In prokaryotes, homologous recombination is essential for the repair of genomic DNA damage and for the integration of DNA taken up during horizontal gene transfer. In Escherichia coli, the exonucleases RecJ (specific for 5′ single-stranded DNA) and RecBCD (degrades duplex DNA) play important roles in recombination and recombinational double-strand break (DSB) repair by the RecF and RecBCD pathways, respectively. The cloned recJ of Acinetobacter baylyi partially complemented an E. coli recJ mutant, suggesting functional similarity of the enzymes. A ΔrecJ mutant of A. baylyi was only slightly altered in transformability and was not affected in UV survival. In contrast, a ΔrecBCD mutant was UV-sensitive, and had a low viability and altered transformation. Compared to wild-type, transformation with large chromosomal DNA fragments was decreased about 5-fold, while transformation with 1.5 kbp DNA fragments was increased 3.3- to 7-fold. A ΔrecD mutation did not affect transformation, viability or UV resistance. However, double mutants recJ recBCD and recJ recD were non-viable, suggesting that the RecJ DNase or the RecBCD DNase (presumably absent in recD) becomes essential for the recombinational repair of spontaneously inactivated replication forks if the other DNase is absent. A model of recombination during genetic transformation is discussed in which the two ends of the single-stranded donor DNA present in the cytoplasm frequently integrate separately and often with a time difference. If replication runs through that genomic region before both ends of the donor DNA are ligated to recipient DNA, a double-strand break (DSB) is formed. In these cases, transformation becomes dependent on DSB repair.
AlonsoJ. C.,
StiegeA. C.,
LüderG.1993; Genetic recombination in Bacillus subtilis 168: effect of recN, recF, recH and addAB mutations on DNA repair and recombination. Mol Gen Genet 239:129–136
AmundsenS. K.,
TaylorA. F.,
ChaudhuryA. M.,
SmithG. R.1986; recD : the gene for an essential third subunit of exonuclease V. Proc Natl Acad Sci U S A 83:5558–5562[CrossRef]
AndersonD. G.,
KowalczykowskiS. C.1997; The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chi-regulated manner. Cell 90:77–86[CrossRef]
AravindL.,
KooninE. V.1998; A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease. Trends Biochem Sci 23:17–19[CrossRef]
BarbeV.,
VallenetD.,
FonknechtenN.,
KreimeyerA.,
OztasS.,
LabarreL.,
CruveillerS.,
RobertC.,
DupratS.other authors2004; Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res 32:5766–5779[CrossRef]
BiekD. P.,
CohenS. N.1986; Identification and characterization of recD , a gene affecting plasmid maintenance and recombination in Escherichia coli. J Bacteriol 167:594–603
BruandC.,
FaracheM.,
McGovernS.,
EhrlichS. D.,
PolardP.2001; DnaB, DnaD and DnaI proteins are components of the Bacillus subtilis replication restart primosome. Mol Microbiol 42:245–255
CampbellE. A.,
ChoiS. Y.,
MasureH. R.1998; A competence regulon in Streptococcus pneumoniae revealed by genomic analysis. Mol Microbiol 27:929–939[CrossRef]
ChurchillJ. J.,
AndersonD. G.,
KowalczykowskiS. C.1999; The RecBC enzyme loads RecA protein onto ssDNA asymmetrically and independently of chi, resulting in constitutive recombination activation. Genes Dev 13:901–911[CrossRef]
ClarkA. J.,
LowK. B.1988; Pathways and systems of homologous recombination in Escherichia coli
. In The Recombination of Genetic Material pp 155–215 Edited by
LowK. B.
San Diego: Academic Press;
CourcelleJ.,
HanawaltP. C.1999; RecQ and RecJ process blocked replication forks prior to the resumption of replication in UV-irradiated Escherichia coli. Mol Gen Genet 262:543–551[CrossRef]
de BoerH. A.,
ConstockL. J.,
VasseM.1983; The tac promoter: a functional hybrid derived from the trp and lac promoters. Proc Natl Acad Sci U S A 80:21–25[CrossRef]
de VriesJ.,
WackernagelW.1998; Detection of nptII (kanamycin resistance) genes in genomes of transgenic plants by marker rescue transformation. Mol Gen Genet 257:606–613[CrossRef]
de VriesJ.,
WackernagelW.2002; Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proc Natl Acad Sci U S A 99:2094–2099[CrossRef]
de VriesJ.,
HeineM.,
HarmsK.,
WackernagelW.2003; Spread of recombinant DNA by roots and pollen of transgenic potato plants, identified by highly specific biomonitoring using natural transformation of Acinetobacter sp. Appl Environ Microbiol 69:4455–4462[CrossRef]
de VriesJ.,
HerzfeldT.,
WackernagelW.2004; Transfer of plastid DNA from tobacco to the soil bacterium Acinetobacter sp. by natural transformation. Mol Microbiol 53:323–334[CrossRef]
DermicD.2006; Functions of multiple exonucleases are essential for cell viability, DNA repair and homologous recombination in recD mutants of Escherichia coli. Genetics 172:2057–2069
Friedman-OhanaR.,
CohenA.1998; Heteroduplex joint formation in Escherichia coli recombination is initiated by pairing of a 3′-ending strand. Proc Natl Acad Sci U S A 95:6909–6914[CrossRef]
GarzónA.,
BeuzónC. R.,
MahanM. J.,
CasadesúsJ.1996; recB recJ mutants of Salmonella typhimurium are deficient in transductional recombination, DNA repair and plasmid maintenance. Mol Gen Genet 250:570–580
GraupnerS.,
WackernagelW.2000; A broad-host-range expression vector series including a P ta c test plasmid and its application in the expression of the dod gene of Serratia marcescens (coding for ribulose-5-phosphate 3-epimerase) in Pseudomonas stutzeri. Biomol Eng 17:11–16[CrossRef]
HaijemaB. J.,
NobackM.,
HesselingA.,
KooistraJ.,
VenemaG.,
MeimaR.1996; Replacement of the lysine residue in the consensus ATP-binding sequence of the AddA subunit of AddAB drastically affects chromosomal recombination in transformation and transduction of Bacillus subtilis. Mol Microbiol 21:989–999[CrossRef]
HarmsK.,
KicksteinE.,
WackernagelW.,
SchönV.2007; The RecJ DNase strongly suppresses genomic integration of short but not long foreign DNA fragments by homology-facilitated illegitimate recombination during transformation of Acinetobacter baylyi. Mol Microbiol 64:691–702[CrossRef]
Ivančić-BaćeI.,
Salaj-ŠmicE.,
Brčić-KostićK.2005; Effects of recJ, recQ , and recFOR mutations on recombination in nuclease-deficient recB recD double mutants of Escherichia coli. J Bacteriol 187:1350–1356[CrossRef]
KooistraJ.,
VenemaG.1976; Effect of adenosine 5′-triphosphate-dependent deoxyribonuclease deficiency on properties and transformation of Haemophilus influenzae strains. J Bacteriol 128:549–556
KowalczykowskiS. C.,
DixonD. A.,
EgglestonA. K.,
LauderS. D.,
RehrauerW. M.1994; Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58:401–465
LloydR. G.,
LowK. B.1996; Homologous recombination. In Escherichia coli and Salmonella pp 2236–2255 Edited by
NeidhardtF. C.
Washington, DC: American Society for Microbiology Press;
LloydR. G.,
PortonM. C.,
BuckmanC.1988; Effect of recF, recJ, recN, recO and ruv mutations on ultraviolet survival and genetic recombination in a recD strain of Escherichia coli K12. Mol Gen Genet 212:317–324[CrossRef]
LovettS. T.,
KolodnerR. D.1989; Identification and purification of a single-stranded DNA-specific exonuclease encoded by the recJ gene of Escherichia coli. Proc Natl Acad Sci U S A 86:2627–2631[CrossRef]
McIlwraithM. J.,
WestS. C.2001; The efficiency of strand invasion by Escherichia coli RecA is dependent upon the length and polarity of ssDNA tails. J Mol Biol 305:23–31[CrossRef]
MehrI. J.,
SeifertH. S.1998; Differential roles of homologous recombination pathways in Neisseria gonorrhoeae pilin antigenic variation, DNA transformation and DNA repair. Mol Microbiol 30:697–710[CrossRef]
MeierP.,
WackernagelW.2005; Impact of mutS inactivation on foreign DNA acquisition by natural transformation in Pseudomonas stutzeri. J Bacteriol 187:143–154[CrossRef]
MendoncaV. M.,
KlepinH. D.,
MatsonS. W.1995; DNA helicases in recombination and repair: construction of a Δ uvrD Δ helD Δ recQ mutant deficient in recombination and repair. J Bacteriol 177:1326–1335
MichelB.,
FloresM.-J.,
VigueraE.,
GromponeG.,
SeigneurM.,
BidnenkoV.2001; Rescue of arrested replication forks by homologous recombination. Proc Natl Acad Sci U S A 98:8181–8188[CrossRef]
MichelB.,
GromponeG.,
FloresM.-J.,
BidnenkoV.2004; Multiple pathways process stalled replication forks. Proc Natl Acad Sci U S A 101:12783–12788[CrossRef]
MorrisonD. A.,
MannarelliB.1979; Transformation in pneumococcus: nuclease resistance of deoxyribonucleic acid in eclipse complex. J Bacteriol 140:655–665
PalmenR.,
VosmanB.,
BuijsmanP.,
BreekC. K.,
HellingwerfK. J.1993; Physiological characterization of natural transformation in Acinetobacter calcoaceticus. J Gen Microbiol 139:295–305[CrossRef]
RajmanL. A.,
LovettS. T.2000; A thermostable single-strand DNase from Methanococcus jannaschii related to the RecJ recombination and repair exonuclease from Escherichia coli. J Bacteriol 182:607–612[CrossRef]
RazavyH.,
SzigetyS. K.,
RosenbergS. M.1996; Evidence for both 3′ and 5′ single-strand DNA ends in intermediates in Chi-stimulated recombination in vivo. Genetics 142:333–339
RinkenR.,
ThomsB.,
WackernagelW.1992; Evidence that recBC -dependent degradation of duplex DNA in Escherichia coli recD mutants involves DNA unwinding. J Bacteriol 174:5424–5429
SuteraV. A.,
HanE. S.,
RajmanL. A.,
LovettS. T.1999; Mutational analysis of the RecJ exonuclease of Escherichia coli : identification of phosphoesterase motifs. J Bacteriol 181:6098–6102
te RieleH. P.,
VenemaG.1982; Molecular fate of heterologous bacterial DNA in competent Bacillus subtilis . I. Processing of B. pumilus and B.licheniformis DNA in B. subtilis. Genetics 101:179–188
ThalerD. S.,
SampsonE.,
SiddiqiI.,
RosenbergS. M.,
ThomasonL. C.,
StahlF. W.,
StahlM. M.1989; Recombination of bacteriophage lambda in recD mutants of Escherichia coli. Genome 31:53–67[CrossRef]
ThomsB.,
WackernagelW.1982; UV-induced alleviation of λ restriction in Escherichia coli K-12: kinetics of induction and specificity of this SOS function. Mol Gen Genet 186:111–117[CrossRef]
VovisG. F.1973; Adenosine triphosphate-dependent deoxyribonuclease from Diplococcus pneumoniae : fate of transforming deoxyribonucleic acid in a strain deficient in the enzymatic activity. J Bacteriol 113:718–723
VovisG. F.,
ButtinG.1970; An ATP-dependent deoxyribonuclease from Diplococcus pneumoniae . II. Evidence for its involvement in bacterial recombination. Biochim Biophys Acta 224:42–54[CrossRef]
WilcoxK. W.,
SmithH. O.1975; Isolation and characterization of mutants of Haemophilus influenzae deficient in an adenosine 5′-triphosphate-dependent deoxyribonuclease activity. J Bacteriol 122:443–453
YoungD. M.,
ParkeD.,
OrnstonL. N.2005; Opportunities for genetic investigation afforded by Acinetobacter baylyi , a nutritionally versatile bacterial species that is highly competent for natural transformation. Annu Rev Microbiol 59:519–551[CrossRef]