INVESTIGATION The Regulation of Cbf1 by PAS Kinase Is a Pivotal Control Point for Lipogenesis vs. Respiration in Saccharomyces cerevisiae Desiree DeMille,* ,1 Jenny A. Pape,* ,1 Benjamin T. Bikman, † Majid Ghassemian, ‡ and Julianne H. Grose* ,2 *Department of Microbiology and Molecular Biology and † Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602 and ‡ Department of Chemistry/Biochemistry, University of California at San Diego, La Jolla, 92093-0378 ORCID IDs: 0000-0001-7924-3379 (D.D.); 0000-0001-8816-6635 (J.H.G.) ABSTRACT PAS kinase 1 (Psk1) is a key regulator of respiration in Saccharomyces cerevisiae. Herein the molecular mechanisms of this regulation are explored through the characterization of its substrate, Centro- mere binding factor 1 (Cbf1). CBF1-deficient yeast displayed a significant decrease in cellular respiration, while PAS kinase-deficient yeast, or yeast harboring a Cbf1 phosphosite mutant (T211A) displayed a sig- nificant increase. Transmission electron micrographs showed an increased number of mitochondria in PAS kinase-deficient yeast consistent with the increase in respiration. Although the CBF1-deficient yeast did not appear to have an altered number of mitochondria, a mitochondrial proteomics study revealed significant differences in the mitochondrial composition of CBF1-deficient yeast including altered Atp3 levels, a sub- unit of the mitochondrial F 1 -ATP synthase complex. Both beta-galactosidase reporter assays and western blot analysis confirmed direct transcriptional control of ATP3 by Cbf1. In addition, we confirmed the reg- ulation of yeast lipid genes LAC1 and LAG1 by Cbf1. The human homolog of Cbf1, Upstream transcription factor 1 (USF1), is also known to be involved in lipid biogenesis. Herein, we provide the first evidence for a role of USF1 in respiration since it appeared to complement Cbf1 in vivo as determined by respiration phenotypes. In addition, we confirmed USF1 as a substrate of human PAS kinase (hPASK) in vitro. Com- bined, our data supports a model in which Cbf1/USF1 functions to partition glucose toward respiration and away from lipid biogenesis, while PAS kinase inhibits respiration in part through the inhibition of Cbf1/USF1. KEYWORDS PAS kinase Cbf1 USF1 respiration lipogenesis mitochondria Proper resource allocation is fundamental to the success of any system. In cellular organisms, it is crucial to sense available nutrients and astutely allocate them among several pathways including growth, storage and energy metabolism. If nutrients are not properly allo- cated, e.g., when too many nutrients are diverted to one pathway, it comes at the expense of another important pathway and often leads to diseases such as obesity, diabetes and cancer. One of the mech- anisms that cells have evolved to help coordinate resource allocation are nutrient sensing protein kinases (Lindsley and Rutter 2004). PAS kinase is a highly conserved sensory kinase with both a sensory PAS (Per-ARNT-Sim) domain and a serine/threonine kinase domain (Rutter et al., 2001). It is a key player in sensing and allocating glucose in eukaryotic cells (reviewed in Cardon and Rutter 2012; DeMille and Grose 2013; Grose and Rutter 2010; Hao and Rutter 2008; Schlafli et al., 2009; Smith and Rutter 2007; Zhang et al., 2015). Additionally, PAS kinase is activated both in yeast and mammalian cells under conditions that ac- tivate respiratory metabolism (da Silva Xavier et al., 2004; Grose et al., 2007). This occurs in yeast when cells are grown on carbon sources other than glucose and in mammalian cells under conditions of high glucose. PAS kinase is not only activated by respiratory conditions, but is also implicated in regulating respiratory metabolism itself. PAS Copyright © 2019 DeMille et al. doi: https://doi.org/10.1534/g3.118.200663 Manuscript received August 10, 2018; accepted for publication October 23, 2018; published Early Online October 31, 2018. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/ licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Supplemental material available at Figshare: https://doi.org/10.25387/g3.6933335. 1 These authors contributed equally to this work. 2 Corresponding author: 4007 LSB, 701 East University Parkway, Provo, UT 84602, grosejulianne@gmail.com, 801-422-4940 Volume 9 | January 2019 | 33