3. Functional clustering in phages T7 and T4

11.3 Functional clustering in phages T7 and T4

Figure 11.5 Phage T7 contains three classes of genes that are expressed sequentially. The genome is ~38 kb.

The genome of phage T7 has three classes of genes, each constituting a group of adjacent loci. As Figure 11.5 shows, the class I genes are the immediate early type, expressed by host RNA polymerase as soon as the phage DNA enters the cell. Among the products of these genes are enzymes that interfere with host gene expression and a phage RNA polymerase. The phage enzyme is responsible for expressing the class II genes (concerned principally with DNA synthesis functions) and the class III genes (concerned with assembling the mature phage particle).

Figure 11.6 The map of T4 is circular. There is extensive clustering of genes coding for components of the phage and processes such as DNA replication, but there is also dispersion of genes coding for a variety of enzymatic and other functions. Essential genes are indicated by numbers. Nonessential genes are identified by letters. Only some representative T4 genes are shown on the map.

Phage T4 has one of the larger genomes (165 kb), organized with extensive functional grouping of genes. Figure 11.6 presents the genetic map. Genes that are numbered are essential: a mutation in any one of these loci prevents successful completion of the lytic cycle. Genes indicated by three-letter abbreviations are nonessential, at least under the usual conditions of infection. We do not really understand the inclusion of many nonessential genes, but presumably they confer a selective advantage in some of T4’s habitats. (In smaller phage genomes, most or all of the genes are essential.)

Figure 11.7 The phage T4 lytic cascade falls into two parts: early and quasi-late functions are concerned with DNA synthesis and gene expression; late functions are concerned with particle assembly.

Figure 11.24 RNA polymerase binds to P_RE only in the presence of CII, which contacts the region around -35.

There are three phases of gene expression. A summary of the functions of the genes expressed at each stage is given in Figure 11.7. The early genes are transcribed by host RNA polymerase. The middle genes are also transcribed by host RNA polymerase, but two phage-encoded products, MotA and AsiA, are also required. The middle promoters lack a consensus V30 sequence, and instead have a binding sequence for MotA. The phage protein is an activator that compensates for the deficiency in the promoter by assisting host RNA polymerase to bind. (This is similar to a mechanism employed by phage lambda, which is illustrated later in Figure 11.24.) The early and middle genes account for virtually all of the phage functions concerned with the synthesis of DNA, modifying cell structure, and transcribing and translating phage genes.

The two essential genes in the "transcription" category fulfill a regulatory function: their products are necessary for late gene expression. Phage T4 infection depends on a mechanical link between replication and late gene expression. Only actively replicating DNA can be used as template for late gene transcription. The connection is generated by introducing a new sigma factor and also by making other modifications in the host RNA polymerase so that it is active only with a template of replicating DNA (because there is an obligatory link between RNA polymerase and the replication apparatus). This link establishes a correlation between the synthesis of phage protein components and the number of genomes available for packaging.