title: Deletion of PHO13, encoding haloacid dehalogenase type IIA phosphatase, results in upregulation of the pentose phosphate pathway in Saccharomyces cerevisiae.
abstract: The haloacid dehalogenase (HAD) superfamily is one of the largest enzyme families, consisting mainly of phosphatases. Although intracellular phosphate plays important roles in many cellular activities, the biological functions of HAD enzymes are largely unknown. Pho13 is 1 of 16 putative HAD enzymes in Saccharomyces cerevisiae. Pho13 has not been studied extensively, but previous studies have identified PHO13 to be a deletion target for the generation of industrially attractive phenotypes, namely, efficient xylose fermentation and high tolerance to fermentation inhibitors. In order to understand the molecular mechanisms underlying the improved xylose-fermenting phenotype produced by deletion of PHO13 (pho13Δ), we investigated the response of S. cerevisiae to pho13Δ at the transcriptomic level when cells were grown on glucose or xylose. Transcriptome sequencing analysis revealed that pho13Δ resulted in upregulation of the pentose phosphate (PP) pathway and NADPH-producing enzymes when cells were grown on glucose or xylose. We also found that the transcriptional changes induced by pho13Δ required the transcription factor Stb5, which is activated specifically under NADPH-limiting conditions. Thus, pho13Δ resulted in the upregulation of the PP pathway and NADPH-producing enzymes as a part of an oxidative stress response mediated by activation of Stb5. Because the PP pathway is the primary pathway for xylose, its upregulation by pho13Δ might explain the improved xylose metabolism. These findings will be useful for understanding the biological function of S. cerevisiae Pho13 and the HAD superfamily enzymes and for developing S. cerevisiae strains with industrially attractive phenotypes.
authors.affiliation: School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea soorinkim@knu.ac.kr ysjin@illinois.edu.
authors.forename: Soo Rin
authors.initials: SR
authors.lastname: Kim
authors.affiliation: Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Haiqing
authors.initials: H
authors.lastname: Xu
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Anastashia
authors.initials: A
authors.lastname: Lesmana
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Uros
authors.initials: U
authors.lastname: Kuzmanovic
authors.affiliation: Department of Chemical Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Au
authors.affiliation: Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Clarissa
authors.initials: C
authors.lastname: Florencia
authors.affiliation: Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Eun Joong
authors.initials: EJ
authors.lastname: Oh
authors.affiliation: Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Guochang
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Department of Biotechnology, Korea University Graduate School, Seoul, Republic of Korea.
authors.forename: Kyoung Heon
authors.identifier: http://orcid.org/0000-0003-4600-8668
authors.initials: KH
authors.lastname: Kim
authors.affiliation: Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA soorinkim@knu.ac.kr ysjin@illinois.edu.
authors.forename: Yong-Su
authors.initials: YS
authors.lastname: Jin
mesh_terms: D017353:Gene Deletion; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D005947:Glucose / Q000378:metabolism; D006867:Hydrolases / Q000235:genetics* / Q000378:metabolism; D010427:Pentose Phosphate Pathway; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000032:analysis / Q000235:genetics; D015854:Up-Regulation; D014994:Xylose / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins; C488251:Stb5 protein, S cerevisiae; D014157:Transcription Factors; D014994:Xylose; D006867:Hydrolases; C000602301:Pho13 protein, S cerevisiae; D010744:Phosphoric Monoester Hydrolases; C034507:2-haloacid dehalogenase; D005947:Glucose