

    Abstract The phylum Cressdnaviricota includes viruses with circular single-stranded DNA (ssDNA) genomes and icosahedral capsids. These viruses display global environmental distribution and infect diverse eukaryotic hosts, including animals, plants, and fungi. Here, we report on the formal creation of two new orders, Rivendellvirales and Rohanvirales, and three new families, Naryaviridae, Nenyaviridae, and Vilyaviridae, of ssDNA viruses associated with protozoan parasites belonging to the genera Entamoeba and Giardia. We describe a sequence-based taxonomic framework, which was used to classify 60 ssDNA viruses into 12 genera (with 18 species) within the family Vilyaviridae; four genera (with five species) within the family Naryaviridae; and five genera (with six species) within the family Nenyaviridae. We also highlight the challenges associated with the classification of chimeric virus genomes, such as those in the families Naryaviridae and Nenyaviridae, where the replication initiation and capsid protein genes have undergone several independent non-orthologous replacements. The described taxonomic changes have been ratified by the International Committee on Taxonomy of Viruses (ICTV) and expand the phylum Cressdnaviricota to eight orders and 11 families.
    Language English
    Publishing date 2022-09-13
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-022-05557-w
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  7. Article ; Online: Megataxonomy and global ecology of the virosphere.

    Koonin, Eugene V / Kuhn, Jens H / Dolja, Valerian V / Krupovic, Mart

    The ISME journal

    2024  Volume 18, Issue 1

    Abstract: Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. ...

    Abstract Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
    MeSH term(s) Viruses/genetics ; Metagenomics/methods ; Ecology ; Phylogeny ; Genome, Viral
    Language English
    Publishing date 2024-02-14
    Publishing country England
    Document type Review ; Journal Article
    ZDB-ID 2406536-5
    ISSN 1751-7370 ; 1751-7362
    ISSN (online) 1751-7370
    ISSN 1751-7362
    DOI 10.1093/ismejo/wrad042
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  8. Article ; Online: The virome of the last eukaryotic common ancestor and eukaryogenesis.

    Krupovic, Mart / Dolja, Valerian V / Koonin, Eugene V

    Nature microbiology

    2023  Volume 8, Issue 6, Page(s) 1008–1017

    Abstract: All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly ... ...

    Abstract All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly understood-we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial-not archaeal-viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.
    MeSH term(s) Eukaryota ; Eukaryotic Cells ; Virome ; Phylogeny ; Archaea/genetics ; Bacteria/genetics ; Viruses/genetics
    Language English
    Publishing date 2023-05-01
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01378-y
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  9. Article ; Online: ICTV Virus Taxonomy Profile:

    Wolf, Yuri I / Krupovic, Mart / Kuhn, Jens H / Koonin, Eugene V

    The Journal of general virology

    2023  Volume 104, Issue 10

    Abstract: ... ...

    Abstract Tosoviridae
    MeSH term(s) RNA Viruses/genetics ; Genome, Viral
    Language English
    Publishing date 2023-10-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 219316-4
    ISSN 1465-2099 ; 0022-1317
    ISSN (online) 1465-2099
    ISSN 0022-1317
    DOI 10.1099/jgv.0.001908
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    Zs.A 610: Show issues Location:
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  10. Article ; Online: ICTV Virus Taxonomy Profile:

    Krupovic, Mart / Wolf, Yuri I / Koonin, Eugene V / Kuhn, Jens H

    The Journal of general virology

    2023  Volume 104, Issue 10

    Abstract: ... ...

    Abstract Yueviridae
    MeSH term(s) RNA Viruses/genetics ; Genome, Viral ; Virion
    Language English
    Publishing date 2023-10-11
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 219316-4
    ISSN 1465-2099 ; 0022-1317
    ISSN (online) 1465-2099
    ISSN 0022-1317
    DOI 10.1099/jgv.0.001904
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