Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway

Abstract
Data availability
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Abstract

Although combinatorial regulation is a common feature in gene regulatory networks, how it evolves and affects network structure and function is not well understood. In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are required for gene induction and survival during phosphate starvation. In the related human commensal C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate starvation and is only partially required for inducing PHO genes. Phylogenetic survey suggests that reduced dependence on Pho2 evolved in C. glabrata and closely related species. In S. cerevisiae, less Pho2-dependent Pho4 orthologs induce more genes. In C. glabrata, its Pho4 binds to more locations and induces three times as many genes as Pho4 in S. cerevisiae does. Our work shows how evolution of combinatorial regulation allows for rapid expansion of a gene regulatory network's targets, possibly extending its physiological functions.

Data availability

The following data sets were generated

1. He BZ
2. Zhou X
3. O'Shea EK
(2017) Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE97801).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97801

The following previously published data sets were used

1. Zhou X
2. O'Shea EK
(2011) Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4.
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE29506).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29506

Article and author information

Author details

Bin Z He

Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Cambridge, United States

For correspondence
binhe@fas.harvard.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-3072-6238
Xu Zhou

Yale School of Medicine, New Haven, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-1692-6823
Erin K O'Shea

Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Cambridge, United States

For correspondence
osheae@hhmi.org

Competing interests
Erin K O'Shea, Chief Scientific Officer and a Vice President at the Howard Hughes Medical Institute, one of the three founding funders of eLife..

"This ORCID iD identifies the author of this article:" 0000-0002-2649-1018

Funding

Howard Hughes Medical Institute

Bin Z He
Xu Zhou
Erin K O'Shea

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.