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Items: 1 to 50 of 287

1.

Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference.

You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y.

Cell. 2018 Nov 26. pii: S0092-8674(18)31451-X. doi: 10.1016/j.cell.2018.10.052. [Epub ahead of print]

PMID:
30503210
2.

Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome.

Sutormin D, Rubanova N, Logacheva M, Ghilarov D, Severinov K.

Nucleic Acids Res. 2018 Dec 4. doi: 10.1093/nar/gky1222. [Epub ahead of print]

PMID:
30517674
3.

Avoidance of Trinucleotide Corresponding to Consensus Protospacer Adjacent Motif Controls the Efficiency of Prespacer Selection during Primed Adaptation.

Musharova O, Vyhovskyi D, Medvedeva S, Guzina J, Zhitnyuk Y, Djordjevic M, Severinov K, Savitskaya E.

MBio. 2018 Dec 4;9(6). pii: e02169-18. doi: 10.1128/mBio.02169-18.

4.

BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site.

Gordeeva J, Morozova N, Sierro N, Isaev A, Sinkunas T, Tsvetkova K, Matlashov M, Truncaite L, Morgan RD, Ivanov NV, Siksnys V, Zeng L, Severinov K.

Nucleic Acids Res. 2018 Nov 12. doi: 10.1093/nar/gky1125. [Epub ahead of print]

PMID:
30418590
5.

Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock.

Klimuk E, Bogdanova E, Nagornykh M, Rodic A, Djordjevic M, Medvedeva S, Pavlova O, Severinov K.

Nucleic Acids Res. 2018 Nov 16;46(20):10810-10826. doi: 10.1093/nar/gky880.

6.

Ultrahigh-throughput functional profiling of microbiota communities.

Terekhov SS, Smirnov IV, Malakhova MV, Samoilov AE, Manolov AI, Nazarov AS, Danilov DV, Dubiley SA, Osterman IA, Rubtsova MP, Kostryukova ES, Ziganshin RH, Kornienko MA, Vanyushkina AA, Bukato ON, Ilina EN, Vlasov VV, Severinov KV, Gabibov AG, Altman S.

Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):9551-9556. doi: 10.1073/pnas.1811250115. Epub 2018 Sep 4.

7.

New Insights Into Functions and Possible Applications of Clostridium difficile CRISPR-Cas System.

Maikova A, Severinov K, Soutourina O.

Front Microbiol. 2018 Jul 31;9:1740. doi: 10.3389/fmicb.2018.01740. eCollection 2018. Review.

8.

Defining the seed sequence of the Cas12b CRISPR-Cas effector complex.

Jain I, Minakhin L, Mekler V, Sitnik V, Rubanova N, Severinov K, Semenova E.

RNA Biol. 2018 Aug 17:1-10. doi: 10.1080/15476286.2018.1495492. [Epub ahead of print]

PMID:
30022698
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.

10.

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.

11.

Biosynthesis of Translation Inhibitor Klebsazolicin Proceeds through Heterocyclization and N-Terminal Amidine Formation Catalyzed by a Single YcaO Enzyme.

Travin DY, Metelev M, Serebryakova M, Komarova ES, Osterman IA, Ghilarov D, Severinov K.

J Am Chem Soc. 2018 Apr 25;140(16):5625-5633. doi: 10.1021/jacs.8b02277. Epub 2018 Apr 11.

PMID:
29601195
12.

Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro.

Krivoy A, Rutkauskas M, Kuznedelov K, Musharova O, Rouillon C, Severinov K, Seidel R.

Nucleic Acids Res. 2018 May 4;46(8):4087-4098. doi: 10.1093/nar/gky219.

13.

Optimal number of spacers in CRISPR arrays.

Martynov A, Severinov K, Ispolatov I.

PLoS Comput Biol. 2017 Dec 18;13(12):e1005891. doi: 10.1371/journal.pcbi.1005891. eCollection 2017 Dec.

14.

A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation.

Ooi WY, Murayama Y, Mekler V, Minakhin L, Severinov K, Yokoyama S, Sekine SI.

Nucleic Acids Res. 2018 Jan 9;46(1):431-441. doi: 10.1093/nar/gkx1162.

15.

Features of CRISPR-Cas Regulation Key to Highly Efficient and Temporally-Specific crRNA Production.

Rodic A, Blagojevic B, Djordjevic M, Severinov K, Djordjevic M.

Front Microbiol. 2017 Nov 3;8:2139. doi: 10.3389/fmicb.2017.02139. eCollection 2017.

16.

Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase.

Petushkov I, Esyunina D, Mekler V, Severinov K, Pupov D, Kulbachinskiy A.

Biochem J. 2017 Dec 1;474(24):4053-4064. doi: 10.1042/BCJ20170436.

PMID:
29101286
17.

The Product of Yersinia pseudotuberculosis mcc Operon Is a Peptide-Cytidine Antibiotic Activated Inside Producing Cells by the TldD/E Protease.

Tsibulskaya D, Mokina O, Kulikovsky A, Piskunova J, Severinov K, Serebryakova M, Dubiley S.

J Am Chem Soc. 2017 Nov 15;139(45):16178-16187. doi: 10.1021/jacs.7b07118. Epub 2017 Oct 31.

PMID:
29045133
18.

The Origins of Specificity in the Microcin-Processing Protease TldD/E.

Ghilarov D, Serebryakova M, Stevenson CEM, Hearnshaw SJ, Volkov DS, Maxwell A, Lawson DM, Severinov K.

Structure. 2017 Oct 3;25(10):1549-1561.e5. doi: 10.1016/j.str.2017.08.006. Epub 2017 Sep 21.

19.

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.

20.

Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel.

Metelev M, Osterman IA, Ghilarov D, Khabibullina NF, Yakimov A, Shabalin K, Utkina I, Travin DY, Komarova ES, Serebryakova M, Artamonova T, Khodorkovskii M, Konevega AL, Sergiev PV, Severinov K, Polikanov YS.

Nat Chem Biol. 2017 Oct;13(10):1129-1136. doi: 10.1038/nchembio.2462. Epub 2017 Aug 28.

21.

Novel Fri1-like Viruses Infecting Acinetobacter baumannii-vB_AbaP_AS11 and vB_AbaP_AS12-Characterization, Comparative Genomic Analysis, and Host-Recognition Strategy.

Popova AV, Lavysh DG, Klimuk EI, Edelstein MV, Bogun AG, Shneider MM, Goncharov AE, Leonov SV, Severinov KV.

Viruses. 2017 Jul 17;9(7). pii: E188. doi: 10.3390/v9070188.

22.

Full shut-off of Escherichia coli RNA-polymerase by T7 phage requires a small phage-encoded DNA-binding protein.

Tabib-Salazar A, Liu B, Shadrin A, Burchell L, Wang Z, Wang Z, Goren MG, Yosef I, Qimron U, Severinov K, Matthews SJ, Wigneshweraraj S.

Nucleic Acids Res. 2017 Jul 27;45(13):7697-7707. doi: 10.1093/nar/gkx370.

23.

Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation.

Mekler V, Minakhin L, Severinov K.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):5443-5448. doi: 10.1073/pnas.1619926114. Epub 2017 May 8.

24.

A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters.

Sokolova M, Borukhov S, Lavysh D, Artamonova T, Khodorkovskii M, Severinov K.

Nucleic Acids Res. 2017 Jun 2;45(10):5958-5967. doi: 10.1093/nar/gkx264.

25.

Spacer-length DNA intermediates are associated with Cas1 in cells undergoing primed CRISPR adaptation.

Musharova O, Klimuk E, Datsenko KA, Metlitskaya A, Logacheva M, Semenova E, Severinov K, Savitskaya E.

Nucleic Acids Res. 2017 Apr 7;45(6):3297-3307. doi: 10.1093/nar/gkx097.

26.

Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases.

Lavysh D, Sokolova M, Slashcheva M, Förstner KU, Severinov K.

MBio. 2017 Feb 14;8(1). pii: e02041-16. doi: 10.1128/mBio.02041-16.

27.

Erratum: Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array.

Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F.

Nat Biotechnol. 2017 Feb 8;35(2):178. doi: 10.1038/nbt0217-178b. No abstract available.

PMID:
28178246
28.

Peptide-nucleotide antibiotic Microcin C is a potent inducer of stringent response and persistence in both sensitive and producing cells.

Piskunova J, Maisonneuve E, Germain E, Gerdes K, Severinov K.

Mol Microbiol. 2017 May;104(3):463-471. doi: 10.1111/mmi.13640. Epub 2017 Feb 24.

29.

The action of Escherichia coli CRISPR-Cas system on lytic bacteriophages with different lifestyles and development strategies.

Strotskaya A, Savitskaya E, Metlitskaya A, Morozova N, Datsenko KA, Semenova E, Severinov K.

Nucleic Acids Res. 2017 Feb 28;45(4):1946-1957. doi: 10.1093/nar/gkx042.

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.

Acinetodin and Klebsidin, RNA Polymerase Targeting Lasso Peptides Produced by Human Isolates of Acinetobacter gyllenbergii and Klebsiella pneumoniae.

Metelev M, Arseniev A, Bushin LB, Kuznedelov K, Artamonova TO, Kondratenko R, Khodorkovskii M, Seyedsayamdost MR, Severinov K.

ACS Chem Biol. 2017 Mar 17;12(3):814-824. doi: 10.1021/acschembio.6b01154. Epub 2017 Feb 3.

PMID:
28106375
32.

Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism.

Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA.

Nucleic Acids Res. 2017 Apr 7;45(6):3580-3590. doi: 10.1093/nar/gkw1354.

33.

Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years.

Savitskaya E, Lopatina A, Medvedeva S, Kapustin M, Shmakov S, Tikhonov A, Artamonova II, Logacheva M, Severinov K.

Mol Ecol. 2017 Apr;26(7):2019-2026. doi: 10.1111/mec.13961. Epub 2017 Jan 17.

34.

Come Together: CRISPR-Cas Immunity Senses the Quorum.

Semenova E, Severinov K.

Mol Cell. 2016 Dec 15;64(6):1013-1015. doi: 10.1016/j.molcel.2016.11.037.

35.

A Trojan-Horse Peptide-Carboxymethyl-Cytidine Antibiotic from Bacillus amyloliquefaciens.

Serebryakova M, Tsibulskaya D, Mokina O, Kulikovsky A, Nautiyal M, Van Aerschot A, Severinov K, Dubiley S.

J Am Chem Soc. 2016 Dec 7;138(48):15690-15698. Epub 2016 Nov 29.

36.

Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array.

Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F.

Nat Biotechnol. 2017 Jan;35(1):31-34. doi: 10.1038/nbt.3737. Epub 2016 Dec 5. Erratum in: Nat Biotechnol. 2017 Feb 8;35(2):178.

37.

Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation.

Kuznedelov K, Mekler V, Lemak S, Tokmina-Lukaszewska M, Datsenko KA, Jain I, Savitskaya E, Mallon J, Shmakov S, Bothner B, Bailey S, Yakunin AF, Severinov K, Semenova E.

Nucleic Acids Res. 2016 Dec 15;44(22):10849-10861. Epub 2016 Oct 13.

38.

The Influence of Copy-Number of Targeted Extrachromosomal Genetic Elements on the Outcome of CRISPR-Cas Defense.

Severinov K, Ispolatov I, Semenova E.

Front Mol Biosci. 2016 Aug 31;3:45. doi: 10.3389/fmolb.2016.00045. eCollection 2016.

39.

Diversity of CRISPR-Cas-Mediated Mechanisms of Adaptive Immunity in Prokaryotes and Their Application in Biotechnology.

Savitskaya EE, Musharova OS, Severinov KV.

Biochemistry (Mosc). 2016 Jul;81(7):653-61. doi: 10.1134/S0006297916070026. Review.

40.

Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex.

Semenova E, Savitskaya E, Musharova O, Strotskaya A, Vorontsova D, Datsenko KA, Logacheva MD, Severinov K.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7626-31. doi: 10.1073/pnas.1602639113. Epub 2016 Jun 20.

41.

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.

42.

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.

43.

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow.

Lopatina A, Medvedeva S, Shmakov S, Logacheva MD, Krylenkov V, Severinov K.

Front Microbiol. 2016 Mar 31;7:398. doi: 10.3389/fmicb.2016.00398. eCollection 2016.

44.

Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3'-terminal segment of guide RNA.

Mekler V, Minakhin L, Semenova E, Kuznedelov K, Severinov K.

Nucleic Acids Res. 2016 Apr 7;44(6):2837-45. doi: 10.1093/nar/gkw138. Epub 2016 Mar 3.

45.

Temporal dynamics of methyltransferase and restriction endonuclease accumulation in individual cells after introducing a restriction-modification system.

Morozova N, Sabantsev A, Bogdanova E, Fedorova Y, Maikova A, Vedyaykin A, Rodic A, Djordjevic M, Khodorkovskii M, Severinov K.

Nucleic Acids Res. 2016 Jan 29;44(2):790-800. doi: 10.1093/nar/gkv1490. Epub 2015 Dec 19.

46.

New Infestin-4 Mutants with Increased Selectivity against Factor XIIa.

Kolyadko VN, Lushchekina SV, Vuimo TA, Surov SS, Ovsepyan RA, Korneeva VA, Vorobiev II, Orlova NA, Minakhin L, Kuznedelov K, Severinov KV, Ataullakhanov FI, Panteleev MA.

PLoS One. 2015 Dec 15;10(12):e0144940. doi: 10.1371/journal.pone.0144940. eCollection 2015.

47.

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.

48.

Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery.

Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E.

Nucleic Acids Res. 2015 Dec 15;43(22):10848-60. doi: 10.1093/nar/gkv1261. Epub 2015 Nov 19.

49.

CRISPR interference and priming varies with individual spacer sequences.

Xue C, Seetharam AS, Musharova O, Severinov K, Brouns SJ, Severin AJ, Sashital DG.

Nucleic Acids Res. 2015 Dec 15;43(22):10831-47. doi: 10.1093/nar/gkv1259. Epub 2015 Nov 19.

50.

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.

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