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Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants.

Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV.

Nat Rev Microbiol. 2020 Feb;18(2):67-83. doi: 10.1038/s41579-019-0299-x. Epub 2019 Dec 19. Review.


Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire.

Koonin EV, Makarova KS, Wolf YI, Krupovic M.

Nat Rev Genet. 2020 Feb;21(2):119-131. doi: 10.1038/s41576-019-0172-9. Epub 2019 Oct 14. Review.


Systematic prediction of functionally linked genes in bacterial and archaeal genomes.

Shmakov SA, Faure G, Makarova KS, Wolf YI, Severinov KV, Koonin EV.

Nat Protoc. 2019 Oct;14(10):3013-3031. doi: 10.1038/s41596-019-0211-1. Epub 2019 Sep 13.


Identification of Dephospho-Coenzyme A (Dephospho-CoA) Kinase in Thermococcus kodakarensis and Elucidation of the Entire CoA Biosynthesis Pathway in Archaea.

Shimosaka T, Makarova KS, Koonin EV, Atomi H.

mBio. 2019 Jul 23;10(4). pii: e01146-19. doi: 10.1128/mBio.01146-19.


RNA-guided DNA insertion with CRISPR-associated transposases.

Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F.

Science. 2019 Jul 5;365(6448):48-53. doi: 10.1126/science.aax9181. Epub 2019 Jun 6.


CRISPR-Cas in mobile genetic elements: counter-defence and beyond.

Faure G, Shmakov SA, Yan WX, Cheng DR, Scott DA, Peters JE, Makarova KS, Koonin EV.

Nat Rev Microbiol. 2019 Aug;17(8):513-525. doi: 10.1038/s41579-019-0204-7.


Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts.

Makarova KS, Wolf YI, Karamycheva S, Zhang D, Aravind L, Koonin EV.

mBio. 2019 May 7;10(3). pii: e00715-19. doi: 10.1128/mBio.00715-19.


Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

Makarova KS, Wolf YI, Koonin EV.

CRISPR J. 2018 Oct;1(5):325-336. doi: 10.1089/crispr.2018.0033. Review.


Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array.

Makarova KS, Karamycheva S, Shah SA, Vestergaard G, Garrett RA, Koonin EV.

FEMS Microbiol Lett. 2019 Apr 1;366(7). pii: fnz079. doi: 10.1093/femsle/fnz079.


Origins and evolution of CRISPR-Cas systems.

Koonin EV, Makarova KS.

Philos Trans R Soc Lond B Biol Sci. 2019 May 13;374(1772):20180087. doi: 10.1098/rstb.2018.0087.


Reply to 'Evolutionary placement of Methanonatronarchaeia'.

Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN, Galinski EA, Ciorda S, Mena MC, Merkel AY, Wolf YI, van Loosdrecht MCM, Koonin EV.

Nat Microbiol. 2019 Apr;4(4):560-561. doi: 10.1038/s41564-019-0358-0. No abstract available.


Integrated mobile genetic elements in Thaumarchaeota.

Krupovic M, Makarova KS, Wolf YI, Medvedeva S, Prangishvili D, Forterre P, Koonin EV.

Environ Microbiol. 2019 Jun;21(6):2056-2078. doi: 10.1111/1462-2920.14564. Epub 2019 Mar 18.


Towards functional characterization of archaeal genomic dark matter.

Makarova KS, Wolf YI, Koonin EV.

Biochem Soc Trans. 2019 Feb 28;47(1):389-398. doi: 10.1042/BST20180560. Epub 2019 Feb 1. Review.


Engineering of CRISPR-Cas12b for human genome editing.

Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F.

Nat Commun. 2019 Jan 22;10(1):212. doi: 10.1038/s41467-018-08224-4.


Functionally diverse type V CRISPR-Cas systems.

Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV, Cheng DR, Scott DA.

Science. 2019 Jan 4;363(6422):88-91. doi: 10.1126/science.aav7271. Epub 2018 Dec 6.


A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition.

Mohr G, Silas S, Stamos JL, Makarova KS, Markham LM, Yao J, Lucas-Elío P, Sanchez-Amat A, Fire AZ, Koonin EV, Lambowitz AM.

Mol Cell. 2018 Nov 15;72(4):700-714.e8. doi: 10.1016/j.molcel.2018.09.013. Epub 2018 Oct 18.


Anti-CRISPRs on the march.

Koonin EV, Makarova KS.

Science. 2018 Oct 12;362(6411):156-157. doi: 10.1126/science.aav2440. No abstract available.


CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity.

Faure G, Makarova KS, Koonin EV.

J Mol Biol. 2019 Jan 4;431(1):3-20. doi: 10.1016/j.jmb.2018.08.030. Epub 2018 Sep 5. Review.


Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems.

Faure G, Shmakov SA, Makarova KS, Wolf YI, Crawley AB, Barrangou R, Koonin EV.

RNA Biol. 2019 Apr;16(4):435-448. doi: 10.1080/15476286.2018.1493331. Epub 2018 Aug 14.


Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X.

Nat Microbiol. 2018 Sep;3(9):1076. doi: 10.1038/s41564-018-0184-9.


Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle.

Wilcox B, Osterman I, Serebryakova M, Lukyanov D, Komarova E, Gollan B, Morozova N, Wolf YI, Makarova KS, Helaine S, Sergiev P, Dubiley S, Borukhov S, Severinov K.

Nucleic Acids Res. 2018 Sep 6;46(15):7873-7885. doi: 10.1093/nar/gky560.


Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis.

Shmakov SA, Makarova KS, Wolf YI, Severinov KV, Koonin EV.

Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):E5307-E5316. doi: 10.1073/pnas.1803440115. Epub 2018 May 21.


Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov.

Sorokin DY, Merkel AY, Abbas B, Makarova KS, Rijpstra WIC, Koenen M, Sinninghe Damsté JS, Galinski EA, Koonin EV, van Loosdrecht MCM.

Int J Syst Evol Microbiol. 2018 Jul;68(7):2199-2208. doi: 10.1099/ijsem.0.002810. Epub 2018 May 29.


Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii.

Ausiannikava D, Mitchell L, Marriott H, Smith V, Hawkins M, Makarova KS, Koonin EV, Nieduszynski CA, Allers T.

Mol Biol Evol. 2018 Aug 1;35(8):1855-1868. doi: 10.1093/molbev/msy075.


DNA silencing by prokaryotic Argonaute proteins adds a new layer of defense against invading nucleic acids.

Willkomm S, Makarova KS, Grohmann D.

FEMS Microbiol Rev. 2018 May 1;42(3):376-387. doi: 10.1093/femsre/fuy010. Review.


Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein.

Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA.

Mol Cell. 2018 Apr 19;70(2):327-339.e5. doi: 10.1016/j.molcel.2018.02.028. Epub 2018 Mar 15.


Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X.

Nat Microbiol. 2018 Apr;3(4):461-469. doi: 10.1038/s41564-018-0120-z. Epub 2018 Mar 5. Erratum in: Nat Microbiol. 2018 Sep;3(9):1076.


Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia".

Ferrer M, Sorokin DY, Wolf YI, Ciordia S, Mena MC, Bargiela R, Koonin EV, Makarova KS.

Genes (Basel). 2018 Jan 23;9(2). pii: E28. doi: 10.3390/genes9020028.


Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.

Galperin MY, Makarova KS, Wolf YI, Koonin EV.

J Bacteriol. 2018 Mar 12;200(7). pii: e00681-17. doi: 10.1128/JB.00681-17. Print 2018 Apr 1.


Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea.

Makarova KS, Galperin MY, Koonin EV.

mBio. 2017 Dec 5;8(6). pii: e01959-17. doi: 10.1128/mBio.01959-17.


Phylogenomics of Cas4 family nucleases.

Hudaiberdiev S, Shmakov S, Wolf YI, Terns MP, Makarova KS, Koonin EV.

BMC Evol Biol. 2017 Nov 28;17(1):232. doi: 10.1186/s12862-017-1081-1.


Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.

Yutin N, Makarova KS, Gussow AB, Krupovic M, Segall A, Edwards RA, Koonin EV.

Nat Microbiol. 2018 Jan;3(1):38-46. doi: 10.1038/s41564-017-0053-y. Epub 2017 Nov 13.


Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.

Petitjean C, Makarova KS, Wolf YI, Koonin EV.

Genome Biol Evol. 2017 Oct 1;9(10):2791-2811. doi: 10.1093/gbe/evx189.


Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back.

Koonin EV, Makarova KS.

Genome Biol Evol. 2017 Oct 1;9(10):2812-2825. doi: 10.1093/gbe/evx192. Review.


Microbial genome analysis: the COG approach.

Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV.

Brief Bioinform. 2019 Jul 19;20(4):1063-1070. doi: 10.1093/bib/bbx117.


Discovery of Oligonucleotide Signaling Mediated by CRISPR-Associated Polymerases Solves Two Puzzles but Leaves an Enigma.

Koonin EV, Makarova KS.

ACS Chem Biol. 2018 Feb 16;13(2):309-312. doi: 10.1021/acschembio.7b00713. Epub 2017 Sep 27.


The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes.

Shmakov SA, Sitnik V, Makarova KS, Wolf YI, Severinov KV, Koonin EV.

mBio. 2017 Sep 19;8(5). pii: e01397-17. doi: 10.1128/mBio.01397-17.


Recruitment of CRISPR-Cas systems by Tn7-like transposons.

Peters JE, Makarova KS, Shmakov S, Koonin EV.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7358-E7366. doi: 10.1073/pnas.1709035114. Epub 2017 Aug 15.


High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.

Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Daligault H, Davenport K, Erkkila T, Goodwin LA, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woolbert M, Gunde-Cimerman N, Wolf YI, Grebenc T, Gostinčar C, Daly MJ.

Stand Genomic Sci. 2017 Jul 28;12:46. doi: 10.1186/s40793-017-0258-y. eCollection 2017.


On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.

Silas S, Makarova KS, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy SR, Fu BXH, Hansen LL, Wang D, Sullivan MB, Millard A, Clokie MR, Bhaya D, Lambowitz AM, Kyrpides NC, Koonin EV, Fire AZ.

mBio. 2017 Jul 11;8(4). pii: e00897-17. doi: 10.1128/mBio.00897-17.


'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.

Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA, La Cono V, Arcadi E, Nechitaylo TY, Ferrer M, Kublanov IV, Wolf YI, Yakimov MM, Golyshin PN.

Nat Commun. 2017 Jul 5;8(1):60. doi: 10.1038/s41467-017-00104-7.


Evolutionary Genomics of Defense Systems in Archaea and Bacteria.

Koonin EV, Makarova KS, Wolf YI.

Annu Rev Microbiol. 2017 Sep 8;71:233-261. doi: 10.1146/annurev-micro-090816-093830. Epub 2017 Jun 28. Review.


Diversity, classification and evolution of CRISPR-Cas systems.

Koonin EV, Makarova KS, Zhang F.

Curr Opin Microbiol. 2017 Jun;37:67-78. doi: 10.1016/j.mib.2017.05.008. Epub 2017 Jun 9. Review.


Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis.

Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN, Galinski EA, Ciordia S, Mena MC, Merkel AY, Wolf YI, van Loosdrecht MCM, Koonin EV.

Nat Microbiol. 2017 May 30;2:17081. doi: 10.1038/nmicrobiol.2017.81.


The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis.

Mekhedov SL, Makarova KS, Koonin EV.

Biol Direct. 2017 May 25;12(1):13. doi: 10.1186/s13062-017-0185-2.


Early vertebrate origin and diversification of small transmembrane regulators of cellular ion transport.

Pirkmajer S, Kirchner H, Lundell LS, Zelenin PV, Zierath JR, Makarova KS, Wolf YI, Chibalin AV.

J Physiol. 2017 Jul 15;595(14):4611-4630. doi: 10.1113/JP274254. Epub 2017 May 29.


Reconstruction of the evolution of microbial defense systems.

Puigbò P, Makarova KS, Kristensen DM, Wolf YI, Koonin EV.

BMC Evol Biol. 2017 Apr 4;17(1):94. doi: 10.1186/s12862-017-0942-y.


SnapShot: Class 1 CRISPR-Cas Systems.

Makarova KS, Zhang F, Koonin EV.

Cell. 2017 Feb 23;168(5):946-946.e1. doi: 10.1016/j.cell.2017.02.018.


Diversity and evolution of class 2 CRISPR-Cas systems.

Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV.

Nat Rev Microbiol. 2017 Mar;15(3):169-182. doi: 10.1038/nrmicro.2016.184. Epub 2017 Jan 23.

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