Penguin

of several different aminoacylation identities may be used within any subfamily. These two familial sublocation preferences imply two modes by which new integration site usage evolves. The tmRNA gene has been adopted as an integration site in both modes, and its distinctive structure imposes some constraints on proposed evolutionary mechanisms.

Genetic elements capable of horizontal transfer and integration into host chromosomes are key agents in the evolution of cellular genomes; bacterial pathogenicity in particular is shaped by integrative elements that can carry with them genes promoting virulence. Integration site specificity is determined primarily by the integrase enzyme typically encoded within elements of several types: temperate bacteriophages, integrative plasmids, pathogenicity islands and conjugative and mobilizable elements. Integrases have also been harnessed for stably inserting foreign genes into bacterial chromosomes in the construction of useful strains. It is therefore important to understand both the mechanism and evolution of integration site usage.

The longest studied integrase, from phage lambda, has the following prototypical properties (1): it (i) catalyzes integration and excision of a genetic element, (ii) has one highly preferred integration site in the host chromosome (attB), (iii) recombines segments of identical sequence within attB and the attP region in the element (2,3), and (iv) belongs to the tyrosine recombinase family. This large protein family, defined by sequence consensus in the C-terminal domain that includes invariant residues involved in catalysis (4,5), contains many members that do not fit the above criteria for a classical integrase; some are involved in resolution of chromosome or plasmi