Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts

Zhenguo Lin, Tzi Yuan Wang, Bing Shi Tsai, Fang Ting Wu, Fu Jung Yu, Yu Jung Tseng, Huang-Mo Sung, Wen Hsiung Li

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Gene regulation change has long been recognized as an important mechanism for phenotypic evolution. We used the evolution of yeast aerobic fermentation as a model to explore how gene regulation has evolved and how this process has contributed to phenotypic evolution and adaptation. Most eukaryotes fully oxidize glucose to CO2 and H2O in mitochondria to maximize energy yield, whereas some yeasts, such as Saccharomyces cerevisiae and its relatives, predominantly ferment glucose into ethanol even in the presence of oxygen, a phenomenon known as aerobic fermentation. We examined the genome-wide gene expression levels among 12 different yeasts and found that a group of genes involved in the mitochondrial respiration process showed the largest reduction in gene expression level during the evolution of aerobic fermentation. Our analysis revealed that the downregulation of these genes was significantly associated with massive loss of binding motifs of Cbf1p in the fermentative yeasts. Our experimental assays confirmed the binding of Cbf1p to the predicted motif and the activator role of Cbf1p. In summary, our study laid a foundation to unravel the long-time mystery about the genetic basis of evolution of aerobic fermentation, providing new insights into understanding the role of cis-regulatory changes in phenotypic evolution.

Original languageEnglish
Pages (from-to)1065-1078
Number of pages14
JournalGenome Biology and Evolution
Volume5
Issue number6
DOIs
Publication statusPublished - 2013 Dec 1

Fingerprint

Fermentation
fermentation
yeast
Yeasts
yeasts
Genes
gene
Gene Expression
Glucose
gene expression
Molecular Evolution
glucose
genes
Eukaryota
Saccharomyces cerevisiae
Mitochondria
Respiration
Ethanol
Down-Regulation
Genome

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Lin, Z., Wang, T. Y., Tsai, B. S., Wu, F. T., Yu, F. J., Tseng, Y. J., ... Li, W. H. (2013). Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts. Genome Biology and Evolution, 5(6), 1065-1078. https://doi.org/10.1093/gbe/evt067
Lin, Zhenguo ; Wang, Tzi Yuan ; Tsai, Bing Shi ; Wu, Fang Ting ; Yu, Fu Jung ; Tseng, Yu Jung ; Sung, Huang-Mo ; Li, Wen Hsiung. / Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts. In: Genome Biology and Evolution. 2013 ; Vol. 5, No. 6. pp. 1065-1078.
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Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts. / Lin, Zhenguo; Wang, Tzi Yuan; Tsai, Bing Shi; Wu, Fang Ting; Yu, Fu Jung; Tseng, Yu Jung; Sung, Huang-Mo; Li, Wen Hsiung.

In: Genome Biology and Evolution, Vol. 5, No. 6, 01.12.2013, p. 1065-1078.

Research output: Contribution to journalArticle

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