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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

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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 α, β, γ, δ, ε 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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References

  • Aigle B, Schneider D, Decaris B (1994) Genbank entry Z30324

  • Akaboshi E, Yip ML, Howard-Flanders P (1989) Nucleotide sequence of the recA gene of Proteus mirabilis. Nucleic Acids Res 17:4390

    Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Angov E, Camerini-Otero RD (1994) The recA gene from the thermophile Thermus aquaticus YT-1: cloning, expression, and characterization. J Bacteriol 176:1405–1412

    Google Scholar 

  • Ball TK, Wasmuth CR, Braunagel SC, Benedik MJ (1990) Expression of Serratia marcescens extracellular proteins requires recA. J Bacteriol 172:342–349

    Google Scholar 

  • Bayles KW, Brunskill EW, Iandolo JJ, Hruska LL, Huang S, Pattee PA, Smiley BK, Yasbin RE (1994) A genetic and molecular characterization of the recA gene from Staphylococcus aureus. Gene 147: 13–20

    Google Scholar 

  • Berson AE, Peters MR, Waleh NS (1990) Nucleotide sequence of recA gene of Aquaspirillum magnetotacticum. Nucleic Acids Res 18:675

    Google Scholar 

  • Billman-Jacobe H (1994) Genbank entry X77384

  • Binet M-N, Osman M, Jagendorf AT (1993) Genomic nucleotide sequence of a gen from Arabidopsis thaliana encoding a protein homolog of Escherichia coli RecA. Plant Physiol 103:673–674

    Google Scholar 

  • Boorstein WR, Ziegelhoffer T, Craig EA (1994) Molecular evolution of the HSP70 multigene family. J Mol Evol 38:1–17

    Google Scholar 

  • Bruns TD and Szaro TM (1992) Rate and mode differences between nuclear and mitochondrial small-subunit rRNA genes in mushrooms. Mol Biol Evol 9:836–855.

    Google Scholar 

  • Burggraf S, Olsen GJ, Stetter KO, Woese CR (1992) A phylogenetic analysis of Aquifex pyrophilus. Syst Appl Microbiol 15:352–356

    Google Scholar 

  • Calero S, Fernandez de Henestrosa AR, Barbe J (1994) Molecular cloning, sequence and regulation of expression of the recA gene of the phototrophic bacterium Rhodobacter sphaeroides. Mol Gen Genet 242:116–120

    Google Scholar 

  • Cerutti H, Osman M, Grandoni P, Jagendorf AT (1992) A homolog of Escherichia coli RecA protein in plastids of higher plants. Proc Natl Acad Sci USA 89:8068–8072

    Google Scholar 

  • Clark AJ, Margulies AD (1965) Isolation and characterization of recombination-deficient mutants of Escherichia coli K-12. Proc Natl Acad Sci USA 53:451–459

    Google Scholar 

  • Clark AJ, Sandler SJ (1994) Homologous genetic recombination: the pieces begin to fall into place. Crit Rev Microbiol 20:125–142

    Google Scholar 

  • Davis EO, Sedgwick SG, Colston MJ (1991) Novel structure of the recA locus of Mycobacterium tuberculosis implies processing of the gene product. J Bacteriol 173:5653–5662

    Google Scholar 

  • Davis EO, Thangaraj HS, Brooks PC, Colston MJ (1994) Evidence of selection for protein introns in the recAs of pathogenic mycobacteria. Embo J 13:699–703

    Google Scholar 

  • Delwiche CF, Kushel M, Palmer JD (1995) Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol Phylogen Evol 4:110–128

    Google Scholar 

  • De Mot R, Laeremans T, Schoofs G, Vanderleyden J (1993) Characterization of the recA gene from Pseudomonas fluorescens OE 28.3 and construction of a recA mutant. J Gen Microbiol 139:49–57

    Google Scholar 

  • De Soete G (1983) A least squares algorithm for fitting additive trees to proximity data. Psychometrika 48:621–626

    Google Scholar 

  • Dunkin SM, Wood DO (1994) Isolation and characterization of the Rickettsia prowazekii recA gene. J Bacteriol 176:1777–1781

    Google Scholar 

  • Duwat P, Ehrlich SD, Gruss A (1992a) A general method for cloning recA genes of gram-positive bacteria by polymerase chain reaction. J Bacteriol 174:5171–5175

    Google Scholar 

  • Duwat P, Ehrlich SD, Gruss A (1992b) Use of degenerate primers for polymerase chain reaction cloning and sequencing of the Lactococcus lactis subsp. lactis recA gene. Appl Environ Microbiol 58: 2674–2678

    Google Scholar 

  • Dybvig K, Hollingshead SK, Heath DG, Clewell DB, Sun F, Woodard A (1992) Degenerate oligonucleotide primers for enzymatic amplification of recA sequences from gram-positive bacteria and mycoplasmas. J Bacteriol 174:2729–2732

    Google Scholar 

  • Dybvig K, Woodard A (1992) Cloning and DNA sequence of a mycoplasmal recA gene. J Bacteriol 174:778–784

    Google Scholar 

  • Eisen JA, Smith SW, Cavanaugh CM (1992) Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum Say (Mollusca: Bivalvia) determined by 16S rRNA sequence analysis. J Bacteriol 174:3416–3421

    Google Scholar 

  • Embley TM, Thomas RH, Williams RAD (1993) Reduced thermophilic bias in the 16S rDNA sequence from Thermus ruber provides further support for a relationship between Thermus and Deinococcus. Syst Appl Microbiol 16:25–29

    Google Scholar 

  • Favre D, Cryz SJ Jr, Viret JF (1991) Cloning of the recA gene of Bordetella pertussis and characterization of its product. Biochimie 73:235–44

    Google Scholar 

  • Favre D, Viret JF (1990) Nucleotide sequence of the recA gene of Bordetella pertussis. Nucleic Acids Res 18:4243

    Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Google Scholar 

  • Felsenstein J (1989) PHYLIP—phylogeny inference package, version 3.2. Cladistics 5:164–166

    Google Scholar 

  • Fernandez de Henestrosa AR (1994) Genbank entry X82183

  • Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279–284

    CAS  PubMed  Google Scholar 

  • Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen LB, Blakemore R, Gupta R, Bonen L, Lewis BJ, Stahl DA, Leuhrsen KH, Chen KN, Woese CR (1980) The phylogeny of prokaryotes. Science 209:457–463

    Google Scholar 

  • Fry NK, Warwick S, Saunders NA, Embley TM (1991) The use of 16S ribosomal RNA analyses to investigate the phylogeny of the family Legionellaceae. J Gen Microbiol 137:1215–1222

    Google Scholar 

  • Fyfe JA, Davies JK (1990) Nucleotide sequence and expression in Escherichia coli of the recA gene of Neisseria gonorrhoeae. Gene 93:151–156

    Google Scholar 

  • Gammie AE, Crosa JH (1991) Co-operative autoregulation of a replication protein gene. Mol Microbiol 5:3015–3023

    Google Scholar 

  • Gatesy J, Desalle R, Wheeler W (1993) Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol Phylog Evol 2:152–157

    Google Scholar 

  • Gomelsky M, Gak E, Chistoserdov A, Bolotin A, Tsygankov YD (1990) Cloning, sequence and expression in Escherichia coli of the Methylobacillus flagellatum recA gene. Gene 94:69–75

    Google Scholar 

  • Goodman HJ, Woods DR (1990) Molecular analysis of the Bacteroides fragilis recA gene. Gene 94:77–82

    Google Scholar 

  • Gregg-Jolly LA, Omston LN (1994) Genbank entry L26100

  • Guerry P, Pope PM, Burr DH, Leifer J, Joseph SW, Bourgeois AL (1994) Development and characterization of recA mutants of Campylobacter jejuni for inclusion in attenuated vaccines. Infect Immunol 62:426–432

    Google Scholar 

  • Gupta RS, Golding GB, Singh B (1994) Hsp70 phylogeny and the relationship between archaebacteria, eubacteria, and eukaryotes. J Mol Evol 39:537–540

    Google Scholar 

  • Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58:10–26

    Google Scholar 

  • Gutman PD, Carroll JD, Masters CI, Minton KW (1994) Sequencing, targeted mutagenesis and expression of a recA gene required for the extreme radioresistance of Deinococcus radiodurans. Gene 141: 31–37

    Google Scholar 

  • Haas R (1994) Genbank entry Z35478

  • Hasegawa M, Hashimoto T (1993) Ribosomal RNA tree misleading? Nature 361:23

    Google Scholar 

  • Henikoff S (1993) Sequence analysis by electronic mail server. Trends Biochem Sci 18:267–268

    Google Scholar 

  • Hillis DM (1995) Approaches for assessing phylogenetic accuracy. Syst Biol 44:3–16

    Google Scholar 

  • Horii T, Ogawa T, Ogawa H (1980) Organization of the recA gene of Escherichia coli. Proc Natl Acad Sci USA 77:313–317

    Google Scholar 

  • Inagaki K, Tomono J, Kishimoto N, Tano T, Tanaka H (1993) Cloning and sequence of the recA gene of Acidiphilium facilis. Nucleic Acids Res 21:4149

    Google Scholar 

  • Jinks-Robertson S, Nomura M (1987) Ribosomes and tRNA, In: Neidhardt FC (ed) Escherichia coli and Salmonella typhimurium cellular and molecular biology. American Society for Microbiology, Washington, DC, pp 1358–1385

    Google Scholar 

  • Kato R, Kuramitsu S (1993) RecA protein from an extremely thermophilic bacterium, Thermus thermophilus HB8. J Biochem 114:926–929

    Google Scholar 

  • Kerins SM, Fitzpatrick R, O'Donohue M, Dunican L (1994) Genbank entry X75085

  • Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  PubMed  Google Scholar 

  • King KW, Woodard A, Dybvig K (1994) Cloning and characterization of the recA genes from Mycoplasma pulmonis and M. mycoides subsp. mycoides. Gene 139:111–115

    Google Scholar 

  • Klenk H-P, Zillig W (1994) DNA-dependent RNA polymerase subunit b as a tool for phylogenetic reconstructions: branching topology of the archaeal domain. J Mol Evol 38:420–432

    Google Scholar 

  • Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SS, Rehrauer WM (1994) Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58:401–465

    Google Scholar 

  • Kowalczykowski SC (1991) Biochemical and biological function of Escherichia coli RecA protein: behavior of mutant RecA proteins. Biochimie 73:289–304

    Google Scholar 

  • Kryukov VM, Suchkov IY, Sazykin IS, Mishankin BN (1993) Genbank entry X75336

  • Lake JA (1991) The order of sequence alignment can bias the selection of tree topology. Mol Biol Evol 8:378–385

    Google Scholar 

  • Lane DJ, Harrison AP, Stahl DA, Pace B, Gíovannoní SJ, Olsen GJ, Pace NR (1992) Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J Bacteriol 174:269–278.

    Google Scholar 

  • Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S rRNA sequences for phylogenetic analysis. Proc Natl Acad Sci USA 82:6955–6959

    CAS  PubMed  Google Scholar 

  • Larsen SH (1994) Genbank entry U16739

  • Lecointre G, Philippe H, Van Le HL, Le Guyader H (1993) Species sampling has a major impact on phylogenetic inference. Mol Phylog Evol 2:205–224

    Google Scholar 

  • Lloyd AT, Sharp PM (1993) Evolution of the recA gene and the molecular phylogeny of bacteria. J Mol Evol 37:399–407

    Google Scholar 

  • Ludwig W, Kirchhof G, Klugbauer N, Weizenegger M, Betzl D, Ehrmann M, Hertel C, Jilg S, Tatzel R, Zitzelsberger H, Liebl S, Hochberger M, Shah J, Lane D, Wallnöfer PR, Shleifer KH (1992) Complete 23S ribosomal RNA sequences of gram-positive bacteria with a low DNA G plus C content. Syst Appl Microbiol 15:487–501

    Google Scholar 

  • Ludwig W, Neumaier J, Klugbauer N, Brockmann E, Roller C, Jilg S, Reetz K, Schachtner I, Ludvigsen A, Bachleitner M, Fischer U, Schleifer KH (1994) Phylogenetic relationships of bacteria based on comparative sequence analysis of elongation factor TU and ATP-synthase beta-subunit genes. Antonie Van Leeuwenhoek 64: 285–305

    Google Scholar 

  • Lon J, Burns G, Sokatch JR (1993) Construction of chromosomal recA mutants of Pseudomonas putida PpG2. Gene 136:263–266

    Google Scholar 

  • Maddison WP, Maddison DR (1992) MacClade version 3. Sinauer Associates, Sunderland, MA

    Google Scholar 

  • Maidak BL, Larsen N, McCaughey MJ, Overbeck R, Olsen GJ, Fogel K, Blandy J, Woese CR (1994) The ribosomal database project. Nucleic Acids Res 22:3485–3487

    Google Scholar 

  • Margraf RL, Roca AI, Cox MM (1995) The deduced Vibrio cholerae RecA amino acid sequence. Gene 152:135–136

    Google Scholar 

  • Martin B, Ruellan JM, Angulo JF, Devoret R, Claverys JP (1992) Identification of the recA gene of Streptococcus pneumoniae. Nucleic Acids Res 20:6412

    Google Scholar 

  • Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like ribosomal RNA-coding regions. Gene 71:491–500

    Google Scholar 

  • Michiels J, Vande Broek A, Vanderleyden J (1991) Molecular cloning and nucleotide sequence of the Rhizobium phaseoli recA gene. Mol Gen Genet 228:486–490

    Google Scholar 

  • Miyamoto MM, Fitch WM (1995) Testing species phylogenies and phylogenetic methods with congruence. Syst Biol 44:64–76

    Google Scholar 

  • Murphy RC, Bryant DA, Porter RD, de Marsac NT (1987) Molecular cloning and characterization of the recA gene from the cyanobacterium Synechococcus sp. strain PCC 7002. J Bacteriol 169:2739–2747

    Google Scholar 

  • Murphy RC, Gasparich GE, Bryant DA, Porter RD (1990) 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 172: 967–976

    Google Scholar 

  • Nakazawa T, Kimoto M, Abe M (1990) Cloning, sequencing, and transcriptional analysis of the recA gene of Pseudomonas cepacia. Gene 94:83–88

    Google Scholar 

  • Nomura M, Morgan EA, Jaskunas S (1977) Genetics of bacterial ribosomes. Anna Rev Genet 11:297–347

    Google Scholar 

  • Nussbaumer B, Wohlleben W (1994) Identification, isolation and sequencing of the recA gene of Streptomyces lividans TK24. FEMS Microbiol Lett 118:57–63

    Google Scholar 

  • Ogawa T, Yu X, Shinohara A, Egelman EH (1993) Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science 259: 1896–1899

    Google Scholar 

  • Olsen GJ (1988) Phylogenefc analysis using ribosomal RNA. Methods Enzymol 164:793–812

    Google Scholar 

  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a rRNA approach. Annu Rev Microbiol 40:337–365

    Google Scholar 

  • Olsen GJ, Woese CR, Overbeck R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1–6

    Google Scholar 

  • Owttrim GW, Coleman JR (1989) Regulation of expression and nucleotide sequence of the Anabaena variabilis recA gene. J Bacteriol 171:5713–5719

    Google Scholar 

  • Pace NR, Olsen GJ, Woese CR (1986) Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45:325–326

    Google Scholar 

  • Pitulle C, Yang Y, Marchiani M, Moore ERB, Siefert JL, Aragno M, Jurtshuk PJ, Fox GE (1994) Phylogenetic position of the genus Hydrogenobacter. Int J Syst Bacteriol 44:620–626

    Google Scholar 

  • Quivey RG Jr, Faustoferri RC (1992) In vivo inactivation of the Streptococcus mutans recA gene mediated by PCR amplification and cloning of a recA DNA fragment. Gene 116:35–42

    Google Scholar 

  • Rainey FA, Toalster R, Stackebrandt E (1993) Desulfurella acetivorans a thermophilic, acetate-oxidizing, and sulfur-reducing organism, represents a distinct lineage within the Proteobacteria. Syst Appl Microbiol 16:373–379.

    Google Scholar 

  • Ramesar RS, Abratt V, Woods DR, Rawlings DE (1989) Nucleotide sequence and expression of a cloned Thiobacillus ferrooxidans recA gene in Escherichia coli. Gene 78:1–8

    Google Scholar 

  • Rappold CSJ, Klingmueller W (1993) Genbank entry P33037

  • Reusing SA, Maier UG (1994) Phylogenetic analysis of the stress-70 protein family. J Mol Evol 39:80–86

    Google Scholar 

  • Ridder R, Marquardt R, Esser K (1991) Molecular cloning and characterization of the recA gene of Methylomonas clara and construction of recA deficient mutant. Appl Microbiol Biotechnol 35:23–31

    Google Scholar 

  • Roca AI, Cox MM (1990) The RecA protein: structure and function. Crit Rev Biochem Mol Biol 25:415–456

    Google Scholar 

  • Rothschild LJ, Ragan MA, Coleman AW, Heywood P, Gerbi SA (1986) Are rRNA sequences the Rosetta stone of phylogenefcs. Cell 47:640

    Google Scholar 

  • Saitou N, Nei M (1987) The neighbor joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sancar A, Stachelek C, Konigsberg W, Rupp WD (1980) Sequences of the recA gene and protein. Proc Natl Acad Sci USA 77:2611–2615

    Google Scholar 

  • Sano Y, Kageyama M (1987) The sequence and function of the recA gene and its protein in Pseudomonas aeruginosa PAO. Mol Gen Genet 208:412–419

    Google Scholar 

  • Schoeniger M, Von Haeseler A (1994) A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylog Evol 3: 240–247

    Google Scholar 

  • Selbitschka W, Arnold W, Priefer UB, Rottschafer T, Schmidt M, Simon R, Puhler A (1991) Characterization of recA genes and recA mutants of Rhizobium meliloti and Rhizobium leguminosarum biovar viciae. Mol Gen Genet 229:86–95

    Google Scholar 

  • Sievers M, Ludwig W, Teuber M (1994) Phylogenetic positioning of Acetobacter, Gluconobacter, Rhodopila and Acidiphilium species as a branch of acidophilic bacteria in the alpha-subclass of proteobacteria based on 16S ribosomal DNA sequences. Syst Appl Microbiol 17:189–196

    Google Scholar 

  • Smith SW (1991) Genetic data environment, version 2.2a. Harvard Genome Laboratory, Cambridge, MA

    Google Scholar 

  • Smith SW, Overbeck R, Woese CR, Gilbert W, Gillevet PM (1994) The genetic data environment: an expandable GUI for multiple sequence analysis. CABIOS 10:671–675

    CAS  PubMed  Google Scholar 

  • Sogin ML (1989) Evolution of eukaryotic microorganisms and their small subunit ribosomal RNA. Am Zool 29:487–500

    Google Scholar 

  • Stackebrandt E, Murray RGE, Traper HG (1988) Proteobacteria classis nov., a name for the phylogenetic taxon that includes ‘purple bacteria and their relatives.’ Int J Syst Bacteriol 38:321–325

    Google Scholar 

  • Story RM, Bishop DK, Kleckner N, Steitz TA (1993) Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast. Science 259:1892–1896

    Google Scholar 

  • Story RM, Steitz TA (1992) Structure of the RecA protein-ADP complex. Nature 355:374–376

    Google Scholar 

  • Story RM, Weber IT, Steitz TA (1992) The structure of the E. coli RecA protein monomer and polymer. Nature 355:318–325

    Google Scholar 

  • Stranathan MC, Bayles KW, Yasbin RE (1990) The nucleotide sequence of the recE+ gene of Bacillus subtilis. Nucleic Acids Res 18:4249

    Google Scholar 

  • Stroeher UH, Lech AJ, Manning PA (1994) Gene sequence of recA+ and construction of recA mutants of Vibrio cholerae. Mol Gen Genet 244:295–302

    Google Scholar 

  • Swofford D (1991) Phylogenetic analysis using parsimony (PAUP), version 3.0d. Illinois Natural History Survey, Champaign, IL

  • Tatum FM, Morfitt DC, Halling SM (1993) Construction of a Brucella abortus recA mutant and its survival in mice. Microbiol Pathogen 14:177–185

    Google Scholar 

  • Tayama K, Fukaya M, Takemura H, Okumura H, Kawamura Y, Horinouchi S, Beppu T (1993) Cloning and sequencing the recA+ genes of Acetobacter polyoxogenes and Acetobacter aceti: construction of recA- mutants of by transformation-mediated gene replacement. Gene 127:47–52

    Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    CAS  PubMed  Google Scholar 

  • Tolmasky ME, Gammie AE, Crosa JH (1992) Characterization of the recA gene of Vibrio anguillarum. Gene 110:41–48

    Google Scholar 

  • Van De Peer Y, Neefs JM, De Rijk P, De Vos P, De Wachter R (1994) About the order of divergence of the major bacterial taxa during evolution. Syst Appl Microbiol 17:32–38

    Google Scholar 

  • Vawter L, Brown WM (1993) Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134:597–608

    Google Scholar 

  • Venkatesh TV, Das HK (1992) The Azotobacter vinelandii recA gene: sequence analysis and regulation of expression. Gene 113:47–53

    Google Scholar 

  • Viale AM, Arakaki AK, Soncini FC, Ferreyra RG (1994) Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons. Int J Syst Bacteriol 44:527–533

    Google Scholar 

  • Wardhan H, McPherson MJ, Harris CA, Sharma E, Sastry GR (1992) Molecular analysis of the recA gene of Agrobacterium tumefaciens C58. Gene 121:133–136

    Google Scholar 

  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    CAS  PubMed  Google Scholar 

  • Weisburg WG, Dobson ME, Samuel JE, Dasch GA, Mallavia LP, Baca O, Mendelco L, Sechrest JE, Weiss E,Woese CR (1989a) Phylogenetic diversity of the Rickettsiae. J Bacteriol 171:4202–4206

    Google Scholar 

  • Weisburg WG, Giovannoni SG, Woese CR (1989b) The Deinococcus Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol 11:128–134

    Google Scholar 

  • Weisburg WG, Tully JG, Rose DL, Petzel JP, Oyaizu H, Yang D, Mandelco L, Sechrest J, Lawrence TG (1989c) A phylogenetic analysis of the mycoplasmas: basis for their classification. J Bacteriol 171:6455–6467

    Google Scholar 

  • Wetmur JG, Wong DM, Ortiz B, Tong J, Reichert F, Gelfand DH (1994) Cloning, sequencing, and expression of RecA proteins from three distantly related thermophilic eubacteria. J Biol Chem 269: 25928–25935

    Google Scholar 

  • Woese CR (1991) The use of ribosomal RNA in reconstructing relationships among bacteria, In: Selander RK, Clark AG, Whittam TS (eds) Evolution at the molecular level. Sinauer Associates, Sunderland, MA, pp 1–24

    Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    CAS  PubMed  Google Scholar 

  • Woese CR, Achenbach L, Rouviere P, Mandelco L (1991) Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in the light of certain coposition-induced artifacts. Syst Appl Microbiol 14:364–371

    Google Scholar 

  • Yao W, Vining LC (1994) Cloning and sequence analysis of a recA-like gene from Streptomyces venezuelae ISP5230. FEMS Microbiol Lett 118:51–56

    Google Scholar 

  • Zhang D, Fan H, McClarty G, Brunham RC (1994) Genbank entry U15281

  • Zhao X, Dreyfus LA (1990) Expression and nucleotide sequence analysis of the Legionella pneumophila recA gene. FEMS Microbial Lett 70:227–232

    Google Scholar 

  • Zhao XJ, McEntee K (1990) DNA sequence analysis of the recA genes from Proteus vulgaris, Erwinia carotovora, Shigella fexneri and Escherichia coli B/r. Mol Gen Genet 222:369–376

    Google Scholar 

  • Zulty JJ, Barcak GJ (1993) Structural organization, nucleotide sequence, and regulation of the Haemophilus infuenzae rec-1+ gene. J Bacteriol 175:7269–7281

    Google Scholar 

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    Jonathan A. Eisen

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Eisen, J.A. 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 41, 1105–1123 (1995). https://doi.org/10.1007/BF00173192

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