Article
Biochemistry & Molecular Biology
Titi Rindi Antika, Kun Rohmatan Nazilah, Yi-Hsueh Lee, Ya-Ting Lo, Chung-Shu Yeh, Fu-Lung Yeh, Tien-Hsien Chang, Tzu-Ling Wang, Chien-Chia Wang
Summary: In this study, it was found that mature native human tRNA(m)(His) contains only G-1. ATP is required for HsThg1 to catalyze the addition of G-1 to tRNA(m)(His). HsThg1 possesses a tRNA-inducible GTPase activity, which can inhibit the incorporation of multiple GTPs into tRNA(m)(His).
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Mineaki Seki, Akihiko Komuro, Tatsuya Ishikawa, Masayuki Takahashi, Masayuki Nashimoto
Summary: The concept of tRNA recycling has emerged from studies of ribosome-associated quality control, where tRNase Z(S) and TRNT1 play essential roles in regenerating intact tRNA molecules. Viral infections, particularly with Theiler's mouse encephalitis virus, can upregulate the expression of tRNase Z(S) and TRNT1, while infections with influenza A virus do not lead to this upregulation. Additionally, there appears to be a positive correlation between IFN-beta mRNA levels and tRNase Z(S) and TRNT1 mRNA levels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Monika Tasak, Eric M. Phizicky
Summary: All tRNAs require modifications for proper function, and lack of these modifications can lead to growth defects and disorders. This study found that specific tRNA body modifications are necessary for tRNA stability and function, and mutants lacking these modifications target hypomodified tRNAs to rapid decay pathways. These findings suggest the importance of these modifications for tRNA biology in different organisms.
Article
Biochemical Research Methods
Guiping Gong, Yueping Zhang, Zibai Wang, Luo Liu, Shuobo Shi, Verena Siewers, Qipeng Yuan, Jens Nielsen, Xu Zhang, Zihe Liu
Summary: This study developed an efficient tool for genome disruption and single-nucleotide conversion, utilizing a gRNAtRNA array and SpCas9-NG (GTR 2.0). The tool achieved near 100% efficiency for gene disruptions in yeast cells covering all 16 possible NGN PAMs and all 12 possible single-nucleotide conversions (N to N). Furthermore, the tool was able to achieve 66.67% mutation efficiency for multiplexed single-nucleotide conversions and 100% mutation efficiency for generating multiple conversions in different genes simultaneously. GTR 2.0 will significantly enhance the scope, efficiency, and capabilities of yeast genome editing, serving as a versatile and valuable addition to the toolbox of synthetic biology and metabolic engineering.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kunal Chatterjee, William A. Marshall, Anita K. Hopper
Summary: This study identifies a new tRNA nuclear exporter and reveals exporter preferences for specific tRNA families. Additionally, it demonstrates the importance of tRNA nuclear import in tRNA quality control.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Cell Biology
Agata Tyczewska, Alicja Rzepczak, Daria Sobanska, Kamilla Grzywacz
Summary: Aging is a gradual decline of various functions of organisms resulting in diminished abilities to protect against environmental damage and reinforce physiological harmony. Recent studies have shown that the mechanisms of lifespan regulation are conserved throughout evolution. This review focuses on the emerging roles of tRNA-associated processes in aging and lifespan regulation, including tRNA metabolism, epitranscriptome, and tRNA-derived fragments. Understanding the basic mechanisms of aging could lead to the development of new diagnostics and treatments for aging-related diseases.
AGEING RESEARCH REVIEWS
(2023)
Review
Microbiology
Antonia Maria Romero, Maria Teresa Martinez-Pastor, Sergi Puig
Summary: Iron is essential for eukaryotic translation, affecting translation initiation, specific transcript translation repression, and various details of the translation process through the action of specific regulators. The influence of iron on different stages of translation and its correlation with protein biosynthesis control are key areas of research interest.
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)
Article
Biotechnology & Applied Microbiology
Morghan C. Lucas, Leszek P. Pryszcz, Rebeca Medina, Ivan Milenkovic, Noelia Camacho, Virginie Marchand, Yuri Motorin, Lluis Ribas de Pouplana, Eva Maria Novoa
Summary: Nano-tRNAseq is a nanopore-based method that allows for simultaneous quantification of tRNA abundance and chemical modifications, providing a new tool for studying tRNA. Re-processing of raw nanopore current intensity signals leads to more accurate tRNA abundance information. Nano-tRNAseq can reveal changes in tRNA populations in response to oxidative stress.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
GeunYoung Sim, Audrey C. Kehling, Mi Seul Park, Jackson Secor, Cameron Divoky, Huaqun Zhang, Nipun Malhotra, Divyaa Bhagdikar, Ekram W. Abd El-Wahab, Kotaro Nakanishi
Summary: MicroRNAs (miRNAs), a type of noncoding RNA with about 22 nucleotides, can form complexes with Argonaute (AGO) proteins to repress gene expression. This study discovered that certain exonucleases, including ISG20, TREX1, and ERI1, are capable of trimming AGO-associated full-length miRNAs to shorter tyRNAs in a manganese-dependent manner. The study also showed that ISG20-mediated trimming converts AGO3 into a slicer. These findings shed light on the roles of manganese-dependent exonucleases in gene silencing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
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
Andy Goldschmidt, James Kunert-Graf, Adrian C. Scott, Zhihao Tan, Aimee M. Dudley, J. Nathan Kutz
Summary: Baker's yeast is a model organism for studying morphology at the scale of multi-cell colonies, with texture score development trajectories used for hierarchical clustering.
Article
Agriculture, Multidisciplinary
Chengcheng Sun, Guangjian Li, Hongbiao Li, Yunbin Lyu, Shiqin Yu, Jingwen Zhou
Summary: This study successfully achieved de novo production of two basic flavan-3-ols by engineering Saccharomyces cerevisiae, demonstrating the potential of engineering strategies in increasing yield.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Vinh G. Tran, Somesh Mishra, Sarang S. Bhagwat, Saman Shafaei, Yihui Shen, Jayne L. Allen, Benjamin A. Crosly, Shih-I Tan, Zia Fatma, Joshua D. Rabinowitz, Jeremy S. Guest, Vijay Singh, Huimin Zhao
Summary: In this study, we successfully engineered yeast to produce succinic acid at high efficiency under low pH conditions. The high titers of succinic acid obtained in the experiments, as well as the economic and environmental benefits demonstrated in the techno-economic and life cycle assessments, indicate the potential of scaling up this process for industrial applications.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Vinh G. Tran, Somesh Mishra, Sarang S. Bhagwat, Saman Shafaei, Yihui Shen, Jayne L. Allen, Benjamin A. Crosly, Shih- Tan, Zia Fatma, Joshua D. Rabinowitz, Jeremy S. Guest, Vijay Singh, Huimin Zhao
Summary: This study presents a metabolic engineering approach to enhance the production of succinic acid (SA) by acid-tolerant yeast, achieving high titers at low pH conditions. The pilot-scale fermentation using sugarcane juice medium resulted in a SA titer of 63.1g/L with a high crystallization yield. Techno-economic analysis and life cycle assessment indicate the financial viability and significant reduction in greenhouse gas emissions of the proposed low-pH SA production process.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Aris-Edda Stachler, Thandi Sarah Schwarz, Sandra Schreiber, Anita Marchfelder
Article
Plant Sciences
Aleksandra Sulkowska, Andor Auber, Pawel J. Sikorski, Daniel Silhavy, Mariann Auth, Ewa Sitkiewicz, Viviane Jean, Remy Merret, Cecile Bousquet-Antonelli, Joanna Kufel
PLANT AND CELL PHYSIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Selom K. Doamekpor, Agnieszka Gozdek, Aleksandra Kwasnik, Joanna Kufel, Liang Tong
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Guillaume Clerget, Valerie Bourguignon-Igel, Nathalie Marmier-Gourrier, Nicolas Rolland, Ludivine Wacheul, Xavier Manival, Christophe Charron, Joanna Kufel, Agnes Mereau, Veronique Senty-Segault, David Tollervey, Denis L. J. Lafontaine, Christiane Branlant, Mathieu Rederstorff
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Sarah J. Berkemer, Lisa-Katharina Maier, Fabian Amman, Stephan H. Bernhart, Julia Woertz, Pascal Maerkle, Friedhelm Pfeiffer, Peter F. Stadler, Anita Marchfelder
Article
Biochemistry & Molecular Biology
Aris-Edda Stachler, Julia Woertz, Omer S. Alkhnbashi, Israela Turgeman-Grott, Rachel Smith, Thorsten Allers, Rolf Backofen, Uri Gophna, Anita Marchfelder
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Lazaros Melidis, Harriet J. Hill, Nicholas J. Coltman, Scott P. Davies, Kinga Winczura, Tasha Chauhan, James S. Craig, Aditya Garai, Catherine A. J. Hooper, Ross T. Egan, Jane A. McKeating, Nikolas J. Hodges, Zania Stamataki, Pawel Grzechnik, Michael J. Hannon
Summary: Researchers have successfully constructed 3D models of the untranslated regions of the SARS-CoV-2 genome and found that metallo-supramolecular helicates can suppress viral replication, highlighting their potential as novel anti-viral agents.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Correction
Biochemistry & Molecular Biology
Selom K. Doamekpor, Agnieszka Gozdek, Aleksandra Kwasnik, Joanna Kufel, Liang Tong
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Dong-Hyuk Heo, Krzysztof Kus, Pawel Grzechnik, Sue Mei Tan-Wong, Adrien Birot, Tea Kecman, Soren Nielsen, Nikolay Zenkin, Lidia Vasiljeva
Summary: Phosphorylation of the RNA polymerase II C-terminal domain Y1S2P3T4S5P6S7 consensus sequence is crucial for coordinating key events in transcription, and its dysregulation can lead to defects in transcription and RNA processing. The histone deacetylase activity of the fission yeast Hos2/Set3 complex has been found to play a significant role in suppressing cryptic initiation of antisense transcription, particularly when RNA polymerase II phosphorylation is dysregulated. Loss of Hos2 or Set3, combined with the absence of Ssu72 phosphatase, results in a synergistic increase in antisense transcription globally and higher sensitivity to genotoxic agents.
Article
Multidisciplinary Sciences
Michal Krzyszton, Joanna Kufel
Summary: Defects in RNA maturation and decay factors can generate substrates for RNA interference machinery. This phenomenon has been observed in plants, where mutations in certain RNA-related factors lead to the production of RNA-quality control small interfering RNAs. However, widespread production of siRNAs from mRNA molecules is only triggered by specific mutations or substantial RNA processing defects.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Anna Golisz, Michal Krzyszton, Monika Stepien, Jakub Dolata, Justyna Piotrowska, Zofia Szweykowska-Kulinska, Artur Jarmolowski, Joanna Kufel
Summary: The study reveals the crucial role of SmD3 in plant immune response, showing that it regulates plant defense against pathogens by affecting mRNA splicing of key pathogenesis factors, particularly in stomatal immunity. SmD3 dysfunction leads to defects in splicing and altered alternative splicing patterns, impacting the plant's ability to combat Pseudomonas infection.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Joanna Kufel, Nataliia Diachenko, Anna Golisz
Summary: Plants, like animals, are exposed to abiotic and biotic stresses which inhibit their growth and development. Alternative splicing plays a crucial role in plant response to biotic stress, although the exact mechanisms are still unclear. The importance of alternative splicing in plant immunity has been established.
MOLECULAR PLANT PATHOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Monika Sledziowska, Kinga Winczura, Matt Jones, Ruba Almaghrabi, Hannah Mischo, Daniel Hebenstreit, Paloma Garcia, Pawel Grzechnik
Summary: Mutations and aberrant gene expression during cellular differentiation lead to neurodevelopmental disorders. This study reveals the importance of SPA-lncRNAs and sno-lncRNAs in controlling gene expression and provides a platform for PWS research.
HUMAN MOLECULAR GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Maria-Bianca Mititelu, Oldrich Hudecek, Agnieszka Gozdek, Roberto Benoni, Ondrej Nesuta, Szymon Krasnodebski, Joanna Kufel, Hana Cahova
Summary: Recent discoveries of various noncanonical RNA caps have changed the understanding of RNA cap function and metabolism. Enzymes from the NudiX family are strong candidates for degrading noncanonically capped RNA. In this study, we focused on four NudiX enzymes in Arabidopsis thaliana and found that they can cleave different types of capped RNA with varying efficiencies.
RSC CHEMICAL BIOLOGY
(2023)
Article
Biology
Onofrio Zanin, Matthew Eastham, Kinga Winczura, Mark Ashe, Rocio T. Martinez-Nunez, Daniel Hebenstreit, Pawel Grzechnik
Summary: The presence of the cap is crucial for initiating the degradation of mRNA, and the levels of non-capped mRNA are inversely correlated with their expression levels.
COMMUNICATIONS BIOLOGY
(2023)
