The microprotein Nrs1 rewires the G1/S transcriptional machinery during nitrogen limitation in budding yeast.

Sylvain Tollis,Jasmin Coulombe-Huntington,Eric Bonneil,Xiaojing Tang,Ghada Ghazal,Catherine A Royer,Deborah Blake,Roger Palou,Mike Tyers,Yogitha Thattikota,Pierre Thibault,Susan Moore,Jaspal Singh,Sophie G Martin

doi:10.1371/journal.pbio.3001548

Abstract

Commitment to cell division at the end of G1 phase, termed Start in the budding yeast Saccharomyces cerevisiae, is strongly influenced by nutrient availability. To identify new dominant activators of Start that might operate under different nutrient conditions, we screened a genome-wide ORF overexpression library for genes that bypass a Start arrest caused by absence of the G1 cyclin Cln3 and the transcriptional activator Bck2. We recovered a hypothetical gene YLR053c, renamed NRS1 for Nitrogen-Responsive Start regulator 1, which encodes a poorly characterized 108 amino acid microprotein. Endogenous Nrs1 was nuclear-localized, restricted to poor nitrogen conditions, induced upon TORC1 inhibition, and cell cycle-regulated with a peak at Start. NRS1 interacted genetically with SWI4 and SWI6, which encode subunits of the main G1/S transcription factor complex SBF. Correspondingly, Nrs1 physically interacted with Swi4 and Swi6 and was localized to G1/S promoter DNA. Nrs1 exhibited inherent transactivation activity, and fusion of Nrs1 to the SBF inhibitor Whi5 was sufficient to suppress other Start defects. Nrs1 appears to be a recently evolved microprotein that rewires the G1/S transcriptional machinery under poor nitrogen conditions.

Highlights

All organisms have evolved adaptive regulatory mechanisms to optimize fitness in the face of ever-changing environmental conditions
On the premise that additional genes may activate Start under suboptimal nutrient conditions, we screened for genes that can circumvent the Start arrest caused by loss of both CLN3 and BCK2 function
We discovered that Nitrogen-Responsive Start regulator 1 (NRS1) overexpression efficiently bypasses the lethality of a cln3Δ bck2Δ strain and activates Start in wild-type cells; that Nrs1 associates with SCB-Binding Factor (SBF) at G1/S promoter DNA and promotes SBF-dependent transcription; that NRS1 overexpression can genetically suppress defects in SBF function; and that Nrs1 is itself a transcriptional activator

Summary

Introduction

All organisms have evolved adaptive regulatory mechanisms to optimize fitness in the face of ever-changing environmental conditions. This ability to adapt is important for unicellular organisms, which lack the capacity to establish the internal homeostatic environments of metazoan species. A nitrogen source-regulated microprotein activates G1/S transcription in yeast images are provided in the supplemental file S1 Raw Images. Raw quantitative data are provided in the supplemental files S1–S7 Data as indicated in the text. The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE [Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, et al The PRIDE database and related tools and resources in 2019: improving support for quantification data. The RNA-sequencing data have been deposited to the Gene Expression Omnibus database (GEO, NCBI, accession number GSE179366)

Methods

Results

Conclusion