Tight Regulation of the intS Gene of the KplE1 Prophage: A New Paradigm for Integrase Gene Regulation

Abstract

Temperate phages have the ability to maintain their genome in their host, a process called lysogeny. For most, passive replication of the phage genome relies on integration into the host's chromosome and becoming a prophage. Prophages remain silent in the absence of stress and replicate passively within their host genome. However, when stressful conditions occur, a prophage excises itself and resumes the viral cycle. Integration and excision of phage genomes are mediated by regulated site-specific recombination catalyzed by tyrosine and serine recombinases. In the KplE1 prophage, site-specific recombination is mediated by the IntS integrase and the TorI recombination directionality factor (RDF). We previously described a sub-family of temperate phages that is characterized by an unusual organization of the recombination module. Consequently, the attL recombination region overlaps with the integrase promoter, and the integrase and RDF genes do not share a common activated promoter upon lytic induction as in the lambda prophage. In this study, we show that the intS gene is tightly regulated by its own product as well as by the TorI RDF protein. In silico analysis revealed that overlap of the attL region with the integrase promoter is widely encountered in prophages present in prokaryotic genomes, suggesting a general occurrence of negatively autoregulated integrase genes. The prediction that these integrase genes are negatively autoregulated was biologically assessed by studying the regulation of several integrase genes from two different Escherichia coli strains. Our results suggest that the majority of tRNA-associated integrase genes in prokaryotic genomes could be autoregulated and that this might be correlated with the recombination efficiency as in KplE1. The consequences of this unprecedented regulation for excisive recombination are discussed.

Author Summary

Temperate bacteriophages are widespread bacterial viruses that have the ability to replicate passively in their hosts as long as no stressful conditions are encountered, a process called lysogeny. Prophage-encoded genes may benefit the host in several ways such as providing resistance to antibiotics, increased pathogenicity, or increased fitness. Most temperate phages insert their genome into the host's chromosome by site-specific recombination. After prophage induction, usually under stressful conditions, the excisive recombination constitutes a key step toward productive phage development. In this paper, we study the regulation of integrase genes that encode the enzyme required for integrative as well as excisive recombination. We noticed that for prophages inserted in or near tRNA genes the orientation of the integrase gene relative to the tRNA is crucial for its regulation.