Editing Genetic transformation (section)

==Natural competence and transformation ==
{{main|Natural competence}}

Naturally competent bacteria carry sets of genes that provide the protein machinery to bring DNA across the cell membrane(s).  The transport of the exogenous DNA into the cells may require proteins that are involved in the assembly of [[Pilus#Type IV pili|type IV pili]] and [[Secretion#Type II secretion system (T2SS)|type II secretion system]], as well as DNA [[translocase]] complex at the cytoplasmic membrane.<ref name=Chen />

Due to the differences in structure of the cell envelope between Gram-positive and Gram-negative bacteria, there are some differences in the mechanisms of DNA uptake in these cells, however most of them share common features that involve related proteins. The DNA first binds to the surface of the competent cells on a DNA receptor, and passes through the [[Cell membrane|cytoplasmic membrane]] via DNA translocase.<ref>{{cite journal | vauthors = Lacks S, Greenberg B, Neuberger M | title = Role of a deoxyribonuclease in the genetic transformation of Diplococcus pneumoniae | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 71 | issue = 6 | pages = 2305–9 | date = June 1974 | pmid = 4152205 | pmc = 388441 | doi = 10.1073/pnas.71.6.2305 | bibcode = 1974PNAS...71.2305L | doi-access = free }}</ref> Only single-stranded DNA may pass through, the other strand being degraded by nucleases in the process. The translocated single-stranded DNA may then be integrated into the bacterial chromosomes by a [[RecA]]-dependent process. In Gram-negative cells, due to the presence of an extra membrane, the DNA requires the presence of a channel formed by secretins on the outer membrane. [[Pilin]] may be required for competence, but its role is uncertain.<ref>{{cite journal | vauthors = Long CD, Tobiason DM, Lazio MP, Kline KA, Seifert HS | title = Low-level pilin expression allows for substantial DNA transformation competence in Neisseria gonorrhoeae | journal = Infection and Immunity | volume = 71 | issue = 11 | pages = 6279–91 | date = November 2003 | pmid = 14573647 | pmc = 219589 | doi = 10.1128/iai.71.11.6279-6291.2003 }}</ref> The uptake of DNA is generally non-sequence specific, although in some species the presence of specific DNA uptake sequences may facilitate efficient DNA uptake.<ref>{{cite journal | vauthors = Sisco KL, Smith HO | title = Sequence-specific DNA uptake in Haemophilus transformation | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 76 | issue = 2 | pages = 972–6 | date = February 1979 | pmid = 311478 | pmc = 383110 | doi = 10.1073/pnas.76.2.972 | bibcode = 1979PNAS...76..972S | doi-access = free }}</ref>

===Natural transformation===

Natural transformation is a bacterial adaptation for DNA transfer that depends on the expression of numerous bacterial genes whose products appear to be responsible for this process.<ref name=Chen>{{cite journal | vauthors = Chen I, Dubnau D | title = DNA uptake during bacterial transformation | journal = Nature Reviews. Microbiology | volume = 2 | issue = 3 | pages = 241–9 | date = March 2004 | pmid = 15083159 | doi = 10.1038/nrmicro844 | s2cid = 205499369 }}</ref><ref name="pmid17997281"/> In general, transformation is a complex, energy-requiring developmental process.  In order for a bacterium to bind, take up and recombine exogenous DNA into its chromosome, it must become competent, that is, enter a special physiological state. Competence development in ''[[Bacillus subtilis]]'' requires expression of about 40 genes.<ref>{{cite journal | vauthors = Solomon JM, Grossman AD | title = Who's competent and when: regulation of natural genetic competence in bacteria | journal = Trends in Genetics | volume = 12 | issue = 4 | pages = 150–5 | date = April 1996 | pmid = 8901420 | doi = 10.1016/0168-9525(96)10014-7 }}</ref> The DNA integrated into the host chromosome is usually (but with rare exceptions) derived from another bacterium of the same species, and is thus homologous to the resident chromosome.

In ''B. subtilis'' the length of the transferred DNA is greater than 1271 kb (more than 1 million bases).<ref>{{cite journal | vauthors = Saito Y, Taguchi H, Akamatsu T | title = Fate of transforming bacterial genome following incorporation into competent cells of Bacillus subtilis: a continuous length of incorporated DNA | journal = Journal of Bioscience and Bioengineering | volume = 101 | issue = 3 | pages = 257–62 | date = March 2006 | pmid = 16716928 | doi = 10.1263/jbb.101.257 }}</ref> The length transferred is likely double stranded DNA and is often more than a third of the total chromosome length of 4215 kb.<ref>{{cite journal | vauthors = Saito Y, Taguchi H, Akamatsu T | title = DNA taken into Bacillus subtilis competent cells by lysed-protoplast transformation is not ssDNA but dsDNA | journal = Journal of Bioscience and Bioengineering | volume = 101 | issue = 4 | pages = 334–9 | date = April 2006 | pmid = 16716942 | doi = 10.1263/jbb.101.334 }}</ref> It appears that about 7-9% of the recipient cells take up an entire chromosome.<ref>{{cite journal | vauthors = Akamatsu T, Taguchi H | title = Incorporation of the whole chromosomal DNA in protoplast lysates into competent cells of Bacillus subtilis | journal = Bioscience, Biotechnology, and Biochemistry | volume = 65 | issue = 4 | pages = 823–9 | date = April 2001 | pmid = 11388459 | doi = 10.1271/bbb.65.823 | s2cid = 30118947 | doi-access = free }}</ref>

The capacity for natural transformation appears to occur in a number of prokaryotes, and thus far 67 prokaryotic species (in seven different phyla) are known to undergo this process.<ref name="pmid17997281"/>

Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth.  Transformation in ''[[Haemophilus influenzae]]'' occurs most efficiently at the end of exponential growth as bacterial growth approaches stationary phase.<ref>{{cite journal | vauthors = Goodgal SH, Herriott RM | title = Studies on transformations of Hemophilus influenzae. I. Competence | journal = The Journal of General Physiology | volume = 44 | issue = 6 | pages = 1201–27 | date = July 1961 | pmid = 13707010 | pmc = 2195138 | doi = 10.1085/jgp.44.6.1201 }}</ref> Transformation in ''[[Streptococcus mutans]]'', as well as in many other streptococci, occurs at high cell density and is associated with [[biofilm]] formation.<ref>{{cite journal | vauthors = Aspiras MB, Ellen RP, Cvitkovitch DG | title = ComX activity of Streptococcus mutans growing in biofilms | journal = FEMS Microbiology Letters | volume = 238 | issue = 1 | pages = 167–74 | date = September 2004 | pmid = 15336418 | doi = 10.1016/j.femsle.2004.07.032 }}</ref> Competence in ''B. subtilis'' is induced toward the end of logarithmic growth, especially under conditions of amino acid limitation.<ref>{{cite journal | vauthors = Anagnostopoulos C, Spizizen J | journal = Journal of Bacteriology | volume = 81 | issue = 5 | pages = 741–6 | date = May 1961 | pmid = 16561900 | pmc = 279084 | title = Requirements for Transformation in Bacillus Subtilis | doi = 10.1128/JB.81.5.741-746.1961 }}</ref> Similarly, in ''[[Micrococcus luteus]]'' (a representative of the less well studied ''[[Actinomycetota]]'' phylum), competence develops during the mid-late exponential growth phase and is also triggered by amino acids starvation.<ref>{{cite journal |last1=Angelov |first1=Angel |last2=Bergen |first2=Paul |last3=Nadler |first3=Florian |last4=Hornburg |first4=Philipp |last5=Lichev |first5=Antoni |last6=Ãœbelacker |first6=Maria |last7=Pachl |first7=Fiona |last8=Kuster |first8=Bernhard |last9=Liebl |first9=Wolfgang |title=Novel Flp pilus biogenesis-dependent natural transformation |journal=Frontiers in Microbiology |date=10 February 2015 |volume=6 |pages=84 |doi=10.3389/fmicb.2015.00084|pmid=25713572 |pmc=4322843 |doi-access=free }}</ref><ref>{{cite journal |last1=Lichev |first1=Antoni |last2=Angelov |first2=Angel |last3=Cucurull |first3=Inigo |last4=Liebl |first4=Wolfgang |title=Amino acids as nutritional factors and (p)ppGpp as an alarmone of the stringent response regulate natural transformation in Micrococcus luteus |journal=Scientific Reports |date=30 July 2019 |volume=9 |issue=1 |pages=11030 |doi=10.1038/s41598-019-47423-x | pmid = 31363120 | pmc = 6667448|bibcode=2019NatSR...911030L }}</ref>

By releasing intact host and plasmid DNA, certain [[bacteriophage]]s are thought to contribute to transformation.<ref name="KeenBliskovsky2017">{{cite journal | vauthors = Keen EC, Bliskovsky VV, Malagon F, Baker JD, Prince JS, Klaus JS, Adhya SL | title = Novel "Superspreader" Bacteriophages Promote Horizontal Gene Transfer by Transformation | journal = mBio | volume = 8 | issue = 1 | pages = e02115–16 | date = January 2017 | pmid = 28096488 | doi = 10.1128/mBio.02115-16 | pmc=5241400}}</ref>

===Transformation, as an adaptation for DNA repair===

Competence is specifically induced by DNA damaging conditions.  For instance, transformation is induced in ''Streptococcus pneumoniae'' by the DNA damaging agents mitomycin C (a DNA cross-linking agent) and fluoroquinolone (a topoisomerase inhibitor that causes double-strand breaks).<ref>{{cite journal | vauthors = Claverys JP, Prudhomme M, Martin B | title = Induction of competence regulons as a general response to stress in gram-positive bacteria | journal = Annual Review of Microbiology | volume = 60 | pages = 451–75 | year = 2006 | pmid = 16771651 | doi = 10.1146/annurev.micro.60.080805.142139 }}</ref>  In ''B. subtilis'', transformation is increased by UV light, a DNA damaging agent.<ref>{{cite journal | vauthors = Michod RE, Wojciechowski MF, Hoelzer MA | title = DNA repair and the evolution of transformation in the bacterium Bacillus subtilis | journal = Genetics | volume = 118 | issue = 1 | pages = 31–9 | date = January 1988 | doi = 10.1093/genetics/118.1.31 | pmid = 8608929 | pmc = 1203263 | url = http://www.genetics.org/cgi/pmidlookup?view=long&pmid=8608929 }}</ref> In ''Helicobacter pylori'', ciprofloxacin, which interacts with DNA gyrase and introduces double-strand breaks, induces expression of competence genes, thus enhancing the frequency of transformation<ref>{{cite journal | vauthors = Dorer MS, Fero J, Salama NR | title = DNA damage triggers genetic exchange in Helicobacter pylori | journal = PLOS Pathogens | volume = 6 | issue = 7 | pages = e1001026 | date = July 2010 | pmid = 20686662 | pmc = 2912397 | doi = 10.1371/journal.ppat.1001026 | editor1-last = Blanke | editor1-first = Steven R | doi-access = free }}</ref> Using ''Legionella pneumophila'', Charpentier et al.<ref name=Charpentier>{{cite journal | vauthors = Charpentier X, Kay E, Schneider D, Shuman HA | title = Antibiotics and UV radiation induce competence for natural transformation in Legionella pneumophila | journal = Journal of Bacteriology | volume = 193 | issue = 5 | pages = 1114–21 | date = March 2011 | pmid = 21169481 | pmc = 3067580 | doi = 10.1128/JB.01146-10 }}</ref> tested 64 toxic molecules to determine which of these induce competence. Of these, only six, all DNA damaging agents, caused strong induction. These DNA damaging agents were mitomycin C (which causes DNA inter-strand crosslinks), norfloxacin, ofloxacin and nalidixic acid (inhibitors of DNA gyrase that cause double-strand breaks<ref>{{cite journal | vauthors = Albertini S, Chételat AA, Miller B, Muster W, Pujadas E, Strobel R, Gocke E | title = Genotoxicity of 17 gyrase- and four mammalian topoisomerase II-poisons in prokaryotic and eukaryotic test systems | journal = Mutagenesis | volume = 10 | issue = 4 | pages = 343–51 | date = July 1995 | pmid = 7476271 | doi = 10.1093/mutage/10.4.343 }}</ref>), bicyclomycin (causes single- and double-strand breaks<ref>{{cite journal | vauthors = Washburn RS, Gottesman ME | title = Transcription termination maintains chromosome integrity | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 2 | pages = 792–7 | date = January 2011 | pmid = 21183718 | pmc = 3021005 | doi = 10.1073/pnas.1009564108 | bibcode = 2011PNAS..108..792W | doi-access = free }}</ref>), and hydroxyurea (induces DNA base oxidation<ref>{{cite journal | vauthors = Sakano K, Oikawa S, Hasegawa K, Kawanishi S | title = Hydroxyurea induces site-specific DNA damage via formation of hydrogen peroxide and nitric oxide | journal = Japanese Journal of Cancer Research | volume = 92 | issue = 11 | pages = 1166–74 | date = November 2001 | pmid = 11714440 | pmc = 5926660 | doi = 10.1111/j.1349-7006.2001.tb02136.x }}</ref>). UV light also induced competence in ''L. pneumophila''. Charpentier et al.<ref name=Charpentier /> suggested that competence for transformation probably evolved as a DNA damage response.  Natural transformation in the extraordinarily radiation resistant bacterium ''[[Deinococcus radiodurans]]'' is associated with the [[DNA repair|repair of DNA damage]] under stressful conditions.<ref>{{cite journal |vauthors=Sharma DK, Soni I, Rajpurohit YS |title=Surviving the storm: exploring the role of natural transformation in nutrition and DNA repair of stressed Deinococcus radiodurans |journal=Appl Environ Microbiol |volume=91 |issue=1 |pages=e0137124 |date=January 2025 |pmid=39651863 |pmc=11784314 |doi=10.1128/aem.01371-24 |url=}}</ref>
 
Logarithmically growing bacteria differ from stationary phase bacteria with respect to the number of genome copies present in the cell, and this has implications for the capability to carry out an important [[DNA repair]] process. During logarithmic growth, two or more copies of any particular region of the chromosome may be present in a bacterial cell, as cell division is not precisely matched with chromosome replication. The process of homologous recombinational repair (HRR) is a key DNA repair process that is especially effective for repairing double-strand damages, such as double-strand breaks. This process depends on a second homologous chromosome in addition to the damaged chromosome. During logarithmic growth, a DNA damage in one chromosome may be repaired by HRR using sequence information from the other homologous chromosome. Once cells approach stationary phase, however, they typically have just one copy of the chromosome, and HRR requires input of homologous template from outside the cell by transformation.<ref name=Bernstein>{{cite book| vauthors = Bernstein H, Bernstein C, Michod RE | year = 2012 | chapter = Chapter 1: DNA repair as the primary adaptive function of sex in bacteria and eukaryotes | title = DNA Repair: New Research | veditors = Kimura S, Shimizu S | publisher =  Nova Sci. Publ., Hauppauge, N.Y. | pages = 1–49 | isbn = 978-1-62100-808-8 | chapter-url =https://www.novapublishers.com/catalog/product_info.php?products_id=31918 }}</ref>
 
To test whether the adaptive function of transformation is repair of DNA damages, a series of experiments were carried out using ''B. subtilis'' irradiated by UV light as the damaging agent (reviewed by Michod et al.<ref>{{cite journal | vauthors = Michod RE, Bernstein H, Nedelcu AM | title = Adaptive value of sex in microbial pathogens | journal = Infection, Genetics and Evolution | volume = 8 | issue = 3 | pages = 267–85 | date = May 2008 | pmid = 18295550 | doi = 10.1016/j.meegid.2008.01.002 | bibcode = 2008InfGE...8..267M | url = http://www.hummingbirds.arizona.edu/Faculty/Michod/Downloads/IGE%20review%20sex.pdf }}</ref> and Bernstein et al.<ref name=Bernstein />) The results of these experiments indicated that transforming DNA acts to repair potentially lethal DNA damages introduced by UV light in the recipient DNA. The particular process responsible for repair was likely HRR.  Transformation in bacteria can be viewed as a primitive sexual process, since it involves interaction of homologous DNA from two individuals to form recombinant DNA that is passed on to succeeding generations. Bacterial transformation in prokaryotes may have been the ancestral process that gave rise to meiotic sexual reproduction in eukaryotes (see [[Evolution of sexual reproduction]]; [[Meiosis]].)