IF 2.6 4区生物学

Yeast Pub Date : 2024-01-01 Epub Date: 2023-11-23 DOI: 10.1002/yea.3910

Alisha G Lewis, Laurin Carmichael, Rebecca Y Wang, Patrick A Gibney

{"title":"Characterizing a panel of amino acid auxotrophs under auxotrophic starvation conditions.","authors":"Alisha G Lewis, Laurin Carmichael, Rebecca Y Wang, Patrick A Gibney","doi":"10.1002/yea.3910","DOIUrl":"10.1002/yea.3910","url":null,"abstract":"Auxotrophic strains starving for their cognate nutrient, termed auxotrophic starvation, are characterized by a shorter lifespan, higher glucose wasting phenotype, and inability to accomplish cell cycle arrest when compared to a \"natural starvation,\" where a cell is starving for natural environmental growth-limiting nutrients such as phosphate. Since evidence of this physiological response is limited to only a subset of auxotrophs, we evaluated a panel of auxotrophic mutants to determine whether these responses are characteristic of a broader range of amino acid auxotrophs. Based on the starvation survival kinetics, the panel of strains was grouped into three categories-short-lived strains, strains with survival similar to a prototrophic wild type strain, and long-lived strains. Among the short-lived strains, we observed that the tyrosine, asparagine, threonine, and aspartic acid auxotrophs rapidly decline in viability, with all strains unable to arrest cell cycle progression. The three basic amino acid auxotrophs had a survival similar to a prototrophic strain starving in minimal media. The leucine, tryptophan, methionine, and cysteine auxotrophs displayed the longest lifespan. We also demonstrate how the phenomenon of glucose wasting is limited to only a subset of the tested auxotrophs, namely the asparagine, leucine, and lysine auxotrophs. Furthermore, we observed pleiotropic phenotypes associated with a subgroup of auxotrophs, highlighting the importance of considering unintended phenotypic effects when using auxotrophic strains especially in chronological aging experiments.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138300148","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

GetPrimers: A generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems. GetPrimers:一个通用的基于pcr的基因靶向引物设计器，可以跨多个系统进行简单和标准化的靶向基因修饰。

IF 2.6 4区生物学

Yeast Pub Date : 2024-01-01 Epub Date: 2023-12-02 DOI: 10.1002/yea.3916

Zepu Miao, Haiting Wang, Xinyu Tu, Zhengshen Huang, Shujing Huang, Xinxin Zhang, Fan Wang, Zhishen Huang, Huihui Li, Yue Jiao, Song Gao, Zhipeng Zhou, Chun-Min Shan, Jing Li, Jia-Xing Yue

{"title":"GetPrimers: A generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems.","authors":"Zepu Miao, Haiting Wang, Xinyu Tu, Zhengshen Huang, Shujing Huang, Xinxin Zhang, Fan Wang, Zhishen Huang, Huihui Li, Yue Jiao, Song Gao, Zhipeng Zhou, Chun-Min Shan, Jing Li, Jia-Xing Yue","doi":"10.1002/yea.3916","DOIUrl":"10.1002/yea.3916","url":null,"abstract":"Genetic targeting (e.g., gene knockout and tagging) based on polymerase chain reaction (PCR) is a simple yet powerful approach for studying gene functions. Although originally developed in classic budding and fission yeast models, the same principle applies to other eukaryotic systems with efficient homologous recombination. One-step PCR-based genetic targeting is conventionally used but the sizes of the homologous arms that it generates for recombination-mediated genetic targeting are usually limited. Alternatively, gene targeting can also be performed via fusion PCR, which can create homologous arms that are orders of magnitude larger, therefore substantially increasing the efficiency of recombination-mediated genetic targeting. Here, we present GetPrimers (https://www.evomicslab.org/app/getprimers/), a generalized computational framework and web tool to assist automatic targeting and verification primer design for both one-step PCR-based and fusion PCR-based genetic targeting experiments. Moreover, GetPrimers by design runs for any given genetic background of any species with full genome scalability. Therefore, GetPrimers is capable of empowering high-throughput functional genomic assays at multipopulation and multispecies levels. Comprehensive experimental validations have been performed for targeting and verification primers designed by GetPrimers across multiple organism systems and experimental setups. We anticipate GetPrimers to become a highly useful and popular tool to facilitate easy and standardized gene modification across multiple systems.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138471021","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

Yeast diversity in open agave fermentations across Mexico. 墨西哥龙舌兰露天发酵中的酵母多样性。

IF 2.2 4区生物学

Yeast Pub Date : 2024-01-01 Epub Date: 2023-12-06 DOI: 10.1002/yea.3913

Porfirio Gallegos-Casillas, Luis F García-Ortega, Adriana Espinosa-Cantú, J Abraham Avelar-Rivas, Carolina G Torres-Lagunes, Adrián Cano-Ricardez, Ángela M García-Acero, Susana Ruiz-Castro, Mayra Flores-Barraza, Alejandra Castillo, Fernando González-Zozaya, América Delgado-Lemus, Francisco Molina-Freaner, Cuauhtémoc Jacques-Hernández, Antonio Hernández-López, Luis Delaye, Xitlali Aguirre-Dugua, Manuel R Kirchmayr, Lucia Morales, Eugenio Mancera, Alexander DeLuna

{"title":"Yeast diversity in open agave fermentations across Mexico.","authors":"Porfirio Gallegos-Casillas, Luis F García-Ortega, Adriana Espinosa-Cantú, J Abraham Avelar-Rivas, Carolina G Torres-Lagunes, Adrián Cano-Ricardez, Ángela M García-Acero, Susana Ruiz-Castro, Mayra Flores-Barraza, Alejandra Castillo, Fernando González-Zozaya, América Delgado-Lemus, Francisco Molina-Freaner, Cuauhtémoc Jacques-Hernández, Antonio Hernández-López, Luis Delaye, Xitlali Aguirre-Dugua, Manuel R Kirchmayr, Lucia Morales, Eugenio Mancera, Alexander DeLuna","doi":"10.1002/yea.3913","DOIUrl":"10.1002/yea.3913","url":null,"abstract":"Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX-1.0 culture collection by isolating 4524 strains from 68 sites with diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and validated a subset of the strains by ITS and D1/D2 sequencing, which also revealed two potential novel species of Saccharomycetales. Overall, the composition of yeast communities was weakly associated with local variables and types of climate, yet a core set of six species was consistently isolated from most producing regions. To explore the intraspecific variation of the yeasts from agave fermentations, we sequenced the genomes of four isolates of the nonconventional yeast Kazachstania humilis. The genomes of these four strains were substantially distinct from a European isolate of the same species, suggesting that they may belong to different populations. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138488581","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

Nakazawaea atacamensis f.a., sp. nov. a novel nonconventional fermentative ascomycetous yeast species from the Atacama Desert. Nakazawaea atacamensis f.a.，sp. nov.来自阿塔卡马沙漠的一种新的非常规发酵子囊酵母菌。

IF 2.6 4区生物学

Yeast Pub Date : 2024-01-01 Epub Date: 2023-12-26 DOI: 10.1002/yea.3920

Macarena Araya, Pablo Villarreal, Tomás Moyano, Ana R O Santos, Francisca P Díaz, Andrea Bustos-Jarufe, Kamila Urbina, Javier E Del Pino, Marizeth Groenewald, Rodrigo A Gutiérrez, Carlos A Rosa, Francisco A Cubillos

{"title":"Nakazawaea atacamensis f.a., sp. nov. a novel nonconventional fermentative ascomycetous yeast species from the Atacama Desert.","authors":"Macarena Araya, Pablo Villarreal, Tomás Moyano, Ana R O Santos, Francisca P Díaz, Andrea Bustos-Jarufe, Kamila Urbina, Javier E Del Pino, Marizeth Groenewald, Rodrigo A Gutiérrez, Carlos A Rosa, Francisco A Cubillos","doi":"10.1002/yea.3920","DOIUrl":"10.1002/yea.3920","url":null,"abstract":"In this study, we describe Nakazawaea atacamensis f. a., sp. nov., a novel species obtained from Neltuma chilensis plant samples in Chile's hyperarid Atacama Desert. In total, three strains of N. atacamensis were obtained from independent N. chilensis samples (synonym Prosopis chilensis, Algarrobo). Two strains were obtained from bark samples, while the third strain was obtained from bark-exuded gum from another tree. The novel species was defined using molecular characteristics and subsequently characterized with respect to morphological, physiological, and biochemical properties. A neighbor-joining analysis using the sequences of the D1/D2 domains of the large subunit ribosomal RNA gene revealed that N. atacamensis clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3%-5.2% in the D1/D2 domains. A phylogenomic analysis based on single-nucleotide polymorphism's data confirms that the novel species belongs to the genus Nakazawaea, where N. atacamensis clustered with N. peltata. Phenotypic comparisons demonstrated that N. atacamensis exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the strain ATA-11A-BT revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of N. atacamensis in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375T . The Mycobank number is MB 849680.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139037981","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

Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription? 塑造 rRNA 和 tRNA 基因的染色质景观，RNA 聚合酶 II 转录的新角色？

IF 2.6 4区生物学

Yeast Pub Date : 2023-12-21 DOI: 10.1002/yea.3921

Carlo Yague-Sanz

{"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":null,"pages":null},"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}

引用次数: 0

Engineering heterothallic strains in fission yeast 裂变酵母中的异型菌株工程

IF 2.6 4区生物学

Yeast Pub Date : 2023-12-15 DOI: 10.1002/yea.3914

Daniel García-Ruano, Ian Hsu, Baptiste Leray, Bénédicte Billard, Gianni Liti, Damien Coudreuse

{"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 Schizosaccharomyces pombe are homothallic. This allows them to naturally switch between the two h− and h+ 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 S. pombe 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":null,"pages":null},"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}

引用次数: 0

Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation 乳酸发酵中絮凝酵母和非絮凝酵母对细胞密度和化学压力的比较反应

IF 2.6 4区生物学

Yeast Pub Date : 2023-12-11 DOI: 10.1002/yea.3917

Radityo Pangestu, Prihardi Kahar, Chiaki Ogino, Akihiko Kondo

{"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 Saccharomyces cerevisiae 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":null,"pages":null},"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}

引用次数: 0

Taxogenomic placement of Rasporella oleae and Rasporella dianae gen. and spp. nov., two insect associated yeast species. 两个昆虫相关酵母种——夹竹桃和二氏桃的分类基因组定位。

IF 2.6 4区生物学

Yeast Pub Date : 2023-12-01 Epub Date: 2023-10-26 DOI: 10.1002/yea.3904

Neža Čadež, Kyria Boundy-Mills, Alfred Botha, Aleksey Kachalkin, Dénes Dlauchy, Gábor Péter

{"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":"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 68-643T , MycoBank no.: 850238) and Rasporella oleae sp. nov. (holotype ZIM 2471T , MycoBank no.: 850126) are provided.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"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}

引用次数: 0

Carbon efficient production of chemicals with yeasts. 利用酵母高效生产化学品。

IF 2.6 4区生物学

Yeast Pub Date : 2023-12-01 Epub Date: 2023-11-23 DOI: 10.1002/yea.3909

Evelyn Vásquez Castro, Golnaz Memari, Özge Ata, Diethard Mattanovich

{"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":"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.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"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}

引用次数: 0

MKT1 alleles regulate stress responses through posttranscriptional modulation of Puf3 targets in budding yeast. MKT1等位基因通过芽殖酵母Puf3靶点的转录后调控胁迫反应。

IF 2.6 4区生物学

Yeast Pub Date : 2023-12-01 Epub Date: 2023-11-22 DOI: 10.1002/yea.3908

Koppisetty Viswa Chaithanya, Himanshu Sinha

{"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":"MKT1 is a pleiotropic stress response gene identified by several quantitative trait studies with MKT189G 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 MKT189G 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 MKT189G allele modulated the differential expression of nuclear-encoded mitochondrial genes in a PBP1- and PUF3-dependent manner. Additionally, MKT189G 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 MKT189G allele contributing to better growth; this response was both PBP1- and PUF3-dependent. Our results indicate that the common allele, MKT189G , regulates stress responses by differentially stabilising Puf3-target mitochondrial genes, which allows for the strain's better growth in stress environments.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"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}

引用次数: 0

Yeast最新文献