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Open Access Highly Accessed Research article

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe

Ian Carter-O’Connell12, Michael T Peel4, Dennis D Wykoff4* and Erin K O’Shea123*

Author Affiliations

1 Howard Hughes Medical Institute, Faculty of Arts and Sciences, Center for Systems Biology, Northwest Labs, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA

2 Department of Molecular and Cellular Biology, Harvard University, Faculty of Arts and Sciences, Center for Systems Biology, Northwest Labs, 52 Oxford Street, Cambridge, MA, 02138, USA

3 Department of Chemistry and Chemical Biology, Harvard University, Faculty of Arts and Sciences, Center for Systems Biology, Northwest Labs, 52 Oxford Street, Cambridge, MA, 02138, USA

4 Department of Biology, Villanova University, 800 Lancaster Ave, Villanova, PA, 19085, USA

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BMC Genomics 2012, 13:697  doi:10.1186/1471-2164-13-697

Published: 12 December 2012

Abstract

Background

Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway, leading to expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway involving genetically identified positive (pho7+) and negative (csk1+) regulators. The genes induced by phosphate limitation and the molecular mechanism by which pho7+ and csk1+ function are unknown. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response.

Results

We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response that contains the ScPHO5 (pho1+), ScPHO84 (SPBC8E4.01c), and ScGIT1 (SPBC1271.09) orthologs. We identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction.

Conclusions

We provide a global analysis of the transcriptional response to phosphate limitation in S. pombe. Our results elucidate the conserved core regulon induced in response to phosphate starvation in this ascomycete distantly related to S. cerevisiae and provide a better understanding of flexibility in environmental stress response networks.

Keywords:
Phosphate starvation pathway; pho7+; csk1+; S. pombe chIp-seq; Gene expression