Chen I, Christie PJ, Dubnau D. The ins and outs of DNA transfer in bacteria. Science. 2005;310(5753):1456–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johnston C, Martin B, Fichant G, Polard P, Claverys JP. Bacterial transformation: distribution, shared mechanisms and divergent control. Nat Rev Microbiol. 2014;12(3):181–96.
Article
CAS
PubMed
Google Scholar
Johnsborg O, Eldholm V, Havarstein LS. Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol. 2007;158(10):767–78.
Article
CAS
PubMed
Google Scholar
Lorenz MG, Wackernagel W. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev. 1994;58(3):563–602.
CAS
PubMed
PubMed Central
Google Scholar
Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol. 2005;3(9):711–21.
Article
CAS
PubMed
Google Scholar
Vos M. Why do bacteria engage in homologous recombination? Trends Microbiol. 2009;17(6):226–32.
Article
CAS
PubMed
Google Scholar
Redfield RJ. Evolution of bacterial transformation - is sex with dead cells ever better than no sex at all. Genetics. 1988;119(1):213–21.
CAS
PubMed
PubMed Central
Google Scholar
Redfield RJ. Do bacteria have sex? Nat Rev Genet. 2001;2(8):634–9.
Article
CAS
PubMed
Google Scholar
Michod RE, Wojciechowski MF, Hoelzer MA. DNA-repair and the evolution of transformation in the Bacterium Bacillus-Subtilis. Genetics. 1988;118(1):31–9.
CAS
PubMed
PubMed Central
Google Scholar
Borgeaud S, Metzger LC, Scrignari T, Blokesch M. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science. 2015;347(6217):63–7.
Article
CAS
PubMed
Google Scholar
Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet. 2013;45(6):656–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Levin BR, Cornejo OE. The population and evolutionary dynamics of homologous gene recombination in bacterial populations. PLoS Genet. 2009;5(8):e1000601.
Article
PubMed
PubMed Central
Google Scholar
Moradigaravand D, Engelstadter J. The evolution of natural competence: disentangling costs and benefits of sex in bacteria. Am Nat. 2013;182(4):E112–26.
Article
PubMed
Google Scholar
Ambur OH, Engelstadter J, Johnsen PJ, Miller EL, Rozen DE. Steady at the wheel: conservative sex and the benefits of bacterial transformation. Phil Trans R Soc B. 2016;371:20150528.
Mell JC, Redfield RJ. Natural competence and the evolution of DNA uptake specificity. J Bacteriol. 2014;196(8):1471–83.
Article
PubMed
PubMed Central
Google Scholar
Treangen TJ, Ambur OH, Tonjum T, Rocha EP. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol. 2008;9(3):R60.
Article
PubMed
PubMed Central
Google Scholar
Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD, Fraser C. Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict. Plos Biol. 2016;14(3):e1002394.
Article
PubMed
PubMed Central
Google Scholar
Baltrus DA, Guillemin K, Phillips PC. Natural transformation increases the rate of adaptation in the human pathogen helicobacter pylori. Evolution. 2008;62(1):39–49.
PubMed
Google Scholar
Perron GG, Lee AE, Wang Y, Huang WE, Barraclough TG. Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations. Proc Biol Sci. 2012;279(1733):1477–84.
Article
PubMed
Google Scholar
Bacher JM, Metzgar D, de Crecy-Lagard V. Rapid evolution of diminished transformability in Acinetobacter baylyi. J Bacteriol. 2006;188(24):8534–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Engelmoer DJ, Donaldson I, Rozen DE. Conservative sex and the benefits of transformation in Streptococcus pneumoniae. PLoS Pathog. 2013;9(11):e1003758.
Article
PubMed
PubMed Central
Google Scholar
Utnes AL, Sorum V, Hulter N, Primicerio R, Hegstad J, Kloos J, Nielsen KM, Johnsen PJ. Growth phase-specific evolutionary benefits of natural transformation in Acinetobacter baylyi. ISME J. 2015;9(10):2221–31.
Article
PubMed
PubMed Central
Google Scholar
Sinha S, Mell J, Redfield R. The availability of purine nucleotides regulates natural competence by controlling translation of the competence activator Sxy. Mol Microbiol. 2013;88(6):1106–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stewart GJ, Carlson CA. The biology of natural transformation. Annu Rev Microbiol. 1986;40:211–35.
Article
CAS
PubMed
Google Scholar
Cameron AD, Redfield RJ. Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria. Nucleic Acids Res. 2006;34(20):6001–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wise EM, Alexander SP, Powers M. Adenosine 3′-5′-cyclic monophosphate as a regulator of bacterial transformation. Proc Natl Acad Sci U S A. 1973;70(2):471–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Blokesch M. Chitin colonization, chitin degradation and chitin-induced natural competence of Vibrio cholerae are subject to catabolite repression. Environ Microbiol. 2012;14(8):1898–912.
Article
CAS
PubMed
Google Scholar
Zheng L, Chen Z, Itzek A, Herzberg MC, Kreth J. CcpA regulates biofilm formation and competence in Streptococcus gordonii. Mol Oral Microbiol. 2012;27(2):83–94.
Article
CAS
PubMed
Google Scholar
Antonova ES, Bernardy EE. Hammer Natural competence in Vibrio cholerae is controlled by a nucleoside scavenging response that requires CytR-dependent anti-activation. Mol Microbiol. 2012;86(5):1215–31.
Article
CAS
PubMed
Google Scholar
Bernstein H, Byerly HC, Hopf FA, Michod RE. Origin of sex. J Theor Biol. 1984;110(3):323–51.
Article
CAS
PubMed
Google Scholar
Hoelzer MA, Michod RE. DNA-repair and the evolution of transformation in bacillus-subtilis.3. Sex with damaged DNA. Genetics. 1991;128(2):215–23.
CAS
PubMed
PubMed Central
Google Scholar
Michod RE, Wojciechowski MF. DNA-repair and the evolution of transformation.4. DNA-damage increases transformation. J Evol Biol. 1994;7(2):147–75.
Article
Google Scholar
Wojciechowski MF, Hoelzer MA, Michod RE. DNA-repair and the evolution of transformation in bacillus-subtilis.2. Role of inducible repair. Genetics. 1989;121(3):411–22.
CAS
PubMed
PubMed Central
Google Scholar
Mongold JA. DNA repair and the evolution of transformation in Haemophilus influenzae. Genetics. 1992;132(4):893–8.
CAS
PubMed
PubMed Central
Google Scholar
Redfield RJ. Evolution of natural transformation: testing the DNA repair hypothesis in Bacillus subtilis and Haemophilus influenzae. Genetics. 1993;133(4):755–61.
CAS
PubMed
PubMed Central
Google Scholar
Engelmoer DJP, Rozen DE. Competence increases survival during stress in streptococcus pneumoniae. Evolution. 2011;65(12):3475–85.
Article
PubMed
Google Scholar
Claverys JP, Prudhomme M, Martin B. Induction of competence regulons as a general response to stress in gram-positive bacteria. Annu Rev Microbiol. 2006;60:451–75.
Article
CAS
PubMed
Google Scholar
Prudhomme M, Attaiech L, Sanchez G, Martin B, Claverys JP. Antibiotic stress induces genetic transformability in the human pathogen Streptococcus pneumoniae. Science. 2006;313(5783):89–92.
Article
CAS
PubMed
Google Scholar
Charpentier X, Kay E, Schneider D, Shuman HA. Antibiotics and UV radiation induce competence for natural transformation in Legionella pneumophila. J Bacteriol. 2011;193(5):1114–21.
Article
CAS
PubMed
Google Scholar
Dorer MS, Fero J, Salama NR. DNA damage triggers genetic exchange in Helicobacter pylori. PLoS Pathog. 2010;6(7):e1001026.
Article
PubMed
PubMed Central
Google Scholar
Hare JM, Ferrell JC, Witkowski TA, Grice AN. Prophage induction and differential RecA and UmuDAb transcriptome regulation in the DNA damage responses of acinetobacter baumannii and acinetobacter baylyi. Plos One. 2014;9(4):e93861.
Article
PubMed
PubMed Central
Google Scholar
Rauch PJG, Palmen R, Burds AA, Gregg-Jolly LA, van der Zee JR, Hellingwerf KJ. The expression of the Acinetobacter calcoaceticus recA gene increases in response to DNA damage independently of RecA and of development of competence for natural transformation. Microbiol-Uk. 1996;142:1025–32.
Palmen R, Vosman B, Kok R, van der Zee JR, Hellingwerf KJ. Characterization of transformation-deficient mutants of acinetobacter-calcoaceticus. Mol Microbiol. 1992;6(13):1747–54.
Palmen R, Vosman B, Buijsman P, Breek CK, Hellingwerf KJ. Physiological characterization of natural transformation in Acinetobacter calcoaceticus. J Gen Microbiol. 1993;139(2):295–305.
Article
CAS
PubMed
Google Scholar
Smith HO, Danner DB, Deich RA. Genetic-transformation. Annu Rev Biochem. 1981;50:41–68.
Article
CAS
PubMed
Google Scholar
Frye SA, Nilsen M, Tonjum T, Ambur OH. Dialects of the DNA uptake sequence in Neisseriaceae. PLoS Genet. 2013;9(4):e1003458.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mell JC, Hall IM, Redfield RJ. Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells. Nucleic Acids Res. 2012;40(17):8536–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Provvedi R, Dubnau D. ComEA is a DNA receptor for transformation of competent Bacillus subtilis. Mol Microbiol. 1999;31(1):271–80.
Article
CAS
PubMed
Google Scholar
Mortier-Barriere I, Velten M, Dupaigne P, Mirouze N, Pietrement O, McGovern S, Fichant G, Martin B, Noirot P, Le Cam E, et al. A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Cell. 2007;130(5):824–36.
Article
CAS
PubMed
Google Scholar
Quevillon-Cheruel S, Campo N, Mirouze N, Mortier-Barriere I, Brooks MA, Boudes M, Durand D, Soulet AL, Lisboa J, Noirot P, et al. Structure-function analysis of pneumococcal DprA protein reveals that dimerization is crucial for loading RecA recombinase onto DNA during transformation. Proc Natl Acad Sci U S A. 2012;109(37):E2466–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harms K, Wackernagel W. The RecBCD and SbcCD DNases suppress homology-facilitated illegitimate recombination during natural transformation of Acinetobacter baylyi. Microbiol-Sgm. 2008;154:2437–45.
Article
CAS
Google Scholar
Kickstein E, Harms K, Wackernagel W. Deletions of recBCD or recD influence genetic transformation differently and are lethal together with a recJ deletion in Acinetobacter baylyi. Microbiology. 2007;153:2259–70.
Article
CAS
PubMed
Google Scholar
de Vries J, Heine M, Harms K, Wackernagel W. Spread of recombinant DNA by roots and pollen of transgenic potato plants, identified by highly specific biomonitoring using natural transformation of an Acinetobacter sp. Appl Environ Microbiol. 2003;69(8):4455–62.
Article
PubMed
PubMed Central
Google Scholar
Sambrook J, Fritsch E, Maniatis T. Molecular cloning : a laboratory manual. 2nd ed. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 1989.
Google Scholar
Barbe V, Vallenet D, Fonknechten N, Kreimeyer A, Oztas S, Labarre L, Cruveiller S, Robert C, Duprat S, Wincker P, et al. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res. 2004;32(19):5766–79.
Article
CAS
PubMed
PubMed Central
Google Scholar
Overballe-Petersen S, Harms K, Orlando LA, Mayar JV, Rasmussen S, Dahl TW, Rosing MT, Poole AM, Sicheritz-Ponten T, Brunak S, et al. Bacterial natural transformation by highly fragmented and damaged DNA. Proc Natl Acad Sci U S A. 2013;110(49):19860–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Horton RM, Cai ZL, Ho SN, Pease LR. Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques. 1990;8(5):528–35.
CAS
PubMed
Google Scholar
Harms K, Schon V, Kickstein E, Wackernagel W. 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. 2007;64(3):691–702.
Article
CAS
PubMed
Google Scholar
Orren DK, Sancar A. The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC subunits in the incision complex. Proc Natl Acad Sci U S A. 1989;86(14):5237–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kok RG, Young DM, Ornston LN. Phenotypic expression of PCR-Generated random mutations in a Pseudomonas putida gene after its introduction into an Acinetobacter chromosome by natural transformation. Appl Environ Microb. 1999;65(4):1675–80.
CAS
Google Scholar
Crawley MJ. Statistical computing. An introduction to data analysis using S-plus. 1st ed. Chichester: Wiley; 2002.
Google Scholar
R core team. R: A language and environment for statistical computing. 321st ed. Vienna: R Foundation for Statistical Computing; 2015.
Google Scholar
Courcelle CT, Chow KH, Casey A, Courcelle J. Nascent DNA processing by RecJ favors lesion repair over translesion synthesis at arrested replication forks in Escherichia coli. Proc Natl Acad Sci U S A. 2006;103(24):9154–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ray JL, Harms K, Wikmark OG, Starikova I, Johnsen PJ, Nielsen KM. Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome. Genetics. 2009;182(4):1165–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van Houten B. Nucleotide excision repair in Escherichia coli. Microbiol Rev. 1990;54(1):18–51.
PubMed
PubMed Central
Google Scholar
Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev. 1994;58(3):401–65.
CAS
PubMed
PubMed Central
Google Scholar
Kuzminov A. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. MMBR. 1999;63(4):751–813.
CAS
PubMed
PubMed Central
Google Scholar
Morimatsu K, Kowalczykowski SC. RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair. Mol Cell. 2003;11(5):1337–47.
Article
CAS
PubMed
Google Scholar
Dillingham MS, Kowalczykowski SC. RecBCD enzyme and the repair of double-stranded DNA breaks. MMBR. 2008;72(4):642–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carrasco B, Fernandez S, Asai K, Ogasawara N, Alonso JC. Effect of the recU suppressors sms and subA on DNA repair and homologous recombination in Bacillus subtilis. Mol Genet Genomics. 2002;266(5):899–906.
Article
CAS
PubMed
Google Scholar
Johnston C, Mortier-Barriere I, Granadel C, Polard P, Martin B, Claverys JP. RecFOR is not required for pneumococcal transformation but together with XerS for resolution of chromosome dimers frequently formed in the process. PLoS Genet. 2015;11(1):e1004934.
Article
PubMed
PubMed Central
Google Scholar
Gupta R, Shuman S, Glickman MS. RecF and recr play critical roles in the homologous recombination and single-strand annealing pathways of mycobacteria. J Bacteriol. 2015;197(19):3121–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang G, Lo LF, Maier RJ. The RecRO pathway of DNA recombinational repair in Helicobacter pylori and its role in bacterial survival in the host. DNA Repair (Amst). 2011;10(4):373–9.
Article
Google Scholar
Sakai A, Cox MM. RecFOR and RecOR as distinct reca loading pathways. J Biol Chem. 2009;284(5):3264–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bakkali M. Could DNA, uptake be a side effect of bacterial adhesion and twitching motility? Arch Microbiol. 2013;195(4):279–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bonura T, Smith KC. Enzymatic production of deoxyribonucleic acid double-strand breaks after ultraviolet irradiation of Escherichia coli K-12. J Bacteriol. 1975;121(2):511–7.
CAS
PubMed
PubMed Central
Google Scholar
Redfield RJ. Genes for breakfast: the have-your-cake-and-eat-it-too of bacterial transformation. J Hered. 1993;84(5):400–4.
Article
CAS
PubMed
Google Scholar