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الانزيمات
Mechanisms of Gene Transfer in Bacteria
المؤلف:
Stefan Riedel, Jeffery A. Hobden, Steve Miller, Stephen A. Morse, Timothy A. Mietzner, Barbara Detrick, Thomas G. Mitchell, Judy A. Sakanari, Peter Hotez, Rojelio Mejia
المصدر:
Jawetz, Melnick, & Adelberg’s Medical Microbiology
الجزء والصفحة:
28e , p111-114
2025-07-07
21
The DNA composition of microorganisms is remarkably fluid. DNA can be transferred from one organism to another, and that DNA can be stably incorporated in the recipient, permanently changing its genetic composition. This process is called horizontal gene transfer (HGT) to differentiate it from the inheritance of parental genes, a process called vertical inheritance. Three broad mechanisms mediate efficient movement of DNA between cells—conjugation, transduction, and transformation.
Conjugation requires donor cell-to-recipient cell con tact to transfer only one strand of DNA (Figure 1). The recipient completes the structure of dsDNA by synthesizing the strand that complements the strand acquired from the donor. In transduction, donor DNA is carried by a phage coat and is transferred into the recipient by the mechanism used for phage infection. Transformation, the direct uptake of “naked” donor DNA by the recipient cell, may be natural or forced. Forced transformation is induced in the laboratory, where, after treatment with high salt and temperature shock, many bacteria are rendered competent for the uptake of extra cellular plasmids. The capacity to force bacteria to incorporate extracellular plasmids by transformation is fundamental to genetic engineering.
Fig1. Mechanism of DNA transfer during conjugation. The donor cell produces a pilus, which is encoded by the plasmid, and contacts a potential recipient cell that does not contain the plasmid. Retraction of the pilus brings the cells into close contact, and a pore forms in the adjoining cell membranes. Formation of the mating pair signals the plasmid to begin transfer from a single stranded nick at oriT. The nick is made by plasmid-encoded tra functions. The 5′ end of a single strand of the plasmid is transferred to the recipient through the pore. During transfer, the plasmid in the donor is replicated, its DNA synthesis being primed by the 3′ OH of the oriT nick. Replication of the single strand in the recipient proceeds by a different mechanism with RNA primers. Both cells now contain double-stranded plasmids, and the mating pair separates. (Reproduced with permission from Snyder L, Champness W: Molecular Genetics of Bacteria, 2nd ed. Washington, DC: ASM Press, 2003. © 2003 American Society for Microbiology.)
A. Conjugation
Plasmids are most frequently transferred by conjugation. Genetic functions required for transfer are encoded by the tra genes, which are carried by self-transmissible plasmids. Some self-transmissible plasmids can mobilize other plasmids or portions of the chromosome for transfer. In some cases, mobilization is achieved because the tra genes provide functions necessary for transfer of an otherwise nontransmissible plasmid (Figures 2 and 3). In other cases, the self-transmissible plasmid integrates with the DNA of another replicon and, as an extension of itself, carries a strand of this DNA into a recipient cell.
Fig2. Mechanism of plasmid mobilization. The donor cell carries two plasmids, a self-transmissible plasmid, F, which encodes the tra functions that promote cell contact and plasmid transfer, and a mobilizable plasmid. The mob functions encoded by the mobilizable plasmid make a single-stranded nick at oriT in the mob region. Transfer and replication of the mobilizable plasmid then occur. The self-transmissible plasmid may also transfer. (Reproduced with permission from Snyder L, Champness W: Molecular Genetics of Bacteria, 2nd ed. Washington, DC: ASM Press, 2003. © 2003 American Society for Microbiology.)
Fig3. A: A male and a female cell joined by an F pilus (sex pilus). B: Mating pairs of E. coli cells. Hfr cells are elongated. C: Electron micrograph of a thin section of a mating pair. The cell walls of the mating partners are in intimate contact in the “bridge” area. (Photograph [A]: Courtesy of Carnahan J and Brinton C. Photographs [B] and [C] reproduced with permission from Gross JD, Caro LG: DNA transfer in bacterial conjugation. J Mol Biol 1966;16:269.)
Genetic analysis of E. coli was greatly advanced by elucidation of fertility factors carried on a plasmid designated F+. This plasmid confers certain donor characteristics upon cells; these characteristics include a sex pilus, an extracellular multimeric protein extrusion that attaches donor cells to recipient organisms lacking the fertility factor. A bridge between the cells allows a strand of the F+ plasmid, synthesized by the donor, to pass into the recipient, where the complementary strand of DNA is formed. The F+ fertility factor can integrate into numerous loci in the chromosome of donor cells. The integrated fertility factor creates high-frequency recombination (Hfr) donors from which chromosomal DNA is transferred (from the site of insertion) in a direction determined by the orientation of insertion (Figure 4).
Fig4. Transfer of chromosomal DNA by an integrated plasmid. Formation of mating pairs, nicking of the F oriT sequence, and transfer of the 5′ end of a single strand of F DNA proceed as in transfer of the F plasmid. Transfer of a covalently linked chromosomal DNA will also occur as long as the mating pair is stable. Complete chromosome transfer rarely occurs, and so the recipient cell remains F−, even after mating. Replication in the donor usually accompanies DNA transfer. Some replication of the transferred single strand may also occur. Once in the recipient cell, the transferred DNA may recombine with homologous sequences in the recipient chromosome. (Reproduced with permission from Snyder L, Champness W: Molecular Genetics of Bacteria, 2nd ed. Washington, DC: ASM Press, 2003. © 2003 American Society for Microbiology.)
The rate of chromosomal transfer from Hfr cells is constant, and compilation of results from many conjugation experiments has allowed preparation of an E. coli genetic map in which distances between loci are measured in number of minutes required for transfer in conjugation. A similar map has been constructed for the related coliform (E. coli like) bacterium Salmonella typhimurium, and comparison of the two maps shows related patterns of genomic organization. This type of mapping has now been replaced by high throughput genomic DNA sequencing.
Integration of chromosomal DNA into a conjugal plasmid can produce a recombinant replicon—an F (fertility) prime, or R (resistance) prime, depending on the plasmid—in which the integrated chromosomal DNA can be replicated on the plasmid independently of the chromosome. This occurs when the integrated plasmid (eg, F) is bracketed by two copies of an IS element. Bacteria carrying gene copies, a full set on the chromosome and a partial set on a prime, are partial dip loids, or merodiploids, and are useful for complementation studies. A wild-type gene frequently complements its mutant homologue, and selection for the wild-type phenotype can allow maintenance of merodiploids in the laboratory. Such strains can allow analysis of interactions between different alleles, genetic variants of the same gene. Merodiploids frequently are genetically unstable because recombination between the plasmid and the homologous chromosome can result in loss or exchange of mutant or wild-type alleles. This problem can frequently be circumvented by maintenance of merodiploids in a genetic background in which recA, a gene required for recombination between homologous segments of DNA, has been inactivated.
Homologous genes from different organisms may have diverged to an extent that prevents homologous recombination between them but does not alter the capacity of one gene to complement the missing activity of another. For example, the genetic origin of an enzyme required for amino acid biosynthesis is unlikely to influence catalytic activity in the cytoplasm of a biologically distant host. A merodiploid carrying a gene for such an enzyme would also carry flanking genes derived from the donor organism. Therefore, conventional microbial genetics, based on selection of prime plasmids, can be used to isolate genes from fastidious (difficult to grow) organisms in easily cultivatable organism such as E. coli or Pseudomonas aeruginosa.
B. Transduction
Transduction is phage-mediated genetic recombination in bacteria. In simplest terms, a transducing particle (phage) is generally regarded as bacterial nucleic acid in a phage-encoded protein coat. In some instances, a lytic-phage population may contain some particles in which the phage coat surrounds DNA derived from the bacterium rather than from the phage. Such populations have been used to transfer genes from one bacterium to another. Temperate phages are preferred vehicles for gene transfer because infection of recipient bacteria under conditions that favor lysogeny minimizes cell lysis and thus favors survival of recombinant strains. Indeed, a recipient bacterium carrying an appropriate prophage may form a repressor that renders the cell immune to lytic super infection; such cells may still take up bacterial DNA from transducing particles. Transducing mixtures carrying donor DNA can be prepared under conditions that favor the lytic phage cycle.
The size of DNA in transducing particles is usually no more than a few percent of the bacterial chromosome, and therefore cotransduction—transfer of more than one gene at a time—is limited to linked bacterial genes. The speed and capacity by which phages recombine and replicate has made them central subjects for study of bacterial genetics and genetic engineering.
In nature, pathogenicity islands are often transported by phages. For example, two phages transport pathogenicity islands responsible for converting a benign form of V. cholerae into the pathogenic form responsible for epidemic cholera . These phages encode genes for cholera toxin (responsible for symptoms) and toxin co-regulated pili (responsible for attachment) that in combination substantially increase the virulence of V. cholerae .
C. Transformation
As described above, forced transformation is typically thought of as a laboratory phenomenon. However, it is now clear that low-frequency HGT has been responsible for common mechanisms of antibiotic resistance among diverse species of bacteria. This is not surprising given the complex diversity and density of the intestinal flora or the biofilms that form on our teeth overnight. Couple this with the therapeutic administration of antibiotics that select for resistant organisms and a “perfect storm” exists for the spread of genetic material across species boundaries.
In contrast to forced transformation (described above), natural competence is unusual among bacteria. Direct uptake of donor DNA by recipient bacteria depends on their competence for transformation. Naturally competent transform able bacteria, of medical importance, are found in several genera and include H. influenzae, Neisseria gonorrhoeae, N. meningitidis, and S. pneumoniae. Natural transformation is an active process demanding specific proteins produced by the recipient cell. In addition, specific DNA sequences (uptake sequences) are required for uptake of the DNA. These uptake sequences are species specific, thus restricting genetic exchange to a single species. The DNA that is not incorporated can be degraded and used as a source of nutrients to support microbial growth. It is clear that genetic transformation is a major force in microbial evolution.
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