Conjugation is the transfer of DNA from one bacterium to another. The F factor can insert into the E. coli chromosome to result in the formation of Hfr bacteria, which donate the chromosome at high frequency to F- bacteria. The F factor inserts at different points in different Hfr strains. The transfer begins in a portion of the F factor and ends with the rest of the F factor being transferred. Time of entry mapping can be used to order genes for a particular Hfr strain. By combining results from multiple Hfr strains it is possible to construct a detailed map ordering the genes.
The F factor may sometimes carry pieces of bacterial DNA with it if it leaves the E. coli chromosome. Such elements are termed F’ (F prime) plasmids. They allow the production of bacteria which are "partial diploids". Such bacteria are important in some genetic studies in which the dominant or recessive nature of mutations is important in making inferences about their function.
Transduction is similar to transformation in that it involves the introduction of DNA into bacteria. However, viruses are the agent which carry the DNA in transduction. There are two types of transduction. Generalized transduction can involve the transfer of any bacterial sequence. Specialized transduction involves the transfer of specific bacterial sequences near the insertion site of viruses which insert into the bacterial chromosome. Generalized transduction is a rare event which allows the mapping of genes based on the frequency with which they are transferred together. Phage P1 is an example of a phage used in these studies. Transfer frequency is about one in a million phage, and as much as 100-115 kb (up to 50 genes) can be transferred. The frequency with which genes are transferred together (co-transduction frequency) is a measure of their proximity. Higher frequencies indicate that genes are closer.
Genes can also be mapped in bacterial viruses based on their recombination frequency during co-infection (simultaneous infection with more than one type of bacteria). The most common phage life cycle is the lytic cycle. Phage replicate, burst the cell, and infect other bacteria, forming a plaque. The easiest types of mutations to study in phage relate to plaque size (r- rapid lysis mutants have large plaques) and host range (ability to grow on different types of bacteria). Other types of mutations studied include conditional mutations such as those able to grow at low temperature but not at high temperature. Map distances for phage genes, as for higher organisms, are based on %recombinant progeny/ total progeny. This data has been used to construct phage genetic maps.
An important study related to these methods was Benzer’s investigation of mutations in the rII region of phage T4. RII mutants have large plaques, can grow on E. coli B, but cannot grow on E. coli K12 (lambda). Wild type phage have small plaques and can grow on both B and K12 (lambda). By infecting two different mutants into K12(lambda) at the same time, it was possible to define two separate genes (cistrons) in the RII region through a complementation test. By infecting two different mutants into E. coli B at the same time and scoring the frequency with which the progeny could grow on K12 (lambda), the genetic distance between the mutants could be determined. The fine structure mapping indicated that the mutations were in a linear array and that some sites had more mutations than others.
In the lysogenic cycle, phage DNA may insert into the E. coli chromosome. Bacteria carrying a phage (e.g., K12 (lambda)) are referred to as lysogens. Phage inserted into the bacterial chromosome are referred to as prophages. Lambda is the best-studied of the phage following this cycle. Lambda codes for a repressor which turns off expression of genes involved in the lytic pathway. This repressor acts to prevent expression of the lambda genes involved in the lytic cycle. However, conditions which threaten survival of the bacteria (e.g., UV light exposure) can also inactivate the repressor and cause the phage to leave the chromosome.
When lambda leaves the host chromosome, it can sometimes take bacterial genes with it. Those are usually the genes adjacent to the insertion site of the phage. That site is located between the gal and bio genes (which do tend to be picked up by the phage at an appreciable frequency). This is termed specialized transduction. Usually either gal or bio (not both) would be picked up.