Кто мы
Мы – команда ученых из Сколковского института науки и технологий, Московского физико-технического института и Центра морских исследований МГУ. Наш главный фокус – метагеномные исследования.
Мы организуем экспедиции для сбора проб из морей, горячих источников и вулканов по всей России, выделяем и культивируем бактерии и вирусы, секвенируем их и проводим биоинформатические исследования.
Наша лаборатория, где мы занимаемся мокрыми исследованиями и анализируем данные, расположена в Сколтехе.
Важное направление нашей работы – гражданская наука; мы привлекаем к проектам школьников и студентов младших курсов, читаем лекции и разрабатываем курсы по биоинформатике и анализу метагеномов.
Мы организуем экспедиции для сбора проб из морей, горячих источников и вулканов по всей России, выделяем и культивируем бактерии и вирусы, секвенируем их и проводим биоинформатические исследования.
Наша лаборатория, где мы занимаемся мокрыми исследованиями и анализируем данные, расположена в Сколтехе.
Важное направление нашей работы – гражданская наука; мы привлекаем к проектам школьников и студентов младших курсов, читаем лекции и разрабатываем курсы по биоинформатике и анализу метагеномов.
Команда
- Констанстин СевериновДиректор лаборатории
- Дмитрий СуторминНаучный сотрудник
- Матвей КолесникНаучный сотрудник
- Дарья СлоноваНаучный сотрудник
- Артём ИсаевНаучный сотрудник
- Михаил СкутельНаучный сотрудник
- Виктор МамонтовНаучный сотрудник
Публикации
2023
[1]
D.Y. Travin, R. Jouan, A. Vigouroux, S. Inaba-Inoue, J. Lachat, F. Haq, T. Timchenko, D. Sutormin, S. Dubiley, K. Beis, S. Moréra, K. Severinov, P. Mergaert, Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition by Gram-Negative Bacteria, MBio 14 (2023) e00217-23. https://doi.org/10.1128/mbio.00217-23.
[2]
D. Sutormin, A. Galivondzhyan, A. Gafurov, K. Severinov, Single-nucleotide resolution detection of Topo IV cleavage activity in the Escherichia coli genome with Topo-Seq, Front. Microbiol. 14 (2023) 1160736. https://doi.org/10.3389/fmicb.2023.1160736.
[3]
A. Olina, A. Agapov, D. Yudin, D. Sutormin, A. Galivondzhyan, A. Kuzmenko, K. Severinov, A.A. Aravin, A. Kulbachinskiy, Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli, Microbiol Spectr 11 (2023) e04146-22. https://doi.org/10.1128/spectrum.04146-22.
[4]
A.A. Kudryavtseva, E. Cséfalvay, E.Y. Gnuchikh, D.D. Yanovskaya, M.A. Skutel, A.B. Isaev, S.V. Bazhenov, A.A. Utkina, I.V. Manukhov, Broadness and specificity: ArdB, ArdA, and Ocr against various restriction-modification systems, Front. Microbiol. 14 (2023) 1133144. https://doi.org/10.3389/fmicb.2023.1133144.
[5]
Moscow State Academy of Veterinary Medicine and Biotechnology – MVA n. a. K.I. Skryabin, R.G. Aksenov, A.V. Komissarova, Financial University under the Government of the Russian Federation, M.A. Skutel, Skolkovo Institute of Science and Technology, A.B. Isaev, Skolkovo Institute of Science and Technology, Genomic variants’ analysis of Escherichia coli K-12 cells resistant to phage T7 infection, P&FPE 16 (2023) 3–12. https://doi.org/10.17586/2310-1164-2023-16-2-3-12.
[6]
A. Kelly, S.C. Went, G. Mariano, L.P. Shaw, D.M. Picton, S.J. Duffner, I. Coates, R. Herdman-Grant, J. Gordeeva, A. Drobiazko, A. Isaev, Y.-J. Lee, Y. Luyten, R.D. Morgan, P. Weigele, K. Severinov, N. Wenner, J.C.D. Hinton, T.R. Blower, Diverse Durham collection phages demonstrate complex BREX defense responses, Appl Environ Microbiol 89 (2023) e00623-23. https://doi.org/10.1128/aem.00623-23.
[7]
A. Andriianov, S. Trigüis, A. Drobiazko, N. Sierro, N.V. Ivanov, M. Selmer, K. Severinov, A. Isaev, Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase, Cell Reports 42 (2023) 112972. https://doi.org/10.1016/j.celrep.2023.112972.
[8]
V.S. Mihailovskaya, D.A. Sutormin, M.O. Karipova, A.B. Trofimova, V.A. Mamontov, K. Severinov, M.V. Kuznetsova, Bacteriocin-Producing Escherichia coli Q5 and C41 with Potential Probiotic Properties: In Silico, In Vitro, and In Vivo Studies, IJMS 24 (2023) 12636. https://doi.org/10.3390/ijms241612636.
[9]
D. Antonova, V.V. Belousova, E. Zhivkoplias, M. Sobinina, T. Artamonova, I.E. Vishnyakov, I. Kurdyumova, A. Arseniev, N. Morozova, K. Severinov, M. Khodorkovskii, M.V. Yakunina, The Dynamics of Synthesis and Localization of Jumbo Phage RNA Polymerases inside Infected Cells, Viruses 15 (2023) 2096. https://doi.org/10.3390/v15102096.
[10]
M. Skutel, A. Andriianov, M. Zavialova, M. Kirsanova, O. Shodunke, E. Zorin, A. Golovshchinskii, K. Severinov, A. Isaev, T5-like phage BF23 evades host-mediated DNA restriction and methylation, MicroLife 4 (2023) uqad044. https://doi.org/10.1093/femsml/uqad044.
[11]
P. Muzyukina, A. Shkaruta, N.M. Guzman, J. Andreani, A.L. Borges, J. Bondy-Denomy, A. Maikova, E. Semenova, K. Severinov, O. Soutourina, Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile, MSphere 8 (2023) e00401-23. https://doi.org/10.1128/msphere.00401-23.
[12]
A. Demkina, D. Slonova, V. Mamontov, O. Konovalova, D. Yurikova, V. Rogozhin, V. Belova, D. Korostin, D. Sutormin, K. Severinov, A. Isaev, Benchmarking DNA isolation methods for marine metagenomics, Sci Rep 13 (2023) 22138. https://doi.org/10.1038/s41598-023-48804-z.
2022
[1]
Alfi, A., Popov, A., Kumar, A., Zhang, K. Y. J., Dubiley, S., Severinov, K., & Tagami, S. (2022). Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2. ACS Synthetic Biology, 11(6), 2022–2028. https://doi.org/10.1021/acssynbio.2c00176
[2]
Bikmetov, D., Hall, A. M. J., Livenskyi, A., Gollan, B., Ovchinnikov, S., Gilep, K., Kim, J. Y., Larrouy-Maumus, G., Zgoda, V., Borukhov, S., Severinov, K., Helaine, S., & Dubiley, S. (2022). GNAT toxins evolve toward narrow tRNA target specificities. Nucleic Acids Research, 50(10), 5807–5817.
https://doi.org/10.1093/nar/gkac356
[3]
Fraser, A., Sokolova, M. L., Drobysheva, A. V., Gordeeva, J. V., Borukhov, S., Jumper, J., Severinov, K. V., & Leiman, P. G. (2022). Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Nature Communications, 13(1), 3526.
https://doi.org/10.1038/s41467-022-31214-6
[4]
Isaev, A., Andriianov, A., Znobishcheva, E., Zorin, E., Morozova, N., & Severinov, K. (2022). Editing of Phage Genomes—Recombineering-assisted SpCas9 Modification of Model Coliphages T7, T5, and T3. Molecular Biology, 56(6), 801–815. https://doi.org/10.1134/S0026893322060073
[5]
Lavysh, D., Mekler, V., Klimuk, E., & Severinov, K. (2022). Regulation of Gene Expression of phiEco32-like Bacteriophage 7-11. Viruses, 14(3), 555. https://doi.org/10.3390/v14030555
[6]
Mamontov, V., Martynov, A., Morozova, N., Bukatin, A., Staroverov, D. B., Lukyanov, K. A., Ispolatov, Y., Semenova, E., & Severinov, K. (2022). Persistence of plasmids targeted by CRISPR interference in bacterial populations. Proceedings of the National Academy of Sciences, 119(15), e2114905119. https://doi.org/10.1073/pnas.2114905119
[7]
Rahlff, J., Bornemann, T. L. V., Lopatina, A., Severinov, K., & Probst, A. J. (2022). Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica. Applied and Environmental Microbiology, 88(10), e0031522. https://doi.org/10.1128/aem.00315-22
[8]
Rusanova, A., Fedorchuk, V., Toshchakov, S., Dubiley, S., & Sutormin, D. (2021). An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics. Life (Basel, Switzerland), 12(1), 25. https://doi.org/10.3390/life12010025
[9]
Sharaev, N., Chacon-Machado, L., Musharova, O., Savitskaya, E., & Severinov, K. (2022). Repair of Double-Stranded DNA Breaks Generated by CRISPR–Cas9 in Pseudomonas putida KT2440. Molecular Biology, 56(6), 842–853. https://doi.org/10.1134/S0026893322060152
[10]
Yagmurov, E., Gilep, K., Serebryakova, M., Wolf, Y. I., Dubiley, S., & Severinov, K. (2022). S51 Family Peptidases Provide Resistance to Peptidyl-Nucleotide Antibiotic McC. MBio, 13(3), e0080522.
https://doi.org/10.1128/mbio.00805-22
[1]
D.Y. Travin, R. Jouan, A. Vigouroux, S. Inaba-Inoue, J. Lachat, F. Haq, T. Timchenko, D. Sutormin, S. Dubiley, K. Beis, S. Moréra, K. Severinov, P. Mergaert, Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition by Gram-Negative Bacteria, MBio 14 (2023) e00217-23. https://doi.org/10.1128/mbio.00217-23.
[2]
D. Sutormin, A. Galivondzhyan, A. Gafurov, K. Severinov, Single-nucleotide resolution detection of Topo IV cleavage activity in the Escherichia coli genome with Topo-Seq, Front. Microbiol. 14 (2023) 1160736. https://doi.org/10.3389/fmicb.2023.1160736.
[3]
A. Olina, A. Agapov, D. Yudin, D. Sutormin, A. Galivondzhyan, A. Kuzmenko, K. Severinov, A.A. Aravin, A. Kulbachinskiy, Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli, Microbiol Spectr 11 (2023) e04146-22. https://doi.org/10.1128/spectrum.04146-22.
[4]
A.A. Kudryavtseva, E. Cséfalvay, E.Y. Gnuchikh, D.D. Yanovskaya, M.A. Skutel, A.B. Isaev, S.V. Bazhenov, A.A. Utkina, I.V. Manukhov, Broadness and specificity: ArdB, ArdA, and Ocr against various restriction-modification systems, Front. Microbiol. 14 (2023) 1133144. https://doi.org/10.3389/fmicb.2023.1133144.
[5]
Moscow State Academy of Veterinary Medicine and Biotechnology – MVA n. a. K.I. Skryabin, R.G. Aksenov, A.V. Komissarova, Financial University under the Government of the Russian Federation, M.A. Skutel, Skolkovo Institute of Science and Technology, A.B. Isaev, Skolkovo Institute of Science and Technology, Genomic variants’ analysis of Escherichia coli K-12 cells resistant to phage T7 infection, P&FPE 16 (2023) 3–12. https://doi.org/10.17586/2310-1164-2023-16-2-3-12.
[6]
A. Kelly, S.C. Went, G. Mariano, L.P. Shaw, D.M. Picton, S.J. Duffner, I. Coates, R. Herdman-Grant, J. Gordeeva, A. Drobiazko, A. Isaev, Y.-J. Lee, Y. Luyten, R.D. Morgan, P. Weigele, K. Severinov, N. Wenner, J.C.D. Hinton, T.R. Blower, Diverse Durham collection phages demonstrate complex BREX defense responses, Appl Environ Microbiol 89 (2023) e00623-23. https://doi.org/10.1128/aem.00623-23.
[7]
A. Andriianov, S. Trigüis, A. Drobiazko, N. Sierro, N.V. Ivanov, M. Selmer, K. Severinov, A. Isaev, Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase, Cell Reports 42 (2023) 112972. https://doi.org/10.1016/j.celrep.2023.112972.
[8]
V.S. Mihailovskaya, D.A. Sutormin, M.O. Karipova, A.B. Trofimova, V.A. Mamontov, K. Severinov, M.V. Kuznetsova, Bacteriocin-Producing Escherichia coli Q5 and C41 with Potential Probiotic Properties: In Silico, In Vitro, and In Vivo Studies, IJMS 24 (2023) 12636. https://doi.org/10.3390/ijms241612636.
[9]
D. Antonova, V.V. Belousova, E. Zhivkoplias, M. Sobinina, T. Artamonova, I.E. Vishnyakov, I. Kurdyumova, A. Arseniev, N. Morozova, K. Severinov, M. Khodorkovskii, M.V. Yakunina, The Dynamics of Synthesis and Localization of Jumbo Phage RNA Polymerases inside Infected Cells, Viruses 15 (2023) 2096. https://doi.org/10.3390/v15102096.
[10]
M. Skutel, A. Andriianov, M. Zavialova, M. Kirsanova, O. Shodunke, E. Zorin, A. Golovshchinskii, K. Severinov, A. Isaev, T5-like phage BF23 evades host-mediated DNA restriction and methylation, MicroLife 4 (2023) uqad044. https://doi.org/10.1093/femsml/uqad044.
[11]
P. Muzyukina, A. Shkaruta, N.M. Guzman, J. Andreani, A.L. Borges, J. Bondy-Denomy, A. Maikova, E. Semenova, K. Severinov, O. Soutourina, Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile, MSphere 8 (2023) e00401-23. https://doi.org/10.1128/msphere.00401-23.
[12]
A. Demkina, D. Slonova, V. Mamontov, O. Konovalova, D. Yurikova, V. Rogozhin, V. Belova, D. Korostin, D. Sutormin, K. Severinov, A. Isaev, Benchmarking DNA isolation methods for marine metagenomics, Sci Rep 13 (2023) 22138. https://doi.org/10.1038/s41598-023-48804-z.
2022
[1]
Alfi, A., Popov, A., Kumar, A., Zhang, K. Y. J., Dubiley, S., Severinov, K., & Tagami, S. (2022). Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2. ACS Synthetic Biology, 11(6), 2022–2028. https://doi.org/10.1021/acssynbio.2c00176
[2]
Bikmetov, D., Hall, A. M. J., Livenskyi, A., Gollan, B., Ovchinnikov, S., Gilep, K., Kim, J. Y., Larrouy-Maumus, G., Zgoda, V., Borukhov, S., Severinov, K., Helaine, S., & Dubiley, S. (2022). GNAT toxins evolve toward narrow tRNA target specificities. Nucleic Acids Research, 50(10), 5807–5817.
https://doi.org/10.1093/nar/gkac356
[3]
Fraser, A., Sokolova, M. L., Drobysheva, A. V., Gordeeva, J. V., Borukhov, S., Jumper, J., Severinov, K. V., & Leiman, P. G. (2022). Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Nature Communications, 13(1), 3526.
https://doi.org/10.1038/s41467-022-31214-6
[4]
Isaev, A., Andriianov, A., Znobishcheva, E., Zorin, E., Morozova, N., & Severinov, K. (2022). Editing of Phage Genomes—Recombineering-assisted SpCas9 Modification of Model Coliphages T7, T5, and T3. Molecular Biology, 56(6), 801–815. https://doi.org/10.1134/S0026893322060073
[5]
Lavysh, D., Mekler, V., Klimuk, E., & Severinov, K. (2022). Regulation of Gene Expression of phiEco32-like Bacteriophage 7-11. Viruses, 14(3), 555. https://doi.org/10.3390/v14030555
[6]
Mamontov, V., Martynov, A., Morozova, N., Bukatin, A., Staroverov, D. B., Lukyanov, K. A., Ispolatov, Y., Semenova, E., & Severinov, K. (2022). Persistence of plasmids targeted by CRISPR interference in bacterial populations. Proceedings of the National Academy of Sciences, 119(15), e2114905119. https://doi.org/10.1073/pnas.2114905119
[7]
Rahlff, J., Bornemann, T. L. V., Lopatina, A., Severinov, K., & Probst, A. J. (2022). Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica. Applied and Environmental Microbiology, 88(10), e0031522. https://doi.org/10.1128/aem.00315-22
[8]
Rusanova, A., Fedorchuk, V., Toshchakov, S., Dubiley, S., & Sutormin, D. (2021). An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics. Life (Basel, Switzerland), 12(1), 25. https://doi.org/10.3390/life12010025
[9]
Sharaev, N., Chacon-Machado, L., Musharova, O., Savitskaya, E., & Severinov, K. (2022). Repair of Double-Stranded DNA Breaks Generated by CRISPR–Cas9 in Pseudomonas putida KT2440. Molecular Biology, 56(6), 842–853. https://doi.org/10.1134/S0026893322060152
[10]
Yagmurov, E., Gilep, K., Serebryakova, M., Wolf, Y. I., Dubiley, S., & Severinov, K. (2022). S51 Family Peptidases Provide Resistance to Peptidyl-Nucleotide Antibiotic McC. MBio, 13(3), e0080522.
https://doi.org/10.1128/mbio.00805-22
Пресса