IF 2.2 4区生物学

Yeast Pub Date : 2024-09-01 Epub Date: 2024-07-30 DOI: 10.1002/yea.3975

Marina E Druseikis, Shay Covo

{"title":"Synthetic lethality between toxic amino acids, RTG-target genes and chaperones in Saccharomyces cerevisiae.","authors":"Marina E Druseikis, Shay Covo","doi":"10.1002/yea.3975","DOIUrl":"10.1002/yea.3975","url":null,"abstract":"The toxicity of non-proteinogenic amino acids has been known for decades. Numerous reports describe their antimicrobial/anticancer potential. However, these molecules are often toxic to the host as well; thus, a synthetic lethality approach that reduces the dose of these toxins while maintaining toxicity can be beneficial. Here we investigate synthetic lethality between toxic amino acids, the retrograde pathway, and molecular chaperones. In Saccharomyces cerevisiae, mitochondrial retrograde (RTG) pathway activation induces transcription of RTG-target genes to replenish alpha-ketoglutarate and its downstream product glutamate; both metabolites are required for arginine and lysine biosynthesis. We previously reported that tolerance of canavanine, a toxic arginine derivative, requires an intact RTG pathway, and low-dose canavanine exposure reduces the expression of RTG-target genes. Here we show that only a few of the examined chaperone mutants are sensitive to sublethal doses of canavanine. To predict synthetic lethality potential between RTG-target genes and chaperones, we measured the expression of RTG-target genes in canavanine-sensitive and canavanine-tolerant chaperone mutants. Most RTG-target genes were induced in all chaperone mutants starved for arginine; the same trend was not observed under lysine starvation. Canavanine exposure under arginine starvation attenuated and even reversed RTG-target-gene expression in the tested chaperone mutants. Importantly, under nearly all tested genetic and pharmacological conditions, the expression of IDH1 and/or IDH2 was induced. In agreement, idh1 and idh2 mutants are sensitive to canavanine and thialysine and show synthetic growth inhibition with chaperone mutants. Overall, we show that inhibiting molecular chaperones, RTG-target genes, or both can sensitize cells to low doses of toxic amino acids.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"549-559"},"PeriodicalIF":2.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Marker-free genomic editing in Saccharomyces cerevisiae using universal donor templates and multiplexing CRISPR-CAS9. 利用通用供体模板和复用 CRISPR-CAS9 在酿酒酵母中进行无标记基因组编辑。

IF 2.2 4区生物学

Yeast Pub Date : 2024-09-01 Epub Date: 2024-08-23 DOI: 10.1002/yea.3977

J H Grissom, S E Moody, R J Chi

{"title":"Marker-free genomic editing in Saccharomyces cerevisiae using universal donor templates and multiplexing CRISPR-CAS9.","authors":"J H Grissom, S E Moody, R J Chi","doi":"10.1002/yea.3977","DOIUrl":"10.1002/yea.3977","url":null,"abstract":"The budding yeast Saccharomyces cerevisiae is an excellent model organism for studying a variety of critical cellular processes. Traditional methods to knock in or -out at specific yeast loci utilize polymerase chain reaction-based techniques, in which marker cassettes with gene-specific homologies are integrated into the genome via homologous recombination. While simple and cost-effective, these methods are limited by marker availability when multiple edits are desired. More recently, CRISPR-Cas9 technology has introduced methods to edit the yeast genome without the need for selectable markers. Although efficient, this method is hindered by additional reagents and lengthy protocols to design and test unique guide RNAs and donor templates for each desired edit. In this study, we have combined these two approaches and have developed a highly efficient economical method to edit the yeast genome marker-free. We have designed two universal donor templates that efficiently repair commonly used selectable markers when targeted by a novel guideRNA-Cas9 designed to promoter regions in Ashbya gossypii found in most integration modules. Furthermore, we find our newly designed guideRNA-Cas9 successfully multiplexes when multiple markers are present. Using these new tools, we have significantly improved the cost and efficiency to generate single or multiple marker-free genetic modifications. In this study, we demonstrate the effectiveness of these new tools by marker-free ablating PRC1, PEP4, and PRB1 vacuolar proteases typically inactivated before many biochemical and membrane-trafficking studies using budding yeast.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"568-579"},"PeriodicalIF":2.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Discovery of novel cellobiose lipid gene clusters from Basidiomycetes: How chemical variation is reflected in gene cluster architecture. 从担子菌中发现新型纤维生物糖脂基因簇：基因簇结构如何反映化学变异。

IF 2.2 4区生物学

Yeast Pub Date : 2024-08-01 Epub Date: 2024-06-14 DOI: 10.1002/yea.3969

Lobke Maria Sips, Laurens Lambrecht, Inge Noëlle Adrienne Van Bogaert

引用次数: 0

Altered S-AdenosylMethionine availability impacts dNTP pools in Saccharomyces cerevisiae. S-AdenosylMethionine 的可用性变化会影响酿酒酵母中的 dNTP 池。

IF 2.2 4区生物学

Yeast Pub Date : 2024-08-01 Epub Date: 2024-07-03 DOI: 10.1002/yea.3973

Warunya Panmanee, Men T H Tran, Serigne N Seye, Erin D Strome

{"title":"Altered S-AdenosylMethionine availability impacts dNTP pools in Saccharomyces cerevisiae.","authors":"Warunya Panmanee, Men T H Tran, Serigne N Seye, Erin D Strome","doi":"10.1002/yea.3973","DOIUrl":"10.1002/yea.3973","url":null,"abstract":"Saccharomyces cerevisiae has long been used as a model organism to study genome instability. The SAM1 and SAM2 genes encode AdoMet synthetases, which generate S-AdenosylMethionine (AdoMet) from Methionine (Met) and ATP. Previous work from our group has shown that deletions of the SAM1 and SAM2 genes cause changes to AdoMet levels and impact genome instability in opposite manners. AdoMet is a key product of methionine metabolism and the major methyl donor for methylation events of proteins, RNAs, small molecules, and lipids. The methyl cycle is interrelated to the folate cycle which is involved in de novo synthesis of purine and pyrimidine deoxyribonucleotides (dATP, dTTP, dCTP, and dGTP). AdoMet also plays a role in polyamine production, essential for cell growth and used in detoxification of reactive oxygen species (ROS) and maintenance of the redox status in cells. This is also impacted by the methyl cycle's role in production of glutathione, another ROS scavenger and cellular protectant. We show here that sam2∆/sam2∆ cells, previously characterized with lower levels of AdoMet and higher genome instability, have a higher level of each dNTP (except dTTP), contributing to a higher overall dNTP pool level when compared to wildtype. Unchecked, these increased levels can lead to multiple types of DNA damage which could account for the genome instability increases in these cells.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"513-524"},"PeriodicalIF":2.2,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pros and cons of auxin-inducible degron as a tool for regulated depletion of telomeric proteins from Saccharomyces cerevisiae. 将辅助素诱导的降解酵母作为一种工具，用于有序消耗酿酒酵母中的端粒蛋白的利弊。

IF 2.2 4区生物学

Yeast Pub Date : 2024-08-01 Epub Date: 2024-06-24 DOI: 10.1002/yea.3971

Tomáš Petrík, Zuzana Brzáčová, Regina Sepšiová, Katarína Veljačiková, Ľubomír Tomáška

{"title":"Pros and cons of auxin-inducible degron as a tool for regulated depletion of telomeric proteins from Saccharomyces cerevisiae.","authors":"Tomáš Petrík, Zuzana Brzáčová, Regina Sepšiová, Katarína Veljačiková, Ľubomír Tomáška","doi":"10.1002/yea.3971","DOIUrl":"10.1002/yea.3971","url":null,"abstract":"To assess the immediate responses of the yeast cells to telomere defects, we employed the auxin-inducible degron (AID) enabling rapid depletion of essential (Rap1, Tbf1, Cdc13, Stn1) and non-essential (Est1, Est2, Est3) telomeric proteins. Using two variants of AID systems, we show that most of the studied proteins are depleted within 10-30 min after the addition of auxin. As expected, depletion of essential proteins yields nondividing cells, provided that the strains are cultivated in an appropriate carbon source and at temperatures lower than 28°C. Cells with depleted Cdc13 and Stn1 exhibit extension of the single-stranded overhang as early as 3 h after addition of auxin. Notably, prolonged incubation of strains carrying AID-tagged essential proteins in the presence of auxin resulted in the appearance of auxin-resistant clones, caused at least in part by mutations within the OsTIR1 gene. Upon assessing the length of telomeres in strains carrying AID-tagged non-essential telomeric proteins, we found that the depletion of Est1 and Est3 leads to auxin-dependent telomere shortening. However, the EST3-AID strain had slightly shorter telomeres even in the absence of auxin. Furthermore, a strain with the AID-tagged version of Est2 (catalytic subunit of telomerase) not only had shorter telomeres in the absence of auxin but also did not exhibit auxin-dependent telomere shortening. Our results demonstrate that while AID can be useful in assessing immediate cellular responses to telomere deprotection, each strain must be carefully evaluated for the effect of AID-tag on the properties of the protein of interest.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"499-512"},"PeriodicalIF":2.2,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141459664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The MAPK homolog, Smk1, promotes assembly of the glucan layer of the spore wall in S. cerevisiae. MAPK 同源物 Smk1 可促进 S. cerevisiae 孢子壁葡聚糖层的组装。

IF 2.2 4区生物学

Yeast Pub Date : 2024-07-01 Epub Date: 2024-06-14 DOI: 10.1002/yea.3967

Julia Y Lee-Soety, Gwendolyn Resch, Abhimannyu Rimal, Erica S Johnson, Jonathan Benway, Edward Winter

{"title":"The MAPK homolog, Smk1, promotes assembly of the glucan layer of the spore wall in S. cerevisiae.","authors":"Julia Y Lee-Soety, Gwendolyn Resch, Abhimannyu Rimal, Erica S Johnson, Jonathan Benway, Edward Winter","doi":"10.1002/yea.3967","DOIUrl":"10.1002/yea.3967","url":null,"abstract":"Smk1 is a MAPK homolog in the yeast Saccharomyces cerevisiae that controls the postmeiotic program of spore wall assembly. During this program, haploid cells are surrounded by a layer of mannan and then a layer of glucan. These inner layers of the spore wall resemble the vegetative cell wall. Next, the outer layers consisting of chitin/chitosan and then dityrosine are assembled. The outer layers are spore-specific and provide protection against environmental stressors. Smk1 is required for the proper assembly of spore walls. However, the protective properties of the outer layers have limited our understanding of how Smk1 controls this morphogenetic program. Mutants lacking the chitin deacetylases, Cda1 and Cda2, form spores that lack the outer layers of the spore wall. In this study, cda1,2∆ cells were used to demonstrate that Smk1 promotes deposition of the glucan layer of the spore wall through the partially redundant glucan synthases Gsc2 and Fks3. Although Gsc2 is localized to sites of spore wall assembly in the wild type, it is mislocalized in the mother cell cytoplasm in the smk1∆ mutant. These findings suggest that Smk1 controls assembly of the spore wall by regulating the localization of Gsc2 during sporogenesis.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"448-457"},"PeriodicalIF":2.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11230851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparison of Xrn1 and Rat1 5' → 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay. 比较了芽殖酵母中的 Xrn1 和 Rat1 5' → 3' 外切核酸酶，证明了 Xrn1 在共翻译 mRNA 衰变中的特殊作用。

IF 2.2 4区生物学

Yeast Pub Date : 2024-07-01 Epub Date: 2024-06-14 DOI: 10.1002/yea.3968

José E Pérez-Ortín, Antonio Jordán-Pla, Yujie Zhang, Jorge Moreno-García, Claudio Bassot, Marina Barba-Aliaga, Leire de Campos-Mata, Mordechai Choder, Juana Díez, Ilaria Piazza, Vicent Pelechano, José García-Martínez

{"title":"Comparison of Xrn1 and Rat1 5' → 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay.","authors":"José E Pérez-Ortín, Antonio Jordán-Pla, Yujie Zhang, Jorge Moreno-García, Claudio Bassot, Marina Barba-Aliaga, Leire de Campos-Mata, Mordechai Choder, Juana Díez, Ilaria Piazza, Vicent Pelechano, José García-Martínez","doi":"10.1002/yea.3968","DOIUrl":"10.1002/yea.3968","url":null,"abstract":"The yeast Saccharomyces cerevisiae and most eukaryotes carry two 5' → 3' exoribonuclease paralogs. In yeast, they are called Xrn1, which shuttles between the nucleus and the cytoplasm, and executes major cytoplasmic messenger RNA (mRNA) decay, and Rat1, which carries a strong nuclear localization sequence (NLS) and localizes to the nucleus. Xrn1 is 30% identical to Rat1 but has an extra ~500 amino acids C-terminal extension. In the cytoplasm, Xrn1 can degrade decapped mRNAs during the last round of translation by ribosomes, a process referred to as \"cotranslational mRNA decay.\" The division of labor between the two enzymes is still enigmatic and serves as a paradigm for the subfunctionalization of many other paralogs. Here we show that Rat1 is capable of functioning in cytoplasmic mRNA decay, provided that Rat1 remains cytoplasmic due to its NLS disruption (cRat1). This indicates that the physical segregation of the two paralogs plays roles in their specific functions. However, reversing segregation is not sufficient to fully complement the Xrn1 function. Specifically, cRat1 can partially restore the cell volume, mRNA stability, the proliferation rate, and 5' → 3' decay alterations that characterize xrn1Δ cells. Nevertheless, cotranslational decay is only slightly complemented by cRat1. The use of the AlphaFold prediction for cRat1 and its subsequent docking with the ribosome complex and the sequence conservation between cRat1 and Xrn1 suggest that the tight interaction with the ribosome observed for Xrn1 is not maintained in cRat1. Adding the Xrn1 C-terminal domain to Rat1 does not improve phenotypes, which indicates that lack of the C-terminal is not responsible for partial complementation. Overall, during evolution, it appears that the two paralogs have acquired specific characteristics to make functional partitioning beneficial.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"458-472"},"PeriodicalIF":2.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-throughput classification of S. cerevisiae tetrads using deep learning. 利用深度学习对 S. cerevisiae tetrads 进行高通量分类。

IF 2.2 4区生物学

Yeast Pub Date : 2024-07-01 Epub Date: 2024-06-08 DOI: 10.1002/yea.3965

Balint Szücs, Raghavendra Selvan, Michael Lisby

引用次数: 0

Spathaspora marinasilvae sp. nov., a xylose-fermenting yeast isolated from galleries of passalid beetles and rotting wood in the Amazonian rainforest biome. Spathaspora marinasilvae sp.

IF 2.2 4区生物学

Yeast Pub Date : 2024-07-01 Epub Date: 2024-06-08 DOI: 10.1002/yea.3966

Katharina O Barros, Thiago M Batista, Rafaela C C Soares, Mariana R Lopes, Flávia B M Alvarenga, Gisele F L Souza, Maxwel A Abegg, Ana Raquel O Santos, Aristóteles Góes-Neto, Heron O Hilário, Rennan G Moreira, Glória R Franco, Marc-André Lachance, Carlos A Rosa

{"title":"Spathaspora marinasilvae sp. nov., a xylose-fermenting yeast isolated from galleries of passalid beetles and rotting wood in the Amazonian rainforest biome.","authors":"Katharina O Barros, Thiago M Batista, Rafaela C C Soares, Mariana R Lopes, Flávia B M Alvarenga, Gisele F L Souza, Maxwel A Abegg, Ana Raquel O Santos, Aristóteles Góes-Neto, Heron O Hilário, Rennan G Moreira, Glória R Franco, Marc-André Lachance, Carlos A Rosa","doi":"10.1002/yea.3966","DOIUrl":"10.1002/yea.3966","url":null,"abstract":"Four yeast isolates were obtained from rotting wood and galleries of passalid beetles collected in different sites of the Brazilian Amazonian Rainforest in Brazil. This yeast produces unconjugated allantoid asci each with a single elongated ascospore with curved ends. Sequence analysis of the internal transcribed spacer-5.8 S region and the D1/D2 domains of the large subunit ribosomal RNA (rRNA) gene showed that the isolates represent a novel species of the genus Spathaspora. The novel species is phylogenetically related to a subclade containing Spathaspora arborariae and Spathaspora suhii. Phylogenomic analysis based on 1884 single-copy orthologs for a set of Spathaspora species whose whole genome sequences are available confirmed that the novel species represented by strain UFMG-CM-Y285 is phylogenetically close to Sp. arborariae. The name Spathaspora marinasilvae sp. nov. is proposed to accommodate the novel species. The holotype of Sp. marinasilvae is CBS 13467 T (MycoBank 852799). The novel species was able to accumulate xylitol and produce ethanol from d-xylose, a trait of biotechnological interest common to several species of the genus Spathaspora.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"437-447"},"PeriodicalIF":2.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On the coupling of intracellular K+ ${{rm{K}}}^{+}$ to glycolytic oscillations in yeast 细胞内 K+ ${{rm{K}}^{+}$ 与酵母中糖酵解振荡的耦合关系

IF 2.6 4区生物学

Yeast Pub Date : 2024-06-21 DOI: 10.1002/yea.3972

Lars F. Olsen, Anita Lunding

{"title":"On the coupling of intracellular K+ ${{rm{K}}}^{+}$ to glycolytic oscillations in yeast","authors":"Lars F. Olsen, Anita Lunding","doi":"10.1002/yea.3972","DOIUrl":"https://doi.org/10.1002/yea.3972","url":null,"abstract":"We have investigated the interplay between glycolytic oscillations and intracellular concentration in the yeast Saccharomyces cerevisiae. Intracellular concentration was measured using the fluorophore potassium‐binding benzofuranisophthalate (PBFI). We found that is an essential ion for the occurrence of glycolytic oscillations and that intracellular concentration oscillates synchronously with other variables such as nicotinamide adenine dinucleotide hydride (NADH), intracellular adenosine triphosphate (ATP), and mitochondrial membrane potential. We also investigated if glycolysis and intracellular concentration oscillate in a number of yeast strains with mutations in transporters in the plasma membrane, mitochondrial membrane and in the vacuolar membrane. Most of these strains are still capable of showing glycolytic oscillations, but two strains are not: (i) a strain with a deletion in the mitochondrial Mdm38p transporter and (ii) a strain with deletion of the late endosomal Nhx1p () transporter. In these two mutant strains intracellular concentration seems to be low, indicating that the two transporters may be involved in transport of into the cytosol. In the strain, Mdm38p oscillations in glycolysis could be restored by addition of the exchange ionophore nigericin. Furthermore, in two nonoscillating mutant strains with a defective V‐ATPase and deletion of the Arp1p protein the intracellular is relatively high, suggesting that the V‐ATPase is essential for transport of out of the cytosol and that the cytoskeleton may be involved in binding to reduce the concentration of free ion in the cytosol. Analyses of the time series of oscillations of NADH, ATP, mitochondrial membrane potential, and potassium concentration using data‐driven modeling corroborate the conjecture that ion is essential for the emergence of oscillations and support the experimental findings using mutant strains.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"8 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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