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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
Biotechnology & Applied Microbiology
Lu Meng, Xu Yang, Xue Lin, Huan-Yuan Jiang, Xiao-Ping Hu, Si-Xin Liu
Summary: The study found that overexpression of SNF1 in baker's yeast enhances cell tolerance and fermentation capacity during freezing by upregulating proteasome, altering carbon source and protectant molecule metabolism, and changing cell membrane components. Before freezing, SNF1 overexpression regulated levels of specific amino acids, glycerol, fatty acids, and phospholipids, while after freezing, it maintained high levels of certain metabolites contributing to freezing resistance. This research provides insights into cellular responses of baker's yeast to freezing and potential for developing low-temperature resistant strains.
MICROBIAL CELL FACTORIES
(2021)
Review
Biochemistry & Molecular Biology
D. Grahame Hardie
Summary: This article reflects on the author's personal research journey, focusing on the early stages of defining AMPK and developing related tools, the exciting period of identifying upstream kinases in the late 1990s and early 2000s, and recent research on the complex role of AMPK in cancer.
BIOCHEMICAL JOURNAL
(2022)
Article
Cell Biology
Stefan Bresson, Vadim Shchepachev, David Tollervey
Summary: The fungal cell wall is a crucial target for antifungal compounds, and the cell wall integrity (CWI) pathway regulates transcriptional responses to cell wall damage. In addition, RNA-binding proteins Mrn1 and Nab6 play a complementary role by stabilizing cell wall-related mRNAs. Lack of Nab6 leads to downregulation of these mRNAs, while CWI signaling and Nab6 work together to maintain appropriate cell wall gene expression during stress. Deletion of MRN1 partially alleviates the growth defects associated with Delta nab6, indicating an opposing function in mRNA destabilization. Our findings highlight the importance of a posttranscriptional pathway in cellular resistance to antifungal compounds.
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
Multidisciplinary Sciences
Qi Yu, Xuanyunjing Gong, Yue Tong, Min Wang, Kai Duan, Xinyu Zhang, Feng Ge, Xilan Yu, Shanshan Li
Summary: In this study, the researchers found that glycolysis regulates histone modifications and gene expression by activating protein kinase A (PKA) pathway. The catalytic subunit of PKA, Tpk2, phosphorylates Jhd2 to affect its localization and function on chromatin, thereby regulating gene expression, lifespan, and autophagy.
NATURE COMMUNICATIONS
(2022)
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Biochemistry & Molecular Biology
Ana I. Garrido-Godino, Abel Cuevas-Bermudez, Francisco Gutierrez-Santiago, Maria del Carmen Mota-Trujillo, Francisco Navarro
Summary: Rtr1 plays a critical role in RNA pol II assembly and mRNA decay regulation by mediating the association between RNA pol II and Rpb4/7. This study reveals new mechanisms in gene regulation and the crosstalk between mRNA synthesis and decay.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Nir Cohen, Amit Kahana, Maya Schuldiner
Summary: Despite our efforts in researching the baker's yeast Saccharomyces cerevisiae, there are still many unknowns in its genome, hindering our understanding of cellular activity and suggesting the presence of unknown processes. However, with advancements in computational methods and the availability of high-quality genomic and structural data, we can now predict and identify candidate enzymes for unannotated proteins in yeast. By using these predictions and experimental validation, we have discovered a new function for an uncharacterized enzyme in the NAD degradation pathway, which has implications in cancer research. This methodology can be applied to other organisms, providing a paradigm for uncovering new enzymatic functions.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
C. Denise Appel, Oya Bermek, Venkata P. Dandey, Makayla Wood, Elizabeth Viverette, Jason G. Williams, Jonathan Bouvette, Amanda A. Riccio, Juno M. Krahn, Mario J. Borgnia, R. Scott Williams
Summary: In this study, the cryo-EM reconstructions of Sen1 reveal its molecular architecture and substrate regulation. The X-ray structure of an activated Sen1 provides insights into its interaction with RNA and its role in the RNA translocation mechanism. These findings have important implications for understanding helicase regulation and the pathogenesis of human diseases.
Article
Biotechnology & Applied Microbiology
Hailong Chen, Xiaoqin Chai, Yan Wang, Jing Liu, Guohai Zhou, Pinghe Wei, Yuhe Song, Lingman Ma
Summary: Background: Saccharomyces cerevisiae is commonly used for the production of S-adenosyl-l-methionine (SAM), but glucose repression negatively affects its production. This study shows that deleting REG1 and overexpressing SNF1 can improve SAM production in S. cerevisiae by enhancing glucose utilization and glycolysis, promoting ethanol conversion, enhancing precursor amino acid biosynthesis, and extending yeast lifespan.
MICROBIAL CELL FACTORIES
(2022)
Review
Biology
Kobi Simpson-Lavy, Martin Kupiec
Summary: Glucose is the preferred carbon source for most cells. Yeast Snf1 is the main regulator of the response to low glucose availability. Three different mechanisms, including phosphorylation, SUMOylation, and protonation, independently control Snf1 activity, allowing a flexible response to carbon source availability.
Article
Biochemistry & Molecular Biology
Riccardo Milanesi, Farida Tripodi, Jacopo Vertemara, Renata Tisi, Paola Coccetti
Summary: This study reveals that glucose-dependent inactivation of Snf1/AMPK is unrelated to the Ras/PKA pathway, and demonstrates a strong coordination between glycolytic metabolism and Snf1/AMPK. The findings support a model in which Snf1/AMPK senses glucose flux independently from PKA activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Alejandro Collin, Araceli Gonzalez-Jimenez, Maria del Carmen Gonzalez-Jimenez, Manuel J. Alfonso, Olga Calvo
Summary: Saccharomyces cerevisiae Sub1 is a transcriptional stimulatory protein that shares homology with the ssDNA binding domain (ssDBD) of human PC4. This study reveals the key residues responsible for DNA-ScSub1 interaction in vivo, localized in the ssDBD, and demonstrates that the carboxyl-terminal (CT) region is required for transcription elongation. These findings indicate that Sub1 plays a dual role in transcription, participating in initiation through the ssDBD and in elongation through the CT region.
Article
Multidisciplinary Sciences
Thoma Itoh, Takashi Makino
Summary: Recent advancements in high throughput single cell RNA-seq have enabled the identification of functional compensation effects of gene perturbations through noise change, which can be measured quantitatively and captured in gene regulatory networks.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Bazile Ravoityte, Juliana Luksa, Ralf Erik Wellinger, Saulius Serva, Elena Serviene
Summary: This study analyzed the impact of L-A virus on gene expression in yeast hosts using high-throughput RNA sequencing data. It was found that the presence of L-A virus resulted in moderate alterations in gene expression, particularly in genes involved in ribosome biogenesis. Additionally, the transcriptional responses to L-A maintenance were similar to those induced by stress or nutrient availability. The study also identified yeast transcriptional regulators that modulate the levels of L-A dsRNA in cells.
Article
Multidisciplinary Sciences
Gregory T. Booth, Pabitra K. Parua, Miriam Sanso, Robert P. Fisher, John T. Lis
NATURE COMMUNICATIONS
(2018)
Article
Biochemistry & Molecular Biology
Pabitra K. Parua, Avisek Mondal, Pradeep Parrack
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2010)
Article
Microbiology
Pabitra K. Parua, Elton T. Young
Article
Biochemistry & Molecular Biology
Pabitra K. Parua, Kenneth M. Dombek, Elton T. Young
JOURNAL OF BIOLOGICAL CHEMISTRY
(2014)
Article
Biotechnology & Applied Microbiology
Pabitra K. Parua, Ajit B. Datta, Pradeep Parrack
JOURNAL OF GENERAL VIROLOGY
(2010)
Article
Biochemistry & Molecular Biology
P. K. Parua, S. Ratnakumar, K. A. Braun, K. M. Dombek, E. Arms, P. M. Ryan, E. T. Young
MOLECULAR AND CELLULAR BIOLOGY
(2010)
Article
Biochemistry & Molecular Biology
Katherine A. Braun, Pabitra K. Parua, Kenneth M. Dombek, Gregory E. Miner, Elton T. Young
MOLECULAR AND CELLULAR BIOLOGY
(2013)
Article
Biochemistry & Molecular Biology
Pabitra K. Parua, Paul M. Ryan, Kayla Trang, Elton T. Young
MOLECULAR MICROBIOLOGY
(2012)
Article
Multidisciplinary Sciences
Pabitra K. Parua, Gregory T. Booth, Miriam Sanso, Bradley Benjamin, Jason C. Tanny, John T. Lis, Robert P. Fisher
Review
Biochemistry & Molecular Biology
Pabitra K. Parua, Robert P. Fisher
NATURE CHEMICAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Miriam Sanso, Pabitra K. Parua, Daniel Pinto, J. Peter Svensson, Viviane Pag, Danny A. Bitton, Sarah MacKinnon, Patricia Garcia, Elena Hidalgo, Jurg Bahler, Jason C. Tanny, Robert P. Fisher
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Pabitra K. Parua, Sampada Kalan, Bradley Benjamin, Miriam Sanso, Robert P. Fisher
NATURE COMMUNICATIONS
(2020)
Review
Cell Biology
Giacomo Cossa, Pabitra K. Parua, Martin Eilers, Robert P. Fisher
Summary: The transcription cycle of RNA polymerase II is regulated by cyclin-dependent kinases and protein phosphatases, with the phosphatases playing a crucial role in ensuring fine control of elongation and termination. The major phosphoprotein phosphatase family members, including PP1, PP2A, and PP4, have decisive roles in the transcription cycle, but there are still unanswered questions about their division of labor and their regulation by transcriptional kinases. CDKs have recently been identified as potential therapeutic targets, raising the possibility that phosphatases could also provide opportunities for new drug development.
GENES & DEVELOPMENT
(2021)