scholarly journals The Chemical Genetic Interactions of Statin Drugs with Their Target Genes in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
◽  
Bede P Busby
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Target Genes ◽  
Genetic Interaction ◽  
Retrograde Transport ◽  
Interaction Networks ◽  
Query Gene ◽  
Yeast Saccharomyces Cerevisiae ◽  
Chemical Genetic ◽  
Genome Wide ◽  
Statin Drugs

<p>Statins, competitive inhibitors of the rate limiting cholesterol/ergosterol enzymes HMG-CoA reductase (HMG1 and HMG2), are the most widely prescribed human therapeutic drugs. They are effective in lowering cholesterol levels in atherosclerosis and related syndromes. However, statins exhibit a range of pleiotropic side effects whose mechanisms are poorly understood. This study investigates statin pleiotropy by analysis of genetic interaction networks in yeast, Saccharomyces cerevisiae, which shows high homology to mammalian pathways affected by statins. Synthetic genetic array (SGA) analysis allows elucidation of functional genetic networks of genes of interest ("query genes") by  measurement of genetic epistasis in double mutants of the query gene with the genome - wide deletion mutant array of ~4800 non-essential strains. Chemicalgenetic profiling is similar where a SMP may effectively replace the query gene in genome wide epistatic analysis. The genetic interaction networks resulting from use of HMG1 and HMG2 as query genes for SGA analysis were compared to the chemical-genetic profiles of atorvastatin, cerivastatin and lovastatin. The genes ARV1, BTS1, OPI3 displaying phenotypic enhancements (i.e. their deletion caused major growth inhibition) with statins became essential in the presence of all the statins. Two mitochondrial genes, COX17 and MMM1, showed phenotypic suppressions (i.e. their deletion allowed better growth) in common to all three statin drugs. An attractive hypothesis is that major pleiotropic effects of statins could be due to variation in function or expression of these enhancing or suppressing genes. Other processes compensating statin use were also elucidated. For example, when HMG1 and its epistatically interacting genes are shut down by deletion coupled with inhibition of HMG2 with statin, there is strong evidence that the cell attempts to maintain membrane/lipid homeostasis via anterograde and retrograde transport mechanisms, including the mobilisation of lipid storage droplets. To aid refinement of genetic analysis in this and future studies, a more direct phenotypic assay was developed for quantifying ergosterol. Such an assay may be used as a phenotype to map the effect of up - and downstream - genes, or network genes affecting ergosterol levels. This assay was used to quantify ergosterol in a drug - resistant mutant developed by others aiding confirmation of the drug target.</p>

scholarly journals The Chemical Genetic Interactions of Statin Drugs with Their Target Genes in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
◽  
Bede P Busby
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Target Genes ◽  
Genetic Interaction ◽  
Retrograde Transport ◽  
Interaction Networks ◽  
Query Gene ◽  
Yeast Saccharomyces Cerevisiae ◽  
Chemical Genetic ◽  
Genome Wide ◽  
Statin Drugs

<p>Statins, competitive inhibitors of the rate limiting cholesterol/ergosterol enzymes HMG-CoA reductase (HMG1 and HMG2), are the most widely prescribed human therapeutic drugs. They are effective in lowering cholesterol levels in atherosclerosis and related syndromes. However, statins exhibit a range of pleiotropic side effects whose mechanisms are poorly understood. This study investigates statin pleiotropy by analysis of genetic interaction networks in yeast, Saccharomyces cerevisiae, which shows high homology to mammalian pathways affected by statins. Synthetic genetic array (SGA) analysis allows elucidation of functional genetic networks of genes of interest ("query genes") by  measurement of genetic epistasis in double mutants of the query gene with the genome - wide deletion mutant array of ~4800 non-essential strains. Chemicalgenetic profiling is similar where a SMP may effectively replace the query gene in genome wide epistatic analysis. The genetic interaction networks resulting from use of HMG1 and HMG2 as query genes for SGA analysis were compared to the chemical-genetic profiles of atorvastatin, cerivastatin and lovastatin. The genes ARV1, BTS1, OPI3 displaying phenotypic enhancements (i.e. their deletion caused major growth inhibition) with statins became essential in the presence of all the statins. Two mitochondrial genes, COX17 and MMM1, showed phenotypic suppressions (i.e. their deletion allowed better growth) in common to all three statin drugs. An attractive hypothesis is that major pleiotropic effects of statins could be due to variation in function or expression of these enhancing or suppressing genes. Other processes compensating statin use were also elucidated. For example, when HMG1 and its epistatically interacting genes are shut down by deletion coupled with inhibition of HMG2 with statin, there is strong evidence that the cell attempts to maintain membrane/lipid homeostasis via anterograde and retrograde transport mechanisms, including the mobilisation of lipid storage droplets. To aid refinement of genetic analysis in this and future studies, a more direct phenotypic assay was developed for quantifying ergosterol. Such an assay may be used as a phenotype to map the effect of up - and downstream - genes, or network genes affecting ergosterol levels. This assay was used to quantify ergosterol in a drug - resistant mutant developed by others aiding confirmation of the drug target.</p>

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 Smy1p, a Kinesin-related Protein That Does Not Require Microtubules

1998 ◽  
Vol 140 (4) ◽  
pp. 873-883 ◽  
Author(s):  
S.H. Lillie ◽  
S.S. Brown
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Motor Activity ◽  
Secretory Pathway ◽  
Genetic Interaction ◽  
Related Protein ◽  
Wild Type ◽  
Yeast Saccharomyces Cerevisiae ◽  
Functional Link ◽  
Specific Step ◽  
Tubulin Mutations

Abstract. We have previously reported that a defect in Myo2p, a myosin in budding yeast (Saccharomyces cerevisiae), can be partially corrected by overexpression of Smy1p, which is by sequence a kinesin-related protein (Lillie, S.H., and S.S. Brown. 1992. Nature. 356:358– 361). Such a functional link between putative actin- and microtubule-based motors is surprising, so here we have tested the prediction that Smy1p indeed acts as a microtubule-based motor. Unexpectedly, we found that abolition of microtubules by nocodazole does not interfere with the ability of Smy1p to correct the mutant Myo2p defect, nor does it interfere with the ability of Smy1p to localize properly. In addition, other perturbations of microtubules, such as treatment with benomyl or introduction of tubulin mutations, do not exacerbate the Myo2p defect. Furthermore, a mutation in SMY1 strongly predicted to destroy motor activity does not destroy Smy1p function. We have also observed a genetic interaction between SMY1 and two of the late SEC mutations, sec2 and sec4. This indicates that Smy1p can play a role even when Myo2p is wild type, and that Smy1p acts at a specific step of the late secretory pathway. We conclude that Smy1p does not act as a microtubule-based motor to localize properly or to compensate for defective Myo2p, but that it must instead act in some novel way.

scholarly journals Retrograde Traffic Out of the Yeast Vacuole to the TGN Occurs via the Prevacuolar/Endosomal Compartment

1998 ◽  
Vol 142 (3) ◽  
pp. 651-663 ◽  
Author(s):  
Nia J. Bryant ◽  
Robert C. Piper ◽  
Lois S. Weisman ◽  
Tom H. Stevens
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Alkaline Phosphatase ◽  
Amino Acid ◽  
Retrograde Transport ◽  
Carboxypeptidase Y ◽  
Hybrid Protein ◽  
Yeast Saccharomyces Cerevisiae ◽  
Endosomal Compartment ◽  
Sorting Motif ◽  
Retrograde Traffic

A large number of trafficking steps occur between the last compartment of the Golgi apparatus (TGN) and the vacuole of the yeast Saccharomyces cerevisiae. To date, two intracellular routes from the TGN to the vacuole have been identified. Carboxypeptidase Y (CPY) travels through a prevacuolar/endosomal compartment (PVC), and subsequently on to the vacuole, while alkaline phosphatase (ALP) bypasses this compartment to reach the same organelle. Proteins resident to the TGN achieve their localization despite a continuous flux of traffic by continually being retrieved from the distal PVC by virtue of an aromatic amino acid–containing sorting motif. In this study we report that a hybrid protein based on ALP and containing this retrieval motif reaches the PVC not by following the CPY sorting pathway, but instead by signal-dependent retrograde transport from the vacuole, an organelle previously thought of as a terminal compartment. In addition, we show that a mutation in VAC7, a gene previously identified as being required for vacuolar inheritance, blocks this trafficking step. Finally we show that Vti1p, a v-SNARE required for the delivery of both CPY and ALP to the vacuole, uses retrograde transport out of the vacuole as part of its normal cellular itinerary.

scholarly journals Antagonism of Chemical Genetic Interaction Networks Resensitize MRSA to β-Lactam Antibiotics

2011 ◽  
Vol 18 (11) ◽  
pp. 1379-1389 ◽  
Author(s):  
Sang Ho Lee ◽  
Lisa Wang Jarantow ◽  
Hao Wang ◽  
Susan Sillaots ◽  
Henry Cheng ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Interaction Networks ◽  
Chemical Genetic

scholarly journals Efficient strategies for screening large-scale genetic interaction networks

2017 ◽  
Author(s):  
Raamesh Deshpande ◽  
Justin Nelson ◽  
Scott W. Simpkins ◽  
Michael Costanzo ◽  
Jeff S. Piotrowski ◽  
...  
Keyword(s):  
Large Scale ◽  
Optimal Algorithm ◽  
Genetic Interaction ◽  
Genetic Screens ◽  
Chemical Genetic ◽  
Genome Wide ◽  
Powerful Approach ◽  
Interaction Screening ◽  
Genetic Interaction Data

Large-scale genetic interaction screening is a powerful approach for unbiased characterization of gene function and understanding systems-level cellular organization. While genome-wide screens are desirable as they provide the most comprehensive interaction profiles, they are resource and time-intensive and sometimes infeasible, depending on the species and experimental platform. For these scenarios, optimal methods for more efficient screening while still producing the maximal amount of information from the resulting profiles are of interest.To address this problem, we developed an optimal algorithm, called COMPRESS-GI, which selects a small but informative set of genes that captures most of the functional information contained within genome-wide genetic interaction profiles. The utility of this algorithm is demonstrated through an application of the approach to define a diagnostic mutant set for large-scale chemical genetic screens, where more than 13,000 compound screens were achieved through the increased throughput enabled by the approach. COMPRESS-GI can be broadly applied for directing genetic interaction screens in other contexts, including in species with little or no prior genetic-interaction data.

scholarly journals Chemical-Genetic Interactions with the Proline Analog L-Azetidine-2-Carboxylic Acid in Saccharomyces cerevisiae

2020 ◽  
Vol 10 (12) ◽  
pp. 4335-4345
Author(s):  
Matthew D. Berg ◽  
Yanrui Zhu ◽  
Joshua Isaacson ◽  
Julie Genereaux ◽  
Raphaël Loll-Krippleber ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Carboxylic Acid ◽  
Cellular Response ◽  
Protein Quality ◽  
Genetic Interaction ◽  
Genetic Interactions ◽  
Temperature Sensitive ◽  
Chemical Genetic ◽  
Proteotoxic Stress

Non-proteinogenic amino acids, such as the proline analog L-azetidine-2-carboxylic acid (AZC), are detrimental to cells because they are mis-incorporated into proteins and lead to proteotoxic stress. Our goal was to identify genes that show chemical-genetic interactions with AZC in Saccharomyces cerevisiae and thus also potentially define the pathways cells use to cope with amino acid mis-incorporation. Screening the yeast deletion and temperature sensitive collections, we found 72 alleles with negative chemical-genetic interactions with AZC treatment and 12 alleles that suppress AZC toxicity. Many of the genes with negative chemical-genetic interactions are involved in protein quality control pathways through the proteasome. Genes involved in actin cytoskeleton organization and endocytosis also had negative chemical-genetic interactions with AZC. Related to this, the number of actin patches per cell increases upon AZC treatment. Many of the same cellular processes were identified to have interactions with proteotoxic stress caused by two other amino acid analogs, canavanine and thialysine, or a mistranslating tRNA variant that mis-incorporates serine at proline codons. Alleles that suppressed AZC-induced toxicity functioned through the amino acid sensing TOR pathway or controlled amino acid permeases required for AZC uptake. Further suggesting the potential of genetic changes to influence the cellular response to proteotoxic stress, overexpressing many of the genes that had a negative chemical-genetic interaction with AZC suppressed AZC toxicity.

scholarly journals Genetic analysis of the bipolar pattern of bud site selection in the yeast Saccharomyces cerevisiae.

1996 ◽  
Vol 16 (4) ◽  
pp. 1857-1870 ◽  
Author(s):  
J E Zahner ◽  
H A Harkins ◽  
J R Pringle
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Interaction ◽  
Previous Analysis ◽  
Intracellular Localization ◽  
Proximal Pole ◽  
Yeast Saccharomyces Cerevisiae ◽  
Novel Gene ◽  
Division Site ◽  
Genes Encoding ◽  
Bud Site

Previous analysis of the bipolar budding pattern of Saccharomyces cerevisiae has suggested that it depends on persistent positional signals that mark the region of the division site and the tip of the distal pole on a newborn daughter cell, as well as each previous division site on a mother cell. In an attempt to identify genes encoding components of these signals or proteins involved in positioning or responding to them, we identified 11 mutants with defects in bipolar but not in axial budding. Five mutants displaying a bipolar budding-specific randomization of budding pattern had mutations in four previously known genes (BUD2, BUD5, SPA2, and BNI1) and one novel gene (BUD6), respectively. As Bud2p and Bud5p are known to be required for both the axial and bipolar budding patterns, the alleles identified here probably encode proteins that have lost their ability to interact with the bipolar positional signals but have retained their ability to interact with the distinct positional signal used in axial budding. The function of Spa2p is not known, but previous work has shown that its intracellular localization is similar to that postulated for the bipolar positional signals. BNI1 was originally identified on the basis of genetic interaction with CDC12, which encodes one of the neck-filament-associated septin proteins, suggesting that these proteins may be involved in positioning the bipolar signals. One mutant with a heterogeneous budding pattern defines a second novel gene (BUD7). Two mutants budding almost exclusively from the proximal pole carry mutations in a fourth novel gene (BUD9). A bud8 bud9 double mutant also buds almost exclusively from the proximal pole, suggesting that Bud9p is involved in positioning the proximal pole signal rather than being itself a component of this signal.

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