Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme

Abstract

For a quantitative understanding of the process of adaptation, we need to understand its “raw material,” that is, the frequency and fitness effects of beneficial mutations. At present, most empirical evidence suggests an exponential distribution of fitness effects of beneficial mutations, as predicted for Gumbel-domain distributions by extreme value theory. Here, we study the distribution of mutation effects on cefotaxime (Ctx) resistance and fitness of 48 unique beneficial mutations in the bacterial enzyme TEM-1 β-lactamase, which were obtained by screening the products of random mutagenesis for increased Ctx resistance. Our contributions are threefold. First, based on the frequency of unique mutations among more than 300 sequenced isolates and correcting for mutation bias, we conservatively estimate that the total number of first-step mutations that increase Ctx resistance in this enzyme is 87 [95% CI 75–189], or 3.4% of all 2,583 possible base-pair substitutions. Of the 48 mutations, 10 are synonymous and the majority of the 38 non-synonymous mutations occur in the pocket surrounding the catalytic site. Second, we estimate the effects of the mutations on Ctx resistance by determining survival at various Ctx concentrations, and we derive their fitness effects by modeling reproduction and survival as a branching process. Third, we find that the distribution of both measures follows a Fréchet-type distribution characterized by a broad tail of a few exceptionally fit mutants. Such distributions have fundamental evolutionary implications, including an increased predictability of evolution, and may provide a partial explanation for recent observations of striking parallel evolution of antibiotic resistance.

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

“…fitness advantage relative to the ancestor (Fig. 1c), values that are substantially larger than any previous estimate of fitness for a synonymous mutation 3,[8][9][10][11] .…”

“…Consistent with this expectation, estimates of fitness from comparative genomics suggest that synonymous sites are under weak purifying selection [13][14][15] , although a recent study suggests that up to 22% of synonymous sites in the Drosophila melanogaster genome may be under strong purifying selection 16 . Direct measures of fitness from site-directed mutagenesis studies tell a similar story: the fitness effects of synonymous mutations are almost always deleterious or, more rarely, weakly beneficial 3,[8][9][10][11] . Deleterious mutations are, by definition, subject to purifying selection, while weakly beneficial mutations are unlikely to be substituted by selection because either they cannot escape drift in small populations or, in large populations, are eliminated in competition with the relatively more abundant class of non-synonymous mutations with larger beneficial effects.…”

“…Pervasive variation in the frequencies of synonymous codons across genes and genomes (codon usage bias) 1 suggests that selection may favour some synonymous codons over others. Moreover, direct measures of the impact of synonymous mutations from nucleotide replacement studies demonstrate that they can impact gene expression 2,3 , presumably through changes to the rate or accuracy of transcription and/or translation 4 , mRNA stability and folding 5 , protein secondary structure 6,7 and even fitness 3,[8][9][10][11] . Taken together, these results suggest that the frequency of at least some synonymous mutations is governed by selection.…”

Bypass of genetic constraints during mutator evolution to antibiotic resistance

“…A : T transitions, one of the two dominant nucleotide changes in the spectrum of mismatch repair-deficient strains, the most prevalent type of strong bacterial mutators [28]. These substitutions include the top-ranked G238S and E104K, which appear combined in many notorious naturally occurring TEM alleles, and substitutions R164H and A237T [24,26]. In addition, the other transition characteristic of these mutators (A : T !…”

Determinants of Genetic Diversity of Spontaneous Drug Resistance in Bacteria

“…However, in most situations of interest the number of different resistance alleles is in the order of tens to hundreds (Garibyan et al 2003;Nilsson et al 2003;Schenk et al 2012;Monti et al 2013;Couce et al 2015). Under such circumstances mutants belonging to independent clones can Figure 4 The effect of phenotypic lag on genetic diversity.…”