title: 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.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220, USA.
authors.forename: Charles M
authors.initials: CM
authors.lastname: Denby
authors.forename: Joo Hyun
authors.initials: JH
authors.lastname: Im
authors.forename: Richard C
authors.initials: RC
authors.lastname: Yu
authors.forename: C Gustavo
authors.initials: CG
authors.lastname: Pesce
authors.forename: Rachel B
authors.initials: RB
authors.lastname: Brem
mesh_terms: D019295:Computational Biology / Q000379:methods; D004252:DNA Mutational Analysis; D005434:Flow Cytometry; D005800:Genes, Fungal; D014644:Genetic Variation; D023281:Genomics; D049452:Green Fluorescent Proteins / Q000378:metabolism; D000860:Hypoxia; D008856:Microscopy, Fluorescence / Q000379:methods; D008957:Models, Genetic; D016366:Open Reading Frames; D012097:Repressor Proteins / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism
chemical_list: C083348:ROX1 protein, S cerevisiae; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D049452:Green Fluorescent Proteins