Analysis of the PRE configuration reveals the constraints in Ste12 oligomerization in mediating pheromone-inducible transcription in Saccharomyces cerevisiae

Abstract

Yeast cell mating is regulated by the transcription factor Ste12, which activates the transcription of mating genes by binding to pheromone response elements (PREs) in their promoters. PREs vary in number and position among different promoters. However, the effect of PRE organization on Ste12-promoter interactions and the possible downstream transcription of mating genes remains to be fully understood. In this study, we analyzed yeast pheromone-induced gene expression using RNA-seq transcription profiling. We retrieved the promoters of the significantly upregulated genes, focusing on the occurrence and arrangement of PREs. PPRM1, which carries three adjacent consensus PREs, was selected as a model for investigating the relative contribution of each PRE to promoter activity through single-base mutation or deletion. We then evaluated the impact of different PRE organizations on pheromone-induced expression by altering their orientations and copy numbers. Subsequently, we proposed a model to explain the mechanism of transcriptional regulation of pheromone-inducible genes, in which the organization of PREs modulates promoter activity by influencing Ste12 oligomerization. This study paves the way for deciphering the transcriptional mechanisms of eukaryotic regulatory systems.

Keywords

Transcription / Pheromone-inducible promoter / PRE configuration / Ste12 oligomerization / DNA looping

Data availability statement

2096-3467The raw data of RNA-seq with a sequencing depth of 2 billion data volumes for each sample had been uploaded to NCBI gene bank under the accession number PRJNA902132.

CRediT authorship contribution statement

2096-3467Yiqing Zhang: Writing - original draft, Visualization, Project administration, Methodology, Investigation, Formal analysis, Data curation, Conceptualization. Yinfeng Wei: Writing - review & editing, Methodology, Formal analysis. Yuxin Huang: Methodology, Investigation. Chenyu Wang: Methodology, Investigation, Data curation. Tao Wang: Methodology, Investigation, Funding acquisition. Yujiao Wang: Methodology, Investigation. Yingxuan Qi: Methodology, Investigation. Guannan Liu: Writing - review & editing, Writing - original draft, Supervision, Project administration, Methodology, Investigation, Funding acquisition, Data curation, Conceptualization.

Declaration of competing interest

2096-3467The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

2096-3467This study was supported by the Jiangsu Basic Research Center for Synthetic Biology (BK20233003), Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture (XTD2214), National Natural Science Foundation of China (21808109), Natural Science Foundation of Jiangsu Province (BK20180703), Natural Science Foundation of Tianjin Municipality (18JCQNJC10200). T.W was supported by the National Students' Platform for Innovation and Entrepreneurship Training Program (202410291018Z).

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