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Rudenko NV, Nagel AS, Melnik BS, Karatovskaya AP, Vetrova OS, Zamyatina AV, Andreeva-Kovalevskaya ZI, Siunov AV, Shlyapnikov MG, Brovko FA, Solonin AS. Utilizing Extraepitopic Amino Acid Substitutions to Define Changes in the Accessibility of Conformational Epitopes of the Bacillus cereus HlyII C-Terminal Domain. Int J Mol Sci 2023; 24:16437. [PMID: 38003626 PMCID: PMC10671226 DOI: 10.3390/ijms242216437] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Hemolysin II (HlyII)-one of the pathogenic factors of Bacillus cereus, a pore-forming β-barrel toxin-possesses a C-terminal extension of 94 amino acid residues, designated as the C-terminal domain of HlyII (HlyIICTD), which plays an important role in the functioning of the toxin. Our previous work described a monoclonal antibody (HlyIIC-20), capable of strain-specific inhibition of hemolysis caused by HlyII, and demonstrated the dependence of the efficiency of hemolysis on the presence of proline at position 324 in HlyII outside the conformational antigenic determinant. In this work, we studied 16 mutant forms of HlyIICTD. Each of the mutations, obtained via multiple site-directed mutagenesis leading to the replacement of amino acid residues lying on the surface of the 3D structure of HlyIICTD, led to a decrease in the interaction of HlyIIC-20 with the mutant form of the protein. Changes in epitope structure confirm the high conformational mobility of HlyIICTD required for the functioning of HlyII. Comparison of the effect of the introduced mutations on the effectiveness of interactions between HlyIICTD and HlyIIC-20 and a control antibody recognizing a non-overlapping epitope enabled the identification of the amino acid residues N339 and K340, included in the conformational antigenic determinant recognized by HlyIIC-20.
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Affiliation(s)
- Natalia V Rudenko
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Alexey S Nagel
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, FRC Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Bogdan S Melnik
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Moscow Region, Russia
| | - Anna P Karatovskaya
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Olesya S Vetrova
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Anna V Zamyatina
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Zhanna I Andreeva-Kovalevskaya
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, FRC Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Alexander V Siunov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, FRC Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Mikhail G Shlyapnikov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, FRC Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Fedor A Brovko
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Alexander S Solonin
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, FRC Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
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2
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Glukhov AS, Krutilina AI, Kaliman AV, Shlyapnikov MG, Ksenzenko VN. [Bacteriophage T5 Mutants Carrying Deletions in tRNA Gene Region]. Mol Biol (Mosk) 2018; 52:3-9. [PMID: 29512629 DOI: 10.7868/s0026898418010019] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 11/23/2022]
Abstract
A new series of heat-stable (st) mutants of bacteriophage T5, which contains deletions in the tRNA gene region, has been isolated. An accurate mapping of the deletion boundaries for more than 30 mutants of phage T5 has been carried out. As a result of the analysis of nucleotide sequences flanking the deleted regions in wild-type phage DNA, it has been shown that they all contain short, direct repeats of different lengths (2-35 nucleotide residues), and that only one repetition is retained in the mutant phage DNA. On the basis of the obtained results, it was suggested that deletion mutants of the phage T5 are formed as a result of illegal recombination occurring with the participation of short repeats in DNA (SHDIR). Based on the example of two mutants, it has been shown that the resistance to thermal inactivation depends on the size of the deleted region.
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Affiliation(s)
- A S Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.,
| | - A I Krutilina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia
| | - A V Kaliman
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia
| | - M G Shlyapnikov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia
| | - V N Ksenzenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia
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3
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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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4
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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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5
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Trutko SM, Akimenko VK, Suzina NE, Anisimova LA, Shlyapnikov MG, Baskunov BP, Duda VI, Boronin AM. Involvement of the respiratory chain of gram-negative bacteria in the reduction of tellurite. Arch Microbiol 2000; 173:178-86. [PMID: 10763749 DOI: 10.1007/s002039900123] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [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: 11/29/2022]
Abstract
The terminal oxidases of the respiratory chain of seven strains of gram-negative bacteria were shown to be involved in the reduction of tellurite. The rate of tellurite reduction correlated with the intensity of respiration. The inhibitors of terminal oxidases, carbon monoxide and cyanide, inhibited the reduction of tellurite. In Pseudomonas aeruginosa PAO ML4262 and P. aeruginosa PAO ML4262 (pBS 10), the respiratory chain was found to contain three types of cytochrome c, one of which (the carbon monoxide-binding cytochrome c) was involved in the reduction of tellurite. Agrobacterium tumefaciens VKM B-1219, P. aeruginosa IBPM B-13, and Escherichia coli G0-102bd++ cells contained oxidases aa3, bb3, and bd, respectively. The respiratory chain of other strains contained two oxidases: E. coli DH5alpha of bb3- and bd-type, and Erwinia carotovora VKM B-567 of bo3- and bd-type. All the strains under study reduced tellurite with the formation of tellurium crystallites. Depending on the position of the active center of terminal oxidases in the plasma membrane, the crystallites appeared either in the periplasmic space [P. aeruginosa PAO ML4262 and P. aeruginosa PAO ML4262 (pBS10)], or on the outer surface of the membrane (A. tumefaciens VKM B-1219 and P. aeruginosa IBPM B-13), its inner surface (E. coli G0-102bd++), or on both surfaces (E. coli DHaalpha and E. carotovora VKM B-567).
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Affiliation(s)
- S M Trutko
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow.
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6
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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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7
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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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8
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Kadyrov FA, Shlyapnikov MG, Kryukov VM. A phage T4 site-specific endonuclease, SegE, is responsible for a non-reciprocal genetic exchange between T-even-related phages. FEBS Lett 1997; 415:75-80. [PMID: 9326373 DOI: 10.1016/s0014-5793(97)01098-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [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: 02/05/2023]
Abstract
The bacteriophage T4 segE gene encoding site-specific endonuclease lies between the hoc.1 and uvsW genes. The similar region of T-even-related phage RB30 lacks the segE gene. Here we demonstrate that the phage T4 segE gene is inherited preferably by progeny of mixed infection with RB30. The preferred inheritance of the segE gene depends on its own expression and is based on a non-reciprocal homologous recombination event providing the transfer of the gene from the segE-containing to the segE-lacking allele. The SegE endonuclease cleaves DNA in a site located at the 5' end of the uvsW gene in the RB30 genome. The T4 DNA is also cleaved by the enzyme, but less efficiently. The cleavage at the RB30 site appears to initiate the observed conversion, which is stimulated by DNA homology and accompanied by co-conversion of flanking markers. Our findings provide a novel example of endonuclease-dependent generation of genetic variation in prokaryotes.
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Affiliation(s)
- F A Kadyrov
- Laboratory of Genetic Enzymology, Institute of Biochemistry and Physiology of Microorganisms of Russian Academy of Sciences, Pushchino, Moscow region.
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9
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Kholod NS, Pan'kova NV, Mayorov SG, Krutilina AI, Shlyapnikov MG, Kisselev LL, Ksenzenko VN. Transfer RNA(Phe) isoacceptors possess non-identical set of identity elements at high and low Mg2+ concentration. FEBS Lett 1997; 411:123-7. [PMID: 9247156 DOI: 10.1016/s0014-5793(97)00608-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [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: 02/04/2023]
Abstract
Primary structures of phage T5- and Escherichia coli-encoded tRNA(Phe) are distinct at four out of 11 positions known as identity elements for E. coli phenylalanyl-tRNA synthetase (FRS). In order to reveal structural requirements for FRS recognition, aminoacylation of wild-type phage T5 tRNA(Phe) gene transcript and mutants containing substitutions of the identity elements at positions 20, 34, 35 and 36 was compared with E. coli tRNA(Phe) gene transcript. The wild-type phage T5 transcript can be aminoacylated with the same catalytic efficiency as the E. coli counterpart. However, the maximal aminoacylation rate for T5 and E. coli transcripts was reached at different Mg2+ concentrations: 4 and 15 mM, respectively. Aminoacylation assays with tRNA(Phe) mutants revealed that (i) phage transcripts with the substituted anticodon bases at positions 35 and 36 were efficient substrates for aminoacylation at 15 mM Mg2+ but not at optimal 4 mM Mg2+; (ii) any change of G34 in phage transcripts dramatically decreased the aminoacylation efficiency at both 4 and 15 mM Mg2+ whereas G34A mutation in the E. coli transcript exhibits virtually no influence on aminoacylation rate at 15 mM Mg2+; (iii) substitution of A20 with U in the phage transcript caused no significant change in the aminoacylation rate at both Mg2+ concentrations; (iv) phage transcripts with double substitutions A20U+A35C and A20U+A36C were very poor substrates for FRS. Collectively, the results indicate the non-identical mode of tRNA(Phe) recognition by E. coli FRS at low and high Mg2+ concentrations. Probably, along with identity elements, the local tRNA conformation is essential for recognition by FRS.
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Affiliation(s)
- N S Kholod
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region
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10
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Abstract
The nucleotide sequence of the bacteriophage T5 Bg/II-BamHI fragment (4,835 bp in length) known to carry a gene encoding the LTF protein which forms the phage L-shaped tail fibers was determined. It was shown to contain an open reading frame for 1,396 amino acid residues that corresponds to a protein of 147.8 kDa. The coding region of ltf gene is preceded by a typical Shine-Dalgarno sequence. Downstream from the ltf gene there is a strong transcription terminator. Data bank analysis of the LTF protein sequence reveals 55.1% identity to the hypothetical protein ORF 401 of bacteriophage lambda in a segment of 118 amino acids overlap.
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Affiliation(s)
- A V Kaliman
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region
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11
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Ivashina TV, Khmelnitsky MI, Shlyapnikov MG, Kanapin AA, Ksenzenko VN. The pss4 gene from Rhizobium leguminosarum by viciae VF39: cloning, sequence and the possible role in polysaccharide production and nodule formation. Gene X 1994; 150:111-6. [PMID: 7959035 DOI: 10.1016/0378-1119(94)90868-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [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: 01/28/2023] Open
Abstract
The Tn5 insertion into the genome of Rhizobium leguminosarum bv viciae VF39, resulting in non-mucoid growth and formation of non-N2-fixing nodule-like structures on Vicia faba plants, was mapped within a 1.4-kb EcoRV-SacI fragment. Nucleotide sequence analysis revealed an ORF (pss4) of 263 amino acids (aa). Three transcription start points (tsp) were determined. Two of them were localized upstream from the first GTG codon; the third tsp was mapped in front of the second putative start codon (GTG) corresponding to Val64 of the Pss4 aa sequence. The expression of pss4 in a T7 RNA polymerase/promoter system produced a single approx. 29-kDa protein. Pss4 reveals similarity to several proteins involved in polysaccharide biosynthesis in various Rhizobium species. A nearly complete homology was found with PssA from Rl biovar phaseoli 8002 [Borthakur et al., Mol. Gen. Genet. 213 (1988) 155-162], except that Pss4 has an additional 63 aa on its N terminus.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/genetics
- Base Sequence
- Cloning, Molecular
- DNA Transposable Elements/genetics
- DNA, Bacterial
- Fabaceae/microbiology
- Genes, Bacterial
- Membrane Proteins/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plants, Medicinal
- Polysaccharides, Bacterial/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Regulatory Sequences, Nucleic Acid
- Rhizobium leguminosarum/genetics
- Rhizobium leguminosarum/physiology
- Sequence Homology, Amino Acid
- Symbiosis
- Transcription, Genetic
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Affiliation(s)
- T V Ivashina
- Institute of Biochemistry and Physiology of Microorganisms, Academy of Sciences, Pushchino, Moscow Region, Russia
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12
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Ksenzenko VN, Wilkens K, Rueger W, Shlyapnikov MG. Nucleotide sequence of the phage T5 DNA segment containing six tRNA genes. Nucleic Acids Res 1992; 20:6104. [PMID: 1461745 PMCID: PMC334483 DOI: 10.1093/nar/20.22.6104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- V N Ksenzenko
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino
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13
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Ksenzenko VN, Shlyapnikov MG, Azbarov VG, Garcia O, Kryukov VM, Bayev AA. Nucleotide sequence of the bacteriophage T5 DNA fragment containing a distal part of tRNA gene region. Nucleic Acids Res 1987; 15:5480-1. [PMID: 3299272 PMCID: PMC305976 DOI: 10.1093/nar/15.13.5480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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14
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Shlyapnikov MG, Ksenzenko VN, Kryukov VM, Bayev AA. Nucleotide sequence of the bacteriophage T5 DNA fragment which contains the gene for tRNAAsp. Eur J Biochem 1986; 156:285-9. [PMID: 3516691 DOI: 10.1111/j.1432-1033.1986.tb09579.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The nucleotide sequence of bacteriophage T5 tRNAAsp has been determined by conventional methods using thin-layer chromatography on cellulose for oligonucleotide fractionation. It exhibits several unusual features, such as (a) the displacement of the constant residues U-8, A-14 and R-15; (b) the presence of three G X U out of four base pairs in the D-stem. The gene for T5 tRNAAsp has been cloned in pBR 322 and sequenced. The analysis of the flanking regions shows the presence of two open reading frames on both sides of this gene. It has also been shown that the cloned gene is expressed in Escherichia coli, and RNase P is involved in the T5 tRNAAsp processing.
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15
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Abstract
Uniformly 32P-labeled bacteriophage T5 leucine tRNA has been isolated by two-dimensional gel electrophoresis from phage-infected E. coli cells. Its nucleotide sequence has been determined by conventional techniques using TLC on cellulose for oligonucleotide fractionation: pGGGGCUAUGCUGGAACDGmGDAGACAAUACGGCCUUAGm6AU psi CCGUAGCUUAAAUGCGUGGGAGT psi CGAGUCUCCCUAGCCCCACCAoh. This tRNA has anticodon sequence UAG, which can presumably recognize all the four leucine-specific codons (CUN). The main feature of T5 tRNALeu is the absence of the A10-C25 and C31-psi 39 pairing in the D and anticodon stems, respectively.
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Shlyapnikov MG, Kaliman AV, Kazantsev SI, Kryukov VM, Bayev AA. The nucleotide sequence of bacteriophage T5 glutamine transfer RNA. Biochim Biophys Acta 1984; 782:313-9. [PMID: 6733112 DOI: 10.1016/0167-4781(84)90067-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Uniformly 32P-labeled phage-specific tRNAGln has been isolated from bacteriophage T5-infected Escherichia coli cells and its nucleotide sequence has been determined using thin-layer chromatography on cellulose to fractionate the oligonucleotides. The sequence is: pUGGGGAUUAGCUUAGCUUGGCCUAAAGCUUCGGCCUUUGAAG psi CGAGAUCAUUGGT psi CAAAUCCAAUAUCCCCUGCCAOH. The main feature of this tRNA is the absence of Watson-Crick pairing between the 5'-terminal base and the fifth base from its 3'-end. The structure of tRNA was confirmed by DNA sequencing of its gene.
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Ksenzenko VN, Kamynina TP, Kazantsev SI, Shlyapnikov MG, Kryukov VM, Bayev AA. Cloning of genes for bacteriophage T5 stable RNAs. Biochim Biophys Acta 1982; 697:235-42. [PMID: 6285979 DOI: 10.1016/0167-4781(82)90082-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
One EcoRI-generated fragment (440 basepairs) and two EcoRI/HindIII fragments (220 and 960 basepairs) from the deletion region of T5 phage have been inserted into the phage lambda XIII and the plasmid pBR322 as vectors. Recombinant DNA molecules were studied by hybridization with in vivo 32P-labeled T5 4-5 S RNAs on nitrocellulose filters. Two-dimensional polyacrylamide gel electrophoretic fractionation and fingerprint analysis of the RNAs eluted from the filters were carried out to identify RNAs coded by cloned fragments. For the accurate localization of the genes for these RNAs, RNA-DNA hybrids were treated with T1 and pancreatic RNAases, and the eluted RNA fragments stable against RNAase action were electrophoresed. It was shown that the EcoRI 440 fragment contains the gene for tRNA 10 (tRNAAsp), the EcoRI/HindIII 220 fragment contains the gene for RNA III (107 bases) and parts of the genes for RNA I (107 bases) and tRNA 12 (tRNAHis), and the EcoRI/HindIII 960 fragment contains only a part of the gene for tRNA 9 (tRNAGln). The arrangement of these genes on the physical map of T5 phage was as follows: -tRNAGln-tRNAHis-RNA III-RNA I-...-tRNAAsp.
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