Faculty Opinions recommendation of A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length.

Lithium hexafluorophosphate (LiPF6) is one of the leading electrolytes in lithium-ion batteries, and its usage has increased tremendously in the past few years. Little is known, however, about its potential environmental and biological impacts. In order to improve our understanding of the cytotoxicity of LiPF6 and the specific cellular response mechanisms to it, we performed a genome-wide screen using a yeast (Saccharomyces cerevisiae) deletion mutant collection and identified 75 gene deletion mutants that showed LiPF6 sensitivity. Among these, genes associated with mitochondria showed the most enrichment. We also found that LiPF6 is more toxic to yeast than lithium chloride (LiCl) or sodium hexafluorophosphate (NaPF6). Physiological analysis showed that a high concentration of LiPF6 caused mitochondrial damage, reactive oxygen species (ROS) accumulation, and ATP content changes. Compared with the results of previous genome-wide screening for LiCl-sensitive mutants, we found that oxidative phosphorylation-related mutants were specifically hypersensitive to LiPF6. In these deletion mutants, LiPF6 treatment resulted in higher ROS production and reduced ATP levels, suggesting that oxidative phosphorylation-related genes were important for counteracting LiPF6-induced toxicity. Taken together, our results identified genes specifically involved in LiPF6-modulated toxicity, and demonstrated that oxidative stress and ATP imbalance maybe the driving factors in governing LiPF6-induced toxicity.

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A genome-wide screen for Schizosaccharomyces pombe deletion mutants that affect telomere length

Cell Research ◽

10.1038/cr.2010.107 ◽

2010 ◽

Vol 20 (8) ◽

pp. 963-965 ◽

Cited By ~ 12

Author(s):

Ning-Ning Liu ◽

Tian Xu Han ◽

Li-Lin Du ◽

Jin-Qiu Zhou

Keyword(s):

Schizosaccharomyces Pombe ◽

Telomere Length ◽

Deletion Mutants ◽

Genome Wide ◽

A Genome

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Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network

Nucleic Acids Research ◽

10.1093/nar/gku576 ◽

2014 ◽

Vol 42 (15) ◽

pp. 9838-9853 ◽

Cited By ~ 6

Author(s):

Saeed Kaboli ◽

Takuya Yamakawa ◽

Keisuke Sunada ◽

Tao Takagaki ◽

Yu Sasano ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Genetic Interaction ◽

Interaction Network ◽

Essential Genes ◽

Genetic Interactions ◽

Lethal Gene ◽

Synthetic Lethal ◽

Genome Wide ◽

A Genome ◽

Wide Scale

Abstract Despite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to delete these regions by PCR-mediated chromosomal deletion technology (PCD), which enables chromosomal segments to be deleted by a one-step transformation. Thirty-three of the 110 regions could be deleted, but the remaining 77 regions could not. To determine whether the 77 undeletable regions are essential, we successfully converted 67 of them to mini-chromosomes marked with URA3 using PCR-mediated chromosome splitting technology and conducted a mitotic loss assay of the mini-chromosomes. Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis. This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome. Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

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Pleiotropic drug-resistance attenuated genomic library improves elucidation of drug mechanisms

Molecular BioSystems ◽

10.1039/c5mb00406c ◽

2015 ◽

Vol 11 (11) ◽

pp. 3129-3136 ◽

Cited By ~ 12

Author(s):

Namal V. C. Coorey ◽

James H. Matthews ◽

David S. Bellows ◽

Paul H. Atkinson

Keyword(s):

Saccharomyces Cerevisiae ◽

Drug Resistance ◽

Mechanism Of Action ◽

Gene Deletion ◽

Genomic Library ◽

Deletion Mutants ◽

Pleiotropic Drug Resistance ◽

Genome Wide

Identifying Saccharomyces cerevisiae genome-wide gene deletion mutants that confer hypersensitivity to a xenobiotic aids the elucidation of its mechanism of action (MoA).

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Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast

Science Advances ◽

10.1126/sciadv.aav1848 ◽

2019 ◽

Vol 5 (1) ◽

pp. eaav1848 ◽

Cited By ~ 24

Author(s):

Xueying C. Li ◽

David Peris ◽

Chris Todd Hittinger ◽

Elaine A. Sia ◽

Justin C. Fay

Keyword(s):

Saccharomyces Cerevisiae ◽

Cold Tolerance ◽

Yeast Species ◽

Saccharomyces Uvarum ◽

Phenotypic Differences ◽

Protein Divergence ◽

Thermal Growth ◽

Genome Wide ◽

A Genome ◽

Moderate Effect

Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species,Saccharomyces cerevisiaeandSaccharomyces uvarum. The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence inCOX1affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence.

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An inducible CRISPR interference library for genetic interrogation of Saccharomyces cerevisiae biology

Communications Biology ◽

10.1038/s42003-020-01452-9 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Amir Momen-Roknabadi ◽

Panos Oikonomou ◽

Maxwell Zegans ◽

Saeed Tavazoie

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcriptional Repression ◽

Nucleosome Occupancy ◽

Design Parameters ◽

Experimental Conditions ◽

Crispr Interference ◽

Cellular Processes ◽

Genome Wide ◽

Reliable Assessment ◽

A Genome

AbstractGenome-scale CRISPR interference (CRISPRi) is widely utilized to study cellular processes in a variety of organisms. Despite the dominance of Saccharomyces cerevisiae as a model eukaryote, an inducible genome-wide CRISPRi library in yeast has not yet been presented. Here, we present a genome-wide, inducible CRISPRi library, based on spacer design rules optimized for S. cerevisiae. We have validated this library for genome-wide interrogation of gene function across a variety of applications, including accurate discovery of haploinsufficient genes and identification of enzymatic and regulatory genes involved in adenine and arginine biosynthesis. The comprehensive nature of the library also revealed refined spacer design parameters for transcriptional repression, including location, nucleosome occupancy and nucleotide features. CRISPRi screens using this library can identify genes and pathways with high precision and a low false discovery rate across a variety of experimental conditions, enabling rapid and reliable assessment of genetic function and interactions in S. cerevisiae.

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A genome-wide screen in Saccharomyces cerevisiae reveals a critical role for the mitochondria in the toxicity of a trichothecene mycotoxin

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0909777106 ◽

2009 ◽

Vol 106 (51) ◽

pp. 21883-21888 ◽

Cited By ~ 45

Author(s):

J. E. McLaughlin ◽

M. A. Bin-Umer ◽

A. Tortora ◽

N. Mendez ◽

S. McCormick ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Critical Role ◽

Trichothecene Mycotoxin ◽

Genome Wide ◽

A Genome

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Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae

PeerJ ◽

10.7717/peerj.9442 ◽

2020 ◽

Vol 8 ◽

pp. e9442 ◽

Cited By ~ 1

Author(s):

Zachary J. Waldrip ◽

Piroon Jenjaroenpun ◽

Oktawia DeYoung ◽

Intawat Nookaew ◽

Sean D. Taverna ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

High Specificity ◽

Genomic Locus ◽

Site Specific ◽

Guide Rna ◽

Genome Wide ◽

A Genome ◽

Wide Scale ◽

Chromosome Iii ◽

Genomic Editing

The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potential for site-specific chromosomal studies in organisms with relatively small genomes such as yeasts.

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