skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae

Abstract

Saccharomyces cerevisiae responds to changes in extracellular inorganic phosphate (Pi) availability by regulating the activity of the phosphate-responsive (PHO) signaling pathway, enabling cells to maintain intracellular levels of the essential nutrient Pi. Pi-limitation induces upregulation of inositol heptakisphosphate (IP7) synthesized by the inositol hexakisphosphate kinase Vip1, triggering inhibition of the Pho80/Pho85 cyclin-cyclin dependent kinase (CDK) complex by the CDK inhibitor Pho81, which upregulates the PHO regulon through the CDK target and transcription factor Pho4. To identify genes that are involved in signaling upstream of the Pho80/Pho85/Pho81 complex and how they interact with each other to regulate the PHO pathway, we performed genome-wide screens with the synthetic genetic array method. We identified more than 300 mutants with defects in signaling upstream of the Pho80/Pho85/Pho81 complex, including AAH1, which encodes an adenine deaminase that negatively regulates the PHO pathway in a Vip1-dependent manner. Moreover, we showed that even in the absence of VIP1, the PHO pathway can be activated under prolonged periods of Pi starvation, suggesting complexity in the mechanisms by which the PHO pathway is regulated.

Authors:
ORCiD logo; ; ; ;
Publication Date:
Research Org.:
Princeton Univ., NJ (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1357715
Alternate Identifier(s):
OSTI ID: 1389780
Grant/Contract Number:  
SC0012461
Resource Type:
Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Name: PLoS ONE Journal Volume: 12 Journal Issue: 5; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; adenine; metabolic pathways; epistasis; genetic screens; phenotypes; gene regulation; genomic signal processing; Saccharomyces cerevisiae

Citation Formats

Choi, Joonhyuk, Rajagopal, Abbhirami, Xu, Yi-Fan, Rabinowitz, Joshua D., and O’Shea, Erin K. A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae. United States: N. p., 2017. Web. doi:10.1371/journal.pone.0176085.
Choi, Joonhyuk, Rajagopal, Abbhirami, Xu, Yi-Fan, Rabinowitz, Joshua D., & O’Shea, Erin K. A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae. United States. doi:10.1371/journal.pone.0176085.
Choi, Joonhyuk, Rajagopal, Abbhirami, Xu, Yi-Fan, Rabinowitz, Joshua D., and O’Shea, Erin K. Wed . "A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae". United States. doi:10.1371/journal.pone.0176085.
@article{osti_1357715,
title = {A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae},
author = {Choi, Joonhyuk and Rajagopal, Abbhirami and Xu, Yi-Fan and Rabinowitz, Joshua D. and O’Shea, Erin K.},
abstractNote = {Saccharomyces cerevisiae responds to changes in extracellular inorganic phosphate (Pi) availability by regulating the activity of the phosphate-responsive (PHO) signaling pathway, enabling cells to maintain intracellular levels of the essential nutrient Pi. Pi-limitation induces upregulation of inositol heptakisphosphate (IP7) synthesized by the inositol hexakisphosphate kinase Vip1, triggering inhibition of the Pho80/Pho85 cyclin-cyclin dependent kinase (CDK) complex by the CDK inhibitor Pho81, which upregulates the PHO regulon through the CDK target and transcription factor Pho4. To identify genes that are involved in signaling upstream of the Pho80/Pho85/Pho81 complex and how they interact with each other to regulate the PHO pathway, we performed genome-wide screens with the synthetic genetic array method. We identified more than 300 mutants with defects in signaling upstream of the Pho80/Pho85/Pho81 complex, including AAH1, which encodes an adenine deaminase that negatively regulates the PHO pathway in a Vip1-dependent manner. Moreover, we showed that even in the absence of VIP1, the PHO pathway can be activated under prolonged periods of Pi starvation, suggesting complexity in the mechanisms by which the PHO pathway is regulated.},
doi = {10.1371/journal.pone.0176085},
journal = {PLoS ONE},
number = 5,
volume = 12,
place = {United States},
year = {2017},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1371/journal.pone.0176085

Save / Share:

Works referenced in this record:

The phosphatase system in Saccharomyces cerevisiae.
journal, January 1997


Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map
journal, February 2007

  • Collins, Sean R.; Miller, Kyle M.; Maas, Nancy L.
  • Nature, Vol. 446, Issue 7137
  • DOI: 10.1038/nature05649

An intracellular phosphate buffer filters transient fluctuations in extracellular phosphate levels
journal, June 2005

  • Thomas, M. R.; O'Shea, E. K.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 27
  • DOI: 10.1073/pnas.0501122102

Regulation of Yeast Pyruvate Kinase by Ultrasensitive Allostery Independent of Phosphorylation
journal, October 2012


Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile
journal, November 2005


Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae
journal, July 2009

  • Camblong, J.; Beyrouthy, N.; Guffanti, E.
  • Genes & Development, Vol. 23, Issue 13
  • DOI: 10.1101/gad.522509

The receptor Msn5 exports the phosphorylated transcription factor Pho4 out of the nucleus
journal, December 1998

  • Kaffman, Arie; Rank, Nicole Miller; O'Neill, Elizabeth M.
  • Nature, Vol. 396, Issue 6710
  • DOI: 10.1038/24898

Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations
journal, January 2010

  • Boer, Viktor M.; Crutchfield, Christopher A.; Bradley, Patrick H.
  • Molecular Biology of the Cell, Vol. 21, Issue 1
  • DOI: 10.1091/mbc.E09-07-0597

Regulation of a Cyclin-CDK-CDK Inhibitor Complex by Inositol Pyrophosphates
journal, April 2007


Metabolic intermediates selectively stimulate transcription factor interaction and modulate phosphate and purine pathways
journal, June 2009

  • Pinson, B.; Vaur, S.; Sagot, I.
  • Genes & Development, Vol. 23, Issue 12
  • DOI: 10.1101/gad.521809

Partially Phosphorylated Pho4 Activates Transcription of a Subset of Phosphate-Responsive Genes
journal, November 2003


Phosphate-regulated inactivation of the kinase PHO80-PHO85 by the CDK inhibitor PHO81
journal, October 1994


A Systematic High-Throughput Screen of a Yeast Deletion Collection for Mutants Defective in PHO5 Regulation
journal, February 2005


Ordering gene function: the interpretation of epistasis in regulatory hierarchies
journal, September 1992


Inositol pyrophosphates: between signalling and metabolism
journal, May 2013

  • Wilson, Miranda S. C.; Livermore, Thomas M.; Saiardi, Adolfo
  • Biochemical Journal, Vol. 452, Issue 3
  • DOI: 10.1042/BJ20130118

Regulation of PHO4 Nuclear Localization by the PHO80-PHO85 Cyclin-CDK Complex
journal, January 1996


Signaling phosphate starvation
journal, October 1996


A Distal, High-affinity Binding Site on the Cyclin-CDK Substrate Pho4 is Important for its Phosphorylation and Regulation
journal, January 2004

  • Byrne, Meghan; Miller, Nicole; Springer, Michael
  • Journal of Molecular Biology, Vol. 335, Issue 1
  • DOI: 10.1016/j.jmb.2003.10.035

Molecular basis of cyclin-CDK-CKI regulation by reversible binding of an inositol pyrophosphate
journal, November 2007

  • Lee, Young-Sam; Huang, Kexin; Quiocho, Florante A.
  • Nature Chemical Biology, Vol. 4, Issue 1
  • DOI: 10.1038/nchembio.2007.52

Exploring genetic interactions and networks with yeast
journal, June 2007

  • Boone, Charles; Bussey, Howard; Andrews, Brenda J.
  • Nature Reviews Genetics, Vol. 8, Issue 6
  • DOI: 10.1038/nrg2085

Positive Feedback Regulates Switching of Phosphate Transporters in S. cerevisiae
journal, September 2007


Multi-site phosphorylation of pho4 by the cyclin-CDK pho80-pho85 is semi-processive with site preference
journal, March 2001

  • Jeffery, Douglas A.; Springer, Michael; King, David S.
  • Journal of Molecular Biology, Vol. 306, Issue 5
  • DOI: 10.1006/jmbi.2000.4417

Chromatin decouples promoter threshold from dynamic range
journal, April 2008

  • Lam, Felix H.; Steger, David J.; O’Shea, Erin K.
  • Nature, Vol. 453, Issue 7192
  • DOI: 10.1038/nature06867

Phosphorylation of the transcription factor PHO4 by a cyclin-CDK complex, PHO80-PHO85
journal, February 1994


The PHO84 gene of Saccharomyces cerevisiae encodes an inorganic phosphate transporter.
journal, June 1991

  • Bun-Ya, M.; Nishimura, M.; Harashima, S.
  • Molecular and Cellular Biology, Vol. 11, Issue 6
  • DOI: 10.1128/MCB.11.6.3229

The Inositol Hexakisphosphate Kinase Family: CATALYTIC FLEXIBILITY AND FUNCTION IN YEAST VACUOLE BIOGENESIS
journal, May 2000

  • Saiardi, Adolfo; Caffrey, James J.; Snyder, Solomon H.
  • Journal of Biological Chemistry, Vol. 275, Issue 32
  • DOI: 10.1074/jbc.M002750200

Comprehensive Characterization of Genes Required for Protein Folding in the Endoplasmic Reticulum
journal, March 2009


Bimodal expression of PHO84 is modulated by early termination of antisense transcription
journal, June 2013

  • Castelnuovo, Manuele; Rahman, Samir; Guffanti, Elisa
  • Nature Structural & Molecular Biology, Vol. 20, Issue 7
  • DOI: 10.1038/nsmb.2598

Phosphorylation regulates association of the transcription factor Pho4 with its import receptor Pse1/Kap121
journal, September 1998


Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer
journal, April 2010

  • Lu, Wenyun; Clasquin, Michelle F.; Melamud, Eugene
  • Analytical Chemistry, Vol. 82, Issue 8
  • DOI: 10.1021/ac902837x

Concentrations of intermediary metabolites in yeast
journal, April 1973


A comprehensive strategy enabling high-resolution functional analysis of the yeast genome
journal, July 2008

  • Breslow, David K.; Cameron, Dale M.; Collins, Sean R.
  • Nature Methods, Vol. 5, Issue 8
  • DOI: 10.1038/nmeth.1234

Yeast AMP Pathway Genes Respond to Adenine through Regulated Synthesis of a Metabolic Intermediate
journal, December 2001


Optimized cassettes for fluorescent protein tagging inSaccharomyces cerevisiae
journal, June 2004


Synthesis and biological actions of diphosphoinositol phosphates (inositol pyrophosphates), regulators of cell homeostasis
journal, September 2012


Nutrient-sensing mechanisms and pathways
journal, January 2015

  • Efeyan, Alejo; Comb, William C.; Sabatini, David M.
  • Nature, Vol. 517, Issue 7534
  • DOI: 10.1038/nature14190

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
journal, December 2008

  • Huang, Da Wei; Sherman, Brad T.; Lempicki, Richard A.
  • Nature Protocols, Vol. 4, Issue 1
  • DOI: 10.1038/nprot.2008.211