An Overview of Tyrosine Site-specific Recombination: From an Flp Perspective

Abstract

Tyrosine site-specific recombinases (YRs) are widely distributed among prokaryotes and their viruses, and were thought to be confined to the budding yeast lineage among eukaryotes. However, YR-harboring retrotransposons (the DIRS and PAT families) and DNA transposons (Cryptons) have been identified in a variety of eukaryotes. The YRs utilize a common chemical mechanism, analogous to that of type IB topoisomerases, to bring about a plethora of genetic rearrangements with important physiological consequences in their respective biological contexts. A subset of the tyrosine recombinases has provided model systems for analyzing the chemical mechanisms and conformational features of the recombination reaction using chemical, biochemical, topological, structural, and single molecule-biophysical approaches. YRs with simple reaction requirements have been utilized to bring about programmed DNA rearrangements for addressing fundamental questions in developmental biology. They have also been employed to trace the topological features of DNA within high-order DNA interactions established by protein machines. The directed evolution of altered specificity YRs, combined with their spatially and temporally regulated expression, heralds their emergence as vital tools in genome engineering projects with wide-ranging biotechnological and medical applications.

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending

“…Tyrosine recombinases promote various programmed DNA rearrangements including the monomerization of phage, plasmid and chromosome multimers, resolution of hairpin telomeres, and the movement of virulence and antibiotic resistance carrying integrative mobile genetic elements (including phages and transposons)(Grindley et al, 2006; Jayaram et al, 2015; Midonet and Barre, 2014). In addition, tyrosine recombinases (as exemplified by Cre and Flp) provide powerful genetic engineering tools that are widely used to carry out mutagenesis and DNA insertion in eukaryotic chromosomes (Nagy, 2000; Turan et al, 2011).…”

Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination

“…The enzymes that carry out these strand breakage/exchange reactions are site-specific recombinases. This review is concerned with ‘conservative site-specific’ recombinases (see below) which are widespread among prokaryotes and mobile DNA elements harbored by them, but are quite rare among eukaryotes [ 39 , 40 ]. They are remarkable for the chemical parsimony with which they bring about diverse, programmed genetic rearrangements resulting in precise physiological consequences.…”

“…Conservative site-specific recombinases belong to two families, namely the serine and tyrosine families—the names indicating the active site nucleophiles utilized by members of each family for the strand cleavage step of recombination [ 39 , 40 , 52 , 53 , 54 ] ( Figure 2 and Figure 3 ). The catalytic serine or tyrosine forms a covalent bond with the phosphate group of the cleaved strand.…”

“…The strand cleavage step using the catalytic tyrosine as nucleophile and the strand joining step using the 5′-hydroxyl as nucleophile are assisted by a catalytic pentad conserved among the members of the tyrosine family recombinases [ 39 ]. These residues in Cre are Arg-173, Lys-201, His-289, Arg-292, and Trp-315, the corresponding ones in Flp being Arg-191, Lys-223, His-305, Arg-308, and Trp-330, respectively.…”

Four genes essential for recombination define GInts, a new type of mobile genomic island widespread in bacteria

“…Tyrosine-based site-specific recombinases (TRases) are exceedingly abundant in prokaryotic and eukaryotic genomes12, carrying out functions as diverse as ensuring proper chromosomal and plasmid segregation, regulating gene expression or determining the life cycle of prophages towards dormancy or cell death3. They are also responsible for the movement of DNA through various types of mobile genetic elements (MGEs), such as integrons, phages, certain transposons, integrative conjugative elements, and genomic islands14.…”