Chapter 3 : Lysogeny, Prophage Induction, and Lysogenic Conversion

Life cycle of phage λ. An infected cell is depicted at the top, in which injected phage DNA has rapidly circularized. Ten to 15 min after infection, a decision is made between two alternative fates. See the text for more details. During the lysogenic response, the circular λ DNA is inserted into the host chromosome by a site-specific recombination event between the phage att site ( Fig. 2A ) and a cognate site on the host genome.

Organization of O R and occupancy patterns of operators. (A) Organization of the O R region. The map is drawn to scale. The locations of promoter elements and O R sites are shown; only the initial parts of cI and cro are shown (see the text for further details). (B) Occupancy patterns of O R operators. (Top) Occupancy by CI at moderate levels. At higher levels, CI binds to O R3, both directly and via looping (C). (Bottom) Occupancy by Cro at moderate levels. At higher levels, Cro binds to O R1 and/or O R2, repressing P R. In each case, the expression of P R and P RM and the resulting regulatory states are indicated. (C) Looping between O R and O L. (Top) Map (to scale) of the immunity region. See the text for more information about rexA and rexB. The cI, rexA, and rexB genes are expressed in an operon; a terminator lies beyond rexB (not shown). O L and O R are about 2.4 kb apart; over this distance, DNA is very flexible. CI binds tightly to O L1 and cooperatively to O L2. (Bottom left) Initial loop between tetramers at O L and tetramers at O R. This structure probably does not repress P RM. (Bottom right) The addition of two more CI dimers, presumably by cooperative interactions, represses P RM.

λ genome organization and transcription patterns. (A) Map of the λ genome. The map is drawn to scale. Genes with related functions are grouped together into modules (see the text for more details). The immunity region, discussed at length in the text, includes the regulatory sites O L, P L,O R, and P R and the regulatory genes cI and cro. The locations of nonessential genes are shown (see the text), as are those of cis-acting sites that are important for the lytic program of gene expression. The GenBank accession number for the λ genome is NC_001416. (B) Lytic gene expression. The map is not drawn to scale. Transcripts are indicated by lines with arrowheads depicting their 3′ ends, except that those indicated by “+N” or “+Q” are anti-terminated and would continue beyond the ends of the map. The T R1 terminator is inefficient; transcripts reading through it terminate at T R2 in the absence of N function. Several other terminators lie to the left of T L1 and are not shown. (C) Expression of cI from two different promoters, P RE and P RM (see the text). The map is drawn to scale.

SOS regulatory system. (A) Normal growth state. LexA represses ~40 genes; in most cases, repression is not complete, and the basal level is 5 to 20% that of the fully induced level. RecA is present at low levels but is not active as a co-protease. (B) Induction pathway. DNA damage or treatments that inhibit DNA replication lead to the production of a signal, probably a single-stranded DNA, to which RecA binds. Binding activates the RecA co-protease activity; this in turn mediates LexA cleavage and inactivation. (C) Induced state. Activated RecA continues to mediate the cleavage of LexA, and the SOS genes are expressed at high levels. If the cell contains a λ prophage, then λ CI is also cleaved. (D) Recovery pathway. When the damage is repaired, the inducing signal disappears and LexA becomes stable. Since LexA is autoregulated (not shown), it can build up rapidly to normal levels.

Threshold behavior of prophage induction. A λ lysogen was exposed to graded doses of DNA damage applied by ultraviolet (UV) irradiation, and the number of phage released was measured (see reference 29 for the methodology used). At high doses, nearly all of the cells were induced. For a phage such as H-19B (see the text), the curve would have a similar shape, but the set point (the dose giving a 50% maximal yield) would be shifted far to the left.