Exploration of essential gene functions via titratable promoter alleles
Cell 2004 Jul 9 118(1) p.31-44

Sanie Mnaimneh,^1,5 Armaity P. Davierwala,^1,5 Jennifer Haynes,^2,5 Jason Moffat,² Wen-Tao Peng,¹ Wen Zhang,^1,2 Xueqi Yang,¹ Jeff Pootoolal,¹ Gordon Chua,¹ Andres Lopez,¹ Miles Trochesset,¹ Darcy Morse,³ Nevan J. Krogan,^1,2 Shawna L. Hiley,¹ Zhijian Li,^1,2 Quaid Morris,¹ Jörg Grigull,¹ Nicholas Mitsakakis,¹ Christopher J. Roberts,⁴ Jack F. Greenblatt,^1,2 Charles Boone,^1,2 Chris A. Kaiser,³ Brenda J. Andrews,² and Timothy R. Hughes^1,2

¹Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
²Department of Medical Genetics and Microbiology, University of Toronto, 1 Kings College Circle, Toronto, ON, Canada
³Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
⁴Rosetta Inpharmatics LLC, a wholly owned supsidiary of Merck & Co., Inc., 401 Terry Avenue North, Seattle, WA 98109 USA

 

Abstract

Nearly 20% of yeast genes are required for viability, hindering genetic analysis with knockouts. We created promoter-shutoff strains for over two-thirds of all essential yeast genes and supjected them to morphological analysis, size profiling, drug sensitivity screening, and microarray expression profiling. We then used this compendium of data to ask which phenotypic features characterized different functional classes and used these to infer potential functions for uncharacterized genes. We identified genes involved in ribosome biogenesis (HAS1, URB1, and URB2), protein secretion (SEC39), mitochondrial import (MIM1), and tRNA charging (GSN1). In addition, apparent negative feedback transcriptional regulation of both ribosome biogenesis and the proteasome was observed. We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection.