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Antonova D, Belousova VV, Zhivkoplias E, Sobinina M, Artamonova T, Vishnyakov IE, Kurdyumova I, Arseniev A, Morozova N, Severinov K, Khodorkovskii M, Yakunina MV. The Dynamics of Synthesis and Localization of Jumbo Phage RNA Polymerases inside Infected Cells. Viruses 2023; 15:2096. [PMID: 37896872 PMCID: PMC10612078 DOI: 10.3390/v15102096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
A nucleus-like structure composed of phage-encoded proteins and containing replicating viral DNA is formed in Pseudomonas aeruginosa cells infected by jumbo bacteriophage phiKZ. The PhiKZ genes are transcribed independently from host RNA polymerase (RNAP) by two RNAPs encoded by the phage. The virion RNAP (vRNAP) transcribes early viral genes and must be injected into the cell with phage DNA. The non-virion RNAP (nvRNAP) is composed of early gene products and transcribes late viral genes. In this work, the dynamics of phage RNAPs localization during phage phiKZ infection were studied. We provide direct evidence of PhiKZ vRNAP injection in infected cells and show that it is excluded from the phage nucleus. The nvRNAP is synthesized shortly after the onset of infection and localizes in the nucleus. We propose that spatial separation of two phage RNAPs allows coordinated expression of phage genes belonging to different temporal classes.
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Affiliation(s)
- Daria Antonova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Viktoriia V. Belousova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Erik Zhivkoplias
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Mariia Sobinina
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Tatyana Artamonova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Innokentii E. Vishnyakov
- Group of Molecular Cytology of Prokaryotes and Bacterial Invasion, Institute of Cytology of the Russian Academy of Science, St. Petersburg 194064, Russia;
| | - Inna Kurdyumova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Anatoly Arseniev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia Morozova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Konstantin Severinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
- Institute of Molecular Genetics National Kurchatov Center, Moscow 123182, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Mikhail Khodorkovskii
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Maria V. Yakunina
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
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Vasileva A, Selkova P, Arseniev A, Abramova M, Shcheglova N, Musharova O, Mizgirev I, Artamonova T, Khodorkovskii M, Severinov K, Fedorova I. Characterization of CoCas9 nuclease from Capnocytophaga ochracea. RNA Biol 2023; 20:750-759. [PMID: 37743659 PMCID: PMC10521337 DOI: 10.1080/15476286.2023.2256578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 09/26/2023] Open
Abstract
Cas9 nucleases are widely used for genome editing and engineering. Cas9 enzymes encoded by CRISPR-Cas defence systems of various prokaryotic organisms possess different properties such as target site preferences, size, and DNA cleavage efficiency. Here, we biochemically characterized CoCas9 from Capnocytophaga ochracea, a bacterium that inhabits the oral cavity of humans and contributes to plaque formation on teeth. CoCas9 recognizes a novel 5'-NRRWC-3' PAM and efficiently cleaves DNA in vitro. Functional characterization of CoCas9 opens ways for genetic engineering of C. ochracea using its endogenous CRISPR-Cas system. The novel PAM requirement makes CoCas9 potentially useful in genome editing applications.
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Affiliation(s)
- A. Vasileva
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - P. Selkova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - A. Arseniev
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - M. Abramova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - N. Shcheglova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - O. Musharova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - I. Mizgirev
- Laboratory of Carcinogenesis and Aging, N.N. Petrov National Medical Research Center of Oncology, St. Petersburg, Russia
| | - T. Artamonova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - M. Khodorkovskii
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - K. Severinov
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - I. Fedorova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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3
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de Martín Garrido N, Orekhova M, Lai Wan Loong YTE, Litvinova A, Ramlaul K, Artamonova T, Melnikov AS, Serdobintsev P, Aylett CHS, Yakunina M. Correction to 'Structure of the bacteriophage PhiKZ non-virion RNA polymerase'. Nucleic Acids Res 2021; 49:10806. [PMID: 34530441 PMCID: PMC8501947 DOI: 10.1093/nar/gkab846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Natàlia de Martín Garrido
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
| | - Mariia Orekhova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | | | - Anna Litvinova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Alexei S Melnikov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | | | - Christopher H S Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, St. Petersburg, Russia
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4
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de Martín Garrido N, Orekhova M, Lai Wan Loong Y, Litvinova A, Ramlaul K, Artamonova T, Melnikov A, Serdobintsev P, Aylett CHS, Yakunina M. Structure of the bacteriophage PhiKZ non-virion RNA polymerase. Nucleic Acids Res 2021; 49:7732-7739. [PMID: 34181731 PMCID: PMC8287921 DOI: 10.1093/nar/gkab539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/04/2021] [Accepted: 06/24/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens of thousands worldwide each year. ΦKZ is an incredibly interesting virus, expressing many systems that the host already possesses. On infection, it forms a ‘nucleus’, erecting a barrier around its genome to exclude host endonucleases and CRISPR-Cas systems. ΦKZ infection is independent of the host transcriptional apparatus. It expresses two different multi-subunit RNA polymerases (RNAPs): the virion RNAP (vRNAP) is injected with the viral DNA during infection to transcribe early genes, including those encoding the non-virion RNAP (nvRNAP), which transcribes all further genes. ΦKZ nvRNAP is formed by four polypeptides thought to represent homologues of the eubacterial β/β′ subunits, and a fifth with unclear homology, but essential for transcription. We have resolved the structure of ΦKZ nvRNAP to better than 3.0 Å, shedding light on its assembly, homology, and the biological role of the fifth subunit: it is an embedded, integral member of the complex, the position, structural homology and biochemical role of which imply that it has evolved from an ancestral homologue to σ-factor.
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Affiliation(s)
| | | | | | - Anna Litvinova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Alexei S Melnikov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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5
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Fedorova I, Vasileva A, Selkova P, Abramova M, Arseniev A, Pobegalov G, Kazalov M, Musharova O, Goryanin I, Artamonova D, Zyubko T, Shmakov S, Artamonova T, Khodorkovskii M, Severinov K. PpCas9 from Pasteurella pneumotropica - a compact Type II-C Cas9 ortholog active in human cells. Nucleic Acids Res 2020; 48:12297-12309. [PMID: 33152077 PMCID: PMC7708072 DOI: 10.1093/nar/gkaa998] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/11/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022] Open
Abstract
CRISPR-Cas defense systems opened up the field of genome editing due to the ease with which effector Cas nucleases can be programmed with guide RNAs to access desirable genomic sites. Type II-A SpCas9 from Streptococcus pyogenes was the first Cas9 nuclease used for genome editing and it remains the most popular enzyme of its class. Nevertheless, SpCas9 has some drawbacks including a relatively large size and restriction to targets flanked by an 'NGG' PAM sequence. The more compact Type II-C Cas9 orthologs can help to overcome the size limitation of SpCas9. Yet, only a few Type II-C nucleases were fully characterized to date. Here, we characterized two Cas9 II-C orthologs, DfCas9 from Defluviimonas sp.20V17 and PpCas9 from Pasteurella pneumotropica. Both DfCas9 and PpCas9 cleave DNA in vitro and have novel PAM requirements. Unlike DfCas9, the PpCas9 nuclease is active in human cells. This small nuclease requires an 'NNNNRTT' PAM orthogonal to that of SpCas9 and thus potentially can broaden the range of Cas9 applications in biomedicine and biotechnology.
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Affiliation(s)
- Iana Fedorova
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, 121205, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Aleksandra Vasileva
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, 121205, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Polina Selkova
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, 121205, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Marina Abramova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
- Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Anatolii Arseniev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Maksim Kazalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
- Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Olga Musharova
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, 121205, Russia
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute’’, Moscow, 123182, Russia
| | - Ignatiy Goryanin
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, 121205, Russia
| | - Daria Artamonova
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, 121205, Russia
| | - Tatyana Zyubko
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Sergey Shmakov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Konstantin Severinov
- Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute’’, Moscow, 123182, Russia
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6
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Selkova P, Vasileva A, Pobegalov G, Musharova O, Arseniev A, Kazalov M, Zyubko T, Shcheglova N, Artamonova T, Khodorkovskii M, Severinov K, Fedorova I. Position of Deltaproteobacteria Cas12e nuclease cleavage sites depends on spacer length of guide RNA. RNA Biol 2020; 17:1472-1479. [PMID: 32564655 PMCID: PMC7549622 DOI: 10.1080/15476286.2020.1777378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/10/2020] [Accepted: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
Cas12e proteins (formerly CasX) form a distinct subtype of Class II type V CRISPR-Cas effectors. Recently, it was shown that DpbCas12e from Deltaproteobacteria and PlmCas12e from Planctomycetes can introduce programmable double-stranded breaks in mammalian genomes. Thus, along with Cas9 and Cas12a Class II effectors, Cas12e could be harnessed for genome editing and engineering. The location of cleavage points in DNA targets is important for application of Cas nucleases in biotechnology. DpbCas12e was reported to produce extensive 5'-overhangs at cleaved targets, which can make it superior for some applications. Here, we used high throughput sequencing to precisely map the DNA cut site positions of DpbCas12e on several DNA targets. In contrast to previous observations, our results demonstrate that DNA cleavage pattern of Cas12e is very similar to that of Cas12a: DpbCas12e predominantly cleaves DNA after nucleotide position 17-19 downstream of PAM in the non-target DNA strand, and after the 22nd position of target strand, producing 3-5 nucleotide-long 5'-overhangs. We also show that reduction of spacer sgRNA sequence from 20nt to 16nt shifts Cas12e cleavage positions on the non-target DNA strand closer to the PAM, producing longer 6-8nt 5'-overhangs. Overall, these findings advance the understanding of Cas12e endonucleases and may be useful for developing of DpbCas12e-based biotechnology instruments.
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Affiliation(s)
- Polina Selkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandra Vasileva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Olga Musharova
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anatolii Arseniev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maksim Kazalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Zyubko
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Nataliia Shcheglova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | | | - Konstantin Severinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Iana Fedorova
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, Russia
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7
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Fedorova I, Arseniev A, Selkova P, Pobegalov G, Goryanin I, Vasileva A, Musharova O, Abramova M, Kazalov M, Zyubko T, Artamonova T, Artamonova D, Shmakov S, Khodorkovskii M, Severinov K. DNA targeting by Clostridium cellulolyticum CRISPR-Cas9 Type II-C system. Nucleic Acids Res 2020; 48:2026-2034. [PMID: 31943070 PMCID: PMC7038990 DOI: 10.1093/nar/gkz1225] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 01/11/2023] Open
Abstract
Type II CRISPR-Cas9 RNA-guided nucleases are widely used for genome engineering. Type II-A SpCas9 protein from Streptococcus pyogenes is the most investigated and highly used enzyme of its class. Nevertheless, it has some drawbacks, including a relatively big size, imperfect specificity and restriction to DNA targets flanked by an NGG PAM sequence. Cas9 orthologs from other bacterial species may provide a rich and largely untapped source of biochemical diversity, which can help to overcome the limitations of SpCas9. Here, we characterize CcCas9, a Type II-C CRISPR nuclease from Clostridium cellulolyticum H10. We show that CcCas9 is an active endonuclease of comparatively small size that recognizes a novel two-nucleotide PAM sequence. The CcCas9 can potentially broaden the existing scope of biotechnological applications of Cas9 nucleases and may be particularly advantageous for genome editing of C. cellulolyticum H10, a bacterium considered to be a promising biofuel producer.
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Affiliation(s)
- Iana Fedorova
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Anatolii Arseniev
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Polina Selkova
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Ignatiy Goryanin
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Aleksandra Vasileva
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Olga Musharova
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Marina Abramova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maksim Kazalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Zyubko
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Daria Artamonova
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
| | - Sergey Shmakov
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | | | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Center of life sciences, Skolkovo, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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8
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Orekhova M, Koreshova A, Artamonova T, Khodorkovskii M, Yakunina M. The study of the phiKZ phage non-canonical non-virion RNA polymerase. Biochem Biophys Res Commun 2019; 511:759-764. [PMID: 30833081 DOI: 10.1016/j.bbrc.2019.02.132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 02/24/2019] [Indexed: 10/27/2022]
Abstract
Non-canonical multisubunit DNA-dependent RNA-polymerases (RNAP) form a new group of the main transcription enzymes, which have only distinct homology to the catalytic subunits of canonical RNAPs of bacteria, archaea and eukaryotes. One of the rare non-canonical RNAP, which was partially biochemically characterized, is non-virion RNAP (nvRNAP) encoded by Pseudomonas phage phiKZ. PhiKZ nvRNAP consists of five subunits, four of which are homologs of β and β' subunit of bacterial RNAP, and the fifth subunits with unknown function. To understand the role of the fifth subunit in phiKZ nvRNAP, we created co-expression system allowing to get recombinant full five-subunit (5s) and four-subunit (4s) complexes and performed their comparison. The 5s recombinant complex is active on phage promoters in vitro as the native nvRNAP. The 4s complex cannot extend RNA, so 4s complex is not a catalytically active core of phiKZ nvRNAP. Thus, the phiKZ fifth subunit is not only a promoter-recognition subunit, but it plays an important role in the formation of active phiKZ nvRNAP.
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Affiliation(s)
- Mariia Orekhova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Alevtina Koreshova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143025, Russia
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
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9
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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. Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel. Nat Chem Biol 2017; 13:1129-1136. [PMID: 28846667 PMCID: PMC5701663 DOI: 10.1038/nchembio.2462] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/19/2017] [Indexed: 12/19/2022]
Abstract
While screening of small-molecular metabolites produced by most cultivatable microorganisms often results in rediscovery of known compounds, genome-mining programs allow to harness much greater chemical diversity and result in discovery of new molecular scaffolds. Here we report genome-guided identification of a new antibiotic klebsazolicin (KLB) from Klebsiella pneumoniae that inhibits growth of sensitive cells by targeting ribosome. A member of ribosomally-synthesized post-translationally modified peptides (RiPPs), KLB is characterized by the presence of unique N-terminal amidine ring essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosome by interfering with translation elongation. Structural analysis of the ribosome-KLB complex reveals the compound bound in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramins-B. KLB adopts compact conformation and largely obstructs the tunnel. Engineered KLB fragments retain in vitro activity and can serve as a starting point for the development of new bioactive compounds.
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Affiliation(s)
- Mikhail Metelev
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Institute of Antimicrobial Chemotherapy, Smolensk State Medical Academy, Smolensk, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya A Osterman
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry Ghilarov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Nelli F Khabibullina
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Alexander Yakimov
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Konstantin Shabalin
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Irina Utkina
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitry Y Travin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina S Komarova
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Marina Serebryakova
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatyana Artamonova
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Mikhail Khodorkovskii
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Andrey L Konevega
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Petr V Sergiev
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Severinov
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
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Yakunina M, Artamonova T, Borukhov S, Makarova KS, Severinov K, Minakhin L. A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage. Nucleic Acids Res 2015; 43:10411-20. [PMID: 26490960 PMCID: PMC4666361 DOI: 10.1093/nar/gkv1095] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/10/2015] [Indexed: 11/21/2022] Open
Abstract
The infection of Pseudomonas aeruginosa by the giant bacteriophage phiKZ is resistant to host RNA polymerase (RNAP) inhibitor rifampicin. phiKZ encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit RNAPs. Polypeptides of one set are encoded by middle phage genes and are found in the phiKZ virions. Polypeptides of the second set are encoded by early phage genes and are absent from virions. Here, we report isolation of a five-subunit RNAP from phiKZ-infected cells. Four subunits of this enzyme are cellular RNAP subunits homologs of the non-virion set; the fifth subunit is a protein of unknown function. In vitro, this complex initiates transcription from late phiKZ promoters in rifampicin-resistant manner. Thus, this enzyme is a non-virion phiKZ RNAP responsible for transcription of late phage genes. The phiKZ RNAP lacks identifiable assembly and promoter specificity subunits/factors characteristic for eukaryal, archaeal and bacterial RNAPs and thus provides a unique model for comparative analysis of the mechanism, regulation and evolution of this important class of enzymes.
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Affiliation(s)
- Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Sergei Borukhov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1501, USA
| | - Kira S Makarova
- National Center for Biotechnology Information NLM, National Institutes of Health Bethesda, MD 20894, USA
| | - Konstantin Severinov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA Skolkovo Institute of Science and Technology, Skolkovo, 143026, Russia
| | - Leonid Minakhin
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA
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