biostudies-arrayexpressÇağla Ece OlgunSaccharomyces cerevisiae S288chttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16090The Yippee-like (YPEL) proteins are a conserved eukaryotic gene family implicated in proliferation, senescence, and stress adaptation. In humans, five paralogs (YPEL1–YPEL5) are widely expressed and encode proteins with high sequence similarity, but the molecular basis of their functions remains poorly defined. Functional redundancy among YPEL paralogs complicates the clarification of their individual roles. The budding yeast Saccharomyces cerevisiae has a single ortholog, MOH1, which is involved in survival and stress responses and can be functionally complemented by human YPELs. However, the cellular function of MOH1 has yet to be elucidated. Here, we investigated the function of MOH1 in S. cerevisiae. Deletion of MOH1 (moh1Δ) conferred sensitivity to sodium azide and sulfuric acid but increased resistance to hydrogen peroxide and acetic acid. Moh1 protein levels decreased upon hydrogen peroxide treatment and increased following sulfuric acid exposure, indicating stress-dependent regulation. Light and scanning electron microscopy analyses revealed that moh1Δ cells are constitutively rounder, tend to form clumps, and exhibit rough surface features, signifying altered cellular architecture. RNA profiling and FTIR spectroscopy revealed transcriptional reprogramming and metabolic remodeling in moh1Δ cells, including alterations in lipid, protein, and cell wall polysaccharide levels and composition. Intracellular ROS assays revealed that resistance to hydrogen peroxide results from reduced cellular uptake caused by altered membrane permeability, rather than from differences in mitochondrial ROS generation. Collectively, our findings identify Moh1 as a regulatory factor linking gene expression to metabolism and cellular architecture, influencing membrane permeability and conferring selective stress resistance in S. cerevisiae.biostudies-arrayexpressGrowth Protocol - Cells grown overnight in YPD at 30 °C with reciprocal shaking at 180 rpm were sub-cultured into fresh YPD at a 1:100 dilution and grown until OD600 reached 0.4-0.6. Cells were subsequently spotted at serial dilution on YPD-agar plates. Plates were incubated at 30 °C for 40 hours. Cells were collected with scraper.Nucleic Acid Extraction - Collected cells were pelleted with centrifugation. To dissolve cell pellets, 25 μl of 20% SDS and 400 μLof ice-cold Acetate-EDTA (AE) buffer containing 50 mM sodium acetate and 10 mM EDTA (pH=8) were added to the cell pellets. Subsequently, 500 μl of acidic 25:24:1 phenol:chloroform:isoamyl alcohol (PCI) solution was added to the cell suspension. The cell suspension was incubated at 65°C for 15 minutes, followed by incubation on ice for 10 minutes. For phase separation, samples were centrifuged at 14000 rpm at 4°C for 15 minutes, and the liquid phase was transferred to a sterile tube containing 500 μLof PCI. The mixture was vortexed for 20 seconds and incubated on ice for 10 minutes. Following centrifugation of the samples at 14000 rpm at 4 °C for 15 minutes, the liquid phase was transferred into a new sterile tube. Then, 1/10 volume of sodium acetate (pH 5.3) and three volumes of 100% ethanol were added. Samples were then incubated at -80 °C for 30 minutes. RNA was precipitated by centrifugation at 14000 rpm at 4 °C for 15 minutes and dissolved in diethylpyrocarbonate (DEPC)-treated water. RNA samples were also treated with DNase I to degrade any remaining DNA. The purity and concentration of RNA were determined using a Nanodrop 2000 spectrophotometer (Thermo-Fisher Sci., California, USA) with A260/A280 and A260/A230 ratios.Sample Collection - S.cerevisiae BY4741 (MATa, his3∆1, leu2∆0, met15∆0, ura3∆0) strain as the wild-type strain (WT) and BY4741 MOH1 knockout mutant strain (moh1∆; MATa, his3∆1, leu2∆0, met15∆0, ura3∆0, Moh1Δ::KanMX4) were used for the RNA-Sequencing.Sequencing - DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.Library Construction - MGIEasy Fast RNA Library Prep Set was used. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Transcript and gene count matrices were generated using featureCounts after the alignment process.Sequence Alignment - RNA-Seq reads were aligned to the most recent version of the Saccharomyces cerevisiae reference genome (Ensembl release 101) using the STAR aligner (Spliced Transcripts Alignment to a Reference).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G400<h4>ABSTRACT</h4> The Yippee-like (YPEL) proteins are a conserved eukaryotic gene family implicated in proliferation, senescence, and stress adaptation. In humans, five paralogs (YPEL1–YPEL5) are widely expressed and encode proteins with high sequence and amino acid similarity, yet the molecular basis of their functions remains poorly defined. While conservation implies possible functional redundancy, the distinct roles of each YPEL paralog have not been defined. The budding yeast S. cerevisiae possesses a single ortholog, MOH1 , which contributes to survival and stress responses and can be functionally complemented by human YPELs. However, the cellular role of MOH1 remains to be elucidated. Here, we investigated the function of MOH1 in S. cerevisiae . MOH1 deletion ( moh1Δ ) conferred sensitivity to sodium azide and sulfuric acid but increased resistance to hydrogen peroxide and acetic acid. Moh1 protein levels decreased upon hydrogen peroxide treatment and increased following sulfuric acid exposure, indicating stress-dependent regulation. Light and scanning electron microscopy showed that moh1Δ cells are constitutively rounder, tend to form clumps, and exhibit rough surface features, indicating altered cellular architecture. RNA profiling and FTIR spectroscopy revealed transcriptional reprogramming and metabolic remodeling in moh1Δ cells, including alterations in lipid, protein, and cell wall polysaccharide levels and composition. Intracellular ROS assays indicated that hydrogen peroxide resistance can be attributed to decreased cellular uptake resulting from altered permeability, rather than changes in mitochondrial ROS production. Collectively, our findings identify Moh1 as a regulatory factor linking gene expression to metabolism and cellular architecture, influencing membrane permeability and conferring selective stress resistance in S. cerevisiae .RNA-seq of coding RNASaccharomyces cerevisiae S288cYippee-like protein Moh1 links gene expression to metabolism and selective stress resistance in Saccharomyces cerevisiaeÇağla Ece OlgunMesut MuyanCagla Ece Olgun, Gizem Turan Duman, Gizem Gupur, Hamit Izgi, Mariam Huda, Demet Cetin, Zekiye Suludere, Fatma Kucuk Baloglu, Ayse Koca Caydasi, Mesut MuyanfalseRNA-Seq profiling of S. Cerevisiae WT BY4741 cells and MOH1-knockout mutants of BY4741 cells (moh1∆) after growth on YPD-Agar for 40 hoursThe Yippee-like (YPEL) proteins are a conserved eukaryotic gene family implicated in proliferation, senescence, and stress adaptation. In humans, five paralogs (YPEL1–YPEL5) are widely expressed and encode proteins with high sequence similarity, but the molecular basis of their functions remains poorly defined. Functional redundancy among YPEL paralogs complicates the clarification of their individual roles. The budding yeast Saccharomyces cerevisiae has a single ortholog, MOH1, which is involved in survival and stress responses and can be functionally complemented by human YPELs. However, the cellular function of MOH1 has yet to be elucidated. Here, we investigated the function of MOH1 in S. cerevisiae. Deletion of MOH1 (moh1Δ) conferred sensitivity to sodium azide and sulfuric acid but increased resistance to hydrogen peroxide and acetic acid. Moh1 protein levels decreased upon hydrogen peroxide treatment and increased following sulfuric acid exposure, indicating stress-dependent regulation. Light and scanning electron microscopy analyses revealed that moh1Δ cells are constitutively rounder, tend to form clumps, and exhibit rough surface features, signifying altered cellular architecture. RNA profiling and FTIR spectroscopy revealed transcriptional reprogramming and metabolic remodeling in moh1Δ cells, including alterations in lipid, protein, and cell wall polysaccharide levels and composition. Intracellular ROS assays revealed that resistance to hydrogen peroxide results from reduced cellular uptake caused by altered membrane permeability, rather than from differences in mitochondrial ROS generation. Collectively, our findings identify Moh1 as a regulatory factor linking gene expression to metabolism and cellular architecture, influencing membrane permeability and conferring selective stress resistance in S. cerevisiae.2026-06-15T00:00:00Z2026-06-15T01:00:59.423Z2025-11-11T16:13:40.545ZE-MTAB-16090ERP184214EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_000418410.1101/2025.10.30.685511