Histone Chaperone Paralogs Have Redundant, Cooperative, and Divergent Functions in Yeast.

Neda Savic,Shawn P Shortill,Joseph M Dobbs,Misha Bilenky,David Dilworth,Martin Hirst,Christopher J Nelson

doi:10.1534/genetics.119.302235

Neda Savic, Shawn P Shortill + Show 5 more

Open Access

https://doi.org/10.1534/genetics.119.302235

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Journal: Genetics	Publication Date: Dec 1, 2019
Citations: 4	License type: cc-by

Affiliation: University of Victoria, BC Cancer Agency

Abstract

Gene duplications increase organismal robustness by providing freedom for gene divergence or by increasing gene dosage. The yeast histone chaperones Fpr3 and Fpr4 are paralogs that can assemble nucleosomes in vitro; however, the genomic locations they target and their functional relationship is poorly understood. We refined the yeast synthetic genetic array approach to enable the functional dissection of gene paralogs. Applying this method to Fpr3 and Fpr4 uncovered redundant, cooperative, and divergent functions. While Fpr3 is uniquely involved in chromosome segregation, Fpr3 and Fpr4 cooperate to regulate genes involved in polyphosphate metabolism and ribosome biogenesis. We find that the TRAMP5 RNA exosome is critical for fitness in Δfpr3Δfpr4 yeast and leverage this information to identify an important role for Fpr4 at the 5′ ends of protein coding genes. Additionally, Fpr4 and TRAMP5 negatively regulate RNAs from the nontranscribed spacers of ribosomal DNA. Yeast lacking Fpr3 and Fpr4 exhibit a genome instability phenotype at the ribosomal DNA, which implies that these histone chaperones regulate chromatin structure and DNA access at this location. Taken together. we provide genetic and transcriptomic evidence that Fpr3 and Fpr4 operate separately, cooperatively, and redundantly to regulate a variety of chromatin environments.

Highlights

GENE duplication events play an important role both in driving protein evolution and in providing a mechanism for ensuring the robustness of biological systems
Through a set of comprehensive genetic interaction screens designed for paralogs and a series of RNA-sequencing (RNA-seq) transcriptome surveys, we demonstrate that Fpr3 and Fpr4 operate separately, cooperatively, and redundantly
The query strain harbored an episomal URA3 plasmid with a functional FPR4 gene to avoid the slow growth phenotype of Dfpr3Dfpr4 dual deletion yeast, and its vulnerability to suppressor mutations. This plasmid was maintained until the final step of the screen, when counterselection with 59FOA created the fpr4 null status. The spores of this single cross were manipulated to generate three separate synthetic genetic array (SGA) screens that identified all genetic interactions with Dfpr3, Dfpr4, and genes whose disruption affected the fitness of yeast lacking both Dfpr3Dfpr4

Summary

Introduction

GENE duplication events play an important role both in driving protein evolution and in providing a mechanism for ensuring the robustness of biological systems. The FPR3 and FPR4 genes encode two Saccharomyces cerevisiae paralogs (Benton et al 1994; Manning-Krieg et al 1994; Shan et al 1994; Dolinski et al 1997) derived from a distant ancestral gene (Wolfe and Shields 1997; Kellis et al 2004; Pemberton 2006) They code for highly similar proteins (58% identical and 72% similar in amino acid residues) with acidic N-terminal nucleoplasmin-like histone chaperone and C-terminal FK506-binding (FKBP) peptidyl-prolyl isomerase domains (Kuzuhara and Horikoshi 2004; Xiao et al 2006; Park et al 2014) (Figure 1A). Taken together we provide genetic and transcriptomic evidence that Fpr and Fpr operate separately, cooperatively, and redundantly to regulate a variety of chromatin environments

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Conclusion