tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector

Jain, I., Kolesnik, M., Kuznedelov, K., Minakhin, L., Morozova, N., Shiriaeva, A., Kirillov, A., Medvedeva, S., Livenskyi, A., Kazieva, L., Makarova, K. S., Koonin, E. V., Borukhov, S., Severinov, K., & Semenova, E. (2024). tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector. Sci Adv, 10(17), eadl0164. doi:10.1126/sciadv.adl0164

Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile

Muzyukina, P., Shkaruta, A., Guzman, N. M., Andreani, J., Borges, A. L., Bondy-Denomy, J., Maikova, A., Semenova, E., Severinov, K., & Soutourina, O. (2023). Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile. mSphere, 8(6), e0040123. doi:10.1128/msphere.00401-23

Host nucleases generate prespacers for primed adaptation in the E. coli type I-E CRISPR-Cas system

Shiriaeva AA, Kuznedelov K, Fedorov I, Musharova O, Khvostikov T, Tsoy Y, Kurilovich E, Smith GR, Semenova E, Severinov K. Host nucleases generate prespacers for primed adaptation in the E. coli type I-E CRISPR-Cas system. Sci Adv. 2022;8(47):eabn8650.

Persistence of plasmids targeted by CRISPR interference in bacterial populations

Mamontov V, Martynov A, Morozova N, Bukatin A, Staroverov DB, Lukyanov KA, Ispolatov Y, Semenova E, Severinov K. Persistence of plasmids targeted by CRISPR interference in bacterial populations. Proc Natl Acad Sci U S A. 2022;119(15):e2114905119.

Prespacers formed during primed adaptation associate with the Cas1-Cas2 adaptation complex and the Cas3 interference nuclease-helicase

Musharova O, Medvedeva S, Klimuk E, Guzman NM, Titova D, Zgoda V, Shiriaeva A, Semenova E, Severinov K, Savitskaya E. Prespacers formed during primed adaptation associate with the Cas1-Cas2 adaptation complex and the Cas3 interference nuclease-helicase. Proc Natl Acad Sci U S A. 2021;118(22).

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. Detection of spacer precursors formed in vivo during primed CRISPR adaptation. Nat Commun. 2019;10(1):4603.

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. Defining the seed sequence of the Cas12b CRISPR-Cas effector complex. RNA Biol. 2019;16(4):413-22.

Interdependencies between the adaptation and interference modules guide efficient CRISPR-Cas immunity

Semenova E, Severinov K. Interdependencies between the adaptation and interference modules guide efficient CRISPR-Cas immunity. Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts. 2017: 51-62.

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

Severinov K, Ispolatov I, Semenova E. The Influence of Copy-Number of Targeted Extrachromosomal Genetic Elements on the Outcome of CRISPR-Cas Defense. Front Mol Biosci. 2016;3:45.

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. Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex. Proc Natl Acad Sci U S A. 2016;113(27):7626-31.

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. Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3'-terminal segment of guide RNA. Nucleic Acids Res. 2016;44(6):2837-45.

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. Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation. Nucleic Acids Res. 2016;44(22):10849-61.

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. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353(6299):aaf5573.

Come Together: CRISPR-Cas Immunity Senses the Quorum

Semenova E, Severinov K. Come Together: CRISPR-Cas Immunity Senses the Quorum. Mol Cell. 2016;64(6):1013-5.

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. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery. Nucleic Acids Res. 2015;43(22):10848-60.

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. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Mol Cell. 2015;60(3):385-97.

The Cas6e ribonuclease is not required for interference and adaptation by the E. coli type I-E CRISPR-Cas system

Semenova E, Kuznedelov K, Datsenko KA, Boudry PM, Savitskaya EE, Medvedeva S, Beloglazova N, Logacheva M, Yakunin AF, Severinov K. The Cas6e ribonuclease is not required for interference and adaptation by the E. coli type I-E CRISPR-Cas system. Nucleic Acids Res. 2015;43(12):6049-61.

Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition

Westra ER*, Semenova E*, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, Brouns SJ. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet. 2013;9(9):e1003742.

CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3

Westra ER, van Erp PB, Kunne T, Wong SP, Staals RH, Seegers CL, Bollen S, Jore MM, Semenova E, Severinov K, de Vos WM, Dame RT, de Vries R, Brouns SJ, van der Oost J. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell. 2012;46(5):595-605.

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system

Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun. 2012;3:945.

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJ, Severinov K. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci U S A. 2011;108(25):10098-103.

Structure-activity analysis of microcinJ25: distinct parts of the threaded lasso molecule are responsible for interaction with bacterial RNA polymerase

Semenova E*, Yuzenkova Y*, Peduzzi J, Rebuffat S, Severinov K. Structure-activity analysis of microcinJ25: distinct parts of the threaded lasso molecule are responsible for interaction with bacterial RNA polymerase. J Bacteriol. 2005;187(11):3859-63.

Transcription regulation of the EcoRV restriction-modification system

Semenova E*, Minakhin L*, Bogdanova E, Nagornykh M, Vasilov A, Heyduk T, Solonin A, Zakharova M, Severinov K. Transcription regulation of the EcoRV restriction-modification system. Nucleic Acids Res. 2005;33(21):6942-51.

The tale of two RNA polymerases: transcription profiling and gene expression strategy of bacteriophage Xp10

Semenova E, Djordjevic M, Shraiman B, Severinov K. The tale of two RNA polymerases: transcription profiling and gene expression strategy of bacteriophage Xp10. Mol Microbiol. 2005;55(3):764-77.

Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah

Minakhin L*, Semenova E*, Liu J, Vasilov A, Severinova E, Gabisonia T, Inman R, Mushegian A, Severinov K. Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah. J Mol Biol. 2005;354(1):1-15.