Editing Genetic transformation (section)

===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>