transformation (genetics) transformation (genetics) in molecular biology and genetics, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). for transformation to take place, the recipient bacterium must be in a state of competence, which might occur in nature as a time-limited response to environmental conditions such as starvation and cell density, and may also be induced in a laboratory. not to be confused with an unrelated process called malignant transformation which occurs in the progression of cancer. in this image, a gene from one bacterial cell is moved to another bacterial cell. this process of the second bacterial cell taking up new genetic material is called transformation. transformation is one of three processes that lead to horizontal gene transfer, in which exogenous genetic material passes from one bacterium to another, the other two being conjugation (transfer of genetic material between two bacterial cells in direct contact) and transduction (injection of foreign dna by a bacteriophage virus into the host bacterium). in transformation, the genetic material passes through the intervening medium, and uptake is completely dependent on the recipient bacterium. as of 2014 about 80 species of bacteria were known to be capable of transformation, about evenly divided between gram-positive and gram-negative bacteria; the number might be an overestimate since several of the reports are supported by single papers. "transformation" may also be used to describe the insertion of new genetic material into nonbacterial cells, including animal and plant cells; however, because "transformation" has a special meaning in relation to animal cells, indicating progression to a cancerous state, the process is usually called "transfection". history transformation in bacteria was first demonstrated in 1928 by the british bacteriologist frederick griffith. griffith was interested in determining whether injections of heat-killed bacteria could be used to vaccinate mice against pneumonia. however, he discovered that a non-virulent strain of streptococcus pneumoniae could be made virulent after being exposed to heat-killed virulent strains. griffith hypothesized that some "transforming principle" from the heat-killed strain was responsible for making the harmless strain virulent. in 1944 this "transforming principle" was identified as being genetic by oswald avery, colin macleod, and maclyn mccarty. they isolated dna from a virulent strain of s. pneumoniae and using just this dna were able to make a harmless strain virulent. they called this uptake and incorporation of dna by bacteria "transformation" (see avery-macleod-mccarty experiment) the results of avery et al.'s experiments were at first skeptically received by the scientific community and it was not until the development of genetic markers and the discovery of other methods of genetic transfer (conjugation in 1947 and transduction in 1953) by joshua lederberg that avery's experiments were accepted. it was originally thought that escherichia coli, a commonly used laboratory organism, was refractory to transformation. however, in 1970, morton mandel and akiko higa showed that e. coli may be induced to take up dna from bacteriophage λ without the use of helper phage after treatment with calcium chloride solution. two years later in 1972, stanley norman cohen, annie chang and leslie hsu showed that cacl2 treatment is also effective for transformation of plasmid dna. the method of transformation by mandel and higa was later improved upon by douglas hanahan. the discovery of artificially induced competence in e. coli created an efficient and convenient procedure for transforming bacteria which allows for simpler molecular cloning methods in biotechnology and research, and it is now a routinely used laboratory procedure. transformation using electroporation was developed in the late 1980s, increasing the efficiency of in-vitro transformation and increasing the number of bacterial strains that could be transformed. transformation of animal and plant cells was also investigated with the first transgenic mouse being created by injecting a gene for a rat growth hormone into a mouse embryo in 1982. in 1897 a bacterium that caused plant tumors, agrobacterium tumefaciens, was discovered and in the early 1970s the tumor-inducing agent was found to be a dna plasmid called the ti plasmid. by removing the genes in the plasmid that caused the tumor and adding in novel genes, researchers were able to infect plants with a. tumefaciens and let the bacteria insert their chosen dna into the genomes of the plants. not all plant cells are susceptible to infection by a. tumefaciens, so other methods were developed, including electroporation and micro-injection. particle bombardment was made possible with the invention of the biolistic particle delivery system (gene gun) by john sanford in the 1980s. definitions transformation is one of three forms of horizontal gene transfer that occur in nature among bacteria, in which dna encoding for a trait passes from one bacterium to another and is integrated into the recipient genome by homologous recombination; the other two are transduction, carried out by means of a bacteriophage, and conjugation, in which a gene is passed through direct contact between bacteria. in transformation, the genetic material passes through the intervening medium, and uptake is completely dependent on the recipient bacterium. competence refers to a temporary state of being able to take up exogenous dna from the environment; it may be induced in a laboratory. it appears to be an ancient process inherited from a common prokaryotic ancestor that is a beneficial adaptation for promoting recombinational repair of dna damage, especially damage acquired under stressful conditions. natural genetic transformation appears to be an adaptation for repair of dna damage that also generates genetic diversity. transformation has been studied in medically important gram-negative bacteria species such as helicobacter pylori, legionella pneumophila, neisseria meningitidis, neisseria gonorrhoeae, haemophilus influenzae and vibrio cholerae. it has also been studied in gram-negative species found in soil such as pseudomonas stutzeri, acinetobacter baylyi, and gram-negative plant pathogens such as ralstonia solanacearum and xylella fastidiosa. transformation among gram-positive bacteria has been studied in medically important species such as streptococcus pneumoniae, streptococcus mutans, staphylococcus aureus and streptococcus sanguinis and in gram-positive soil bacterium bacillus subtilis. it has also been reported in at least 30 species of pseudomonadota distributed in several different classes. the best studied pseudomonadota with respect to transformation are the medically important human pathogens neisseria gonorrhoeae, haemophilus influenzae, and helicobacter pylori. "transformation" may also be used to describe the insertion of new genetic material into nonbacterial cells, including animal and plant cells; however, because "transformation" has a special meaning in relation to animal cells, indicating progression to a cancerous state, the process is usually called "transfection". natural competence and transformation as of 2014 about 80 species of bacteria were known to be capable of transformation, about evenly divided between gram-positive and gram-negative bacteria; the number might be an overestimate since several of the reports are supported by single papers. 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 type iv pili and type ii secretion system, as well as dna translocase complex at the cytoplasmic membrane. 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 cytoplasmic membrane via dna translocase. 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. 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. 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. 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. 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). the length transferred is likely double stranded dna and is often more than a third of the total chromosome length of 4215 kb. it appears that about 7-9% of the recipient cells take up an entire chromosome. 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. 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. transformation in streptococcus mutans, as well as in many other streptococci, occurs at high cell density and is associated with biofilm formation. competence in b. subtilis is induced toward the end of logarithmic growth, especially under conditions of amino acid limitation. 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. by releasing intact host and plasmid dna, certain bacteriophages are thought to contribute to transformation. 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). in b. subtilis, transformation is increased by uv light, a dna damaging agent. 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 using legionella pneumophila, charpentier et al. 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), bicyclomycin (causes single- and double-strand breaks), and hydroxyurea (induces dna base oxidation). uv light also induced competence in l. pneumophila. charpentier et al. suggested that competence for transformation probably evolved as a dna damage response. 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. 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. and bernstein et al.) 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