Integrated analysis of the yeast NADPH-regulator Stb5 reveals distinct differences in NADPH requirements and regulation in different states of yeast metabolism

Liming Ouyang, Petter Holland, Hongzhong Lu, David Bergenholm, Jens Nielsen*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

The Saccharomyces cerevisiae transcription factor (TF) Stb5 is known to be involved in regulating NADPH generation. We explored its role by combining DNA binding studies with transcriptome analysis at four environmental conditions that were selected to cover a range of different metabolic states. Using ChIP-exo, DNA binding targets of Stb5 were found to confirm many previously proposed binding targets, in particular genes encoding enzymes involved in NADPH generation and the pentose-phosphate (PP) pathway. Transcriptome analysis of an STB5 deletion strain revealed transcriptional changes in direct regulation targets of Stb5, including several PP pathway genes as well as additional novel regulatory targets, but interestingly not including the proposed PP pathway flux controlling enzyme Zwf1. Consistently, NADPH levels were found to decrease significantly with STB5 deletion in cultures with aerobic, glucose metabolism. We also found reduced growth for the STB5 deletion strain in similar conditions as those with reduced NADPH levels, supporting a role for Stb5 in NADPH generation through the PP pathway. We finally explored the flux distribution by genome scale modelling simulations and found a decreased flux in both NADPH generating as well as consuming reactions in the STB5 deletion strain.
Original languageEnglish
Article numberfoy091
JournalFEMS Yeast Research
Volume18
Issue number8
Number of pages12
ISSN1567-1356
DOIs
Publication statusPublished - 2018

Keywords

  • CHIP-exo
  • genome scale metabolic modelling
  • NADPH
  • pentose phosphate pathway
  • RNA-seq
  • Stb5
  • yeast Saccharomyces cerevisiae

Cite this

@article{cfdcd13b624d4eebb7eb3db918561466,
title = "Integrated analysis of the yeast NADPH-regulator Stb5 reveals distinct differences in NADPH requirements and regulation in different states of yeast metabolism",
abstract = "The Saccharomyces cerevisiae transcription factor (TF) Stb5 is known to be involved in regulating NADPH generation. We explored its role by combining DNA binding studies with transcriptome analysis at four environmental conditions that were selected to cover a range of different metabolic states. Using ChIP-exo, DNA binding targets of Stb5 were found to confirm many previously proposed binding targets, in particular genes encoding enzymes involved in NADPH generation and the pentose-phosphate (PP) pathway. Transcriptome analysis of an STB5 deletion strain revealed transcriptional changes in direct regulation targets of Stb5, including several PP pathway genes as well as additional novel regulatory targets, but interestingly not including the proposed PP pathway flux controlling enzyme Zwf1. Consistently, NADPH levels were found to decrease significantly with STB5 deletion in cultures with aerobic, glucose metabolism. We also found reduced growth for the STB5 deletion strain in similar conditions as those with reduced NADPH levels, supporting a role for Stb5 in NADPH generation through the PP pathway. We finally explored the flux distribution by genome scale modelling simulations and found a decreased flux in both NADPH generating as well as consuming reactions in the STB5 deletion strain.",
keywords = "CHIP-exo, genome scale metabolic modelling, NADPH, pentose phosphate pathway, RNA-seq, Stb5, yeast Saccharomyces cerevisiae",
author = "Liming Ouyang and Petter Holland and Hongzhong Lu and David Bergenholm and Jens Nielsen",
year = "2018",
doi = "10.1093/femsyr/foy091",
language = "English",
volume = "18",
journal = "F E M S Yeast Research",
issn = "1567-1356",
publisher = "Oxford University Press",
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Integrated analysis of the yeast NADPH-regulator Stb5 reveals distinct differences in NADPH requirements and regulation in different states of yeast metabolism. / Ouyang, Liming; Holland, Petter; Lu, Hongzhong; Bergenholm, David; Nielsen, Jens.

In: FEMS Yeast Research, Vol. 18, No. 8, foy091, 2018.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - Integrated analysis of the yeast NADPH-regulator Stb5 reveals distinct differences in NADPH requirements and regulation in different states of yeast metabolism

AU - Ouyang, Liming

AU - Holland, Petter

AU - Lu, Hongzhong

AU - Bergenholm, David

AU - Nielsen, Jens

PY - 2018

Y1 - 2018

N2 - The Saccharomyces cerevisiae transcription factor (TF) Stb5 is known to be involved in regulating NADPH generation. We explored its role by combining DNA binding studies with transcriptome analysis at four environmental conditions that were selected to cover a range of different metabolic states. Using ChIP-exo, DNA binding targets of Stb5 were found to confirm many previously proposed binding targets, in particular genes encoding enzymes involved in NADPH generation and the pentose-phosphate (PP) pathway. Transcriptome analysis of an STB5 deletion strain revealed transcriptional changes in direct regulation targets of Stb5, including several PP pathway genes as well as additional novel regulatory targets, but interestingly not including the proposed PP pathway flux controlling enzyme Zwf1. Consistently, NADPH levels were found to decrease significantly with STB5 deletion in cultures with aerobic, glucose metabolism. We also found reduced growth for the STB5 deletion strain in similar conditions as those with reduced NADPH levels, supporting a role for Stb5 in NADPH generation through the PP pathway. We finally explored the flux distribution by genome scale modelling simulations and found a decreased flux in both NADPH generating as well as consuming reactions in the STB5 deletion strain.

AB - The Saccharomyces cerevisiae transcription factor (TF) Stb5 is known to be involved in regulating NADPH generation. We explored its role by combining DNA binding studies with transcriptome analysis at four environmental conditions that were selected to cover a range of different metabolic states. Using ChIP-exo, DNA binding targets of Stb5 were found to confirm many previously proposed binding targets, in particular genes encoding enzymes involved in NADPH generation and the pentose-phosphate (PP) pathway. Transcriptome analysis of an STB5 deletion strain revealed transcriptional changes in direct regulation targets of Stb5, including several PP pathway genes as well as additional novel regulatory targets, but interestingly not including the proposed PP pathway flux controlling enzyme Zwf1. Consistently, NADPH levels were found to decrease significantly with STB5 deletion in cultures with aerobic, glucose metabolism. We also found reduced growth for the STB5 deletion strain in similar conditions as those with reduced NADPH levels, supporting a role for Stb5 in NADPH generation through the PP pathway. We finally explored the flux distribution by genome scale modelling simulations and found a decreased flux in both NADPH generating as well as consuming reactions in the STB5 deletion strain.

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