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.

Dynamics of the SetCD-Regulated Integration and Excision of Genomic Islands Mobilized by Integrating Conjugative Elements of the SXT/R391 Family

“…Yet while the recombination functions of MGIs and KplE1 seem to be organized alike, they are functionally unrelated. In KplE1, the intS gene is tightly regulated by its own product as well as by the TorI protein (34). In contrast, we showed that in MGIs, rdfM is not a transcriptional regulator of int MGI .…”

“…The integrase gene intV2 (VC1758) and the RDF gene vefA (VC1809) of the Vibrio pathogenicity island 2 (VPI-2) are organized in a similar manner (2). This organization also resembles that of the KplE1 prophage, in which the attL site overlaps with the promoter of the intS gene, and the gene coding for the RDF TorI is remotely located, near the attR site (34). Yet while the recombination functions of MGIs and KplE1 seem to be organized alike, they are functionally unrelated.…”

Transcription termination controls prophage maintenance in Escherichia coli genomes

“…The integrase gene of KplE1 is transcribed independently from the RDF gene and is always expressed at a sufficient level to support prophage excision in the presence of the cognate RDF (24). However, under noninduced conditions, expression of the torI gene is not sufficient to allow for KplE1 excision.…”

“…These prophages integrate into the same argW locus, share a similar genetic organization of the recombination module, and their respective integrase genes are always expressed at low but sufficient levels to promote prophage excision as long as the RDF genes are expressed. A bioinformatics search allowed us to generalize this genetic organization to many prophages in bacterial genomes (24). This analysis, recently updated to more than 2,000 prokaryotic genomes, shows that 57% of the integrase genes associated with tRNA are self-regulated.…”

“…Two genes are required for excisive recombination: the integrase gene, which encodes the specific recombinase, and the recombination directionality factor (RDF) gene, which is necessary for directing the reaction toward excision (22,23). We recently characterized the regulation of intS gene expression and found that, like numerous integrase genes in prokaryotic genomes, intS was self-regulated to allow for optimal integrase production (24). We thus hypothesized that if prophage maintenance was controlled at the gene regulation level, the target should be the RDF gene.…”