Genes VII

Phages have a lytic life cycle, in which infection of a host bacterium is followed by production of a large number of phage particles, lysis of the cell, and release of the viruses. Some phages also can exist in lysogenic form, in which the phage genome is integrated into the bacterial chromosome and is inherited in this inert, latent form like any other bacterial gene.

Lytic infection falls typically into three phases. In the first phase a small number of phage genes are transcribed by the host RNA polymerase. One or more of these genes is a regulator that controls expression of the group of genes expressed in the second phase. The pattern is repeated in the second phase, when one or more genes is a regulator needed for expression of the genes of the third phase. Genes of the first two phases code for enzymes needed to reproduce phage DNA; genes of the final phase code for structural components of the phage particle. It is common for the very early genes to be turned off during the later phases.

In phage lambda, the genes are organized into groups whose expression is controlled by individual regulatory events. The immediate early gene N codes for an antiterminator that allows transcription of the leftward and rightward groups of delayed early genes from the early promoters P_R and P _L. The delayed early gene Q has a similar antitermination function that allows transcription of all late genes from the promoter P_R′. The lytic cycle is repressed, and the lysogenic state maintained, by expression of the cI gene, whose product is a repressor protein that acts at the operators O_R and O_L to prevent use of the promoters P_R and P_L, respectively. A lysogenic phage genome expresses only the cI gene, from its promoter P_RM. Transcription from this promoter involves positive autogenous regulation, in which repressor bound at O_R activates RNA polymerase at P_RM.

Each operator consists of three binding sites for repressor. Each site is palindromic, consisting of symmetrical half-sites. Repressor functions as a dimer. Each half binding site is contacted by a repressor monomer. The N-terminal domain of repressor contains a helix-turn-helix motif that contacts DNA. Helix-3 is the recognition helix, responsible for making specific contacts with base pairs in the operator. Helix-2 is involved in positioning helix-3; it is also involved in contacting RNA polymerase at P_RM. The C-terminal domain is required for dimerization. Induction is caused by cleavage between the N- and C-terminal domains, which prevents the DNA-binding regions from functioning in dimeric form, thereby reducing their affinity for DNA and making it impossible to maintain lysogeny. Repressor-operator binding is cooperative, so that once one dimer has bound to the first site, a second dimer binds more readily to the adjacent site.

The helix-turn-helix motif is used by other DNA-binding proteins, including lambda Cro, which binds to the same operators, but has a different affinity for the individual operator sites, determined by the sequence of helix-3. Cro binds individually to operator sites, starting with O_R3, in a noncooperative manner. It is needed for progression through the lytic cycle. Its binding to O_R first prevents synthesis of repressor from P_RM; then it prevents continued expression of early genes, an effect also seen in its binding to O_L.

Establishment of repressor synthesis requires use of the promoter P_RE, which is activated by the product of the cII gene. The product of cIII is required to stabilize the cII product against degradation. By turning off cII and cIII expression, Cro acts to prevent lysogeny. By turning off all transcription except that of its own gene, repressor acts to prevent the lytic cycle. The choice between lysis and lysogeny depends on whether repressor or Cro gains occupancy of the operators in a particular infection. The stability of CII protein in the infected cell is a primary determinant of the outcome.