scholarly journals Synthetic Lethal Screens Identify Gene Silencing Processes in Yeast and Implicate the Acetylated Amino Terminus of Sir3 in Recognition of the Nucleosome Core

2008 ◽  
Vol 28 (11) ◽  
pp. 3861-3872 ◽  
Author(s):  
Tibor van Welsem ◽  
Floor Frederiks ◽  
Kitty F. Verzijlbergen ◽  
Alex W. Faber ◽  
Zara W. Nelson ◽  
...  
Keyword(s):  
Nonspecific Binding ◽  
Synthetic Lethal ◽  
Nucleosome Core ◽  
Growth Defects ◽  
Sir Proteins ◽  
Epistasis Analysis ◽  
Genome Wide ◽  
Bah Domain ◽  
H3k79 Methylation ◽  
Synthetic Growth

ABSTRACT Dot1 methylates histone H3 lysine 79 (H3K79) on the nucleosome core and is involved in Sir protein-mediated silencing. Previous studies suggested that H3K79 methylation within euchromatin prevents nonspecific binding of the Sir proteins, which in turn facilitates binding of the Sir proteins in unmethylated silent chromatin. However, the mechanism by which the Sir protein binding is influenced by this modification is unclear. We performed genome-wide synthetic genetic array (SGA) analysis and identified interactions of DOT1 with SIR1 and POL32. The synthetic growth defects found by SGA analysis were attributed to the loss of mating type identity caused by a synthetic silencing defect. By using epistasis analysis, DOT1, SIR1, and POL32 could be placed in different pathways of silencing. Dot1 shared its silencing phenotypes with the NatA N-terminal acetyltransferase complex and the conserved N-terminal bromo adjacent homology (BAH) domain of Sir3 (a substrate of NatA). We classified all of these as affecting a common silencing process, and we show that mutations in this process lead to nonspecific binding of Sir3 to chromatin. Our results suggest that the BAH domain of Sir3 binds to histone H3K79 and that acetylation of the BAH domain is required for the binding specificity of Sir3 for nucleosomes unmethylated at H3K79.

scholarly journals Genetic Interactions WithCLF1Identify Additional Pre-mRNA Splicing Factors and a Link Between Activators of Yeast Vesicular Transport and Splicing

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 895-907 ◽  
Author(s):  
Kevin Vincent ◽  
Qiang Wang ◽  
Steven Jay ◽  
Kathryn Hobbs ◽  
Brian C Rymond
Keyword(s):  
Mrna Splicing ◽  
Splicing Factors ◽  
Sequence Information ◽  
Specific Sequence ◽  
Synthetic Lethal ◽  
Growth Defects ◽  
Mrna Maturation ◽  
Assembly Factor ◽  
Gtpase Activation ◽  
Synthetic Growth

AbstractClf1 is a conserved spliceosome assembly factor composed predominately of TPR repeats. Here we show that the TPR elements are not functionally equivalent, with the amino terminus of Clf1 being especially sensitive to change. Deletion and add-back experiments reveal that the splicing defect associated with TPR removal results from the loss of TPR-specific sequence information. Twelve mutants were found that show synthetic growth defects when combined with an allele that lacks TPR2 (i.e., clf1Δ2). The identified genes encode the Mud2, Ntc20, Prp16, Prp17, Prp19, Prp22, and Syf2 splicing factors and four proteins without established contribution to splicing (Bud13, Cet1, Cwc2, and Rds3). Each synthetic lethal with clf1Δ2 (slc) mutant is splicing defective in a wild-type CLF1 background. In addition to the splicing factors, SSD1, BTS1, and BET4 were identified as dosage suppressors of clf1Δ2 or selected slc mutants. These results support Clf1 function through multiple stages of the spliceosome cycle, identify additional genes that promote cellular mRNA maturation, and reveal a link between Rab/Ras GTPase activation and the process of pre-mRNA splicing.

scholarly journals Sec3p is involved in secretion and morphogenesis in Saccharomyces cerevisiae.

1997 ◽  
Vol 8 (4) ◽  
pp. 647-662 ◽  
Author(s):  
F P Finger ◽  
P Novick
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Temperature Sensitive ◽  
Synthetic Lethal ◽  
Growth Defects ◽  
Actin Structure ◽  
Synthetically Lethal ◽  
Bud Site ◽  
Slow Growing ◽  
Late Stages ◽  
Synthetic Growth

Two new temperature-sensitive alleles of SEC3, 1 of 10 late-acting SEC genes required for targeting or fusion of post-Golgi secretory vesicles to the plasma membrane in Saccharomyces cerevisiae, were isolated in a screen for temperature-sensitive secretory mutants that are synthetically lethal with sec4-8. The new sec3 alleles affect early as well as late stages of secretion. Cloning and sequencing of the SEC3 gene revealed that it is identical to profilin synthetic lethal 1 (PSL1). The SEC3 gene is not essential because cells depleted of Sec3p are viable although slow growing and temperature sensitive. All of the sec3 alleles genetically interact with a profilin mutation, pfy1-111. The SEC3 gene in high copy suppresses pfy1-111 and sec5-24 and causes synthetic growth defects with ypt1, sec8-9, sec10-2, and sec15-1. Actin structure is only perturbed in conditions of chronic loss of Sec3p function, implying that Sec3p does not directly regulate actin. All alleles of sec3 cause bud site selection defects in homozygous diploids, as do sec4-8 and sec9-4. This suggests that SEC gene products are involved in determining the bud site and is consistent with a role for Sec3p in determining the correct site of exocytosis.

scholarly journals Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Molly Brothers ◽  
Jasper Rine
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Fusion Protein ◽  
Protein A ◽  
Temperature Sensitive ◽  
Sir Proteins ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Long Read ◽  
Bah Domain ◽  
Sensitive Allele

The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. We developed a method to study these two processes at single base-pair resolution. Using a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, we mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein. A silencing-deficient mutant of Sir3 lacking its Bromo-Adjacent Homology (BAH) domain, sir3-bahΔ, was still recruited to HML, HMR, and telomeres. However, in the absence of the BAH domain, it was unable to spread away from those recruitment sites. Overexpression of Sir3 did not lead to further spreading at HML, HMR, and most telomeres. A few exceptional telomeres, like 6R, exhibited a small amount of Sir3 spreading, suggesting that boundaries at telomeres responded variably to Sir3 overexpression. Finally, by using a temperature-sensitive allele of SIR3 fused to M.ECOGII, we tracked the positions first methylated after induction and found that repression of genes at HML and HMR began before Sir3 occupied the entire locus.

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

2014 ◽  
Vol 42 (15) ◽  
pp. 9838-9853 ◽  
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.

scholarly journals Genome-wide synthetic lethal screen unveils novel CAIX-NFS1/xCT axis as a targetable vulnerability in hypoxic solid tumors

2021 ◽  
Vol 7 (35) ◽  
Author(s):  
Shawn C. Chafe ◽  
Frederick S. Vizeacoumar ◽  
Geetha Venkateswaran ◽  
Oksana Nemirovsky ◽  
Shannon Awrey ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Synthetic Lethal ◽  
Genome Wide

scholarly journals DCA for genome-wide epistasis analysis: the statistical genetics perspective

2019 ◽  
Vol 16 (2) ◽  
pp. 026002 ◽  
Author(s):  
Chen-Yi Gao ◽  
Fabio Cecconi ◽  
Angelo Vulpiani ◽  
Hai-Jun Zhou ◽  
Erik Aurell
Keyword(s):  
Statistical Genetics ◽  
Epistasis Analysis ◽  
Genome Wide

scholarly journals Genome-wide synthetic lethal CRISPR screen identifies FIS1 as a genetic interactor of ALS-linked C9ORF72

2020 ◽  
Vol 1728 ◽  
pp. 146601 ◽  
Author(s):  
Noori Chai ◽  
Michael S. Haney ◽  
Julien Couthouis ◽  
David W. Morgens ◽  
Alyssa Benjamin ◽  
...  
Keyword(s):  
Synthetic Lethal ◽  
Genome Wide ◽  
Crispr Screen

scholarly journals Induction of protein aggregation and starvation response by tRNA modification defects

2020 ◽  
Vol 66 (6) ◽  
pp. 1053-1057
Author(s):  
Roland Klassen ◽  
Alexander Bruch ◽  
Raffael Schaffrath
Keyword(s):  
Cellular Response ◽  
Anticodon Loop ◽  
Protein Aggregate ◽  
Starvation Response ◽  
Codon Recognition ◽  
Growth Defects ◽  
Yeast Strains ◽  
Transcriptional Changes ◽  
Decoding Efficiency ◽  
Synthetic Growth

Abstract Posttranscriptional modifications of anticodon loops contribute to the decoding efficiency of tRNAs by supporting codon recognition and loop stability. Consistently, strong synthetic growth defects are observed in yeast strains simultaneously lacking distinct anticodon loop modifications. These phenotypes are accompanied by translational inefficiency of certain mRNAs and disturbed protein homeostasis resulting in accumulation of protein aggregates. Different combinations of anticodon loop modification defects were shown to affect distinct tRNAs but provoke common transcriptional changes that are reminiscent of the cellular response to nutrient starvation. Multiple mechanisms may be involved in mediating inadequate starvation response upon loss of critical tRNA modifications. Recent evidence suggests protein aggregate induction to represent one such trigger.

scholarly journals Ups1p and Ups2p antagonistically regulate cardiolipin metabolism in mitochondria

2009 ◽  
Vol 185 (6) ◽  
pp. 1029-1045 ◽  
Author(s):  
Yasushi Tamura ◽  
Toshiya Endo ◽  
Miho Iijima ◽  
Hiromi Sesaki
Keyword(s):  
Fatty Acid ◽  
Molecular Mechanism ◽  
Protein Import ◽  
Protein Complexes ◽  
Mitochondrial Protein ◽  
Intermembrane Space ◽  
Mitochondrial Protein Import ◽  
Growth Defects ◽  
Mitochondrial Inner Membrane ◽  
Synthetic Growth

Cardiolipin, a unique phospholipid composed of four fatty acid chains, is located mainly in the mitochondrial inner membrane (IM). Cardiolipin is required for the integrity of several protein complexes in the IM, including the TIM23 translocase, a dynamic complex which mediates protein import into the mitochondria through interactions with the import motor presequence translocase–associated motor (PAM). In this study, we report that two homologous intermembrane space proteins, Ups1p and Ups2p, control cardiolipin metabolism and affect the assembly state of TIM23 and its association with PAM in an opposing manner. In ups1Δ mitochondria, cardiolipin levels were decreased, and the TIM23 translocase showed altered conformation and decreased association with PAM, leading to defects in mitochondrial protein import. Strikingly, loss of Ups2p restored normal cardiolipin levels and rescued TIM23 defects in ups1Δ mitochondria. Furthermore, we observed synthetic growth defects in ups mutants in combination with loss of Pam17p, which controls the integrity of PAM. Our findings provide a novel molecular mechanism for the regulation of cardiolipin metabolism.

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