{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Leo Zeef"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"organism":["Maudiozyma bulderi"],"species":["Maudiozyma bulderi"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15136"],"description":["Non-conventional yeasts represent a great genetic and phenotypic diversity with potential for industrial strain development in the bio-production of green chemicals. In recent years, mass genome sequencing of non-conventional yeasts has opened avenues to improved understanding of transcriptional networks and phenotypic plasticity and gene function, including the discovery of novel genes. Here, we investigated the gene expression changes at low-pH in three strains of the acidophilic yeast Maudiozyma bulderi (previously Kazachstania bulderi): CBS8638, CBS8639 and NRRL-Y27205. The comparison of the transcriptome of cells growing in a bioreactor at pH=5.5 vs pH= 2.5, primarily showed dysregulation of genes involved in cell wall integrity, with NRRL-Y27205, the least acidophilic strain, showing the largest transcriptional response when compared to the other two strains. We identified four uncharacterised genes, unique to M. bulderi ,and predicted function as transporters, upregulated at low pH. We also showed that M. bulderi cell wall and membrane lipid composition is not significantly affected by low pH unlike Saccharomyces cerevisiae. Overall, our data on transcriptional variability in M. bulderi highlights genes and cellular pathways involved in the acidophilic adaptation of this species and can aid further strain development."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Libraries were prepared from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) following the manufacturer’s instructions.","Nucleic Acid Extraction - Total RNA was extracted from 1x10^7 cells of three biological replicates harvested at the logarithmic growth phase (OD600 0.5-1.0) using the RNeasy Mini Kit (QIAGEN, Germany) following the manufacturer’s protocol for enzymatic digestion of the cell wall followed by lysis of spheroplasts. The concentration of lyticase was optimized to 50U per 107 cells for efficient cell lysis. To eliminate genomic DNA contamination, an additional DNase treatment was performed using the RNase-free DNase set (QIAGEN, Germany) according to the manufacturer’s instructions. The extracted RNA was quantified using a NanoDrop Lite Spectrophotometer (Thermo Fisher Scientific, United States).","Sample Collection - Three Maudiozyma bulderi strains used in this study CBS 8638, CBS 8639, and NRRL Y-27205 were obtained from the Agricultural Research Service (ARS-NRRL) culture collection. The yeasts were cultured and maintained on YPD agar medium (15 g/L agar, 10 g/L yeast extract, 20 g/L peptone, 20 g/L glucose) or in SD minimal media (Yeast nitrogen base with ammonium sulphate and amino acids 6.7g/L)  Bioreactor fermentations for RNA extraction were conducted using one litre stirred tank bioreactors (Multifors, Infors-HT, Bottmingen, Switzerland). All fermentation experiments were carried out with cells grown in 500 mL of SD minimal media supplemented with 20g/l glucose. Fermentations were inoculated with cells from YPD overnight culture, washed twice in sterile deionised water, to achieve an initial optical density (OD) of 0.1. Three replicates of each strain were then cultured in 500 mL of YNB supplemented with 20g/l glucose and adjusted to either pH 5.5 or 2.5 with H2SO4. The pH was maintained at 5.5 and 2.5 using either 10 M NaOH or 1 M H3PO4 for pH adjustment. Temperature was maintained at 25°C, with agitation set at 300 rpm. For RNA extraction, 10-20 mL of cells with OD between 0.7 and 1.0 were harvested and promptly snap-frozen with liquid nitrogen.","Sequencing - Paired-end sequencing was conducted on an Illumina HiSeq 4000 instrument"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Leo Zeef"],"additional_accession":[]},"is_claimable":false,"name":"Unveiling the genetic basis of the low pH response in the acidophilic yeast Maudiozyma bulderi (previously Kazachstania bulderi) via transcriptomic analysis","description":"Non-conventional yeasts represent a great genetic and phenotypic diversity with potential for industrial strain development in the bio-production of green chemicals. In recent years, mass genome sequencing of non-conventional yeasts has opened avenues to improved understanding of transcriptional networks and phenotypic plasticity and gene function, including the discovery of novel genes. Here, we investigated the gene expression changes at low-pH in three strains of the acidophilic yeast Maudiozyma bulderi (previously Kazachstania bulderi): CBS8638, CBS8639 and NRRL-Y27205. The comparison of the transcriptome of cells growing in a bioreactor at pH=5.5 vs pH= 2.5, primarily showed dysregulation of genes involved in cell wall integrity, with NRRL-Y27205, the least acidophilic strain, showing the largest transcriptional response when compared to the other two strains. We identified four uncharacterised genes, unique to M. bulderi ,and predicted function as transporters, upregulated at low pH. We also showed that M. bulderi cell wall and membrane lipid composition is not significantly affected by low pH unlike Saccharomyces cerevisiae. Overall, our data on transcriptional variability in M. bulderi highlights genes and cellular pathways involved in the acidophilic adaptation of this species and can aid further strain development.","dates":{"release":"2025-10-22T00:00:00Z","modification":"2025-10-22T15:43:42.927Z","creation":"2025-05-19T09:40:30.831Z"},"accession":"E-MTAB-15136","cross_references":{"ENA":["ERP172704"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}