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Items: 1 to 50 of 176

1.

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 Jun 21. doi: 10.1038/s41564-018-0184-9. [Epub ahead of print]

PMID:
29934592
2.

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 Jun 21. doi: 10.1093/nar/gky560. [Epub ahead of print]

PMID:
29931259
3.

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.

PMID:
29784811
4.

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.

PMID:
29781801
5.

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 Apr 16. doi: 10.1093/molbev/msy075. [Epub ahead of print]

PMID:
29668953
6.

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.

7.

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.

PMID:
29551514
8.

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 Jun 21;:.

PMID:
29507349
9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

Microbial genome analysis: the COG approach.

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

Brief Bioinform. 2017 Sep 14. doi: 10.1093/bib/bbx117. [Epub ahead of print]

PMID:
28968633
17.

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.

PMID:
28937734
18.

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.

19.

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.

20.

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.

21.

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.

22.

'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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

Myosin-driven transport network in plants.

Kurth EG, Peremyslov VV, Turner HL, Makarova KS, Iranzo J, Mekhedov SL, Koonin EV, Dolja VV.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1385-E1394. doi: 10.1073/pnas.1620577114. Epub 2017 Jan 17.

32.

SnapShot: Class 2 CRISPR-Cas Systems.

Makarova KS, Zhang F, Koonin EV.

Cell. 2017 Jan 12;168(1-2):328-328.e1. doi: 10.1016/j.cell.2016.12.038. Epub 2017 Jan 12.

33.

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28.

Smargon AA, Cox DBT, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, Abudayyeh OA, Essletzbichler P, Shmakov S, Makarova KS, Koonin EV, Zhang F.

Mol Cell. 2017 Feb 16;65(4):618-630.e7. doi: 10.1016/j.molcel.2016.12.023. Epub 2017 Jan 5.

34.

Two fundamentally different classes of microbial genes.

Wolf YI, Makarova KS, Lobkovsky AE, Koonin EV.

Nat Microbiol. 2016 Nov 7;2:16208. doi: 10.1038/nmicrobiol.2016.208.

PMID:
27819663
35.

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems.

Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J.

Science. 2016 Aug 5;353(6299):aad5147. doi: 10.1126/science.aad5147. Review.

PMID:
27493190
36.

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.

Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F.

Science. 2016 Aug 5;353(6299):aaf5573. doi: 10.1126/science.aaf5573. Epub 2016 Jun 2.

37.

The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases.

Lavysh D, Sokolova M, Minakhin L, Yakunina M, Artamonova T, Kozyavkin S, Makarova KS, Koonin EV, Severinov K.

Virology. 2016 Aug;495:185-96. doi: 10.1016/j.virol.2016.04.030. Epub 2016 May 26.

38.

Diversity and Evolution of Type IV pili Systems in Archaea.

Makarova KS, Koonin EV, Albers SV.

Front Microbiol. 2016 May 6;7:667. doi: 10.3389/fmicb.2016.00667. eCollection 2016.

39.

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA.

Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O.

Cell. 2016 May 5;165(4):949-62. doi: 10.1016/j.cell.2016.04.003. Epub 2016 Apr 21.

40.

Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity.

Krupovic M, Shmakov S, Makarova KS, Forterre P, Koonin EV.

Genome Biol Evol. 2016 Jan 13;8(2):375-86. doi: 10.1093/gbe/evw006.

41.

ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs.

Kapitonov VV, Makarova KS, Koonin EV.

J Bacteriol. 2015 Dec 28;198(5):797-807. doi: 10.1128/JB.00783-15.

42.

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.

Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV.

Mol Cell. 2015 Nov 5;60(3):385-97. doi: 10.1016/j.molcel.2015.10.008. Epub 2015 Oct 22.

43.

A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage.

Yakunina M, Artamonova T, Borukhov S, Makarova KS, Severinov K, Minakhin L.

Nucleic Acids Res. 2015 Dec 2;43(21):10411-20. doi: 10.1093/nar/gkv1095. Epub 2015 Oct 20.

44.

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.

Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F.

Cell. 2015 Oct 22;163(3):759-71. doi: 10.1016/j.cell.2015.09.038. Epub 2015 Sep 25.

45.

An updated evolutionary classification of CRISPR-Cas systems.

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV.

Nat Rev Microbiol. 2015 Nov;13(11):722-36. doi: 10.1038/nrmicro3569. Epub 2015 Sep 28. Review.

46.

Evolution of plant δ(1)-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives.

Forlani G, Makarova KS, Ruszkowski M, Bertazzini M, Nocek B.

Front Plant Sci. 2015 Aug 3;6:567. doi: 10.3389/fpls.2015.00567. eCollection 2015.

47.

A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase.

Liu B, Ouyang S, Makarova KS, Xia Q, Zhu Y, Li Z, Guo L, Koonin EV, Liu ZJ, Huang L.

Nat Commun. 2015 Jun 22;6:7300. doi: 10.1038/ncomms8300.

48.

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF.

J Biol Chem. 2015 Jul 24;290(30):18678-98. doi: 10.1074/jbc.M115.657916. Epub 2015 Jun 12.

49.

Annotation and Classification of CRISPR-Cas Systems.

Makarova KS, Koonin EV.

Methods Mol Biol. 2015;1311:47-75. doi: 10.1007/978-1-4939-2687-9_4. Review.

50.

Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae.

Pagnier I, Yutin N, Croce O, Makarova KS, Wolf YI, Benamar S, Raoult D, Koonin EV, La Scola B.

Biol Direct. 2015 Mar 31;10:13. doi: 10.1186/s13062-015-0043-z.

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