Article
Multidisciplinary Sciences
Tomoaki Mizuno, Kenji Irie
Summary: Selective autophagy of the endoplasmic reticulum in yeast, known as ER-phagy, is regulated by multiple signaling pathways and transcription factors, with Atg39 and Atg40 serving as receptors and Msn2/4 transcription factors identified as regulators of ATG39 transcription.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Zhiling Kuang, Jiyuan Ke, Jiong Hong, Zhongliang Zhu, Liwen Niu
Summary: PCI domain proteins play important roles in post-transcriptional gene regulation. In this study, the structure of yeast Thp3-Csn12-Sem1 ternary complex was determined, revealing significant structural differences compared to the Sac3-Thp1-Sem1 complex. This structure provides a foundation for further exploring its specific recruitment to the spliceosome.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Food Science & Technology
Gang Du, Xingyu Zhang, Yuting Gao, Cunying Sun, Liwen Wang, Wei Zhao, Dan Meng, Wenqiang Guan, Hui Zhao
Summary: Ginger is commonly used in traditional Chinese medicine as a natural remedy for cold, and it has thermogenic effects when consumed. This study revealed that ginger oleoresin stress and heat stress had similar effects on yeast and shared genes. The transcription factor Hsf1 was found to be phosphorylated and activated in response to ginger oleoresin stress, leading to increased expression of heat shock proteins.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sandra Klama, Anna G. Hirsch, Ulla M. Schneider, Gesa Zander, Anika Seel, Heike Krebber
Summary: Efficient gene expression requires properly matured mRNAs for translation. The guard protein Npl3 monitors the 5' capping of transcripts and plays a role in degrading improperly capped transcripts.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Joana I. Rodrigues, Emma Lorentzon, Sansan Hua, Andrew Boucher, Markus J. Tamas
Summary: Arsenite induces proteotoxicity by causing misfolding and aggregation of nascent proteins. Loss of ribosome-associated chaperones Zuo1, Ssz1, and Ssb1/Ssb2 reduces protein aggregation and increases arsenite resistance. Defective aggregate clearance and arsenite sensitivity are observed with loss of cytosolic GimC/prefoldin function. Ribosome-associated ubiquitin ligases have little contribution to proteostasis during arsenite stress, while cytosolic ubiquitin ligase Rsp5 plays an important role in aggregate clearance and resistance. Our study highlights the importance of damage prevention and elimination mechanisms in maintaining proteostasis during arsenite stress.
Article
Multidisciplinary Sciences
Shiladitya Chattopadhyay, Jose Garcia-Martinez, Gal Haimovich, Jonathan Fischer, Aya Khwaja, Oren Barkai, Silvia Gabriela Chuartzman, Maya Schuldiner, Ron Elran, Miriam Rosenberg, Shira Urim, Shubham Deshmukh, Katherine E. Bohnsack, Markus T. Bohnsack, Jose E. Perez-Ortin, Mordechai Choder
Summary: This study reveals the crucial role of nucleocytoplasmic shuttling of yeast mRNA decay factors in regulating both transcription and mRNA decay. The shuttling process is controlled by decaying RNA and is essential for coping with environmental changes.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Sean L. Beckwith, Emily J. Nomberg, Abigail C. Newman, Jeannette V. Taylor, Ricardo C. Guerrero-Ferreira, David J. Garfinkel
Summary: A study found an intrinsically disordered N-terminal prion-like domain (PrLD) within the Gag protein of Ty1 retrotransposons, which is required for retrotransposition. Deleting the PrLD leads to defects in virus-like particle (VLP) assembly and retrotransposition. Chimeras of Ty1 Gag with PrLD replaced by other sequences display different retrotransposition phenotypes. This study provides a genetically tractable in vivo platform for studying PrLDs and encourages further research on the prevalence of PrLDs in other mobile elements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Anna Greta Hirsch, Daniel Becker, Jan-Philipp Lamping, Heike Krebber
Summary: Telomerases elongate chromosome ends through a series of maturation steps involving transcription, cytoplasmic cycling, import, and exosome trimming. Cse1 plays a key role in supporting both TLC1 import and Sm-ring stabilization, acting as a quality control factor in telomerase maturation.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Xiang Meng, Alan Reed, Sandie Lai, Juraj Szavits-Nossan, John E. G. McCarthy
Summary: Gene expression stochasticity is an inherent feature of biological systems, creating non-genetic cellular variation and influencing various processes. In this study, the researchers discovered a distinct form of non-transcriptional noise associated with the translation machinery and mRNA 5'UTR of the GCN4 gene in yeast. They characterized the heterogeneity of translation initiation mediated by GCN4-5'UTR using different techniques and found a subpopulation of cells that consistently exhibited enhanced GCN4 translation under non-starvation conditions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Matthew P. Swaffer, Georgi K. Marinov, Huan Zheng, Lucas Fuentes Valenzuela, Crystal Yee Tsui, Andrew W. Jones, Jessica Greenwood, Anshul Kundaje, William J. Greenleaf, Rodrigo Reyes-Lamothe, Jan M. Skotheim
Summary: A fundamental feature of cellular growth is that protein and RNA amounts increase with cell size to maintain constant concentrations. In budding yeast, RNA polymerase II (RNAPII) is identified as the limiting factor scaling mRNA transcription with cell size. The global RNAPII transcription is determined by the mass action recruitment kinetics of unengaged nucle-oplasmic RNAPII to the genome. However, this increase in transcription with size is partially compensated for by a decrease in mRNA decay rates as cells enlarge.
Article
Green & Sustainable Science & Technology
Dagnew Bitew, Marye Alemu, Anteneh Tesfaye, Berhanu Andualem
Summary: This study aimed to isolate efficient ethanologenic microbes from Ethiopian traditional fermented beverages, evaluate their ethanol yield using banana peel as a substrate, and optimize fermentation conditions. The selected yeast strains Saccharomyces cerevisiae showed high tolerance to stress conditions and produced significant amounts of ethanol from banana peel waste. The results suggest that these strains are promising candidates for bioethanol production.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2024)
Article
Multidisciplinary Sciences
James M. Burke, Alison R. Gilchrist, Sara L. Sawyer, Roy Parker
Summary: The study demonstrates that RNase L-mediated mRNA decay does not completely limit protein synthesis of dengue virus and influenza A virus, as their mRNAs largely escape this process. However, activation of RNase L inhibits nuclear mRNA export, thereby restricting influenza A virus protein synthesis and cytokine production.
Review
Parasitology
Susanne Kramer
Summary: The passage of mRNAs through nuclear pores into the cytoplasm is essential for all eukaryotes, with mRNA export tightly connected to nuclear mRNA processing. Trypanosoma brucei exhibits unusual features in nuclear mRNA processing, lacking key complexes and proteins found in opisthokonts. Further investigation is needed to determine the extent of mRNA export regulation in trypanosomes and the evolutionary implications of mRNA export across eukaryotes.
Review
Cell Biology
Pierre Bensidoun, Daniel Zenklusen, Marlene Oeffinger
Summary: The nuclear pore complex (NPC) is the central gate for mRNA transportation from the nucleus to the cytoplasm. The export competence of mRNAs is linked to upstream nuclear processes, and recent evidence suggests that the NPC may be more heterogeneous than previously believed, providing functional plasticity to mRNA export. Interconnected processes of nuclear mRNA metabolism and NPC heterogeneity play crucial roles in regulating export competence.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Biochemistry & Molecular Biology
Ryoga Ishii, Ayu Fukui, Yuri Sakihama, Shoko Kitsukawa, Ayami Futami, Takahiro Mochizuki, Makoto Nagano, Jiro Toshima, Fumiyoshi Abe
Summary: This study found that Tat2 is rapidly degraded in a Rsp5-Bul1-dependent manner upon the addition of tryptophan, phenylalanine, or tyrosine, while Tat1 is unaffected. The expression of a ubiquitination-deficient variant of Tat2 leads to a reduction in cell yield. Tryptophan addition causes the rapid dissociation of Tat2 from eisosomes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Biochemistry & Molecular Biology
Yuki Yoshikawa, Ryo Nasuno, Hiroshi Takagi
Summary: The study found that yeast cells lacking NADPH exhibited increased tolerance to oxidative and nitrosative stress. This was primarily due to the upregulation of Ctt1 expression in ZWF1-deficient cells, enhancing their antioxidant capacity.
Article
Biotechnology & Applied Microbiology
Shota Isogai, Tomonori Matsushita, Hiroyuki Imanishi, Jirasin Koonthongkaew, Yoichi Toyokawa, Akira Nishimura, Xiao Yi, Romas Kazlauskas, Hiroshi Takagi
Summary: In this study, a feedback inhibition-insensitive HCS variant was designed and analyzed using in silico docking and enzymatic assays. The engineered HCS showed significantly higher lysine production in yeast cells compared to the wild-type HCS and another variant, demonstrating the potential for rational engineering of key enzymes in metabolic engineering for improved amino acid productivity.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shota Isogai, Hiroshi Takagi
Summary: The study showed that lysine supplementation and enhancement of lysine biosynthesis improved the high-temperature stress tolerance of E. coli cells. Lysine-overproducing strains have the potential as stress-tolerant microorganisms and can be used as robust host cells for microbial production of useful compounds.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shota Isogai, Akira Nishimura, Atsushi Kotaka, Naoyuki Murakami, Natsuki Hotta, Hiroki Ishida, Hiroshi Takagi
Summary: The study found that a yeast strain with a specific mutation can lead to the accumulation of isoleucine, resulting in increased production of 2-methyl-1-butanol. This discovery is valuable for engineering yeast strains to enhance the production of isoleucine and its derived fusel alcohols.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Akira Nishimura, Shota Isogai, Naoyuki Murakami, Natsuki Hotta, Atsushi Kotaka, Kengo Matsumura, Yoji Hata, Hiroki Ishida, Hiroshi Takagi
Summary: The research identified a sake yeast mutant that accumulates phenylalanine and decreases 2-phenylethanol production, which may lead to the creation of unique new sake varieties.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Microbiology
Masataka Ohashi, Shota Isogai, Hiroshi Takagi
Summary: This study revealed the crucial role of key residues in the formation of the arginine-binding cavity for arginine recognition of NAGK. Additionally, novel arginine feedback inhibition-insensitive variants of NAGK in sake yeast mutants with ornithine overproduction were analyzed, suggesting that amino acid substitutions in the NAGK variants destabilize the arginine-binding cavity, leading to lower sensitivity to arginine feedback inhibition of NAGK activity.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biotechnology & Applied Microbiology
Jirasin Koonthongkaew, Nontawat Ploysongsri, Yoichi Toyokawa, Vithaya Ruangpornvisuti, Hiroshi Takagi
Summary: In this study, we successfully increased the production of branched-chain higher alcohols (BCHAs) by designing variants of Bat1 and Bat2 with altered enzyme activity. Our results showed that these engineered BCATs decreased catalytic activities and increased BCHA production. This study provides new insights into the functions of BCATs and has practical applications in the future construction of enzymes for high-level BCHAs production.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ryoya Tanahashi, Akira Nishimura, Fumika Morita, Hayate Nakazawa, Atsuki Taniguchi, Kazuki Ichikawa, Kazuki Nakagami, Kyria Boundy-Mills, Hiroshi Takagi
Summary: Proline, the most abundant amino acid in wine and beer, is hardly assimilated by Saccharomyces cerevisiae during fermentation. The study found that arginine, ornithine, and lysine inhibit proline utilization by inducing endocytosis of the proline transporter Put4, while citrulline does not. By genetic screening, it was revealed that the arginine transporter Can1 is involved in the arginine-dependent inhibition of proline utilization. Further biochemical analyses showed that Can1 activates signaling cascades of protein kinase A in response to extracellular arginine, suggesting its role as a transceptor regulating proline utilization.
Editorial Material
Biochemistry & Molecular Biology
Andriy A. Sibirny, Terrance G. Cooper, Hiroshi Takagi
Article
Biotechnology & Applied Microbiology
Shota Isogai, Akira Nishimura, Naoyuki Murakami, Natsuki Hotta, Atsushi Kotaka, Yoichi Toyokawa, Hiroki Ishida, Hiroshi Takagi
Summary: This study identified a valine-accumulating sake yeast mutant and found a novel amino acid substitution. The mutant yeast accumulated valine and produced more isobutanol. This research provides insights for brewing distinctive Japanese sake by increasing the production of valine-derived compounds.
FEMS YEAST RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Akira Nishimura, Ryoya Tanahashi, Tomoki Oi, Kyoyuki Kan, Hiroshi Takagi
Summary: The current CRISPR/Cas9 systems in Saccharomyces cerevisiae cannot be considered non-genetic modification technology due to the need for plasmid expression systems. However, our study demonstrates that editing the yeast genome can be achieved without plasmid expression systems, using a commercially available protein transfection reagent and chemically modified sgRNAs.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Ryoya Tanahashi, Akira Nishimura, Minh Nguyen, Irnayuli Sitepu, Glen Fox, Kyria Boundy-Mills, Hiroshi Takagi
Summary: Proline contributes to taste and flavor of foods. Saccharomyces cerevisiae poorly assimilates proline during fermentation, resulting in its accumulation in fermented products. Our screening of 1138 yeasts revealed that Zygoascus, Galactomyces, and Magnusiomyces genera are better at utilizing proline.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Masatoshi Tsukahara, Shota Isogai, Haruna Azuma, Keiko Tsukahara, Yoichi Toyokawa, Hiroshi Takagi
Summary: A new strain of yeast, Saccharomyces cerevisiae 35a14, was isolated from banana stems in Okinawa. This strain did not belong to any industrial yeast groups and had high alcohol production. Furthermore, a mutant derived from 35a14, which overproduces l-leucine, resulted in a high concentration of isoamyl acetate when used in brewing awamori, an Okinawa's traditional distilled alcoholic beverage.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Akira Nishimura, Kazuki Nakagami, Kyoyuki Kan, Fumika Morita, Hiroshi Takagi
Summary: This study elucidated the inhibitory effect of arginine on yeast biofilm formation and its underlying mechanism, providing insights into the molecular mechanism and control of yeast biofilm formation.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Akira Nishimura, Kazuki Ichikawa, Hayate Nakazawa, Ryoya Tanahashi, Fumika Morita, Irnayuli Sitepu, Kyria Boundy-Mills, Glen Fox, Hiroshi Takagi
Summary: This study clarifies the inhibitory mechanism of proline utilization in yeast during wine-making processes, revealing the involvement of glucose response and the Ras/PKA pathway. The research indicates the existence of crosstalk between carbon and proline metabolisms and provides valuable insights and directions for developing wine yeast strains that can efficiently assimilate proline.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
