E V Koonin
Affiliation: National Institutes of Health
- Koonin E, Makarova K, Wolf Y. Evolutionary Genomics of Defense Systems in Archaea and Bacteria. Annu Rev Microbiol. 2017;71:233-261 pubmed publisher....
- Lobkovsky A, Wolf Y, Koonin E. Estimation of prokaryotic supergenome size and composition from gene frequency distributions. BMC Genomics. 2014;15 Suppl 6:S14 pubmed publisher....
- Puigbò P, Makarova K, Kristensen D, Wolf Y, Koonin E. Reconstruction of the evolution of microbial defense systems. BMC Evol Biol. 2017;17:94 pubmed publisher..Apart from the paucity and the low flux of defense genes in parasitic bacteria with deteriorating genomes, there is no clear connection between the evolutionary regime of defense systems and microbial life style. ..
- 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. ..
- ..Together with the unexpected discoveries of the first putative archaeal RNA virus and a RNA-DNA virus hybrid, this work shows that RNA viral genomics has major surprises to deliver. ..
- Lavysh D, Sokolova M, Minakhin L, Yakunina M, Artamonova T, Kozyavkin S, et al. The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases. Virology. 2016;495:185-96 pubmed publisher..Purification of one of PBS1/AR9 RNAPs has been reported previously, which makes AR9 a promising object for further studies of RNAP evolution, assembly and mechanism...
- Koonin E, Wolf Y, Katsnelson M. Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states. Biol Direct. 2017;12:31 pubmed publisher..This article has been reviewed by Yitzhak Pilpel, Bojan Zagrovic, and Eric van Nimwegen. ..
- Yutin N, Makarova K, Gussow A, Krupovic M, Segall A, Edwards R, et al. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat Microbiol. 2018;3:38-46 pubmed publisher..These findings provide for experimental characterization of the most abundant but poorly understood members of the human-associated virome. ..
- 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. ..
- Shmakov S, Sitnik V, Makarova K, Wolf Y, SEVERINOV K, Koonin E. The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes. MBio. 2017;8: pubmed publisher..We further demonstrate that spacers with no matches have the same properties as those of identifiable origins, strongly suggesting that all spacers originate from mobile elements. ..
- 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. ..
- Koonin E, Makarova K. CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes. RNA Biol. 2013;10:679-86 pubmed publisher..Such coupling could manifest in the persistence state being induced and potentially providing conditions for more effective action of the immune system or in cell death being triggered when immunity fails. ..
- Koonin E, Wolf Y, Puigbò P. The phylogenetic forest and the quest for the elusive tree of life. Cold Spring Harb Symp Quant Biol. 2009;74:205-13 pubmed publisher..The totality of gene trees comprising the FOL appears to be a natural representation of the history of life given the inherent tree-like character of the replication process...
- Makarova K, Ponomarev V, Koonin E. Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol. 2001;2:RESEARCH 0033 pubmed..The recurrent theme of emergence and disruption of Zn-ribbons in bacterial ribosomal proteins awaits a functional interpretation. ..
- Koonin E, Rudd K. Two domains of superfamily I helicases may exist as separate proteins. Protein Sci. 1996;5:178-80 pubmed..It is speculated that PhoH and YjhR have evolved from helicases through deletion of the portions of the helicase genes coding for the C- and N-terminal domain, respectively. ..
- Koonin E. Viruses and mobile elements as drivers of evolutionary transitions. Philos Trans R Soc Lond B Biol Sci. 2016;371: pubmed publisher..This article is part of the themed issue 'The major synthetic evolutionary transitions'. ..
- Koonin E, Wolf Y. Evolution of microbes and viruses: a paradigm shift in evolutionary biology?. Front Cell Infect Microbiol. 2012;2:119 pubmed....
- Koonin E, Novozhilov A. Origin and Evolution of the Universal Genetic Code. Annu Rev Genet. 2017;: pubmed publisher..Expected final online publication date for the Annual Review of Genetics Volume 51 is November 23, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. ..
- Koonin E. Intron-dominated genomes of early ancestors of eukaryotes. J Hered. 2009;100:618-23 pubmed publisher..An organism with such an unusual genome architecture could survive only under conditions of a severe population bottleneck...
- Belinky F, Rogozin I, Koonin E. Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions. Sci Rep. 2017;7:12422 pubmed publisher..Together, all these findings indicate that in prokaryotes, translation start signals are subject to weak but significant selection for maximization of initiation rate and, consequently, protein production...
- Koonin E. Evolution of genome architecture. Int J Biochem Cell Biol. 2009;41:298-306 pubmed publisher..Selection for specific gene arrangements (elements of genome architecture) seems only to modulate the results of these processes...
- Koonin E, Makarova K, Elkins J. Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota". Biol Direct. 2007;2:38 pubmed..These findings suggest that all 12 core subunits of eukaryotic RNAPs were already present in the last common ancestor of the extant archaea...
- Hudaiberdiev S, Shmakov S, Wolf Y, Terns M, Makarova K, Koonin E. Phylogenomics of Cas4 family nucleases. BMC Evol Biol. 2017;17:232 pubmed publisher..Experimental characterization of the solo and MGE-encoded Cas4 nucleases is expected to reveal currently uncharacterized defense and anti-defense systems and their interactions with CRISPR-Cas systems. ..