Yeast最新文献

{"title":"Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription?","authors":"Carlo Yague-Sanz","doi":"10.1002/yea.3921","DOIUrl":"https://doi.org/10.1002/yea.3921","url":null,"abstract":"Eukaryotic genes must be condensed into chromatin while remaining accessible to the transcriptional machinery to support gene expression. Among the three eukaryotic RNA polymerases (RNAP), RNAPII is unique, partly because of the C-terminal domain (CTD) of its largest subunit, Rpb1. Rpb1 CTD can be extensively modified during the transcription cycle, allowing for the co-transcriptional recruitment of specific interacting proteins. These include chromatin remodeling factors that control the opening or closing of chromatin. How the CTD-less RNAPI and RNAPIII deal with chromatin at rRNA and tRNA genes is less understood. Here, we review recent advances in our understanding of how the chromatin at tRNA genes and rRNA genes can be remodeled in response to environmental cues in yeast, with a particular focus on the role of local RNAPII transcription in recruiting chromatin remodelers at these loci. In fission yeast, RNAPII transcription at tRNA genes is important to re-establish a chromatin environment permissive to tRNA transcription, which supports growth from stationary phase. In contrast, local RNAPII transcription at rRNA genes correlates with the closing of the chromatin in starvation in budding and fission yeast, suggesting a role in establishing silent chromatin. These opposite roles might support a general model where RNAPII transcription recruits chromatin remodelers to tRNA and rRNA genes to promote the closing and reopening of chromatin in response to the environment.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"7 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138824838","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}

{"title":"Engineering heterothallic strains in fission yeast","authors":"Daniel García-Ruano, Ian Hsu, Baptiste Leray, Bénédicte Billard, Gianni Liti, Damien Coudreuse","doi":"10.1002/yea.3914","DOIUrl":"https://doi.org/10.1002/yea.3914","url":null,"abstract":"In poor nitrogen conditions, fission yeast cells mate, undergo meiosis and form spores that are resistant to deleterious environments. Natural isolates of <i>Schizosaccharomyces pombe</i> are homothallic. This allows them to naturally switch between the two <i>h−</i> and <i>h+</i> mating types with a high frequency, thereby ensuring the presence of both mating partners in a population of cells. However, alteration of the mating type locus can abolish mating type switching or reduce it to a very low frequency. Such heterothallic strains have been isolated and are common in research laboratories due to the simplicity of their use for Mendelian genetics. In addition to the standard laboratory strains, a large collection of natural <i>S. pombe</i> isolates is now available, representing a powerful resource for investigating the genetic diversity and biology of fission yeast. However, most of these strains are homothallic, and only tedious or mutagenic strategies have been described to obtain heterothallic cells from a homothallic parent. Here, we describe a simple approach to generate heterothallic strains. It takes advantage of an alteration of the mating type locus that was previously identified in a mating type switching-deficient strain and the CRISPR-Cas9 editing tool, allowing for a one-step engineering of heterothallic cells with high efficiency.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"10 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687440","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}

{"title":"Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation","authors":"Radityo Pangestu, Prihardi Kahar, Chiaki Ogino, Akihiko Kondo","doi":"10.1002/yea.3917","DOIUrl":"https://doi.org/10.1002/yea.3917","url":null,"abstract":"While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating <i>Saccharomyces cerevisiae</i> strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"55 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138630574","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}

{"title":"Taxogenomic placement of Rasporella oleae and Rasporella dianae gen. and spp. nov., two insect associated yeast species.","authors":"Neža Čadež, Kyria Boundy-Mills, Alfred Botha, Aleksey Kachalkin, Dénes Dlauchy, Gábor Péter","doi":"10.1002/yea.3904","DOIUrl":"10.1002/yea.3904","url":null,"abstract":"<p><p>During the course of independent studies in Europe, North America, and Africa, seven yeast strains were isolated from insect frass, decaying wood, tree flux, and olive oil sediment. Phylogenetic analysis of two barcoding DNA regions (internal transcribed spacer and the D1/D2 domain of the LSU rRNA gene) revealed that they belong to two closely related undescribed species distinct from all genera in the family Debaryomycetaceae. For reliable taxonomic placement the genomes of four strains of the two novel species and six type strains of closely related species were sequenced. Orthologous genes from 54 genomes of representatives of the Pichiomycetes and 23 outgroup taxa were concatenated to construct a fully supported phylogenetic tree. Consistent with the assumptions, we found that the two new species belong to a novel genus. In addition, the delimitation of the novel species was supported by genetic distance calculations from average nucleotide identity (ANI) and digital DNA:DNA hybridization (dDDH) values. The physiological characterization of the novel species was generally consistent with their genomic content. All strains had two alleles encoding secretory lipase in either two or three copies depending on the species. However, lipolytic activity was detected only in strains with three copies of the secretory lipase gene. Nevertheless, lipolytic activity might be related to their association with the insect gut. Based on these results, formal descriptions of the new genus Rasporella gen. nov. and of two new species Rasporella dianae sp. nov. (holotype UCDFST 68-643^T , MycoBank no.: 850238) and Rasporella oleae sp. nov. (holotype ZIM 2471^T , MycoBank no.: 850126) are provided.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"594-607"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54231274","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}

{"title":"MKT1 alleles regulate stress responses through posttranscriptional modulation of Puf3 targets in budding yeast.","authors":"Koppisetty Viswa Chaithanya, Himanshu Sinha","doi":"10.1002/yea.3908","DOIUrl":"10.1002/yea.3908","url":null,"abstract":"<p><p>MKT1 is a pleiotropic stress response gene identified by several quantitative trait studies with MKT1^89G as a causal variant, contributing to growth advantage in multiple stress environments. MKT1 has been shown to regulate HO endonuclease posttranscriptionally via the Pbp1-Pab1 complex. RNA-binding protein Puf3 modulates a set of nuclear-encoded mitochondrial transcripts whose expression was found to be affected by MKT1 alleles. This study attempts to relate the MKT1 allele-derived growth advantage with the stability of Puf3 targets during stress and elucidate the roles of Pbp1 and Puf3 in this mechanism. Our results showed that the growth advantage of the MKT1^89G allele in cycloheximide and H₂ O₂ was PBP1-dependent, whereas in 4-nitroquinoline 1-oxide, the growth advantage was dependent on both PUF3 and PBP1. We compared the messenger RNA decay kinetics of a set of Puf3 targets in multiple stress environments to understand the allele-specific regulation by MKT1. In oxidative stress, the MKT1^89G allele modulated the differential expression of nuclear-encoded mitochondrial genes in a PBP1- and PUF3-dependent manner. Additionally, MKT1^89G stabilised Puf3 targets, namely, COX17, MRS1 and RDL2, in an allele and stress-specific manner. Our results showed that COX17, MRS1 and RDL2 had a stress-specific response in stress environments, with the MKT1^89G allele contributing to better growth; this response was both PBP1- and PUF3-dependent. Our results indicate that the common allele, MKT1^89G , regulates stress responses by differentially stabilising Puf3-target mitochondrial genes, which allows for the strain's better growth in stress environments.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"616-627"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138291941","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}

{"title":"Carbon efficient production of chemicals with yeasts.","authors":"Evelyn Vásquez Castro, Golnaz Memari, Özge Ata, Diethard Mattanovich","doi":"10.1002/yea.3909","DOIUrl":"10.1002/yea.3909","url":null,"abstract":"<p><p>Microbial metabolism offers a wide variety of opportunities to produce chemicals from renewable resources. Employing such processes of industrial biotechnology provides valuable means to fight climate change by replacing fossil feedstocks by renewable substrate to reduce or even revert carbon emission. Several yeast species are well suited chassis organisms for this purpose, illustrated by the fact that the still largest microbial production of a chemical, namely bioethanol is based on yeast. Although production of ethanol and some other chemicals is highly efficient, this is not the case for many desired bulk chemicals. One reason for low efficiency is carbon loss, which decreases the product yield and increases the share of total production costs that is taken by substrate costs. Here we discuss the causes for carbon loss in metabolic processes, approaches to avoid carbon loss, as well as opportunities to incorporate carbon from CO₂ , based on the electron balance of pathways. These aspects of carbon efficiency are illustrated for the production of succinic acid from a diversity of substrates using different pathways.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"583-593"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10946752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138300147","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}

{"title":"High nitrogen concentration causes G2/M arrest in Hanseniaspora vineae.","authors":"Luisa Vivian Schwarz, Fernanda Knaach Sandri, Fernando Scariot, Ana Paula Longaray Delamare, Maria Jose Valera, Francisco Carrau, Sergio Echeverrigaray","doi":"10.1002/yea.3911","DOIUrl":"10.1002/yea.3911","url":null,"abstract":"<p><p>Yeasts have been widely used as a model to better understand cell cycle mechanisms and how nutritional and genetic factors can impact cell cycle progression. While nitrogen scarcity is well known to modulate cell cycle progression, the relevance of nitrogen excess for microorganisms has been overlooked. In our previous work, we observed an absence of proper entry into the quiescent state in Hanseniaspora vineae and identified a potential link between this behavior and nitrogen availability. Furthermore, the Hanseniaspora genus has gained attention due to a significant loss of genes associated with DNA repair and cell cycle. Thus, the aim of our study was to investigate the effects of varying nitrogen concentrations on H. vineae's cell cycle progression. Our findings demonstrated that nitrogen excess, regardless of the source, disrupts cell cycle progression and induces G2/M arrest in H. vineae after reaching the stationary phase. Additionally, we observed a viability decline in H. vineae cells in an ammonium-dependent manner, accompanied by increased production of reactive oxygen species, mitochondrial hyperpolarization, intracellular acidification, and DNA fragmentation. Overall, our study highlights the events of the cell cycle arrest in H. vineae induced by nitrogen excess and attempts to elucidate the possible mechanism triggering this absence of proper entry into the quiescent state.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"640-650"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138300149","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}

{"title":"Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov.","authors":"Dana A Opulente, Quinn K Langdon, Martin Jarzyna, Kelly V Buh, Max A B Haase, Marizeth Groenewald, Chris Todd Hittinger","doi":"10.1002/yea.3905","DOIUrl":"10.1002/yea.3905","url":null,"abstract":"<p><p>A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446^T (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"608-615"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10841356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71427439","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}

{"title":"Strain diversity in Saccharomyces cerevisiae thiamine production capacity.","authors":"Rebecca Rocchi, Judith C M Wolkers-Rooijackers, Zhuotong Liao, Marcel H Tempelaars, Eddy J Smid","doi":"10.1002/yea.3906","DOIUrl":"10.1002/yea.3906","url":null,"abstract":"<p><p>Vitamin B₁ , also known as thiamine, is an important vitamin that, besides its role in human health, is converted to meat aromas upon exposure to high temperatures. Therefore, it is relevant for the production of vegan meat-like flavours. In this study, we investigated 48 Saccharomyces cerevisiae strains for their thiamine production capacity by measuring the intracellular and extracellular vitamins produced in the thiamine-free minimal medium after 72 h of growth. We found approximately an 8.2-fold difference in overall thiamine yield between the highest and lowest-producing strains. While the highest thiamine yield was 254.6 nmol/L, the highest thiamine-specific productivity was 160.9 nmol/g DW. To assess whether extracellular thiamine was due to leakage caused by cell damage, we monitored membrane permeabilization using propidium iodide (PI) staining and flow cytometry. We found a good correlation between the percentage of extracellular thiamine and PI-stained cells (Spearman's ρ = 0.85). Finally, we compared S. cerevisiae CEN.PK113-7D (wild type [WT]) to three strains evolved in a thiamine-free medium for their thiamine production capacity. On average, we saw an increase in the amount of thiamine produced. One of the evolved strains had a 49% increase in intracellular thiamine-specific productivity and a biomass increase of 20% compared with the WT. This led to a total increase in thiamine yield of 60% in this strain, reaching 208 nmol/L. This study demonstrated that it is possible to achieve thiamine overproduction in S. cerevisiae via strain selection and adaptive laboratory evolution.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"628-639"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71486677","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}

{"title":"Histomorphological Study of Thyroidectomy Specimens in Tertiary Care Hospital -A Retrospective Study.","authors":"Santosh U P, Ashwini Kuruwatti, Srivaibhava V, Jemima H","doi":"10.1007/s12070-023-03916-w","DOIUrl":"10.1007/s12070-023-03916-w","url":null,"abstract":"<p><p>Thyroid disorders are the most common endocrine disorder affecting the general population. Diseases of the thyroid glands present with either an alteration of hormone secretion or as an enlargement of the thyroid gland. They vary from non-neoplastic to neoplastic lesions. The prevalence and pattern of these disorders depend on the factors like age, sex and geographic patterns. The aim of the study is to determine the histomorphological features of thyroid lesions in thyroidectomy specimens in patients who underwent thyroidectomy in tertiary care hospital. This is a retrospective study, conducted in tertiary care centre attached to government hospital. All thyroidectomy specimens received in the Department of Pathology, from January 2021 to January 2023 were included in the study. The patients who underwent thyroidectomy in view of thyroid swelling, over a period of 2 years, were selected. Data was collected from histopathological examinations done on the thyroidectomy specimens. Different histomorphological patterns were observed on microscopy. The thyroid lesions were classified into Neoplastic and Non-neoplastic based on histomorphological features and the data was segregated according to this and analysed. There was a total of 194 specimens, of which 175 were from female and 19 were from male patients. Maximum number of thyroid lesions were seen in the age group of 30-50 years. Among 194 patients, 52 (26.8%) were found to have neoplastic lesions, of whom, 25 (12.8%) patients had benign and 27(14%) patients had malignant lesion. 141(72.7%) patients had non neoplastic conditions. One patient had lymphoproliferative disorder (0.5%). In Neoplastic lesions, Among Benign lesions, Follicular adenoma was found be present in 25 patients. In malignant lesions, Papillary carcinoma was the most commonly found lesion (25 cases, 12.9%). 141(73%) patients had Non neoplastic conditions. Most commonly occurring Non neoplastic lesions were Nodular goiter (50 cases, 25.8%) followed by Colloid goiter (34cases, 17.5%), Multinodular goiter (33 cases, 17%), Hashimoto's thyroiditis (5 cases, 2.6%). Followed by Chronic lymphocytic thyroiditis (4 cases, 2.1%). The frequency of carcinoma is more common in females amongst the total thyroid lesions. Papillary carcinoma was the most frequent malignancy (12.9%) among the thyroidectomy specimens. Papillary carcinoma was the commonest malignant lesion with female preponderance whereas, nodular goiter and colloid goiter were the commonest non neoplastic lesions with female preponderance.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"20 1","pages":"3205-3210"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10645978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73023357","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}