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The Transcriptional Regulator Ume6 is a Major Driver of Gene Expression during Gametogenesis in Budding Yeast

ABSTRACT: Early meiotic genes (EMGs) encompass an important subset within the developmental program of gametogenesis. Regulation of EMGs is achieved through the recognition of a common regulatory element in their promoters by the transcription factor Ume6. Proper meiotic execution requires the timely expression of EMGs, which is achieved through the adoption of the meiotic regulator Ime1 by Ume6. While it is known that Ime1’s binding to Ume6 promotes EMG expression, the mechanism of EMG activation remains unclear. Two competing models have been proposed: (1) Ime1 converts Ume6 to a coactivator complex, and (2) Ime1 binding targets Ume6 for degradation. Using a combination of tools including meiotic synchronization, temporally controlled protein depletion, protein-protein interaction engineering, and transcriptomics, here we address this conundrum. We identify 160 genes that are directly regulated by Ime1-Ume6, including UME6 itself. Removal of Ume6 shortly before meiotic entry is detrimental to EMG activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger EMG expression and to generate viable gametes in the absence of Ime1. We conclude that Ime1-Ume6 functions as a coactivator complex. While Ume6 is indispensable for EMGs expression, Ime1 primarily serves as an evolutionarily tuned activation domain for Ume6.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE226769 | GEO | 2023/06/30

REPOSITORIES: GEO

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Project description:Ray2013 - Meiotic initiation in S. cerevisiae A mathematical representation of early meiotic events, particularly feedback mechanisms at the system level and phosphorylation of signalling molecules for regulating protein activities, is described here This model is described in the article: Dynamic modeling of yeast meiotic initiation. Ray D, Su Y, Ye P. BMC Syst Biol. 2013 May 1;7:37 Abstract: BACKGROUND: Meiosis is the sexual reproduction process common to eukaryotes. The diploid yeast Saccharomyces cerevisiae undergoes meiosis in sporulation medium to form four haploid spores. Initiation of the process is tightly controlled by intricate networks of positive and negative feedback loops. Intriguingly, expression of early meiotic proteins occurs within a narrow time window. Further, sporulation efficiency is strikingly different for yeast strains with distinct mutations or genetic backgrounds. To investigate signal transduction pathways that regulate transient protein expression and sporulation efficiency, we develop a mathematical model using ordinary differential equations. The model describes early meiotic events, particularly feedback mechanisms at the system level and phosphorylation of signaling molecules for regulating protein activities. RESULTS: The mathematical model is capable of simulating the orderly and transient dynamics of meiotic proteins including Ime1, the master regulator of meiotic initiation, and Ime2, a kinase encoded by an early gene. The model is validated by quantitative sporulation phenotypes of single-gene knockouts. Thus, we can use the model to make novel predictions on the cooperation between proteins in the signaling pathway. Virtual perturbations on feedback loops suggest that both positive and negative feedback loops are required to terminate expression of early meiotic proteins. Bifurcation analyses on feedback loops indicate that multiple feedback loops are coordinated to modulate sporulation efficiency. In particular, positive auto-regulation of Ime2 produces a bistable system with a normal meiotic state and a more efficient meiotic state. CONCLUSIONS: By systematically scanning through feedback loops in the mathematical model, we demonstrate that, in yeast, the decisions to terminate protein expression and to sporulate at different efficiencies stem from feedback signals toward the master regulator Ime1 and the early meiotic protein Ime2. We argue that the architecture of meiotic initiation pathway generates a robust mechanism that assures a rapid and complete transition into meiosis. This type of systems-level regulation is a commonly used mechanism controlling developmental programs in yeast and other organisms. Our mathematical model uncovers key regulations that can be manipulated to enhance sporulation efficiency, an important first step in the development of new strategies for producing gametes with high quality and quantity. This model is hosted on BioModels Database and identified by: BIOMD0000000626 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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The Transcriptional Regulator Ume6 is a Major Driver of Gene Expression during Gametogenesis in Budding Yeast

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