IF 2.6 4区生物学

Yeast Pub Date : 2024-06-01 Epub Date: 2024-05-06 DOI: 10.1002/yea.3940

Syed Azhar Ali, Pattanan Songdech, Wiwan Samakkarn, Orawan Duangphakdee, Nitnipa Soontorngun

{"title":"New regulatory role of Znf1 in transcriptional control of pentose phosphate pathway and ATP synthesis for enhanced isobutanol and acid tolerance.","authors":"Syed Azhar Ali, Pattanan Songdech, Wiwan Samakkarn, Orawan Duangphakdee, Nitnipa Soontorngun","doi":"10.1002/yea.3940","DOIUrl":"10.1002/yea.3940","url":null,"abstract":"To develop a cost-effective microbial cell factory for the production of biofuels and biochemicals, an understanding of tolerant mechanisms is vital for the construction of robust host strains. Here, we characterized a new function of a key metabolic transcription factor named Znf1 and its involvement in stress response in Saccharomyces cerevisiae to enhance tolerance to advanced biofuel, isobutanol. RNA-sequencing analysis of the wild-type versus the znf1Δ deletion strains in glucose revealed a new role for transcription factor Znf1 in the pentose phosphate pathway (PPP) and energy generation. The gene expression analysis confirmed that isobutanol induces an adaptive cell response, resulting in activation of ATP1-3 and COX6 expression. These genes were Znf1 targets that belong to the electron transport chain, important to produce ATPs. Znf1 also activated PPP genes, required for the generation of key amino acids, cellular metabolites, and maintenance of NADP/NADPH redox balance. In glucose, Znf1 also mediated the upregulation of valine biosynthetic genes of the Ehrlich pathway, namely ILV3, ILV5, and ARO10, associated with the generation of key intermediates for isobutanol production. Using S. cerevisiae knockout collection strains, cells with deleted transcriptional regulatory gene ZNF1 or its targets displayed hypersensitivity to isobutanol and acid inhibitors; in contrast, overexpression of ZNF1 enhanced cell survival. Thus, the transcription factor Znf1 functions in the maintenance of energy homeostasis and redox balance at various checkpoints of yeast metabolic pathways. It ensures the rapid unwiring of gene transcription in response to toxic products/by-products generated during biofuel production. Importantly, we provide a new approach to enhance strain tolerance during the conversion of glucose to biofuels.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"401-417"},"PeriodicalIF":2.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140852348","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

MiniRead: A simple and inexpensive do-it-yourself device for multiple analyses of micro-organism growth kinetics. 迷你阅读器用于微生物生长动力学多重分析的简单而廉价的 DIY 设备。

IF 2.2 4区生物学

Yeast Pub Date : 2024-05-01 Epub Date: 2024-02-21 DOI: 10.1002/yea.3932

Matthieu Falque, Aurélie Bourgais, Fabrice Dumas, Mickaël de Carvalho, Célian Diblasi

{"title":"MiniRead: A simple and inexpensive do-it-yourself device for multiple analyses of micro-organism growth kinetics.","authors":"Matthieu Falque, Aurélie Bourgais, Fabrice Dumas, Mickaël de Carvalho, Célian Diblasi","doi":"10.1002/yea.3932","DOIUrl":"10.1002/yea.3932","url":null,"abstract":"Fitness in micro-organisms can be proxied by growth parameters on different media and/or temperatures. This is achieved by measuring optical density at 600 nm using a spectrophotometer, which measures the effect of absorbance and side scattering due to turbidity of cells suspensions. However, when growth kinetics must be monitored in many 96-well plates at the same time, buying several 96-channel spectrophotometers is often beyond budgets. The MiniRead device presented here is a simple and inexpensive do-it-yourself 96-well temperature-controlled turbidimeter designed to measure the interception of white light via absorption or side scattering through liquid culture medium. Turbidity is automatically recorded in each well at regular time intervals for up to several days or weeks. Output tabulated text files are recorded into a micro-SD memory card to be easily transferred to a computer. We propose also an R package which allows (1) to compute the nonlinear calibration curves required to convert raw readings into cell concentration values, and (2) to analyze growth kinetics output files to automatically estimate proxies of growth parameters such as lag time, maximum growth rate, or cell concentration at the plateau.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"307-314"},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139913617","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

Let it stick: Strategies and applications for intracellular plasma membrane targeting of proteins in Saccharomyces cerevisiae. 让它粘住：酿酒酵母细胞内质膜靶向蛋白质的策略和应用。

IF 2.2 4区生物学

Yeast Pub Date : 2024-05-01 Epub Date: 2024-03-05 DOI: 10.1002/yea.3933

Liv Teresa Muth, Inge Noëlle Adriënne Van Bogaert

{"title":"Let it stick: Strategies and applications for intracellular plasma membrane targeting of proteins in Saccharomyces cerevisiae.","authors":"Liv Teresa Muth, Inge Noëlle Adriënne Van Bogaert","doi":"10.1002/yea.3933","DOIUrl":"10.1002/yea.3933","url":null,"abstract":"Lipid binding domains and protein lipidations are essential features to recruit proteins to intracellular membranes, enabling them to function at specific sites within the cell. Membrane association can also be exploited to answer fundamental and applied research questions, from obtaining insights into the understanding of lipid metabolism to employing them for metabolic engineering to redirect fluxes. This review presents a broad catalog of membrane binding strategies focusing on the plasma membrane of Saccharomyces cerevisiae. Both lipid binding domains (pleckstrin homology, discoidin-type C2, kinase associated-1, basic-rich and bacterial phosphoinositide-binding domains) and co- and post-translational lipidations (prenylation, myristoylation and palmitoylation) are introduced as tools to target the plasma membrane. To provide a toolset of membrane targeting modules, respective candidates that facilitate plasma membrane targeting are showcased including their in vitro and in vivo properties. The relevance and versatility of plasma membrane targeting modules are further highlighted by presenting a selected set of use cases.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"315-329"},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140040468","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

Identification of heparin-binding proteins expressed on Trichosporon asahii cell surface. 鉴定旭三代孢子虫细胞表面表达的肝素结合蛋白。

IF 2.6 4区生物学

Yeast Pub Date : 2024-05-01 Epub Date: 2024-01-31 DOI: 10.1002/yea.3928

Tomoe Ichikawa, Yuka Ikeda, Jumpei Sadanaga, Ayano Kikuchi, Kohei Kawamura, Reiko Ikeda, Yoshio Ishibashi

引用次数: 0

Yeast-insect interactions in southern Africa: Tapping the diversity of yeasts for modern bioprocessing. 南部非洲酵母与昆虫的相互作用：利用酵母的多样性进行现代生物加工。

IF 2.2 4区生物学

Yeast Pub Date : 2024-05-01 Epub Date: 2024-03-07 DOI: 10.1002/yea.3935

Tawanda P Makopa, Thembekile Ncube, Saleh Alwasel, Teun Boekhout, Nerve Zhou

{"title":"Yeast-insect interactions in southern Africa: Tapping the diversity of yeasts for modern bioprocessing.","authors":"Tawanda P Makopa, Thembekile Ncube, Saleh Alwasel, Teun Boekhout, Nerve Zhou","doi":"10.1002/yea.3935","DOIUrl":"10.1002/yea.3935","url":null,"abstract":"Yeast-insect interactions are one of the most interesting long-standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect-derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern-day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"330-348"},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140050449","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 Crf1p is an activator with different roles in regulation of target genes 酵母 Crf1p 是一种激活剂，在靶基因调控中发挥不同作用

IF 2.6 4区生物学

Yeast Pub Date : 2024-04-19 DOI: 10.1002/yea.3939

Sanjay Kumar, Muneera Mashkoor, Priya Balamurugan, Anne Grove

{"title":"Yeast Crf1p is an activator with different roles in regulation of target genes","authors":"Sanjay Kumar, Muneera Mashkoor, Priya Balamurugan, Anne Grove","doi":"10.1002/yea.3939","DOIUrl":"https://doi.org/10.1002/yea.3939","url":null,"abstract":"Under stress conditions, ribosome biogenesis is downregulated. This process requires that expression of ribosomal RNA, ribosomal protein, and ribosome biogenesis genes be controlled in a coordinated fashion. The mechanistic Target of Rapamycin Complex 1 (mTORC1) participates in sensing unfavorable conditions to effect the requisite change in gene expression. In Saccharomyces cerevisiae, downregulation of ribosomal protein genes involves dissociation of the activator Ifh1p in a process that depends on Utp22p, a protein that also functions in pre‐rRNA processing. Ifh1p has a paralog, Crf1p, which was implicated in communicating mTORC1 inhibition and hence was perceived as a repressor. We focus here on two ribosomal biogenesis genes, encoding Utp22p and the high mobility group protein Hmo1p, both of which are required for communication of mTORC1 inhibition to target genes. Crf1p functions as an activator on these genes as evidenced by reduced mRNA abundance and RNA polymerase II occupancy in a crf1Δ strain. Inhibition of mTORC1 has distinct effects on expression of HMO1 and UTP22; for example, on UTP22, but not on HMO1, the presence of Crf1p promotes the stable depletion of Ifh1p. Our data suggest that Crf1p functions as a weak activator, and that it may be required to prevent re‐binding of Ifh1p to some gene promoters after mTORC1 inhibition in situations when Ifh1p is available. We propose that the inclusion of genes encoding proteins required for mTORC1‐mediated downregulation of ribosomal protein genes in the same regulatory circuit as the ribosomal protein genes serves to optimize transcriptional responses during mTORC1 inhibition.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"25 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140626062","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 transcriptome analysis reveals the redirection of metabolic flux from cell growth to astaxanthin biosynthesis in Yarrowia lipolytica 比较转录组分析揭示了脂肪溶解亚罗维氏菌中从细胞生长到虾青素生物合成的代谢通量的重新定向

IF 2.6 4区生物学

Yeast Pub Date : 2024-04-13 DOI: 10.1002/yea.3938

Dan‐Ni Wang, Chen‐Xi Yu, Jie Feng, Liu‐Jing Wei, Jun Chen, Zhijie Liu, Liming Ouyang, Lixin Zhang, Feng Liu, Qiang Hua

{"title":"Comparative transcriptome analysis reveals the redirection of metabolic flux from cell growth to astaxanthin biosynthesis in Yarrowia lipolytica","authors":"Dan‐Ni Wang, Chen‐Xi Yu, Jie Feng, Liu‐Jing Wei, Jun Chen, Zhijie Liu, Liming Ouyang, Lixin Zhang, Feng Liu, Qiang Hua","doi":"10.1002/yea.3938","DOIUrl":"https://doi.org/10.1002/yea.3938","url":null,"abstract":"Engineering Yarrowia lipolytica to produce astaxanthin provides a promising route. Here, Y. lipolytica M2 producing a titer of 181 mg/L astaxanthin was isolated by iterative atmospheric and room‐temperature plasma mutagenesis and diphenylamine‐mediated screening. Interestingly, a negative correlation was observed between cell biomass and astaxanthin production. To reveal the underlying mechanism, RNA‐seq analysis of transcriptional changes was performed in high producer M2 and reference strain M1, and a total of 1379 differentially expressed genes were obtained. Data analysis revealed that carbon flux was elevated through lipid metabolism, acetyl‐CoA and mevalonate supply, but restrained through central carbon metabolism in strain M2. Moreover, upregulation of other pathways such as ATP‐binding cassette transporter and thiamine pyrophosphate possibly provided more cofactors for carotenoid hydroxylase and relieved cell membrane stress caused by astaxanthin insertion. These results suggest that balancing cell growth and astaxanthin production may be important to promote efficient biosynthesis of astaxanthin in Y. lipolytica.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"32 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140581142","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

Gene transcription in yeasts: From molecules to integrated processes 酵母中的基因转录：从分子到综合过程

IF 2.6 4区生物学

Yeast Pub Date : 2024-04-08 DOI: 10.1002/yea.3936

Domenico Libri, Jane Mellor, Françoise Stutz, Benoit Palancade

引用次数: 0

Live‐cell fluorescence imaging and optogenetic control of PKA kinase activity in fission yeast Schizosaccharomyces pombe 裂殖酵母中 PKA 激酶活性的活细胞荧光成像和光遗传控制

IF 2.6 4区生物学

Yeast Pub Date : 2024-04-07 DOI: 10.1002/yea.3937

Keiichiro Sakai, Kazuhiro Aoki, Yuhei Goto

{"title":"Live‐cell fluorescence imaging and optogenetic control of PKA kinase activity in fission yeast Schizosaccharomyces pombe","authors":"Keiichiro Sakai, Kazuhiro Aoki, Yuhei Goto","doi":"10.1002/yea.3937","DOIUrl":"https://doi.org/10.1002/yea.3937","url":null,"abstract":"The cAMP‐PKA signaling pathway plays a crucial role in sensing and responding to nutrient availability in the fission yeast Schizosaccharomyces pombe. This pathway monitors external glucose levels to control cell growth and sexual differentiation. However, the temporal dynamics of the cAMP‐PKA pathway in response to external stimuli remains unclear mainly due to the lack of tools to quantitatively visualize the activity of the pathway. Here, we report the development of the kinase translocation reporter (KTR)‐based biosensor spPKA‐KTR1.0, which allows us to measure the dynamics of PKA activity in fission yeast cells. The spPKA‐KTR1.0 is derived from the transcription factor Rst2, which translocates from the nucleus to the cytoplasm upon PKA activation. We found that spPKA‐KTR1.0 translocates between the nucleus and cytoplasm in a cAMP‐PKA pathway‐dependent manner, indicating that the spPKA‐KTR1.0 is a reliable indicator of the PKA activity in fission yeast cells. In addition, we implemented a system that simultaneously visualizes and manipulates the cAMP‐PKA signaling dynamics by introducing bPAC, a photoactivatable adenylate cyclase, in combination with spPKA‐KTR1.0. This system offers an opportunity for investigating the role of the signaling dynamics of the cAMP‐PKA pathway in fission yeast cells with higher temporal resolution.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"47 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140581449","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

Transcription as source of genetic heterogeneity in budding yeast. 转录是芽殖酵母遗传异质性的来源。

IF 2.6 4区生物学

Yeast Pub Date : 2024-04-01 Epub Date: 2024-01-09 DOI: 10.1002/yea.3926

Baptiste Piguet, Jonathan Houseley

{"title":"Transcription as source of genetic heterogeneity in budding yeast.","authors":"Baptiste Piguet, Jonathan Houseley","doi":"10.1002/yea.3926","DOIUrl":"10.1002/yea.3926","url":null,"abstract":"Transcription presents challenges to genome stability both directly, by altering genome topology and exposing single-stranded DNA to chemical insults and nucleases, and indirectly by introducing obstacles to the DNA replication machinery. Such obstacles include the RNA polymerase holoenzyme itself, DNA-bound regulatory factors, G-quadruplexes and RNA-DNA hybrid structures known as R-loops. Here, we review the detrimental impacts of transcription on genome stability in budding yeast, as well as the mitigating effects of transcription-coupled nucleotide excision repair and of systems that maintain DNA replication fork processivity and integrity. Interactions between DNA replication and transcription have particular potential to induce mutation and structural variation, but we conclude that such interactions must have only minor effects on DNA replication by the replisome with little if any direct mutagenic outcome. However, transcription can significantly impair the fidelity of replication fork rescue mechanisms, particularly Break Induced Replication, which is used to restart collapsed replication forks when other means fail. This leads to de novo mutations, structural variation and extrachromosomal circular DNA formation that contribute to genetic heterogeneity, but only under particular conditions and in particular genetic contexts, ensuring that the bulk of the genome remains extremely stable despite the seemingly frequent interactions between transcription and DNA replication.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"171-185"},"PeriodicalIF":2.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139404621","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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