Advances in bacterial and phage genetics within the past 50 years have provided the foundation for molecular biology and cloning (discussed in later chapters). Early in this period, gene transfer and recombination were found to take place between different strains of bacteria. In bacteria, however, genetic material is passed in only one direction—for example, in Escherichia coli, from a donor cell (F⁺ or Hfr) to a recipient cell (F⁻). Donor ability is determined by the presence in the cell of a fertility factor (F), a type of plasmid. On occasion, the F factor present in the free state in F⁺ cells can integrate into the E. coli chromosome and form an Hfr cell. When this occurs, a fragment of donor chromosome can transfer into a recipient cell and subsequently recombine with the recipient chromosome. Because the F factor can insert at different places on the host chromosome, early investigators were able to piece the transferred fragments together to show that the E. coli chromosome is a single circle, or ring. Interruption of the transfer at different times has provided geneticists with an unconventional method (interrupted mating) for constructing a linkage map of the single chromosome of E. coli and other similar bacteria, in which the map unit is a unit of time (minutes). In an extension of this technique, the frequency of recombinants between markers known to have entered the recipient can provide a finer-scale map distance.

Several types of plasmids other than F can be found. R plasmids carry antibiotic-resistance alleles, often within a mobile element called a transposon. Rapid plasmid spread causes population-wide resistance to medically important drugs. Derivatives of such natural plasmids have become important cloning vectors, useful for gene isolation and study in all organisms.

Genetic traits can also be transferred from one bacterial cell to another in the form of pieces of DNA taken into the cell from the extracellular environment. This process of transformation in bacterial cells was the first demonstration that DNA is the genetic material. For transformation to occur, DNA must be taken into a recipient cell, and recombination must then take place between a recipient chromosome and the incorporated DNA.

Bacteria can be infected by viruses called bacteriophages. In one method of infection, the phage chromosome may enter the bacterial cell and, by using the bacterial metabolic machinery, produce progeny phages that burst the host bacterium. The new phages can then infect other cells. If two phages of different genotypes infect the same host, recombination between their chromosomes can take place.

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In another mode of infection, lysogeny, the injected phage lies dormant in the bacterial cell. In many cases, this dormant phage (the prophage) incorporates into the host chromosome and replicates with it. Either spontaneously or under appropriate stimulation, the prophage can leave its dormant state and lyse the bacterial host cell.

A phage can carry bacterial genes from a donor to a recipient. In generalized transduction, random host DNA is incorporated alone into the phage head during lysis. In specialized transduction, faulty excision of the prophage from a unique chromosomal locus results in the inclusion of specific host genes as well as phage DNA in the phage head.

Today, a physical map in the form of the complete genome sequence is available for many bacterial species. With the use of this physical genome map, the map position of a mutation of interest can be precisely located. First, appropriate mutations are produced by the insertion of transposons (insertional mutagenesis). Then, the DNA sequence surrounding the inserted transposon is obtained and matched to a sequence in the physical map. This technique provides the locus, the sequence, and possibly the function of the gene of interest.