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Liu YT, Chen CG, Chao DC, Lee F, Liao CL, Sytwu HK, Chou CF, Ji DD. Sequence analysis of theGluconobacter oxydansRecA protein and construction of arecA-deficient mutant. Can J Microbiol 1999. [DOI: 10.1139/w99-009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The deduced amino acid sequence of Gluconobacter oxydans RecA protein shows 75.2, 69.4, and 66.2% homology with those from Aquaspirillum magnetotacticum, Escherichia coli, andPseudomonas aeruginosa, respectively. The amino acid residues essential for function of the recombinase, protease, and ATPase in E. coli recA protein are conserved in G. oxydans. Of 24 amino acid residues believed to be the ATP binding domain of E. coli RecA, 17 are found to be identical in G. oxydans RecA. Interestingly, nucleotide sequence alignment between the SOS box of G. orphans recA gene and those from different microorganisms revealed that all the DNA sequences examined have dyad symmetry that can form a stem-loop structure. A G. oxydans recA-deficient mutant (LCC96) was created by allelic exchange using the cloned recA gene that had been insertionally inactivated by a kanamycin-resistance cassette. Such replacement of the wild-type recA with a kanamycin resistance gene in the chromosome was further verified by Southern hybridization. Phenotypically, the recA-deficient mutant is significantly more sensitive to UV irradiation than the wild-type strain, suggesting that the recA gene of G. oxydans ATCC9324 plays a role in repairing DNA damage caused by UV irradiation. Moreover, the mutant strain is much more plasmid transformable than its parent strain, illustrating that G. oxydans LCC96 could be used as a host to take up the recombinant plasmid for gene manipulation.Key words: Gluconobacter orphans, recA gene, DNA repair, recA mutant, SOS box.
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2
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Liu YT, Chao DC, Lee F, Chen CG, Ji DD. Molecular characterization ofGluconobacter oxydans recAgene and its inhibitory effect on the function of the host wild-typerecAgene. Can J Microbiol 1998. [DOI: 10.1139/w97-140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A DNA fragment containing the recA gene of Gluconobacter oxydans was isolated and further characterized for its nucleotide sequence and ability to functionally complement various recA mutations. When expressed in an Escherichia coli recA host, the G. oxydans recA protein could efficiently function in homologous recombination and DNA damage repair. The recA gene's nucleotide sequence analysis revealed a protein of 344 amino acids with a molecular mass of 38 kDa. We observed an E. coli-like LexA repressor-binding site in the G. oxydans recA gene promoter region, suggesting that a LexA-like mediated response system may exist in G. oxydans. The expression of G. oxydans recA in E. coli RR1, a recA+strain, surprisingly caused a remarkable reduction of the host wild-type recA gene function, whereas the expression of both Serratia marcescens recA and Pseudomonas aeruginosa recA gene caused only a slight inhibitory effect on function of the host wild-typerecA gene product. Compared with the E. coli RecA protein, the identity of the amino acid sequence of G. oxydans RecA protein is much lower than those RecA proteins of both S. marcescens and Pseudomonas aeruginosa. This result suggests that the expression of another wild-type RecA could interfere with host wild-type recA gene's function, and the extent of such an interference is possibly correlated to the identity of the amino acid sequence between the two classes of RecA protein.Key words: Gluconobacter oxydans, recA gene, recombination, SOS function, interference.
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3
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Eisen JA. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 1995; 41:1105-23. [PMID: 8587109 PMCID: PMC3188426 DOI: 10.1007/bf00173192] [Citation(s) in RCA: 179] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The evolution of the RecA protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete RecA proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The RecA trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the alpha, beta, gamma, delta, epsilon proteobacteria, cyanobacteria, high-GC gram-positives, and the Deinococcus-Thermus group. However, there are interesting differences between the RecA trees and these other trees. For example, in all the RecA trees the proteins from gram-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the RecA analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make RecA useful for molecular systematics and for studies of protein evolution are also discussed.
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Affiliation(s)
- J A Eisen
- Department of Biological Sciences, Stanford University, CA 94305-5020, USA
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4
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Schmitt W, Odenbreit S, Heuermann D, Haas R. Cloning of the Helicobacter pylori recA gene and functional characterization of its product. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:563-72. [PMID: 7476856 DOI: 10.1007/bf02423452] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The RecA protein is a key enzyme involved in DNA recombination in bacteria. Using a polymerase chain reaction (PCR) amplification we cloned a recA homolog from Helicobacter pylori. The gene revealed an open reading frame (ORF) encoding a putative protein of 37.6 kDa showing closest homology to the Campylobacter jejuni RecA (75.5% identity). A putative ribosome binding site and a near-consensus sigma 70 promoter sequence was found upstream of recA. A second ORF, encoding a putative protein with N-terminal sequence homology to prokaryotic and eukaryotic enolases, is located directly downstream of recA. Compared to the wild-type strains, isogenic H. pylori recA deletion mutants of strains 69A and NCTC11637 displayed increased sensitivity to ultraviolet light and abolished general homologous recombination. The recombinant H. pylori RecA protein produced in Escherichia coli strain GC6 (recA-) was 38 kDa in size but inactive in DNA repair, whereas the corresponding protein in H. pylori 69A migrated at the greater apparent molecular weight of approx. 40 kDa in SDS-polyacrylamide gels. However, complementation of the H. pylori mutant using the cloned recA gene on a shuttle vector resulted in a RecA protein of the original size and fully restored the general functions of the enzyme. These data can be best explained by a modification of RecA in H. pylori which is crucial for its function. The potential modification seems not to occur when the protein is produced in E. coli, giving rise to a smaller but inactive protein.
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Affiliation(s)
- W Schmitt
- Max-Planck-Institut für Biologie, Abteilung Infektionsbiologie, Tübingen, Germany
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5
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Affiliation(s)
- E C Conley
- Department of Biochemistry, University of Leicester, UK
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6
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Wardhan H, McPherson MJ, Harris CA, Sharma E, Sastry GR. Molecular analysis of the recA gene of Agrobacterium tumefaciens C58. Gene 1992; 121:133-6. [PMID: 1427086 DOI: 10.1016/0378-1119(92)90171-k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The complete nucleotide sequence of the Agrobacterium tumefaciens recA gene was determined. A comparison of the translated open reading frame of the gene with other known recA sequences revealed significant sequence conservation. However, unlike its Escherichia coli equivalent, A. tumefaciens recA lacks the upstream 'SOS box', suggesting a different mechanism of regulation for this gene.
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Affiliation(s)
- H Wardhan
- Department of Genetics, University of Leeds, UK
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7
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Quivey RG, Faustoferri RC. In vivo inactivation of the Streptococcus mutans recA gene mediated by PCR amplification and cloning of a recA DNA fragment. Gene 1992; 116:35-42. [PMID: 1628842 DOI: 10.1016/0378-1119(92)90626-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The inactivation of the RecA protein in pathogenic oral streptococci would facilitate genetic analysis of potential virulence factors in these strains. Comparison of recA nucleotide (nt) sequences from a number of bacteria has suggested that two regions of highly conserved RecA amino acid (aa) sequence could be used as a basis for synthesizing degenerate oligodeoxyribonucleotide primers with which to amplify recA homologues from the streptococci. Accordingly, primer mixtures were used to amplify a 693-bp fragment of the Streptococcus mutans chromosome by PCR. The amplified fragment was cloned and its identity confirmed via hybridization to an Escherichia coli recA gene probe and by nt sequence determination. The recA homologue fragment from S. mutans GS-5 was 63% and 75% homologous to the deduced aa sequences of the E. coli and Bacillus subtilis RecA enzymes, respectively. The S. mutans recA fragment was mutagenized in vitro via insertional inactivation and returned to the chromosome using allelic exchange. The resulting strains of S. mutans were shown to be substantially more sensitive to UV irradiation than the wild-type strain. Further, the ability to incorporate linear markers into the chromosome was abolished in putative S. mutans recA strains, thus indicating the functional inactivation of RecA in these microorganisms.
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Affiliation(s)
- R G Quivey
- Department of Dental Research, University of Rochester School of Medicine and Dentistry, NY 14642
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Abstract
We have cloned and sequenced the recA gene from two strains, 775 and 531A, of the fish pathogen, Vibrio anguillarum. Although both strains showed different sensitivities to methyl methanesulfonate (MMS), the recA genes were identical. In vitro expression of the V. anguillarum recA gene produced a polypeptide of about 40 kDa, in agreement with the value obtained from the nucleotide sequence. We identified the transcription start point by primer extension. The promoter for the recA gene mapped to an SOS regulatory element. The presence of an SOS box suggests that a LexA-like mediated response system may exist in V. anguillarum. The deduced RecA amino acid sequence is highly homologous with Escherichia coli RecA and other RecA proteins. Domains important in RecA function are conserved. We provide a comparative analysis of the activities and features of RecA analogs from a variety of species. We observed that certain residues that could be important in protein conformation are conserved in RecA proteins across a diverse range of bacterial species.
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Affiliation(s)
- M E Tolmasky
- Department of Microbiology and Immunology, Oregon Health Sciences University, Portland 97201-3098
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Selbitschka W, Arnold W, Priefer UB, Rottschäfer T, Schmidt M, Simon R, Pühler A. Characterization of recA genes and recA mutants of Rhizobium meliloti and Rhizobium leguminosarum biovar viciae. MOLECULAR & GENERAL GENETICS : MGG 1991; 229:86-95. [PMID: 1896024 DOI: 10.1007/bf00264217] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA fragments carrying the recA genes of Rhizobium meliloti and Rhizobium leguminosarum biovar viciae were isolated by complementing a UV-sensitive recA- Escherichia coli strain. Sequence analysis revealed that the coding region of the R. meliloti recA gene consists of 1044 bp coding for 348 amino acids whereas the coding region of the R. leguminosarum bv. viciae recA gene has 1053 bp specifying 351 amino acids. The R. meliloti and R. leguminosarum bv. viciae recA genes show 84.8% homology at the DNA sequence level and of 90.1% at the amino acid sequence level. recA- mutant strains of both Rhizobium species were constructed by inserting a gentamicin resistance cassette into the respective recA gene. The resulting recA mutants exhibited an increased sensitivity to UV irradiation, were impaired in their ability to perform homologous recombination and showed a slightly reduced growth rate when compared with the respective wild-type strains. The Rhizobium recA strains did not have altered symbiotic nitrogen fixation capacity. Therefore, they represent ideal candidates for release experiments with impaired strains.
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Affiliation(s)
- W Selbitschka
- Lehrstuhl für Genetik, Universität Bielefeld, Federal Republic of Germany
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Abstract
Processes fundamental to all models of genetic recombination include the homologous pairing and subsequent exchange of DNA strands. Biochemical analysis of these events has been conducted primarily on the recA protein of Escherichia coli, although proteins which can promote such reactions have been purified from many sources, both prokaryotic and eukaryotic. The activities of these homologous pairing and DNA strand exchange proteins are either ATP-dependent, as predicted based on the recA protein paradigm, or, more unexpectedly, ATP-independent. This review examines the reactions promoted by both classes of proteins and highlights their similarities and differences. The mechanistic implications of the apparent existence of 2 classes of strand exchange protein are discussed.
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Affiliation(s)
- A K Eggleston
- Department of Cell, Molecular, and Structural Biology, Northwestern University Medical School, IL 60611
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11
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Favre D, Cryz SJ, Viret JF. Cloning of the recA gene of Bordetella pertussis and characterization of its product. Biochimie 1991; 73:235-44. [PMID: 1832021 DOI: 10.1016/0300-9084(91)90208-i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A recA gene of Bordetella pertussis was identified in a plasmid library by complementation of a recA mutation in E coli and subcloned as a 2.1-kb Sph I DNA fragment. Southern hybridization experiments showed no similarity to the E coli recA gene, but very strong similarity to other Bordetella species. E coli recA mutant cells containing the B pertussis recA gene at high gene dosage were resistant to DNA-damaging agents such as methyl methane sulfonate or 4-nitroquinoline-N-oxide, displayed induction of SOS functions, and were able to promote DNA recombination, but not induction of phage lambda. The latter phenotype distinguishes the B pertussis recA gene product from the corresponding proteins from most other Gram-negative organisms. Amino acid sequence comparisons revealed a high degree of structural conservation between prokaryotic RecA proteins.
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Affiliation(s)
- D Favre
- Swiss Serum and Vaccine Institute, Berne, Switzerland
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12
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Gomelsky M, Gak E, Chistoserdov A, Bolotin A, Tsygankov YD. Cloning, sequence and expression in Escherichia coli of the Methylobacillus flagellatum recA gene. Gene 1990; 94:69-75. [PMID: 2227454 DOI: 10.1016/0378-1119(90)90469-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
By means of interspecific complementation of an Escherichia coli recA- mutation with phasmids containing a gene bank from an obligate methylotroph, Methylobacillus flagellatum (Mf), the recA+ gene from this bacterium was identified. When expressed in an E. coli recA- host, it can function in recombination, DNA repair, and prophage induction. The nucleotide sequence of the gene has been determined. The coding region consists of 1032 bp specifying 344 amino acids. The deduced RecA protein structure shows a striking homology with RecA from other bacteria, except for the C-terminal region and some residues which were proposed to be responsible for the coprotease ability of RecA proteins. The region preceding the recA-Mf gene start codon has no SOS box--the LexA repressor binding site. Expression of the recA-Mf gene in E. coli proved to be DNA-damage independent.
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Affiliation(s)
- M Gomelsky
- Institute of Genetics and Selection of Industrial Microorganisms, Moscow, U.S.S.R
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13
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Abstract
The nucleotide sequence of a 2.5-kb DNA segment containing the Bacteroides fragilis recA gene was determined. The coding region of the recA gene specifies a protein of 318 amino acids. The RecA protein of B. fragilis shows significant homology with that of Escherichia coli, Thiobacillus ferrooxidans, Pseudomonas aeruginosa and Proteus mirabilis. No SOS box characteristic of LexA-regulated promoters could be identified in the 5'-noncoding region of the B. fragilis recA gene. Promoter activity of the cloned recA gene in E. coli was located within a 113-bp fragment of the B. fragilis DNA by in vitro construction of operon fusions with a promoterless lacZ gene. The transcription start point for this gene in B. fragilis was determined by primer extension analysis.
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Affiliation(s)
- H J Goodman
- Department of Microbiology, University of Cape Town, Rondebosch, South Africa
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14
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Fyfe JA, Davies JK. Nucleotide sequence and expression in Escherichia coli of the recA gene of Neisseria gonorrhoeae. Gene 1990; 93:151-6. [PMID: 2121608 DOI: 10.1016/0378-1119(90)90151-g] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The nucleotide sequence of the recA gene of Neisseria gonorrhoeae MS11 has been determined. The product of this gene can act as a recombinase in Escherichia coli, but does so with a decreased efficiency, probably because of the formation of mixed multimers with the equivalent E. coli protein.
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Affiliation(s)
- J A Fyfe
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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15
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Zhao X, Dreyfus LA. Expression and nucleotide sequence analysis of the Legionella pneumophila recA gene. FEMS Microbiol Lett 1990; 58:227-31. [PMID: 2121588 DOI: 10.1111/j.1574-6968.1990.tb13983.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nucleotide sequence of the L pneumophila recA gene was determined. The coding region was 1044 nucleotides (348 codons), specifying a 37,934 Da protein. Preceding the recA gene was a tandem set of transcription regulatory sequences and putative LexA binding sites. When expressed in E. coli, the cloned recA gene yield two proteins with molecular weights of approximately 38,000 and 35,500 Da. The larger of these two proteins shared 70.4% and 74.6% identity with the E. coli and Pseudomonas aeruginosa RecA proteins, respectively. The 35,500 Da recA encoded protein was presumed to be the product of translation from Met26 which was preceded by an alternate ribosomal binding site.
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Affiliation(s)
- X Zhao
- Department of Microbiology, University of Texas Medical Branch, Galveston 77550
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Zhao XJ, McEntee K. DNA sequence analysis of the recA genes from Proteus vulgaris, Erwinia carotovora, Shigella flexneri and Escherichia coli B/r. MOLECULAR & GENERAL GENETICS : MGG 1990; 222:369-76. [PMID: 2274037 DOI: 10.1007/bf00633842] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complete nucleotide sequences of the recA genes from Escherichia coli B/r, Shigella flexneri, Erwinia carotovora and Proteus vulgaris were determined. The DNA sequence of the coding region of the E. coli B/r gene contained a single nucleotide change compared with the E. coli K12 gene sequence whereas the S. flexneri gene differed at 7 residues. In both cases, the predicted proteins were identical in primary structure to the E. coli K12 RecA protein. The DNA sequences of the recA genes from E. carotovora and P. vulgaris were 80% and 74% homologous, respectively, to the E. coli K12 gene. The predicted amino acid sequences of the E. carotovora and P. vulgaris RecA proteins were 91% and 85% identical respectively, to that of E. coli K12. The RecA proteins from both P. vulgaris and E. carotovora diverged significantly in sequence in the last 50 residues whereas they showed striking conservation throughout the first 300 amino acids which include an ATP-binding region and a subunit interaction domain. A putative LexA repressor binding site was localized upstream of each of the heterologous genes.
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Affiliation(s)
- X J Zhao
- Department of Biological Chemistry, UCLA School of Medicine, University of California 90024
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Murphy RC, Gasparich GE, Bryant DA, Porter RD. Nucleotide sequence and further characterization of the Synechococcus sp. strain PCC 7002 recA gene: complementation of a cyanobacterial recA mutation by the Escherichia coli recA gene. J Bacteriol 1990; 172:967-76. [PMID: 2105307 PMCID: PMC208525 DOI: 10.1128/jb.172.2.967-976.1990] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nucleotide sequence and transcript initiation site of the Synechococcus sp. strain PCC 7002 recA gene have been determined. The deduced amino acid sequence of the RecA protein of this cyanobacterium is 56% identical and 73% similar to the Escherichia coli RecA protein. Northern (RNA) blot analysis indicates that the Synechococcus strain PCC 7002 recA gene is transcribed as a monocistronic transcript 1,200 bases in length. The 5' endpoint of the recA mRNA was mapped by primer extension by using synthetic oligonucleotides of 17 and 27 nucleotides as primers. The nucleotide sequence 5' to the mapped endpoint contained sequence motifs bearing a striking resemblance to the heat shock (sigma 32-specific) promoters of E. coli but did not contain sequences similar to the E. coli SOS operator recognized by the LexA repressor. An insertion mutation introduced into the recA locus of Synechococcus strain PCC 7002 via homologous recombination resulted in the formation of diploids carrying both mutant and wild-type recA alleles. A variety of growth regimens and transformation procedures failed to produce a recA Synechococcus strain PCC 7002 mutant. However, introduction into these diploid cells of the E. coli recA gene in trans on a biphasic shuttle vector resulted in segregation of the cyanobacterial recA alleles, indicating that the E. coli recA gene was able to provide a function required for growth of recA Synechococcus strain PCC 7002 cells. This interpretation is supported by the observation that the E. coli recA gene is maintained in these cells when antibiotic selection for the shuttle vector is removed.
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Affiliation(s)
- R C Murphy
- Department of Molecular and Cell Biology, Pennsylvania State University, University Park 16802
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Affiliation(s)
- A I Roca
- Department of Biochemistry, University of Wisconsin-Madison 53706
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