TY - JOUR T1 - On the illusion of auxotrophy: <em>met15Δ</em> yeast cells can grow on inorganic sulfur thanks to the previously uncharacterized homocysteine synthase Yll058w JF - bioRxiv DO - 10.1101/2022.01.19.476918 SP - 2022.01.19.476918 AU - S. Branden Van Oss AU - Saurin Bipin Parikh AU - Nelson Castilho Coelho AU - Aaron Wacholder AU - Ivan Belashov AU - Sara Zdancewicz AU - Manuel Michaca AU - Jiazhen Xu AU - Yun Pyo Kang AU - Nathan P. Ward AU - Sang Jun Yoon AU - Katherine M. McCourt AU - Jake McKee AU - Trey Ideker AU - Andrew P. VanDemark AU - Gina M. DeNicola AU - Anne-Ruxandra Carvunis Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/11/08/2022.01.19.476918.abstract N2 - Organisms must either synthesize or assimilate essential organic compounds to survive. The homocysteine synthase Met15 has been considered essential for inorganic sulfur assimilation in yeast since its discovery in the 1970s. As a result, MET15 has served as a genetic marker for hundreds of experiments that play a foundational role in eukaryote genetics and systems biology. Nevertheless, we demonstrate here through structural and evolutionary modeling, in vitro kinetic assays, and genetic complementation, that an alternative homocysteine synthase encoded by the previously uncharacterized gene YLL058W enables cells lacking Met15 to assimilate enough inorganic sulfur for survival and proliferation. These cells however fail to grow in patches or liquid cultures unless provided with exogenous methionine or other organosulfurs. We show that this growth failure, which has historically justified the status of MET15 as a classic auxotrophic marker, is largely explained by toxic accumulation of the gas hydrogen sulfide due to a metabolic bottleneck. When patched or cultured with a hydrogen sulfide chelator, and when propagated as colony grids, cells without Met15 assimilate inorganic sulfur and grow, and cells with Met15 achieve even higher yields. Thus, Met15 is not essential for inorganic sulfur assimilation in yeast. Instead, MET15 is the first example of a yeast gene whose loss conditionally prevents growth in a manner that depends on local gas exchange. Our results have broad implications for investigations of sulfur metabolism, including studies of stress response, methionine restriction, and aging. More generally, our findings illustrate how unappreciated experimental variables can obfuscate biological discovery.Competing Interest StatementA.-R. C. is a member of the scientific advisory board for Flagship Labs 69, Inc. T.I. is a co-founder of Data4Cure and has an equity interest. T.I. is on the Scientific Advisory Board of Ideaya BioSciences, Inc., has an equity interest, and receives income. The terms of these arrangements have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies. ER -