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

Budding yeast as an ideal model for elucidating the role of N⁶-methyladenosine in regulating gene expression. 芽殖酵母是阐明 N6 -甲基腺苷调控基因表达作用的理想模型。

IF 2.6 4区生物学

Yeast Pub Date : 2024-04-01 Epub Date: 2024-01-18 DOI: 10.1002/yea.3925

Waleed S Albihlal, Wei Yee Chan, Folkert J van Werven

{"title":"Budding yeast as an ideal model for elucidating the role of N6-methyladenosine in regulating gene expression.","authors":"Waleed S Albihlal, Wei Yee Chan, Folkert J van Werven","doi":"10.1002/yea.3925","DOIUrl":"10.1002/yea.3925","url":null,"abstract":"N6-methyladenosine (m6A) is a highly abundant and evolutionarily conserved messenger RNA (mRNA) modification. This modification is installed on RRACH motifs on mRNAs by a hetero-multimeric holoenzyme known as m6A methyltransferase complex (MTC). The m6A mark is then recognised by a group of conserved proteins known as the YTH domain family proteins which guide the mRNA for subsequent downstream processes that determine its fate. In yeast, m6A is installed on thousands of mRNAs during early meiosis by a conserved MTC and the m6A-modified mRNAs are read by the YTH domain-containing protein Mrb1/Pho92. In this review, we aim to delve into the recent advances in our understanding of the regulation and roles of m6A in yeast meiosis. We will discuss the potential functions of m6A in mRNA translation and decay, unravelling their significance in regulating gene expression. We propose that yeast serves as an exceptional model organism for the study of fundamental molecular mechanisms related to the function and regulation of m6A-modified mRNAs. The insights gained from yeast research not only expand our knowledge of mRNA modifications and their molecular roles but also offer valuable insights into the broader landscape of eukaryotic posttranscriptional regulation of gene expression.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139492266","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

How is polyadenylation restricted to 3'-untranslated regions? 聚腺苷化如何局限于3'-非翻译区?

IF 2.6 4区生物学

Yeast Pub Date : 2024-04-01 Epub Date: 2023-12-02 DOI: 10.1002/yea.3915

Kevin Struhl

{"title":"How is polyadenylation restricted to 3'-untranslated regions?","authors":"Kevin Struhl","doi":"10.1002/yea.3915","DOIUrl":"10.1002/yea.3915","url":null,"abstract":"Polyadenylation occurs at numerous sites within 3'-untranslated regions (3'-UTRs) but rarely within coding regions. How does Pol II travel through long coding regions without generating poly(A) sites, yet then permits promiscuous polyadenylation once it reaches the 3'-UTR? The cleavage/polyadenylation (CpA) machinery preferentially associates with 3'-UTRs, but it is unknown how its recruitment is restricted to 3'-UTRs during Pol II elongation. Unlike coding regions, 3'-UTRs have long AT-rich stretches of DNA that may be important for restricting polyadenylation to 3'-UTRs. Recognition of the 3'-UTR could occur at the DNA (AT-rich), RNA (AU-rich), or RNA:DNA hybrid (rU:dA- and/or rA:dT-rich) level. Based on the nucleic acid critical for 3'-UTR recognition, there are three classes of models, not mutually exclusive, for how the CpA machinery is selectively recruited to 3'-UTRs, thereby restricting where polyadenylation occurs: (1) RNA-based models suggest that the CpA complex directly (or indirectly through one or more intermediary proteins) binds long AU-rich stretches that are exposed after Pol II passes through these regions. (2) DNA-based models suggest that the AT-rich sequence affects nucleosome depletion or the elongating Pol II machinery, resulting in dissociation of some elongation factors and subsequent recruitment of the CpA machinery. (3) RNA:DNA hybrid models suggest that preferential destabilization of the Pol II elongation complex at rU:dA- and/or rA:dT-rich duplexes bridging the nucleotide addition and RNA exit sites permits preferential association of the CpA machinery with 3'-UTRs. Experiments to provide evidence for one or more of these models are suggested.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11001523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138471022","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

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