Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion.

Meghan M McLean,Reid C Johnson,John K Heiss,Gautam Dhar,Yong Chang

doi:10.7554/elife.01211

Abstract

Serine recombinases are often tightly controlled by elaborate, topologically-defined, nucleoprotein complexes. Hin is a member of the DNA invertase subclass of serine recombinases that are regulated by a remote recombinational enhancer element containing two binding sites for the protein Fis. Two Hin dimers bound to specific recombination sites associate with the Fis-bound enhancer by DNA looping where they are remodeled into a synaptic tetramer competent for DNA chemistry and exchange. Here we show that the flexible beta-hairpin arms of the Fis dimers contact the DNA binding domain of one subunit of each Hin dimer. These contacts sandwich the Hin dimers to promote remodeling into the tetramer. A basic region on the Hin catalytic domain then contacts enhancer DNA to complete assembly of the active Hin tetramer. Our results reveal how the enhancer generates the recombination complex that specifies DNA inversion and regulates DNA exchange by the subunit rotation mechanism. DOI:http://dx.doi.org/10.7554/eLife.01211.001.

Highlights

Site-specific recombination reactions have evolved as a relatively simple solution to a myriad of biological problems including gene regulation, viral integration, DNA transposition, chromosome segregation, and the programmed creation of genetic diversity (Craig, 2002)
We show that Fis contacts to inactive Hin dimers at an early step of invertasome formation lead to assembly of catalytically-active tetramers
We show that the Hin recombinase contacts the Fis/enhancer element at four distinct locations, which together promote assembly of the chemically-active Hin tetramer

Summary

Introduction

Site-specific recombination reactions have evolved as a relatively simple solution to a myriad of biological problems including gene regulation, viral integration, DNA transposition, chromosome segregation, and the programmed creation of genetic diversity (Craig, 2002). Most site-specific recombinases can be classified into two structurally and mechanistically unrelated groups that are named for the use of either a serine or tyrosine as the active site residue (Grindley et al, 2006). Some reactions, such as those mediated by the tyrosine recombinases Cre and FLP, only require the recombinase and its cognate DNA binding sites, whereas others involve additional accessory proteins and assemble elaborate synaptic complexes that provide tight control over chemical and mechanical steps of the reaction. Attack of the phosphoserine by the free 3′ OH ligates the DNA in the recombinant configuration

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Conclusion