Negative feedback confers mutational robustness in yeast transcription factor regulation

Abstract

Organismal fitness depends on the ability of gene networks to function robustly in the face of environmental and genetic perturbations. Understanding the mechanisms of this stability is one of the key aims of modern systems biology. Dissecting the basis of robustness to mutation has proven a particular challenge, with most experimental models relying on artificial DNA sequence variants engineered in the laboratory. In this work, we hypothesized that negative regulatory feedback could stabilize gene expression against the disruptions that arise from natural genetic variation. We screened yeast transcription factors for feedback and used the results to establish ROX1 (Repressor of hypOXia) as a model system for the study of feedback in circuit behaviors and its impact across genetically heterogeneous populations. Mutagenesis experiments revealed the mechanism of Rox1 as a direct transcriptional repressor at its own gene, enabling a regulatory program of rapid induction during environmental change that reached a plateau of moderate steady-state expression. Additionally, in a given environmental condition, Rox1 levels varied widely across genetically distinct strains; the ROX1 feedback loop regulated this variation, in that the range of expression levels across genetic backgrounds showed greater spread in ROX1 feedback mutants than among strains with the ROX1 feedback loop intact. Our findings indicate that the ROX1 feedback circuit is tuned to respond to perturbations arising from natural genetic variation in addition to its role in induction behavior. We suggest that regulatory feedback may be an important element of the network architectures that confer mutational robustness across biology.R obustness of organismal function in the face of perturbations is critical for fitness. Since the seminal work of Waddington (1), biologists have remarked on the stability of phenotypes against environmental and genetic variation, and understanding how organisms achieve robustness remains one of the major challenges in systems biology (2-4). Much of the search for molecular mechanisms of robustness has focused on gene regulation. Characteristics of regulatory networks that confer robustness include pathway redundancy and master regulatory organization (5), phenotypic capacitors (6-8), paired activating and inhibiting inputs (9), and cooperative and feed-forward regulation (10). Additionally, negative regulatory feedback, in which a biomolecule represses its own abundance, can buffer variation in gene expression (11,12), and negative feedback loops have been shown to underlie robustness to variable environmental conditions and stochastic intracellular change (13-15). Negative feedback may also confer network stability against the effects of mutations (3, 16), but evidence for negative feedback as a driver of mutational robustness in vivo has been at a premium (17); the relevance of this principle to natural genetic variation remains largely unknown.In this work, we focused on negative feedback in yeast hypoxia regulation motiva...

Buffering of Genetic Regulatory Networks inDrosophila melanogaster

“…Denby et al (2012) have proposed that negative feedback controlling the level of RNA expression could be a common mechanism to buffer effects of regulatory variants in yeast. Screening for autoregulated transcription factors in yeast, Denby et al (2012) found ROX1 to be under strong negative feedback.…”

“…Denby et al (2012) have proposed that negative feedback controlling the level of RNA expression could be a common mechanism to buffer effects of regulatory variants in yeast. Screening for autoregulated transcription factors in yeast, Denby et al (2012) found ROX1 to be under strong negative feedback. Mutant experiments showed that this negative feedback confers robustness to the expression of ROX1 in the face of naturally occurring allelic variants present in a set of divergent yeast strains.…”

“…GRN robustness has been explicitly formulated to account for the prevalence of compensatory cis-trans interactions (Denby et al 2012;Bader et al 2015). Denby et al (2012) have proposed that negative feedback controlling the level of RNA expression could be a common mechanism to buffer effects of regulatory variants in yeast.…”

Negative Feedback in Genetic Circuits Confers Evolutionary Resilience and Capacitance

“…However, nearly all the subsequent theoretical and experimental investigations focus upon negative feedback's dynamic properties within the cell without examining its effect upon mutational robustness. More recently, negative feedback was experimentally shown, in Saccharomyces cerevisiae, to reduce the variation in gene expression levels after the system-wide introduction of genomic mutations (Denby et al, 2012). However, it is unknown what role negative feedback has upon the capacity of an individual transcriptional circuit or transcription factor to tolerate variation in the form of amino acid changes.…”

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

“…Many biological systems, including gene regulatory networks, are known to exhibit robustness to genetic and environmental perturbation (Stark et al 2005;Levy and Siegal 2008;Masel and Siegal 2009;MacNeil and Walhout 2011;Denby et al 2012). By increasing the robustness of protein production, translational buffering could reduce the phenotypic impacts of variation in mRNA abundance.…”