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Items: 1 to 50 of 307

1.

Virus-borne mini-CRISPR arrays are involved in interviral conflicts.

Medvedeva S, Liu Y, Koonin EV, Severinov K, Prangishvili D, Krupovic M.

Nat Commun. 2019 Nov 15;10(1):5204. doi: 10.1038/s41467-019-13205-2.

2.

'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses.

Boon M, De Zitter E, De Smet J, Wagemans J, Voet M, Pennemann FL, Schalck T, Kuznedelov K, Severinov K, Van Meervelt L, De Maeyer M, Lavigne R.

Nucleic Acids Res. 2019 Nov 14. pii: gkz1048. doi: 10.1093/nar/gkz1048. [Epub ahead of print]

PMID:
31724707
3.

Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas System.

Kurilovich E, Shiriaeva A, Metlitskaya A, Morozova N, Ivancic-Bace I, Severinov K, Savitskaya E.

Genes (Basel). 2019 Oct 31;10(11). pii: E872. doi: 10.3390/genes10110872.

4.

Detection of spacer precursors formed in vivo during primed CRISPR adaptation.

Shiriaeva AA, Savitskaya E, Datsenko KA, Vvedenskaya IO, Fedorova I, Morozova N, Metlitskaya A, Sabantsev A, Nickels BE, Severinov K, Semenova E.

Nat Commun. 2019 Oct 10;10(1):4603. doi: 10.1038/s41467-019-12417-w.

5.

Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.

Travin DY, Watson ZL, Metelev M, Ward FR, Osterman IA, Khven IM, Khabibullina NF, Serebryakova M, Mergaert P, Polikanov YS, Cate JHD, Severinov K.

Nat Commun. 2019 Oct 8;10(1):4563. doi: 10.1038/s41467-019-12589-5.

6.

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.

PMID:
31520072
7.

Using an Endogenous CRISPR-Cas System for Genome Editing in the Human Pathogen Clostridium difficile.

Maikova A, Kreis V, Boutserin A, Severinov K, Soutourina O.

Appl Environ Microbiol. 2019 Oct 1;85(20). pii: e01416-19. doi: 10.1128/AEM.01416-19. Print 2019 Oct 15.

PMID:
31399410
8.

Structural Basis of Leader Peptide Recognition in Lasso Peptide Biosynthesis Pathway.

Sumida T, Dubiley S, Wilcox B, Severinov K, Tagami S.

ACS Chem Biol. 2019 Jul 19;14(7):1619-1627. doi: 10.1021/acschembio.9b00348. Epub 2019 Jun 24.

PMID:
31188556
9.

Cytological Immunostaining of HMGA2, LRP1B, and TP63 as Potential Biomarkers for Triaging Human Papillomavirus-Positive Women.

Jiang Y, Zhu C, He D, Gao Q, Tian X, Ma X, Wu J, Das BC, Severinov K, Hitzeroth II, Debata PR, Liu R, Zou L, Shi L, Xu H, Wang K, Bao Y, Ka-Kit LR, You Z, Cui Z, Hu Z.

Transl Oncol. 2019 Jul;12(7):959-967. doi: 10.1016/j.tranon.2019.04.012. Epub 2019 May 16.

10.

Risk stratification of cervical lesions using capture sequencing and machine learning method based on HPV and human integrated genomic profiles.

Tian R, Cui Z, He D, Tian X, Gao Q, Ma X, Yang JR, Wu J, Das BC, Severinov K, Hitzeroth II, Debata PR, Xu W, Zhong H, Fan W, Chen Y, Jin Z, Cao C, Yu M, Xie W, Huang Z, Bao Y, Xie H, Yao S, Hu Z.

Carcinogenesis. 2019 Oct 16;40(10):1220-1228. doi: 10.1093/carcin/bgz094.

PMID:
31102403
11.

Reiterative Synthesis by the Ribosome and Recognition of the N-Terminal Formyl Group by Biosynthetic Machinery Contribute to Evolutionary Conservation of the Length of Antibiotic Microcin C Peptide Precursor.

Zukher I, Pavlov M, Tsibulskaya D, Kulikovsky A, Zyubko T, Bikmetov D, Serebryakova M, Nair SK, Ehrenberg M, Dubiley S, Severinov K.

MBio. 2019 Apr 30;10(2). pii: e00768-19. doi: 10.1128/mBio.00768-19.

12.

Natural diversity of CRISPR spacers of Thermus: evidence of local spacer acquisition and global spacer exchange.

Lopatina A, Medvedeva S, Artamonova D, Kolesnik M, Sitnik V, Ispolatov Y, Severinov K.

Philos Trans R Soc Lond B Biol Sci. 2019 May 13;374(1772):20180092. doi: 10.1098/rstb.2018.0092.

13.

Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor.

Dong SH, Kulikovsky A, Zukher I, Estrada P, Dubiley S, Severinov K, Nair SK.

Chem Sci. 2018 Dec 26;10(8):2391-2395. doi: 10.1039/c8sc03173h. eCollection 2019 Feb 28.

14.

Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation.

Musharova O, Sitnik V, Vlot M, Savitskaya E, Datsenko KA, Krivoy A, Fedorov I, Semenova E, Brouns SJJ, Severinov K.

Mol Microbiol. 2019 Jun;111(6):1558-1570. doi: 10.1111/mmi.14237. Epub 2019 Apr 6.

PMID:
30875129
15.

Xenogeneic Regulation of the Bacterial Transcription Machinery.

Tabib-Salazar A, Mulvenna N, Severinov K, Matthews SJ, Wigneshweraraj S.

J Mol Biol. 2019 Feb 15. pii: S0022-2836(19)30085-3. doi: 10.1016/j.jmb.2019.02.008. [Epub ahead of print] Review.

16.

Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids.

Bayfield OW, Klimuk E, Winkler DC, Hesketh EL, Chechik M, Cheng N, Dykeman EC, Minakhin L, Ranson NA, Severinov K, Steven AC, Antson AA.

Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3556-3561. doi: 10.1073/pnas.1813204116. Epub 2019 Feb 8.

17.

CRISPR-Cas molecular beacons as tool for studies of assembly of CRISPR-Cas effector complexes and their interactions with DNA.

Mekler V, Kuznedelov K, Minakhin L, Murugan K, Sashital DG, Severinov K.

Methods Enzymol. 2019;616:337-363. doi: 10.1016/bs.mie.2018.10.026. Epub 2018 Dec 1.

PMID:
30691650
18.

Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison.

Ghilarov D, Stevenson CEM, Travin DY, Piskunova J, Serebryakova M, Maxwell A, Lawson DM, Severinov K.

Mol Cell. 2019 Feb 21;73(4):749-762.e5. doi: 10.1016/j.molcel.2018.11.032. Epub 2019 Jan 17.

19.

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. 2019 Feb 20;47(3):1601. doi: 10.1093/nar/gky1312. No abstract available.

20.

Effects of Population Dynamics on Establishment of a Restriction-Modification System in a Bacterial Host.

Graovac S, Rodic A, Djordjevic M, Severinov K, Djordjevic M.

Molecules. 2019 Jan 7;24(1). pii: E198. doi: 10.3390/molecules24010198.

21.

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. 2019 Jan 10;176(1-2):239-253.e16. doi: 10.1016/j.cell.2018.10.052. Epub 2018 Nov 29.

PMID:
30503210
22.

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. 2019 Feb 20;47(3):1373-1388. doi: 10.1093/nar/gky1222. Erratum in: Nucleic Acids Res. 2019 Feb 20;47(3):1601.

23.

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.

24.

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. 2019 Jan 10;47(1):253-265. doi: 10.1093/nar/gky1125.

25.

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.

26.

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.

27.

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.

28.

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. 2019 Apr;16(4):413-422. doi: 10.1080/15476286.2018.1495492. Epub 2018 Aug 17.

29.

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.

30.

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.

31.

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
32.

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.

33.

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.

34.

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.

35.

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.

36.

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
37.

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
38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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
48.

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.

49.

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.

50.

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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