Asymmetrical dose responses shape the evolutionary trade-off between antifungal resistance and nutrient use

URA6 mutations provide an alternative mechanism for 5-FOA resistance in Saccharomyces cerevisiae

URA3 is frequently used in the yeast community as the mutation target for 5-fluoroorotic acid (5-FOA) resistance. We identified a novel class of ura6 mutants that can grow in the presence of 5-FOA. Unlike ura3 mutants, ura6 mutants remain prototrophic and grow in the absence of uracil. In addition to 5-FOA resistance, we found that mutations to URA6 also confer resistance to 5-fluorocytosine (5-FC) and 5-fluorouracil (5-FU). In total, we identified 50 unique missense mutations across 32 residues of URA6. We found that 28 out of the 32 affected residues are located in regions conserved between Saccharomyces cerevisiae and three clinically relevant pathogenic fungi. These findings suggest that mutations to URA6 present a second target for mutation screens utilizing 5-FOA as a selection marker as well as a potential mode of resistance to the antifungal therapeutic 5-FC.

Shaping of microbial phenotypes by trade-offs

Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.

Dose-response curves: the next frontier in plant ecology

A large fraction of experimental work in plant ecology, and thus also on ecosystem functioning and the delivery of ecosystem services, describes experiments that have been carried out under controlled (glasshouse) conditions. Controlled growth settings commonly sacrifice realism through, for example, reducing the densities of plant species in the pots and controlling how environmental settings such as moisture and light vary in favor of a higher mechanistic resolution, which makes these studies particularly suitable for subsequent syntheses. We explore the possibility that further integration of dose-response curves can maximize the impact of existing studies. We suggest that we can expand considerably the scope of the dose and response variables that are considered in plant ecology.

Variability in competitive fitness among environmental and clinical azole-resistant Aspergillus fumigatus isolates

Azoles are the primary antifungal drugs used to treat infections caused by Aspergillus fumigatus. However, the emergence of azole resistance in A. fumigatus has become a global health concern despite the low proportion of resistant isolates in natural populations. In bacteria, antibiotic resistance incurs a fitness cost that renders strains less competitive in the absence of antibiotics. Consequently, fitness cost is a key determinant of the spread of resistant mutations. However, the cost of azole resistance and its underlying causes in A. fumigatus remain poorly understood. In this observation, we revealed that the 10 out of 15 screened azole-resistant isolates, which possessed the most common azole-targeted cyp51A mutations, particularly the presence of tandem repeats in the promoter region, exhibit fitness cost when competing with the susceptible isolates in azole-free environments. These results suggest that fitness cost may significantly influence the dynamics of azole resistance, which ultimately contributes to the low prevalence of azole-resistant A. fumigatus isolates in the environment and clinic. By constructing in situ cyp51A mutations in a parental azole-susceptible strain and reintroducing the wild-type cyp51A gene into the azole-resistant strains, we demonstrated that fitness cost is not directly dependent on cyp51A mutations but is instead associated with the evolution of variable mutations related to conidial germination or other unknown development-related processes. Importantly, our observations unexpectedly revealed that some azole-resistant isolates showed no detectable fitness cost, and some even exhibited significantly increased competitive fitness in azole-free environments, highlighting the potential risk associated with the prevalence of these isolates.

IMPORTANCE

Azole resistance in the human fungal pathogen Aspergillus fumigatus presents a global public health challenge. Understanding the epidemic trends and evolutionary patterns of azole resistance is critical to prevent and control the spread of azole-resistant isolates. The primary cause is the mutation of the drug target 14α-sterol-demethylase Cyp51A, yet its impact on competitive ability remains uncertain. Our competition assays revealed a diverse range of fitness outcomes for environmental and clinical cyp51A-mutated isolates. We have shown that this fitness cost is not reliant on cyp51A mutations but might be linked to unknown mutations induced by stress conditions. Among these isolates, the majority displayed fitness costs, while a few displayed enhanced competitive ability, which may have a potential risk of spread and the need to closely monitor these isolates. Our observation reveals the variation in fitness costs among azole-resistant isolates of A. fumigatus, highlighting the significant role of fitness cost in the spread of resistant strains.

Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network

Paralogous genes are often redundant for long periods of time before they diverge in function. While their functions are preserved, paralogous proteins can accumulate mutations that, through epistasis, could impact their fate in the future. By quantifying the impact of all single-amino acid substitutions on the binding of two myosin proteins to their interaction partners, we find that the future evolution of these proteins is highly contingent on their regulatory divergence and the mutations that have silently accumulated in their protein binding domains. Differences in the promoter strength of the two paralogs amplify the impact of mutations on binding in the lowly expressed one. While some mutations would be sufficient to non-functionalize one paralog, they would have minimal impact on the other. Our results reveal how functionally equivalent protein domains could be destined to specific fates by regulatory and cryptic coding sequence changes that currently have little to no functional impact.

Measuring differential fitness costs and interactions between genetic cassettes using fluorescent spectrophotometry

In this article, we present a method for designing, executing, and analyzing data from a microbial competition experiment. We use fluorescent reporters to label different competing strains and resolve individual growth curves using a fluorescent spectrophotometer. Our comprehensive data analysis pipeline integrates multiple experiments to simultaneously infer sources of variation, extract selection coefficients, and estimate the genetic contributions to fitness for various synthetic genetic cassettes (SGCs). To demonstrate the method, we employ a synthetic biological system based on Escherichia coli. Strains carry 1 of 10 different plasmids and one of three genomically integrated fluorescent markers. All strains are co-cultured to obtain real-time measurements of optical density (total population density) and fluorescence (sub-population densities). We identify challenges in calibrating between fluorescence and density and of fluorescent proteins maturing at different rates. To resolve these issues, we compare two methods of fluorescence calibration and correct for maturation by measuring in vivo maturation times. We provide evidence of genetic interactions occurring between our SGCs and further show how to use our statistical model to test some hypotheses about microbial growth and the costs of protein expression.IMPORTANCEFluorescently labeled co-cultures are becoming increasingly popular. The approach proposed here offers a high standard for experimental design and data analysis to measure selection coefficients and growth rates in competition. Measuring competitive differences is useful in many laboratory studies, allowing for fitness cost-correction of growth rates and ecological interactions and testing hypotheses in synthetic biology. Using time-resolved growth curves, rather than endpoint measurements, for competition assays allows us to construct a detailed scientific model that can be used to ask questions about fine-grained phenomena, such as bacterial growth dynamics, as well as higher-level phenomena, such as the interactions between synthetic cassette expression.

Compensatory mutations potentiate constructive neutral evolution by gene duplication

Protein functions generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicate and evolve an homodimeric enzyme to examine if and how this could happen. We identify hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when co-expressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate.

Cross-feeding affects the target of resistance evolution to an antifungal drug

Pathogenic fungi are a cause of growing concern. Developing an efficient and safe antifungal is challenging because of the similar biological properties of fungal and host cells. Consequently, there is an urgent need to better understand the mechanisms underlying antifungal resistance to prolong the efficacy of current molecules. A major step in this direction would be to be able to predict or even prevent the acquisition of resistance. We leverage the power of experimental evolution to quantify the diversity of paths to resistance to the antifungal 5-fluorocytosine (5-FC), commercially known as flucytosine. We generated hundreds of independent 5-FC resistant mutants derived from two genetic backgrounds from wild isolates of Saccharomyces cerevisiae. Through automated pin-spotting, whole-genome and amplicon sequencing, we identified the most likely causes of resistance for most strains. Approximately a third of all resistant mutants evolved resistance through a pleiotropic drug response, a potentially novel mechanism in response to 5-FC, marked by cross-resistance to fluconazole. These cross-resistant mutants are characterized by a loss of respiration and a strong tradeoff in drug-free media. For the majority of the remaining two thirds, resistance was acquired through loss-of-function mutations in FUR1, which encodes an important enzyme in the metabolism of 5-FC. We describe conditions in which mutations affecting this particular step of the metabolic pathway are favored over known resistance mutations affecting a step upstream, such as the well-known target cytosine deaminase encoded by FCY1. This observation suggests that ecological interactions may dictate the identity of resistance hotspots.

Epistasis between promoter activity and coding mutations shapes gene evolvability

The evolution of protein-coding genes proceeds as mutations act on two main dimensions: regulation of transcription level and the coding sequence. The extent and impact of the connection between these two dimensions are largely unknown because they have generally been studied independently. By measuring the fitness effects of all possible mutations on a protein complex at various levels of promoter activity, we show that promoter activity at the optimal level for the wild-type protein masks the effects of both deleterious and beneficial coding mutations. Mutations that are deleterious at low activity but masked at optimal activity are slightly destabilizing for individual subunits and binding interfaces. Coding mutations that increase protein abundance are beneficial at low expression but could potentially incur a cost at high promoter activity. We thereby demonstrate that promoter activity in interaction with protein properties can dictate which coding mutations are beneficial, neutral, or deleterious.