Primary and promiscuous functions coexist during evolutionary innovation through whole protein domain acquisitions.

José Antonio Escudero,Harry E Kemble,Céline Loot,Aleksandra Nivina,Didier Mazel,Olivier Tenaillon

doi:10.7554/elife.58061

Abstract

Molecular examples of evolutionary innovation are scarce and generally involve point mutations. Innovation can occur through larger rearrangements, but here experimental data is extremely limited. Integron integrases innovated from double-strand- toward single-strand-DNA recombination through the acquisition of the I2 α-helix. To investigate how this transition was possible, we have evolved integrase IntI1 to what should correspond to an early innovation state by selecting for its ancestral activity. Using synonymous alleles to enlarge sequence space exploration, we have retrieved 13 mutations affecting both I2 and the multimerization domains of IntI1. We circumvented epistasis constraints among them using a combinatorial library that revealed their individual and collective fitness effects. We obtained up to 104-fold increases in ancestral activity with various asymmetrical trade-offs in single-strand-DNA recombination. We show that high levels of primary and promiscuous functions could have initially coexisted following I2 acquisition, paving the way for a gradual evolution toward innovation.

Highlights

Integrons are genetic elements that enhance bacterial evolvability through the acquisition of new genes encoded in integron cassettes (Francia et al, 1997; Escudero et al, 2015; Mazel, 2006; Hall and Stokes, 1993; Figure 1a)
After minor modifications aiming to decrease the stability of secondary structures in their transcripts, these low energy alternative genes, named alt1l.e. and alt2l.e., showed recombination activities comparable to those of IntI1 encoding gene (intI1) and were used as a starting point for directed evolution experiments (Escudero et al, 2018)
For the intI1 allele, we used a library of randomized intI1 that had been previously constructed in our laboratory (Demarre et al, 2007)

Summary

Introduction

Integrons are genetic elements that enhance bacterial evolvability through the acquisition of new genes encoded in integron cassettes (Francia et al, 1997; Escudero et al, 2015; Mazel, 2006; Hall and Stokes, 1993; Figure 1a). Recombination reactions leading to cassette acquisition and reshuffling are governed by integron integrases (herafter, integrases). Phylogenetic studies show that integrases belong to the family of tyrosine (Y)-recombinases, but form a discrete cluster within it, that evolved recently (Mazel, 2006; Nunes-Duby et al, 1998). Y-recombinases are a large family of DNA-recombinases.

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