Affiliation: Institut Pasteur
- Krupovic M, Dolja V, Koonin E. Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes. Biol Direct. 2015;10:12 pubmed publisher..The chimeric genomes of amalgaviruses are a testament to the effectively limitless gene exchange between viruses that shaped the evolution of the virosphere. ..
- Philippe C, Krupovic M, Jaomanjaka F, Claisse O, Petrel M, Le Marrec C. Bacteriophage GC1, a Novel Tectivirus Infecting Gluconobacter Cerinus, an Acetic Acid Bacterium Associated with Wine-Making. Viruses. 2018;10: pubmed publisher..Furthermore, GC1 helps to bridge the gap in the sequence space between alphatectiviruses and betatectiviruses. ..
- Koonin E, Dolja V, Krupovic M. Origins and evolution of viruses of eukaryotes: The ultimate modularity. Virology. 2015;479-480:2-25 pubmed publisher..Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes. ..
- Beguin P, Charpin N, Koonin E, Forterre P, Krupovic M. Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems. Nucleic Acids Res. 2016;44:10367-10376 pubmed..These findings reinforce the mechanistic similarities and evolutionary connection between the casposons and the adaptation module of the prokaryotic adaptive immunity systems. ..
- Iranzo J, Koonin E, Prangishvili D, Krupovic M. Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements. J Virol. 2016;90:11043-11055 pubmed..This finding could reflect actual independent origins of the distinct groups of archaeal viruses from different nonviral elements, providing important insights into the emergence and evolution of the archaeal virome. ..
- Krupovic M, Kuhn J, Fischer M. A classification system for virophages and satellite viruses. Arch Virol. 2016;161:233-47 pubmed publisher..For double-stranded DNA virophages, we propose to establish the family Lavidaviridae, including two genera, Sputnikvirus and Mavirus. ..
- Krupovic M, Shmakov S, Makarova K, Forterre P, Koonin E. Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity. Genome Biol Evol. 2016;8:375-86 pubmed publisher..Finally, besides identifying additional representatives in each of the three originally defined families, we describe a new, fourth, family of casposons. ..
- Krupovic M. Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses. Bioessays. 2012;34:867-70 pubmed publisher..It also substantiates the hypothesis that certain groups of DNA viruses could have emerged from plasmids via acquisition of capsid protein-coding genes from RNA viruses...
- Krupovic M, Cvirkaite Krupovic V, Prangishvili D, Koonin E. Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease. Biol Direct. 2015;10:65 pubmed publisher..To our knowledge, this is the first described case of exaptation of an enzyme for a virus capsid protein function. ..
- Krupovic M, Koonin E. Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems. Curr Opin Microbiol. 2016;31:25-33 pubmed publisher..The casposons are thought to have played a pivotal role in the origin of the prokaryotic adaptive immunity, giving rise to the adaptation module of the CRISPR-Cas systems. ..
- Krupovic M. Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol. 2013;3:578-86 pubmed publisher..This scenario places structurally related viruses with DNA and RNA genomes into an evolutionary continuum and highlights general evolutionary trends in the virosphere. ..
- Krupovic M, Bamford D, Koonin E. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol Direct. 2014;9:6 pubmed publisher..We propose the name 'Polintoviruses' to denote these putative viruses that could have played a central role in the evolution of several groups of DNA viruses of eukaryotes. ..
- Krupovic M, Koonin E. Cellular origin of the viral capsid-like bacterial microcompartments. Biol Direct. 2017;12:25 pubmed publisher..This article was reviewed by Igor Zhulin, Jeremy Selengut and Narayanaswamy Srinivasan. For complete reviews, see the Reviewers' reports section. ..
- Redrejo Rodríguez M, Ordóñez C, Berjón Otero M, Moreno González J, Aparicio Maldonado C, Forterre P, et al. Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements. Cell Rep. 2017;21:1574-1587 pubmed publisher..We suggest that piPolBs are involved in self-replication of pipolins and may also contribute to bacterial DNA damage tolerance. ..
- Koonin E, Krupovic M. Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity. Curr Opin Virol. 2017;25:7-15 pubmed publisher..Taken together, these findings show that Polintons, PLV, virophages and transpovirons form a dynamic network of integrating mobile genetic elements that contribute to the cellular antivirus defense and host-virus coevolution. ..
- Krupovic M, Cvirkaite Krupovic V. Virophages or satellite viruses?. Nat Rev Microbiol. 2011;9:762-3 pubmed..However, Mart Krupovic and Virginija Cvirkaite-Krupovic argue here that these smaller viruses should be classified with the satellite ..
- Krupovic M, Zhi N, Li J, Hu G, Koonin E, Wong S, et al. Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing. Genome Biol Evol. 2015;7:993-1001 pubmed publisher..Our results underscore the importance of horizontal gene transfer in the evolution of ssDNA viruses and the role of genetic recombination in the emergence of novel virus groups. ..
- Kazlauskas D, Dayaram A, Kraberger S, Goldstien S, Varsani A, Krupovic M. Evolutionary history of ssDNA bacilladnaviruses features horizontal acquisition of the capsid gene from ssRNA nodaviruses. Virology. 2017;504:114-121 pubmed publisher..Considering the sequence diversity within the expanding Bacilladnavirus genus, we argue that classification of these viruses has to be revised and the current genus upgraded to the family level. ..
- Krupovic M, Cvirkaite Krupovic V, Iranzo J, Prangishvili D, Koonin E. Viruses of archaea: Structural, functional, environmental and evolutionary genomics. Virus Res. 2018;244:181-193 pubmed publisher..Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome. ..
- Krupovic M, Bamford D. Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly. Curr Opin Virol. 2011;1:118-24 pubmed publisher..We note that viruses belonging to 20 different families fall into only five distinct structural groups, suggesting that optimal virus classification approach should equally rely on both sequence and structural information. ..
- Krupovic M, Prangishvili D, Hendrix R, Bamford D. Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev. 2011;75:610-35 pubmed publisher..We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions...