Optimization of gene expression through divergent mutational paths

Abstract

Adaptation under similar selective pressure often leads to comparable phenotypes. A longstanding question is whether such phenotypic repeatability entails similar (parallelism) or different genotypic changes (convergence). To better understand this, we characterized mutations that optimized expression of a plasmid-borne metabolic pathway during laboratory evolution of a bacterium. Expressing these pathway genes was essential for growth but came with substantial costs. Starting from overexpression, replicate populations founded by this bacterium all evolved to reduce expression. Despite this phenotypic repetitiveness, the underlying mutational spectrum was highly diverse. Analysis of these plasmid mutations identified three distinct means to modulate gene expression: (1) reducing the gene copy number, (2) lowering transcript stability, and (3) integration of the pathway-bearing plasmid into the host genome. Our study revealed diverse molecular changes beneath convergence to a simple phenotype. This complex genotype-phenotype mapping presents a challenge to inferring genetic evolution based solely on phenotypic changes.

Figure 1. Diverse Mutations Occurred on the pCM410 Plasmid

(A) Structure of pCM410. Seven ISMex25 insertion sites of Class C halotypes (pCM410^C) are indicated by white arrowheads. trfA, plasmid replication gene encoding 33 or 44 kDa TrfA proteins; P_mxaF, promoter of the flhA-fghA gene cassette (see also Figure S1 and Table S1); P_traJ, promoter of trfA; oriV, origin of replication recognized by TrfA proteins; oriT, origin of transfer; ColE1, high-copy origin of replication in E. coli; kan, kanamycin resistance marker. (B) Class A haplotypes with mutations in fghA, predicted RBS (bold text), and its upstream region. The fghA start codon is underlined. (C) Class B haplotypes with mutations in regions controlling plasmid replication. (D) The process of forming Class C plasmid cointegrates and mini-plasmids. SNPs, IS insertion sites, and deletions are indicated by black asterisks, dashed arrows, and black bars, respectively. Haplotypes chosen for detailed analysis are indicated by colored index numbers.

Figure 2. Fitness Ranges of pCM410 Derivatives

Empty triangles, pCM410^B2 and pCM410^B3 containing just the 1.1 kb deletion and the SNP of pCM410^B1, respectively. Error bars are 95% confidence intervals. See also Figure S2 and Extended Experimental Procedures.

Figure 3. Expression of the GSH-Linked Pathway Exhibits an Intermediate Fitness Optimum

Enzymatic activities of plasmid haplotypes are indicated by their index numbers (0, ancestral pCM410; A1–A3, Class A haplotypes; B1–B5, Class B haplotypes; C1–C3, Class C haplotypes). Grey dots denote expression levels explored by the inducible expression plasmid pHC112. The corresponding fitness value of each data point is shown in black text. The inset shows the correspondence between enzyme activity (E) and fitness (W). pCM410° (yellow dot) and pHC112 (gray dots) are perpendicularly projected onto the orthogonal regression line (dashed line) of their FlhA and FghA enzyme activities. The yellow line in the inset denotes the fitness value of 1.0. Enzyme activity shown in the inset is expressed in terms of the relative distance between each projected point and the y axis intercept of the regression line. Error bars are 95% confidence intervals.

Figure 4. Three Plasmid Haplotype Classes Exhibit Distinct Molecular Phenotypes

(A) Cluster analysis of molecular phenotypes of plasmid haplotypes. Values of each molecular phenotype shown here are normalized to that of pCM410°, then weighted equally and analyzed together by hierarchical clustering. Molecular phenotypes are shown in their normalized values as a grayscale heat map. Transcript levels and enzyme activities are indicated by italicized and capitalized letters, respectively. Fitness, though not included in the cluster analysis, is shown as a red-scale heat map in the bottom. Two color bars on the side denote the scale for heat maps. Two cases in which pCM410 derivatives switch haplotype classes due to the acquisition of further mutations are indicated by dashed arrows. (B) Principle component (PC) analysis of molecular phenotypes. The data variation captured by PCs is shown as percentage in parenthesis. The loadings of PC1 and PC2 on the five molecular phenotypes are indicated by gray arrows. See also Figure S3, Tables S1 and S2, and Extended Experimental Procedures. Plasmid haplotypes are indicated by their index numbers as described in Figure 3.