Article
Cell Biology
Sherif Ismail, Dirk Flemming, Matthias Thoms, Jose Vicente Gomes-Filho, Lennart Randau, Roland Beckmann, Ed Hurt
Summary: The synthesis of ribosomes in the nucleolus involves the formation of pre-ribosomes, from which the 40S and 60S pathways diverge. However, it is unknown how the earliest pre-60S subunit continues to develop after this separation. This study reveals a large-subunit intermediate, connected to the 90S pre-ribosome, that contains specific proteins and RNAs. The inability to disconnect from the 90S in a mutant allows for the visualization of a 70nm 90S-pre-60S particle. This research provides insights into the assembly pathway of the still-connected nascent 40S and 60S subunits.
Article
Multidisciplinary Sciences
Mustafa Malik Ghulam, Mathieu Catala, Gaspard Reulet, Michelle S. Scott, Sherif Abou Elela
Summary: We demonstrate that gene duplication in yeast serves as a stress-adaptation mechanism by modulating the global proteome through differential expression of ribosomal protein paralogs. This mechanism controls translation through differential acetylation of ribosomal proteins, favoring the translation of genes with short open reading frames under normal conditions and increasing translation of genes with long open reading frames after exposure to drugs. This study identifies a natural program where changing the ratio of proteins produced from duplicated genes modifies translation in response to drugs, regardless of ribosome number.
NATURE COMMUNICATIONS
(2022)
Article
Food Science & Technology
Junyan Liu, Tengyi Huang, Wei Hong, Fang Peng, Zerong Lu, Gongyong Peng, Xin Fu, Gongliang Liu, Zhi Wang, Qingmei Peng, Xiangjun Gong, Lizhen Zhou, Lin Li, Bing Li, Zhenbo Xu, Haifeng Lan
Summary: The study found that HPUL treatment induced stress response and altered cell metabolism of S. cerevisiae, potentially leading to failure of deactivation.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Agnes Baudin-Baillieu, Olivier Namy
Summary: Ribosomal RNA is a crucial component of ribosomes, playing a key role in peptide bond formation and accurate genetic code decoding. Recent research suggests that ribosomal RNA modifications are not 100% complete, leading to heterogeneous populations of ribosomes. Accumulated knowledge from yeast is valuable in understanding the role of ribosomal RNA modifications in humans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Francisco Gutierrez-Santiago, Francisco Navarro
Summary: Ribosomes are vital for protein production, and their biogenesis is regulated by cellular energy status and stress signals. In eukaryotic cells, stress signals and newly-synthesized ribosomes require transcription by RNA polymerases. The Target of Rapamycin pathway in eukaryotes influences RNA polymerase transcription to ensure proper ribosome production. This review focuses on how TOR regulates transcription in Saccharomyces cerevisiae and the coordination of three RNA polymerases.
Article
Microbiology
Yan Yang, Ganglong Yang, Zi-Jie Li, Yi-Shi Liu, Xiao-Dong Gao, Hideki Nakanishi
Summary: The surface of Saccharomyces cerevisiae spore wall has a ridged appearance. The outermost layer, believed to be a dityrosine layer composed of crosslinked dipeptide bisformyl dityrosine, is impervious to protease digestion. However, the ridged structure is removed by protease treatment. Hydrophilin proteins present in the spore wall, such as Sip18, Gre1, and Hsp12, are required for the proper organization of the ridged and proteinaceous structure.
Article
Biotechnology & Applied Microbiology
Lingjie Zeng, Jinxiang Huang, Pixue Feng, Xuemei Zhao, Zaiyong Si, Xiufeng Long, Qianwei Cheng, Yi Yi
Summary: This study revealed the transcriptional response of Saccharomyces cerevisiae to formic acid stress using RNA-Seq technology. The study found that formic acid stress induces oxidative stress, inhibits protein biosynthesis, and activates cellular autophagy. Additionally, formic acid was shown to induce sexual reproduction and spore formation.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Pharmacology & Pharmacy
Jianxun Zhu, Tianyue An, Wenlong Zha, Ke Gao, Ting Li, Jiachen Zi
Summary: Metabolic engineering has been widely used for the production of natural medicinal molecules. However, the limited knowledge of the complex regulatory machinery of the metabolic network hindered the engineering of high-yield platforms. The N6-methyladenosine (m6A) modification of RNA plays a critical role in the regulation of gene expression. Overexpression of the yeast m6A methyltransferase IME4 remarkably altered the transcript levels of genes involved in pathways optimized for chemical production, such as glycolysis, acetyl-CoA synthesis, and shikimate/ aromatic amino acid synthesis. Furthermore, IME4 overexpression induced the key genes ACS1 and ADH2 responsible for acetyl-CoA synthesis in a transcription factor-mediated manner and significantly increased the production of isoprenoids and aromatic compounds. Manipulation of m6A adds a new layer of metabolic regulatory machinery and has the potential to be widely used in the bioproduction of various medicinal molecules.
ACTA PHARMACEUTICA SINICA B
(2023)
Article
Biochemical Research Methods
Pavani Vamsi Krishna Nittala, Allison Hohreiter, Emilio Rosas Linhard, Ryan Dohn, Suryakant Mishra, Abhiteja Konda, Ralu Divan, Supratik Guha, Anindita Basu
Summary: The paper presents fabrication methodologies that integrate silicon components into soft microfluidic devices for cell lysis. The integration methodology involves a silicon chip with microstructure arrays embedded in a microfluidic device, which is actuated by piezoelectric force to physically break microbial cell walls. Different silicon microarray geometries, fabrication techniques, integration methods, and efficacy evaluation using synthetic microbeads and yeast species are presented. The proposed integration methodology can serve as an important process step for future hybrid silicon-polymeric devices in cellular processing applications.
Article
Biochemistry & Molecular Biology
Hong Zhang, Parker Murphy, Jason Yu, Sukyeong Lee, Francis T. F. Tsai, Ambro van Hoof, Jiqiang Ling
Summary: Aminoacyl-tRNA synthetases (aaRSs), essential enzymes for protein synthesis, can cause neurological disorders when mutated. This study investigates the mechanism behind these mutations and found that combined defects in aminoacylation and editing result in severe proteotoxicity. The results show that aminoacylation deficiency predisposes cells to proteotoxic stress and impairs ribosome-associated quality control.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Paraskevi Kritsiligkou, Tzu Keng Shen, Tobias P. Dick
Summary: Genetically encoded fluorescent H2O2 probes have advanced the field of redox biology. A comparison between the HyPer7 and roGFP2-Tsa2 Delta CR probes in yeast as a model system revealed significant differences in the dynamics of intracellular probe reduction, with HyPer7 being rapidly reduced by the thioredoxin system and roGFP2-Tsa2 Delta CR being reduced more slowly by the glutathione system. Future side-by-side measurements with both probes may provide insights into the relative activity of the two major cellular reducing systems.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Yanyan Wang, Xiaowei Li, Xin Chen, Jens Nielsen, Dina Petranovic, Verena Siewers
Summary: Monoclonal antibodies, antibody fragments, and fusion proteins have revolutionized medicine, but challenges in the biopharmaceutical industry include high production costs and low productivity in mammalian cell lines. Saccharomyces cerevisiae has been used as a secretion host for various products, but due to incompatible surface glycosylation, non-glycosylated antibody fragments need to be chosen. The secretion level of antibody fragments in yeast strains is correlated with their secretory capacity and unique physiological needs.
MICROBIAL CELL FACTORIES
(2021)
Article
Multidisciplinary Sciences
Jakob Peder Pettersen, Eivind Almaas
Summary: Improvements have been made to a new model for predicting the temperature dependence of an organism's metabolic network, addressing the issue of multimodality and highlighting the model's inadequacy in predicting metabolic flux with current experimental data.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Michelle Lindstrom, Lihua Chen, Shan Jiang, Dan Zhang, Yuan Gao, Ju Zheng, Xinxin Hao, Xiaoxue Yang, Arpitha Kabbinale, Johannes Thoma, Lisa C. Metzger, Deyuan Y. Zhang, Xuefeng Zhu, Huisheng Liu, Claes M. Gustafsson, Bjorn M. Burmann, Joris Winderickx, Per Sunnerhagen, Beidong Liu
Summary: This study identifies a yeast protein, Lsm7, that facilitates stress granule formation through dynamic liquid-liquid phase separation condensates induced by 2-deoxy-D-glucose stress. The Lsm7 phase-separated condensates appear to function as seeding scaffolds, promoting Pab1 demixing and subsequent stress granule initiation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
David Bunk, Julian Moriasy, Felix Thoma, Christopher Jakubke, Christof Osman, David Hoerl
Summary: YeastMate is a user-friendly deep learning-based application that can automatically detect and segment Saccharomyces cerevisiae cells and their mating and budding events in microscopy images. It uses Mask R-CNN with a custom segmentation head for subclassification of mother and daughter cells during lifecycle transitions. YeastMate can be used as a Python library or through a standalone application with a graphical user interface (GUI) and a Fiji plugin.
Article
Biochemistry & Molecular Biology
Miriam Olombrada, Cohue Pena, Olga Rodriguez-Galan, Purnima Klingauf-Nerurkar, Daniela Portugal-Calisto, Michaela Oborska-Oplova, Martin Altvater, Jose G. Gavilanes, Alvaro Martinez-del-Pozo, Jesus de la Cruz, Lucia Garcia-Ortega, Vikram Govind Panse
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Sara Martin-Villanueva, Jose Fernandez-Fernandez, Olga Rodriguez-Galan, Julia Fernandez-Boraita, Eduardo Villalobo, Jesus de La Cruz
Article
Biochemistry & Molecular Biology
Carlos Calafi, Maria Lopez-Malo, Diego Velazquez, Chunyi Zhang, Jose Fernandez-Fernandez, Olga Rodriguez-Galan, Jesus de la Cruz, Joaquin Arino, Antonio Casamayor
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2020)
Article
Multidisciplinary Sciences
Vitan Blagotinsek, Meike Schwan, Wieland Steinchen, Devid Mrusek, John C. Hook, Florian Rossmann, Sven A. Freibert, Hanna Kratzat, Guillaume Murat, Dieter Kressler, Roland Beckmann, Morgan Beeby, Kai M. Thormann, Gert Bange
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Olga Rodriguez-Galan, Juan J. Garcia-Gomez, Ivan Rosado, Wu Wei, Alfonso Mendez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M. Steinmetz, Vicent Pelechano, Dieter Kressler, Jesus de la Cruz
Summary: The study reveals a cooperative relationship between ribosomal protein uL3 and the ribosome-associated Ssb-RAC chaperone system to prevent excessive accumulation of 80S ribosomes in the 5' region of mRNAs during translation.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Sara Martin-Villanueva, Gabriel Gutierrez, Dieter Kressler, Jesus de la Cruz
Summary: Ubiquitin is a highly conserved small protein in eukaryotes that functions as a post-translational modifier through ubiquitination. It plays a crucial role in ribosome biogenesis and function, along with other ubiquitin-like proteins such as SUMO. The fusion of ubiquitin moieties to specific ribosomal proteins is evolutionarily significant and helps regulate cellular processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ladislav Dokladal, Michael Stumpe, Benjamin Pillet, Zehan Hu, Guillermo Miguel Garcia Osuna, Dieter Kressler, Joern Dengjel, Claudio De Virgilio
Summary: Gcn2 protein kinase mediates cellular adaptations to amino acid limitation by phosphorylating eIF2 alpha, as well as targeting auxiliary effectors such as eIF2 G protein complex for translational control. This mechanism contributes to the inhibition of translation initiation in amino-acid-starved cells and plays a more intricate role in translation control than previously understood.
Article
Multidisciplinary Sciences
Mariam Jaafar, Julia Contreras, Carine Dominique, Sara Martin-Villanueva, Regine Capeyrou, Patrice Vitali, Olga Rodriguez-Galan, Carmen Velasco, Odile Humbert, Nicholas J. Watkins, Eduardo Villalobo, Katherine E. Bohnsack, Markus T. Bohnsack, Yves Henry, Raghida Abou Merhi, Jesus de la Cruz, Anthony K. Henras
Summary: This study investigates the functions of box C/D snoRNP snR190 and helicase Dbp7 in eukaryotic ribosome biogenesis. The snR190 snoRNA acts as an RNA chaperone to assist in structuring 25S rRNA, while Dbp7 is crucial for facilitating remodeling events in the peptidyl transferase center region of 25S rRNAs. The molecular events underlying the assembly and maturation of early pre-60S particles during eukaryotic ribosome synthesis are complex and not well understood.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Jelena Micic, Olga Rodriguez-Galan, Reyes Babiano, Fiona Fitzgerald, Jose Fernandez-Fernandez, Yunyang Zhang, Ning Gao, John L. Woolford, Jesus de la Cruz
Summary: This study investigates the role of ribosomal protein eL39 in tunnel construction, 60S subunit biogenesis, and protein synthesis. The findings suggest that eL39 plays a critical role in proper protein folding, as well as in various stages of ribosome assembly.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ingrid Roessler, Sarah Weigl, Jose Fernandez-Fernandez, Sara Martin-Villanueva, Daniela Strauss, Ed Hurt, Jesus de la Cruz, Brigitte Pertschy
Summary: The small ribosomal subunit protein Rps15/uS19 is involved in both nucleolar ribosome assembly and cytoplasmic pre-40S maturation. The C-terminal tail of Rps15 plays a role in quality control during late pre-40S maturation, ensuring functional Rps15 C-terminal tail in 40S ribosomal subunits entering translation.
Article
Oncology
Laura Contreras, Alfonso Rodriguez-Gil, Jordi Muntane, Jesus de la Cruz
Summary: Hepatocellular carcinoma (HCC) is the fourth most common cause of cancer-related mortality worldwide. Sorafenib (Sfb) is the current first-line treatment for advanced HCC, but its therapeutic benefit is limited. This study analyzed the gene expression changes in two liver cancer cell lines upon Sfb treatment and found similar responses in both cell lines. The results provide valuable information on the molecular action of Sfb and suggest potential strategies to improve clinical outcomes.
Article
Biochemistry & Molecular Biology
Julia Contreras, Oscar Ruiz-Blanco, Carine Dominique, Odile Humbert, Yves Henry, Anthony K. Henras, Jesus de la Cruz, Eduardo Villalobo
Summary: Ribosome synthesis involves various protein trans-acting factors, including DEx(D/H)-box helicases, such as Dbp7. Dbp7 is an RNA helicase that regulates the base-pairing between snR190 small nucleolar RNA and ribosomal RNA during early ribosome biogenesis. The N- and C-terminal domains of Dbp7 are important for its nuclear import, normal growth, and 60S ribosomal subunit synthesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jose Fernandez-Fernandez, Sara Martin-Villanueva, Jorge Perez-Fernandez, Jesus de la Cruz
Summary: Ribosomal proteins play crucial roles in maintaining the structure and function of ribosomes. The depletion of yeast eL15 affects the formation of 60S ribosomal subunits and inhibits the nucleocytoplasmic export of pre-60S particles.
JOURNAL OF MOLECULAR BIOLOGY
(2023)