A Novel Plasmid-Based Microarray Screen Identifies Suppressors of rrp6Δ in Saccharomyces cerevisiae

Abstract

Genetic screens in Saccharomyces cerevisiae provide novel information about interacting genes and pathways. We screened for high-copy-number suppressors of a strain with the gene encoding the nuclear exosome component Rrp6p deleted, with either a traditional plate screen for suppressors of rrp6Δ temperature sensitivity or a novel microarray enhancer/suppressor screening (MES) strategy. MES combines DNA microarray technology with high-copy-number plasmid expression in liquid media. The plate screen and MES identified overlapping, but also different, suppressor genes. Only MES identified the novel mRNP protein Nab6p and the tRNA transporter Los1p, which could not have been identified in a traditional plate screen; both genes are toxic when overexpressed in rrp6Δ strains at 37°C. Nab6p binds poly(A)⁺ RNA, and the functions of Nab6p and Los1p suggest that mRNA metabolism and/or protein synthesis are growth rate limiting in rrp6Δ strains. Microarray analyses of gene expression in rrp6Δ strains and a number of suppressor strains support this hypothesis.

SUPPLEMENTAL MATERIAL

We thank colleagues in the Rosbash and Jensen laboratories, as well as former colleagues K. Dower and N. Kuperwasser, for helpful suggestions and encouragement. We are particularly grateful to Sebastian Kadener for help with the Affymetrix microarray analysis. We thank B. Goode for providing the arp2-1 mutant strain (Y721).

The work was supported in part by grants from the NIH (GM23549) to M.R. and from the Danish National Research Foundation and the Novo Nordisk Foundation to T.H.J. K.A. was partially supported by an NIH postdoctoral fellowship (GM66640).