Challenging a Paradigm: the Role of DNA Homology in Tyrosine Recombinase Reactions

Abstract

SUMMARY A classical feature of the tyrosine recombinase family of proteins catalyzing site-specific recombination, as exemplified by the phage lambda integrase and the Cre and Flp recombinases, is the ability to recombine substrates sharing very limited DNA sequence identity. Decades of research have established the importance of this short stretch of identity within the core regions of the substrates. Since then, several new enzymes that challenge this paradigm have been discovered and require the role of sequence identity in site-specific recombination to be reconsidered. The integrases of the conjugative transposons such as Tn916, Tn1545, and CTnDOT recombine substrates with heterologous core sequences. The integrase of the mobilizable transposon NBU1 performs recombination more efficiently with certain core mismatches. The integration of CTX phage and capture of gene cassettes by integrons also occur by altered mechanisms. In these systems, recombination occurs between mismatched sequences by a single strand exchange. In this review, we discuss literature that led to the formulation of the current strand-swapping isomerization model for tyrosine recombinases. The review then focuses on recent developments on the recombinases that challenged the paradigm that was derived from the studies of early systems.

Mechanisms of DNA Transposition

“…The second major type of catalytic domain is seen for those transposases that act on single-stranded DNA (ssDNA) and is known as an HUH domain (8). The serine transposases (such as those of IS607, Tn5397, and Tn5541 (9, 10)) and tyrosine transposases (exemplified by those of CTnDOT and Tn916 (11)) are predicted to have the same catalytic domain folds as serine and tyrosine site-specific recombinases, respectively. This last aspect is illustrated in Table 1: the four catalytic nuclease domains found in DNA transposases are also used by other enzymes that rearrange DNA such as retroviral integrases, invertases, resolvases, site-specific recombinases, and the RAG-1 recombinase involved in V(D)J recombination.…”

“…By analogy to tyrosine recombinases, a tetrameric complex is believed to assemble in which each subunit cleaves one of the four strands of the recombining sites ( Conjugative transposons display a spectrum of targeting specificity in their requirements for homology between the attL/attR junction and the attB site (11). Some insert essentially randomly, others display relatively strict specificity reflecting the site-specific recombinase machinery at work, and yet others occupy a middle ground with strict albeit usually very short sequence requirements for where they will integrate (11,61,62). While most conjugative transposons use tyrosine or serine transposases, it has recently been discovered that some conjugative transposons are mobilized by RNase H-like transposases (63,64).…”

Cre Recombinase

“…In molecular terms, formation of canonical base-pairs during strand exchange is thought to be required to establish a geometry that promotes efficient ligation and formation of stable intermediates or products. It is worth noting, however, that crossover sequence identity is not required for all tyrosine recombinases (72).…”

Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae

“…About 80 % of human S. agalactiae isolates are resistant to tetracycline due to the presence of Tn916 or related ICEs (Achard & Leclercq, 2007;Le Bouguénec et al, 1990;Poyart et al, 2003). However, with the exception of the TnGBS conjugative transposons described below, transposition of Tn916 and of all S. agalactiae ICEs described so far is not mediated by a DDE transposase, but by a serine recombinase, such as Tn5397 from Clostridium difficile or a tyrosine recombinase such as Tn916 (Brochet et al, 2008a;Chuzeville et al, 2012;Da Cunha et al, 2013;Haenni et al, 2010;Puymège et al, 2013;Rajeev et al, 2009;Wang et al, 2006).…”