The presence of prophage DNA in a cell constitutes a genetic alteration to the cell. Usually the only phage gene that is expressed is that which codes for production of the repressor, which switches off all the others. This in itself confers two new properties on the cell, super infection immunity and the liability to revert to the lytic cycle with the production of new phage. It is worth noting that bacteriophages are not necessarily harmful to bacteria; temperate phages at least confer immunity to lysis by other phages of the same type. In practice, it is not easy to be certain whether any particular bacterial strain is lysogenic or not without fairly intensive investigation, but it is probable that lysogeny is quite widespread in nature.
In certain cases it can be shown that other prophage genes are also expressed so that the lysogenized cell has acquired other properties as well (lysogenic conversion). Non-lysogenized Salmonella anatumforms receptors that can absorb phage ε 15 but not phage ε 34 (ε =epsilon). However Salmonella anatum lysogenized by ε 15 forms different receptor that can absorb phage e34 but not ε 15. If the cells are now doubly lysogenized by the addition of phage ε34 to cells that are already lysogenic for ε 15, the receptors are changed again so that neither phage can be adsorbed. In this particular case the presence of a prophage directs the cell to alter its surface receptors so that the cell becomes resistant to that phage (cf. the more normal super infection immunity).
This is a particularly interesting model as the effects of the prophages can be analyzed in terms of the production of new phage-coded enzymes and the shut-off of host-coded enzymes involved in the synthesis of polysaccharides side chains on the bacterial surface. This allows a detailed analysis of the chemical structure of the cell surface components that make up the O-antigens and bacteriophage receptors of the cell. The system is also interesting in that such phage-coded alterations in the bacterial surface appear to be similar to the alterations in eukaryotic cell surface properties that occur after infection with integrated tumor viruses.
Another example of lysogenic conversion has been found with Corynebacterium diphtheriae, which produces diphtheria toxin only when it is lysogenized by a specific phage (β-phage). The toxin is specified by one of the phage genes. It is probable that the production of certain toxins by staphylococci, streptococci and clostridia is also dependent on the presence of specific temperate prophages. In these cases, lysogeny not only gives the cell superinfection immunity, it also actively influences the virulence of the bacterium for man.
One may speculate, with Hayes, to what extent we unjustly incriminate bacteria in general for the sins of their viruses.