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Zagoskin AA, Zakharova MV, Nagornykh MO. [Structural Elements of DNA and RNA Eukaryotic Expression Vectors for In Vitro and In Vivo Genome Editor Delivery]. Mol Biol (Mosk) 2022; 56:1023-1038. [PMID: 36475486 DOI: 10.31857/s002689842206026x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/28/2022] [Indexed: 12/13/2022]
Abstract
Gene editing with programmable nucleases opens new perspectives in important practice areas, such as healthcare and agriculture. The most challenging problem for the safe and effective therapeutic use of gene editing technologies is the proper delivery and expression of gene editors in cells and tissues of different organisms. Virus-based and nonviral systems can be used for the successful delivery of gene editors. Here we have reviewed structural elements of nonviral DNA- and RNA-based expression vectors for gene editing and delivery methods in vitro and in vivo.
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Affiliation(s)
- A A Zagoskin
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290 Russia
| | - M V Zakharova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290 Russia
| | - M O Nagornykh
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290 Russia.,Sirius University of Science and Technology, Sirius, Sochi, 354349 Russia.,
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2
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Zakharova MV, Beletskaya IV, Ibryashkina EM, Solonin AS. An alternative approach to study the enzymatic specificities of the CfrBI restriction-modification system. Heliyon 2019; 5:e01846. [PMID: 31198872 PMCID: PMC6556831 DOI: 10.1016/j.heliyon.2019.e01846] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/18/2019] [Accepted: 05/24/2019] [Indexed: 11/20/2022] Open
Abstract
Restriction–modification systems (RMS) are the main gene-engineering tools and a suitable model to study the molecular mechanisms of catalysis and DNA–protein interactions. Research into the catalytic properties of these enzymes, determination of hydrolysis and DNA-methylation sites remain topical. In our previous work we have cloned and sequenced the CfrBI restriction–modification system (strain Citrobacter freundii), which recognizes the nucleotide sequence 5′-CCWWGG-3′. In this article we describe the cloning of the methyltransferase and restriction endonuclease genes (gene encoding CfrBI DNA methyltransferase (cfrBIM) and gene encoding CfrBI restriction endonuclease (cfrBIR)) separately to obtain strains overproducing the enzymes of this system. His6-CfrBI, which had been purified to homogeneity, was used to establish the DNA-hydrolysis point in its recognition site. CfrBI was shown to cleave DNA after just the first 5′C within the recognition site and then to generate 4-nt 3′ cohesive ends (5′-C/CWWGG-3′). To map the site of methylation by M.CfrBI, we exploited the fact that the CfrBI site partially overlaps with the recognition sites of the well-documented enzymes KpnI and ApaI. The M.CfrBI- induced hemimethylation of the internal C residue of the ApaI recognition sequence (GGGCN4mCC) was observed to block cleavage by ApaI. In contrast, KpnI was able to digest its M.CfrBI-hemimethylated site (GGTAN4mCC). KpnI was used to restrict a fragment of DNA harbouring the CfrBI and KpnI sites, in which the CfrBI site was methylated in vitro by His6-M.CfrBI using [3H]-SAM. The subsequent separation of hydrolysis products by electrophoresis and the enumeration of incorporated [H3]-methyl groups in each of the fragments made it possible to determine that external cytosine undergoes modification in the recognition site.
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3
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Lisov AV, Belova OV, Lisova ZA, Vinokurova NG, Nagel AS, Andreeva-Kovalevskaya ZI, Budarina ZI, Nagornykh MO, Zakharova MV, Shadrin AM, Solonin AS, Leontievsky AA. Xylanases of Cellulomonas flavigena: expression, biochemical characterization, and biotechnological potential. AMB Express 2017; 7:5. [PMID: 28050845 PMCID: PMC5209306 DOI: 10.1186/s13568-016-0308-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/19/2016] [Indexed: 11/10/2022] Open
Abstract
Four xylanases of Cellulomonas flavigena were cloned, expressed in Escherichia coli and purified. Three enzymes (CFXyl1, CFXyl2, and CFXyl4) were from the GH10 family, while CFXyl3 was from the GH11 family. The enzymes possessed moderate temperature stability and a neutral pH optimum. The enzymes were more stable at alkaline pH values. CFXyl1 and CFXyl2 hydrolyzed xylan to form xylobiose, xylotriose, xylohexaose, xylopentaose, and xylose, which is typical for GH10. CFXyl3 (GH11) and CFXyl4 (GH10) formed the same xylooligosaccharides, but xylose was formed in small amounts. The xylanases made efficient saccharification of rye, wheat and oat, common components of animal feed, which indicates their high biotechnological potential.
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4
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Filatova IY, Kazakov AS, Muzafarov EN, Zakharova MV. Protein SgpR of Pseudomonas putida strain AK5 is a LysR-type regulator of salicylate degradation through gentisate. FEMS Microbiol Lett 2017; 364:3924860. [DOI: 10.1093/femsle/fnx112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/03/2017] [Indexed: 11/13/2022] Open
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5
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Ibryashkina EM, Solonin AS, Zakharova MV. Protein NCRII-18: the role of gene fusion in the molecular evolution of restriction endonucleases. FEBS Lett 2017; 591:1702-1711. [DOI: 10.1002/1873-3468.12669] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Elena M. Ibryashkina
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; Pushchino Moscow Region Russia
| | - Alexander S. Solonin
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; Pushchino Moscow Region Russia
| | - Marina V. Zakharova
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; Pushchino Moscow Region Russia
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6
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Trubitsina LI, Tishchenko SV, Gabdulkhakov AG, Lisov AV, Zakharova MV, Leontievsky AA. Structural and functional characterization of two-domain laccase from Streptomyces viridochromogenes. Biochimie 2015; 112:151-9. [PMID: 25778839 DOI: 10.1016/j.biochi.2015.03.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 11/03/2014] [Accepted: 03/05/2015] [Indexed: 11/30/2022]
Abstract
Laccase (EC 1.10.3.2) is one of the most common copper-containing oxidases found in many organisms and catalyses oxidation of primarily phenolic compounds by oxygen. A recently found bacterial laccase whose molecule is formed by two domains - the so called two-domain laccase (2DLac) or small laccase - has unusual resistance to inhibitors and an alkaline optimum of activity. The causes of these properties, as well as the biological function of two-domain laccases, are poorly understood. We performed an enzymatic and structural characterization of 2DLac from Streptomyces viridochromogenes (SvSL). It was cloned and overproduced in Escherichia coli. Phenolic compounds were oxidized in the presence of the enzyme under alkaline but not acidic conditions. Conversely, nonphenolic compounds were oxidized at acidic but not alkaline pH. SvSL catalysed oxidation of nonphenolic compounds more efficiently than that of phenols. Moreover, this two-domain laccase displayed a cytochrome c oxidase activity and exhibited no ferroxidase activity. The enzyme was resistant to specific inhibitors of copper-containing oxidases, such as NaN3 and NaF. We succeeded in generating X-ray quality crystals and solved their structure to a resolution of 2.4 Å. SvSL is a homotrimer in its native state. Comparison of its structure with that of a three-domain laccase revealed differences in the second coordination sphere of the T2/T3 centre and solvent channels. The role of these differences in the resistance of the enzyme to inhibitors and the activity at alkaline pH is under discussion.
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Affiliation(s)
- L I Trubitsina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (IBPM RAS), Pushchino, Russia; Pushchino State Institute of Life Sciences, Pushchino, Russia
| | - S V Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A G Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A V Lisov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (IBPM RAS), Pushchino, Russia.
| | - M V Zakharova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (IBPM RAS), Pushchino, Russia
| | - A A Leontievsky
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (IBPM RAS), Pushchino, Russia; Pushchino State Institute of Life Sciences, Pushchino, Russia
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7
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Fedotova EA, Protsenko AS, Zakharova MV, Lavrova NV, Alekseevsky AV, Oretskaya TS, Karyagina AS, Solonin AS, Kubareva EA. SsoII-like DNA-methyltransferase Ecl18kI: interaction between regulatory and methylating functions. Biochemistry (Mosc) 2009; 74:85-91. [PMID: 19232054 DOI: 10.1134/s0006297909010131] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The interaction of DNA-methyltransferase Ecl18kI (M.Ecl18kI) with a fragment of promoter region of restriction-modification system SsoII was studied. It is shown that dissociation constants of M.Ecl18kI and M.SsoII complexes with DNA ligand carrying a regulatory site previously characterized for M.SsoII have comparable values. A deletion derivative of M.Ecl18kI, Delta(72-379)Ecl18kI, representing the N-terminal protein region responsible for regulation, was obtained. It is shown that such polypeptide fragment has virtually no interaction with the regulatory site. Therefore, the existence of a region responsible for methylation is necessary for maintaining M.Ecl18kI regulatory function. The properties of methyltransferase NlaX, which is actually a natural deletion derivative of M.Ecl18kI and M.SsoII lacking the first 70 amino acid residues and not being able to regulate gene expression of the SsoII restriction-modification system, were studied. The ability of mutant forms of M.Ecl18kI incorporating single substitutions in regions responsible for regulation and methylation to interact with both sites of DNA recognition was characterized. The data show a correlation between DNA-binding activity of two M.Ecl18kI regions-regulatory and methylating.
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Affiliation(s)
- E A Fedotova
- Chemical Faculty, Lomonosov Moscow State University, Moscow, 119991, Russia
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8
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Ibryashkina EM, Sasnauskas G, Solonin AS, Zakharova MV, Siksnys V. Oligomeric structure diversity within the GIY-YIG nuclease family. J Mol Biol 2009; 387:10-6. [PMID: 19361436 DOI: 10.1016/j.jmb.2009.01.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 12/30/2008] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
Abstract
The GIY-YIG nuclease domain has been identified in homing endonucleases, DNA repair and recombination enzymes, and restriction endonucleases. The Type II restriction enzyme Eco29kI belongs to the GIY-YIG nuclease superfamily and, like most of other family members, including the homing endonuclease I-TevI, is a monomer. It recognizes the palindromic sequence 5'-CCGC/GG-3' ("/" marks the cleavage position) and cuts it to generate 3'-staggered ends. The Eco29kI monomer, which contains a single active site, either has to nick sequentially individual DNA strands or has to form dimers or even higher-order oligomers upon DNA binding to make a double-strand break at its target site. Here, we provide experimental evidence that Eco29kI monomers dimerize on a single cognate DNA molecule forming the catalytically active complex. The mechanism described here for Eco29kI differs from that of Cfr42I isoschisomer, which also belongs to the GIY-YIG family but is functional as a tetramer. This novel mechanism may have implications for the function of homing endonucleases and other enzymes of the GIY-YIG family.
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Affiliation(s)
- Elena M Ibryashkina
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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9
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Nagornykh MO, Bogdanova ES, Protsenko AS, Zakharova MV, Solonin AS, Severinov KV. [Regulation of gene expression in type II restriction-modification system]. RUSS J GENET+ 2008; 44:606-615. [PMID: 18672793 DOI: 10.1134/s1022795408050037] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Type II restriction-modification systems are comprised of a restriction endonuclease and methyltransferase. The enzymes are coded by individual genes and recognize the same DNA sequence. Endonuclease makes a double-stranded break in the recognition site, and methyltransferase covalently modifies the DNA bases within the recognition site, thereby down-regulating endonuclease activity. Coordinated action of these enzymes plays a role of primitive immune system and protects bacterial host cell from the invasion of foreign (for example, viral) DNA. However, uncontrolled expression of the restriction-modification system genes can result in the death of bacterial host cell because of the endonuclease cleavage of host DNA. In the present review, the data on the expression regulation of the type II restriction-modification enzymes are discussed.
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10
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Rebrikov DV, Rebrikov DN, Stepanova EV, Koroleva OV, Budarina ZI, Zakharova MV, Iurkova TV, Solonin AS, Belova OV, Pozhidaeva ZA, Leont'evskiĭ AA. [Laccase of the lignolytic fungus Trametes hirsuta: purification and characterization of the enzyme, and cloning and primary structure of the gene]. Prikl Biokhim Mikrobiol 2006; 42:645-53. [PMID: 17168293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The main physicochemical characteristics of the major isoform of the laccase secreted by the fungu, Trametes hirsuta 072 were studied. The enzyme belongs to the group of high redox potential laccases (E(T1) = 790 +/- 5), and it oxidizes with high efficiency various substrates of phenolic nature. The gene of this isoform was cloned, and its nucleotide sequence was determined. The length of the complete gene is 2134 bp. It comprises 11 exons and 10 introns. Analysis of the amino acid sequence of T. hirsuta 072 laccase demonstrated a high homology (to 96.9%) to the other laccases secreted by fungi of the genus Trametes.
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11
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Zakharova MV, Beletskaya IV, Bolovin DV, Yurkova TV, Semenova LM, Solonin AS. Structural plasmid evolution as a result of coupled recombinations at bom and cer sites. Mol Genet Genomics 2003; 270:415-9. [PMID: 14564507 DOI: 10.1007/s00438-003-0933-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2003] [Accepted: 09/16/2003] [Indexed: 10/26/2022]
Abstract
We have studied the recombination of plasmids bearing bom and cer sites. The bom ( basis of mobilization) site is required for conjugative transfer, while the cer ( Col E1 resolution) site is involved in the resolution of plasmid multimers, which increases plasmid stability. We constructed a pair of parent plasmids in such a way as to allow us select clones containing recombinant plasmids directly. Clone selection was based on the McrA sensitivity of recipient host DNA modified by M. Ecl18kI, which is encoded by one of the parent plasmids. The recombinant plasmid contains segments originating from both parental DNAs, which are bounded by bom and cer sites. Its structure is in accordance with our previously proposed model for recombination mediated by bom and cer sequences. The frequency of recombinant plasmid formation coincided with the frequency of recombination at the bom site. We also show that bom-mediated recombination in trans, unlike in cis, is independent of other genetic determinants on the conjugative plasmids.
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Affiliation(s)
- M V Zakharova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia.
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12
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Zakharova MV, Beletskaya IV, Denjmukhametov MM, Yurkova TV, Semenova LM, Shlyapnikov MG, Solonin AS. Characterization of pECL18 and pKPN2: a proposed pathway for the evolution of two plasmids that carry identical genes for a Type II restriction-modification system. Mol Genet Genomics 2002; 267:171-8. [PMID: 11976960 DOI: 10.1007/s00438-002-0644-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2001] [Accepted: 01/14/2001] [Indexed: 11/30/2022]
Abstract
The primary structures of the plasmids pECL18 (5571 bp) and pKPN2 (4196 bp) from Escherichia coli and Klebsiella pneumoniae, respectively, which carry genes for a Type II restriction-modification system (RMS2) with the specificity 5'-CCNGG-3', were determined in order to elucidate the structural relationship between them. The data suggest a possible role for recombination events at bom (basis of mobility) regions and the sites of resolution of multimer plasmid forms (so-called cer sequences) in the structural evolution of multicopy plasmids. Analysis of the sequences of pECL18 and pKPN2 showed that the genes for RM* Ecl18kI and RM* Kpn2kI, and the sequences of the rep (replication) regions in the two plasmids, are almost identical. In both plasmids, these regions are localized between the bom regions and the cer sites. The rest of the pECL18 sequence is almost identical to that of the mob (mobilization) region of ColE1, and the corresponding segment of pKPN2 is almost identical to part of pHS-2 from Shigella flexneri. The difference in primary structures results in different mobilization properties of pECL18 and pKPN2. The complete sequences of pECL18, pKPN2 and the pairwise comparison of the sequences of pECL18, pKPN2, ColE1 and pHS-2 suggest that plasmids may exchange DNA units via site-specific recombination events at bom and cer sites. In the course of BLASTN database searches using the cer sites of pECL18 and pKPN2 as queries, we found twenty cer sites of natural plasmids. Alignment of these sequences reveals that they fall into two classes. The plasmids in each group possess related segments between their cer and bom sites.
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Affiliation(s)
- M V Zakharova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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13
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Beletskaya IV, Zakharova MV, Shlyapnikov MG, Semenova LM, Solonin AS. DNA methylation at the CfrBI site is involved in expression control in the CfrBI restriction-modification system. Nucleic Acids Res 2000; 28:3817-22. [PMID: 11000275 PMCID: PMC110769 DOI: 10.1093/nar/28.19.3817] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have previously found that genes of the CFR:BI restriction-modification (R-M) system from Citrobacter freundii are oriented divergently and that their promoter regions overlap. The overlapping promoters suggest regulation of gene expression at the transcriptional level. In this study the transcription regulation of CFR:BI R-M genes was analyzed in vivo and in vitro in Escherichia coli. It was shown that in the presence of CFR:BI methyltransferase (M.CFR:BI), cell galactokinase activity decreases 10-fold when the galactokinase gene (galK) is under the control of the cfrBIM promoter and increases 20-fold when galK is under the control of the cfrBIR promoter. The CFR:BI site, proven to be unique for the entire CFR:BI R-M gene sequence, is located in the -35 cfrBIM promoter region and is in close vicinity of the -10 cfrBIR promoter region. A comparison of the cfrBIM and the cfrBIR promoter activities in the in vitro transcription system using methylated and unmethylated DNA fragments as templates demonstrated that the efficiency of CFR:BI R-M gene transcription is regulated by enzymatic modification at the N-4-position of cytosine bases of the CFR:BI site by M.CFR:BI. From the results of the in vivo and in vitro experiments we suggest a new model of gene expression regulation in type II R-M systems.
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MESH Headings
- Base Sequence
- Binding Sites
- Citrobacter freundii/enzymology
- Citrobacter freundii/genetics
- Cytosine/chemistry
- Cytosine/metabolism
- DNA Methylation
- DNA Modification Methylases/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Deoxyribonucleases, Type II Site-Specific/genetics
- Escherichia coli/genetics
- Galactokinase/genetics
- Galactokinase/metabolism
- Gene Expression Regulation, Bacterial
- Genes, Bacterial/genetics
- Genes, Reporter/genetics
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Conformation
- Promoter Regions, Genetic/genetics
- Regulatory Sequences, Nucleic Acid/genetics
- Sequence Deletion/genetics
- Templates, Genetic
- Transcription, Genetic/genetics
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Affiliation(s)
- I V Beletskaya
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
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14
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Denjmukhametov MM, Brevnov MG, Zakharova MV, Repyk AV, Solonin AS, Petrauskene OV, Gromova ES. The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes. FEBS Lett 1998; 433:233-6. [PMID: 9744801 DOI: 10.1016/s0014-5793(98)00921-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ecl18kI is a type II restriction-modification system isolated from Enterobacter cloaceae 18kI strain. Genes encoding Ecl18kI methyltransferase (M.Ecl18kI) and Ecl18kI restriction endonuclease (R.Ecl18kI) have been cloned and expressed in Escherichia coli. These enzymes recognize the 5'.../CCNGG...3' sequence in DNA; M.Ecl18kI methylates the C5 carbon atom of the inner dC residue and R.Ecl18kI cuts DNA as shown by the arrow. The restriction endonuclease and the methyltransferase were purified from E. coli B834 [p18Ap1] cells to near homogeneity. The restriction endonuclease is present in the solution as a tetramer, while the methyltransferase is a monomer. The interactions of M.Ecl18kI and R.Ecl18kI with 1,2-dideoxy-D-ribofuranose containing DNA duplexes were investigated. The target base flipping-out mechanism is applicable in the case of M.Ecl18kI. Correct cleavage of the abasic substrates by R.Ecl18kI is accompanied by non-canonical hydrolysis of the modified strand.
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Affiliation(s)
- M M Denjmukhametov
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region
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15
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Zakharova MV, Pertzev AV, Kravetz AN, Beletskaya IV, Shlyapnikov MG, Solonin AS. Complete nucleotide sequence of the Hsd plasmid pECO29 and identification of its functional regions. Biochim Biophys Acta 1998; 1398:106-12. [PMID: 9689911 DOI: 10.1016/s0167-4781(98)00051-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The complete nucleotide sequence of the Hsd plasmid pECO29 has been determined. The plasmid DNA consists of 3895 base pairs. These include 4 genes and 5 sites. Two genes encoding the proteins (restriction endonuclease and DNA methyltransferase) have been fully characterized. The pECO29 comprises a Co1El-type replication system coding for untranslated genes RNAI and RNAII, the emr recombination site containing palindromic sequences and involved in stable maintenance of the plasmid, two pseudo oriT sites homologous to the oriT site of R64 and F plasmids, as well as the bom locus of a Co1El-like plasmid. There are no genes involved in the mobilization of pECO29 plasmid.
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Affiliation(s)
- M V Zakharova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
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16
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Kravets AN, Pertsev AV, Tarutina ZE, Krendelev ID, Zakharova MV, Beletskaia IV, Solonin AS. [Novel isoschizomers of restriction endonucleases from Pseudomonas aeruginosa strains]. Mol Gen Mikrobiol Virusol 1998:14-7. [PMID: 9611755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Testing of Pseudomonas aeruginosa strains from the collection of the L. V. Gromashevsky Institute of Epidemiology and Infectious Diseases (Kiev) for specific endonucleases resulted in isolation of five class II restriction endonucleases, which were partially purified and their recognition targets were determined. Two of these endonucleases, Pae2kI and Pae18kI, are isoschizomers of Bg1II (5'-AGACTC-3'). Pae5kI and Pae14kI recognize the 5'-CCGC/GG-3' sequence and are therefore true isoschizomers of SacII. Hence, Pae17kI is an isoschizomer of PvuII and cleaves the DNA within the recognition sequence 5'-CAG/CTG-3'. Bg1II and PvuII are for the first time detected in Pseudomonas aeruginosa.
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Zakharova MV, Beletskaya IV, Kravetz AN, Pertzev AV, Mayorov SG, Shlyapnikov MG, Solonin AS. Cloning and sequence analysis of the plasmid-borne genes encoding the Eco29kI restriction and modification enzymes. Gene X 1998; 208:177-82. [PMID: 9524260 DOI: 10.1016/s0378-1119(97)00637-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Eco29kI restriction-modification system (RMS2) has been found to be localized on the plasmid pECO29 occurring naturally in the Escherichia coli strain 29k (Pertzev, A.V., Ruban, N.M., Zakharova, M.V., Beletskaya, I.V., Petrov, S.I., Kravetz, A.N., Solonin, A.S., 1992. Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli. Nucleic Acids Res. 20, 1991). The genes coding for this RMS2, a SacII isoschizomer recognizing the sequence CCGCGG have been cloned in Escherichia coli K802 and sequenced. The DNA sequence predicts the restriction endonuclease (ENase) of 214 amino acids (aa) (24,556 Da) and the DNA-methyltransferase (MTase) of 382 aa (43,007 Da) where the genes are separated by 2 bp and arranged in tandem with eco29kIR preceding eco29kIM. The recombinant plasmid with eco29kIR produces a protein of expected size. MEco29kI contains all the conserved aa sequence motifs characteristic of m5C-MTases. Remarkably, its variable region exhibits a significant similarity to the part of the specific target-recognition domain (TRD) from MBssHII--multispecific m5C-MTase (Schumann, J.J., Walter, J., Willert, J., Wild, C., Koch D., Trautner, T.A., 1996. MBssHII: a multispecific cytosine-C5-DNA-methyltransferase with unusual target recognizing properties. J. Mol. Biol. 257, 949-959), which recognizes five different sites on DNA (HaeII, MluI, Cfr10I, SacII and BssHII), and the comparison of the nt sequences of its variable regions allowed us to determine the putative TRD of MEco29kI.
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Affiliation(s)
- M V Zakharova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Den'mukhametov MM, Zakharova MV, Kravets AN, Pertsev AV, Sineva EV, Repik AV, Beletskaia IV, Gromova ES, Solonin AS. [Characteristics of a plasmid bearing a gene of a restriction modification type II system--the SsoII isoschizomer]. Mol Biol (Mosk) 1997; 31:831-8. [PMID: 9454069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Pertzev AV, Kravetz AN, Mayorov SG, Zakharova MV, Solonin AS. Isolation of a strain overproducing endonuclease Eco29kI: purification and characterization of the homogeneous enzyme. Biochemistry (Mosc) 1997; 62:732-41. [PMID: 9331965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The physical map of the plasmid pSACII1 carrying the genes of restriction-modification system Eco29kI (isoschizomer of SacII) was determined. The cloning of the Eco29kI endonuclease and methylase genes into the plasmid vector pUC129 produced recombinant strain Escherichia coli K802[pECO29A15] with Eco29kI synthesis level about 100 times higher than in the parent strain. The restriction endonuclease was purified from Escherichia coli K802 [pECO29A15] cells to near homogeneity using column chromatography sequentially on phosphocellulose, hydroxyapatite, and heparin-Sepharose and rechromatography on phosphocellulose. Biochemical characterization of the homogeneous R Eco29kI is given. The enzyme has molecular mass 24.5 kD and is present in the solution as a monomer.
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Affiliation(s)
- A V Pertzev
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow Region, Russia
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Zakharova MV, Shkurupiĭ VA, Grek OR. [Effect of preliminary phenobarbital and ziksorin administration on reparative processes in the liver parenchyma after ischemic damage]. Biull Eksp Biol Med 1994; 117:185-8. [PMID: 8012029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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21
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Grek OR, Rybakova TA, Sharapov VI, Zakharova MV, Shkurupiĭ VA. [The correction of the liver detoxifying function with phenobarbital and ziksorin before and after ischemia]. Eksp Klin Farmakol 1993; 56:30-3. [PMID: 8312805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Rat experiments have shown preliminary administration of phenobarbital and zixoryn (before ischemia) fails to prevent the hepatic monoxygenase system from ischemic lesion, followed by profound destructive changes in the liver, though the functional activity of the microsomal system remained high. Phenobarbital and zixoryn induction of monooxygenases in the postischemic period contributed to the complete restoration of the levels of microsomal cytochromes and the metabolic activity of xenobiotics in the liver just in its early periods. It is concluded that it is advisable to use the inductors in the postischemic restorative period to correct the detoxifying function of the liver.
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Zakharova MV, Kravetz AN, Beletzkaja IV, Repyk AV, Solonin AS. Cloning and sequences of the genes encoding the CfrBI restriction-modification system from Citrobacter freundii. Gene 1993; 129:77-81. [PMID: 8335262 DOI: 10.1016/0378-1119(93)90698-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The genes encoding the CfrBI restriction and modification (R-M) systems from Citrobacter freundii and recognizing the sequence 5'-CCWWGG-3' (W = A or T) were cloned in Escherichia coli McrBC- cells. The nucleotide (nt) sequences of the genes were determined. Two large open reading frames were found. Deletion analysis showed that one of them [1128 nt coding for 376 amino acids (aa)] corresponds to a methyltransferase (MTase)-encoding gene and the other (1065 nt coding for 355 aa) to a restriction endonuclease-encoding gene. The genes are oriented divergently and separated by 76 bp. A CfrBI site (5'-m4CCATGG) was found in the intergenic region of the cfrBIRM genes. Analysis of the deduced aa sequence of M.CfrBI made it possible to determine the typical features of a m4C-specific MTase. Limited homology between the M.CfrBI and R.CfrBI proteins was also found.
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Affiliation(s)
- M V Zakharova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region
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Kravetz AN, Zakharova MV, Beletskaya IV, Sineva EV, Denjmuchametov MM, Petrov SI, Glatman LI, Solonin AS. The cleavage sites and localization of genes encoding the restriction endonucleases Eco1831I and EcoHI. Gene 1993; 129:153-4. [PMID: 8335254 DOI: 10.1016/0378-1119(93)90712-c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The restriction endonucleases Eco1831I and EcoHI cleave before the first 5'-cytosine in the recognition sequence 5'-decreases CCSGG--3'/3'--GGSCC increases-5' (where S = G or C), generate 5-base 5' cohesive ends, and are encoded by homologous plasmids that are restricted in McrA+ hosts. Thus, they differ in their cleavage specificity from that of the BcnI isoschizomer, which cleaves after the second 5' cytosine.
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Affiliation(s)
- A N Kravetz
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region
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Kravetz AN, Zakharova MV, Beljetzkaja IV, Pertzev AV, Spivak OI, Solonin AS. Two novel restriction endonucleases from Klebsiella pneumoniae. Nucleic Acids Res 1993; 21:1501. [PMID: 8385321 PMCID: PMC309349 DOI: 10.1093/nar/21.6.1501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- A N Kravetz
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region
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Kravets AN, Solonin AS, Zakharova MV, Tarutina ZE. [Plasmid localization and cloning of restriction modification genes from Citrobacter freundii 4111 strain]. Mol Gen Mikrobiol Virusol 1992:4-7. [PMID: 1338550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Over 60 producing strains of restriction endonucleases type II have been found among 500 different strains, mostly Enterobacteriaceae. The strain Citrobacter freundii 4111 produces restriction endonuclease CfrBI, a new isoschisomer of StyI. The genes of the restriction-modification system CfrBI were located on the multicopy plasmid pZE8 containing the Co1E1-type replicon and cloned to E. coli K802. The deletion variant of 3.2-kb pZE8 which contains intact restriction-modification and a DNA fragment responsible for autonomous plasmid replication was selected among the recombinant plasmids. The strain with higher R. CfrBI production (at least 10,000,000 U/g cells, which is 500-fold higher than the wild strain) was constructed.
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Pertzev AV, Ruban NM, Zakharova MV, Beletzkaja IV, Petrov SI, Kravetz AN, Solonin AS. Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli. Nucleic Acids Res 1992; 20:1991. [PMID: 1579502 PMCID: PMC312317 DOI: 10.1093/nar/20.8.1991] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- A V Pertzev
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region, Puschino
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Denjmuchametov MM, Ruban NM, Zakharova MV, Beletzkaja IV, Kravetz AN, Solonin AS. Eco27kI, a new isoschizomer of AvaI from Escherichia coli. Nucleic Acids Res 1992; 20:1992. [PMID: 1579503 PMCID: PMC312318 DOI: 10.1093/nar/20.8.1992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- M M Denjmuchametov
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region
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Kravets AN, Zakharova MV, Solonin AS, Kuz'min NP, Taniashin VI, Glatman LI, Moroz AF, Baev AA. [Cloning and regulation of gene expression of EcoRV restriction- modification system]. Mol Biol (Mosk) 1990; 24:438-47. [PMID: 2194115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A number of recombinant plasmids, containing EcoRV restriction-modification genes have been constructed. Individual genes of this system were introduced into plasmids of various incompatibility groups. Promoter regions of genes encoding methylase and restrictase have been cloned and studied. With the use of specialized vector pVE8 it was shown that the efficiency of the endonuclease gene promoter is comparable with early lambda phage promoters and produced about 70% of PL efficiency. The efficiency of the methylase gene promoter region was twice less than the efficiency of the restriction endonuclease gene promoter. Plasmid with restriction endonuclease gene promoter located downstream in relation to the additional regulatable phage lambda promoter PL has been obtained. It enabled us to construct strains 30-40 fold overproducing this enzyme under conditions of inactivation of the temperature sensitive phage repressor c1857. This construction directs the production of a high level (10%) of the total cellular soluble proteins) of the EcoRV restriction enzyme. The factors that influenced the level of enzyme synthesis under induction are discussed.
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