Article
Physics, Multidisciplinary
Jorge Fernandez-de-Cossio-Diaz, Simona Cocco, Remi Monasson
Summary: The goal of unsupervised machine learning is to build disentangled representations of complex high-dimensional data, making it easier to interpret latent factors of variation and generate new data. We propose a simple, effective way to disentangle representations without the need for adversarial training, using constraints on weights during training. Our approach is demonstrated on various datasets and allows for the computation of the cost associated with representation disentanglement.
Article
Chemistry, Medicinal
Nicolette Valdez, Casey Hughes, Stephanie O. Palmer, Alyssa Sepulveda, Frank B. Dean, Yaritza Escamilla, James M. Bullard, Yonghong Zhang
Summary: Bacterial infections remain a major global health risk, especially with the increasing antibiotic resistance in Pseudomonas aeruginosa, necessitating the discovery of new antibiotic candidates. Research has identified the interaction mechanism between P. aeruginosa initiation factor 1 and the 30S ribosomal subunit, and proposed a new strategy for designing antimicrobials.
ACS INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Chatchai Phoomak, Natalie Rinis, Marta Baro, Shiteshu Shrimal, Daniel Bennett, Scott A. Shaffer, Mark Lehrman, Reid Gilmore, Joseph N. Contessa
Summary: Proteins targeted for secretion are translocated into the endoplasmic reticulum in a cotranslational manner. N-glycosylation is an important co- and posttranslational modification for these proteins, ensuring proper folding, stability, solubility, and localization. The beta subunit of the signal recognition particle receptor (SR) is found to be crucial for the assembly of the N-glycosylation-competent translocon. Chemical probes and mutation of the SR-beta guanosine triphosphate binding site both result in a deficiency in N-glycosylation, suggesting that SR-beta coordinates endoplasmic reticulum translation with N-glycosylation.
Article
Biochemistry & Molecular Biology
Ryo Murakami, Tetsutaro Sumiyoshi, Lumi Negishi, Mikiko C. Siomi
Summary: This study identifies DDX43 as a key protein in regulating the piRNA amplification pathway in Bombyx, functionally similar to Vasa. DDX43 contains a KH domain that enhances its ATPase activity, while its helicase core is responsible for Ago3-piRISC interaction and ATP hydrolysis. Both domains are required for maximal DDX43 RNA-binding activity, shedding light on unique collaborations within the pathway.
Article
Biochemistry & Molecular Biology
Cristina Remes, Anas Khawaja, Sarah F. Pearce, Adam M. Dinan, Shreekara Gopalakrishna, Miriam Cipullo, Vasileios Kyriakidis, Jingdian Zhang, Xaquin Castro Dopico, Olessya Yukhnovets, Ilian Atanassov, Andrew E. Firth, Barry Cooperman, Joanna Rorbach
Summary: The detailed mechanism of mitochondrial translation in human mitochondria remains unclear. This study reveals that leaderless mRNA transcripts can be directly loaded onto assembled 55S mitochondrial ribosomes in human mitochondria, but not onto the small subunit, and this process requires initiator fMet-tRNA(Met) binding. Furthermore, this study demonstrates that mtIF3 is not involved in translation of leaderless mitochondrial transcripts but is essential for translation of ATP6 in the bicistronic ATP8/ATP6 transcript. These findings provide insights into the evolutionary divergence of mitochondrial translation and enhance our understanding of a critical process in eukaryotic metabolism.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xiangxiang Zhang, Qinyu Xie, Lijun Xiang, Zhonghua Lei, Qixiu Huang, Juncheng Zhang, Maohong Cai, Tao Chen
Summary: The plant-specific protein AtSIEK responds to salt stress and acts as a positive regulator in stress response.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Plant Sciences
Achala Bakshi, Mazahar Moin, Meher B. Gayatri, Aramati B. M. Reddy, Raju Datla, Maganti S. Madhav, Pulugurtha B. Kirti
Summary: Experimental results in rice and Arabidopsis plants indicate that the TOR protein regulates ribosome biogenesis and translation initiation by phosphorylating S6K1. The study also demonstrates the transcriptional upregulation of RP genes in TOR overexpressing transgenic plants. Furthermore, analysis of mutants suggests that the regulation of RP function may involve phosphorylation of S6K1.
Article
Plant Sciences
Pau Boher, Marcal Soler, Sandra Fernandez-Pinan, Xenia Torrent, Sebastian Y. Muller, Krystyna A. Kelly, Olga Serra, Merce Figueras
Summary: Researchers used potato tuber periderm as a model to study the function of RIK in periderm development, and found that StRIK may play a general regulatory role in plant developmental processes. The analysis of the transcriptome suggests that StRIK might be involved in RNA maturation and stress response in the periderm.
Article
Agronomy
Kunneng Zhou, Caijuan Zhang, Jiafa Xia, Peng Yun, Yuanlei Wang, Tingchen Ma, Zefu Li
Summary: The mutant asl4 disrupts early chloroplast development and chlorophyll biosynthesis, with some genes involved in chloroplast biogenesis being up-regulated and others down-regulated. Plastid transcription is impaired in asl4 mutant tissues, leading to reduced levels of most plastid-encoded genes and proteins. The decreased contents of chloroplast rRNAs and ribosomal proteins indicate impaired chloroplast ribosome biogenesis in the asl4 mutant.
Article
Biology
Margarita Belinite, Iskander Khusainov, Stefano Marzi
Summary: The ribosome is a crucial cellular machinery and its solved structure has greatly advanced the field of structural biology. This study presents a detailed protocol for the purification of intact and functional 30S ribosomes, and successfully obtained the high-resolution structure of 30S-mRNA complex from Staphylococcus aureus using cryo-electron microscopy.
Article
Biochemistry & Molecular Biology
Mariusz Popenda, Tomasz Zok, Joanna Sarzynska, Agnieszka Korpeta, Ryszard W. Adamiak, Maciej Antczak, Marta Szachniuk
Summary: Computational methods for predicting RNA 3D structures have practical applications in molecular biology and medicine, highlighting the need to improve accuracy. The RNA-Puzzles initiative plays a significant role in collecting and evaluating computationally built RNAs, allowing for the analysis of prediction methods. This study focuses on entangled RNA fragments in predicted structures, proposing a classification based on topology and components.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Mariusz Popenda, Tomasz Zok, Joanna Sarzynska, Agnieszka Korpeta, Ryszard W. Adamiak, Maciej Antczak, Marta Szachniuk
Summary: Computational methods for predicting RNA 3D structure are increasingly important in molecular biology and medicine. The RNA-Puzzles initiative evaluates and shares computationally built RNAs, allowing for better understanding of strengths and weaknesses in prediction methods. This study focuses on the issue of entangled RNA fragments in predicted 3D models, proposing a classification system for different types of entanglements.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biology
Marcell Lederer, Simon Mueller, Markus Glass, Nadine Bley, Christian Ihling, Andrea Sinz, Stefan Huettelmaier
Summary: RNA-binding proteins (RBPs) play crucial roles in post-transcriptional control of gene expression and cellular processes, especially in cancer where dysregulation of RBPs, such as the MEX3 family member MEX3A, can impact proliferation, migration, and tumorigenesis. The unique domain structure of MEX3 proteins allows them to modulate both RNA and protein fate, and their oncogenic potential is supported by their impact on tumor cell behaviors and growth.
Review
Microbiology
Anusha Naganathan, Gloria M. Culver
Summary: The production of ribosomal subunits directly affects the fitness of bacteria, and extra-ribosomal protein factors play a crucial role in this process.
ANNUAL REVIEW OF MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Ravi Shankar Singh, Ananna Bhadra Arna, He Dong, Manisha Yadav, Aanchal Aggarwal, Yuliang Wu
Summary: DDX43, a member of the DEAD-box protein family, exhibits ATP-dependent RNA and DNA helicase activity. Its KH domain selectively binds pyrimidine-rich ssDNA and ssRNA. DDX43 is overexpressed in many tumors and thus holds potential as a target for cancer therapy.
Article
Genetics & Heredity
Xia Ding, Subha Philip, Betty K. Martin, Yan Pang, Sandra Burkett, Deborah A. Swing, Chinmayi Pamala, Daniel A. Ritt, Ming Zhou, Deborah K. Morrison, Xinhua Ji, Shyam K. Sharan
Article
Oncology
Krishna B. Singh, Xinhua Ji, Shivendra V. Singh
MOLECULAR CANCER THERAPEUTICS
(2018)
Article
Biochemistry & Molecular Biology
Chao Wang, Genbin Shi, Xinhua Ji
Review
Cell Biology
Sherif Abou Elela, Xinhua Ji
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2019)
Article
Biochemistry & Molecular Biology
Lan Jin, He Song, Joseph E. Tropea, Danielle Needle, David S. Waugh, Shuo Gu, Xinhua Ji
NUCLEIC ACIDS RESEARCH
(2019)
Article
Multidisciplinary Sciences
He Song, Xinhua Ji
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
He Song, Madushini N. Dharmasena, Chao Wang, Gary X. Shaw, Scott Cherry, Joseph E. Tropea, Ding J. Jin, Xinhua Ji
Article
Microbiology
Xiaomei Zhou, Howard K. Peters, Xintian Li, Nina Costantino, Vandana Kumari, Genbin Shi, Chao Tu, Todd A. Cameron, Daniel P. Haeusser, Daniel E. Vega, Xinhua Ji, William Margolin, Donald L. Court
JOURNAL OF BACTERIOLOGY
(2020)
Article
Chemistry, Medicinal
Jacynthe L. Toulouse, Genbin Shi, Claudele Lemay-St-Denis, Maximilian C. C. J. C. Ebert, Daniel Deon, Marc Gagnon, Edward Ruediger, Kevin Saint-Jacques, Delphine Forge, Jean Jacques Vanden Eynde, Anne Marinier, Xinhua Ji, Joelle N. Pelletier
ACS MEDICINAL CHEMISTRY LETTERS
(2020)
Article
Biochemistry & Molecular Biology
Genbin Shi, Gary X. Shaw, Fengxia Zhu, Sergey G. Tarasov, Xinhua Ji
Summary: HPPK is a key enzyme in the folate biosynthesis pathway, essential for microorganisms. Researchers have developed third-generation inhibitors to mimic the transition state, advancing the development of bisubstrate analog inhibitors.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Christopher E. Smith, Yien Che Tsai, Yu-He Liang, Domarin Khago, Jennifer Mariano, Jess Li, Sergey G. Tarasov, Emma Gergel, Borong Tsai, Matthew Villaneuva, Michelle E. Clapp, Valentin Magidson, Raj Chari, R. Andrew Byrd, Xinhua Ji, Allan M. Weissman
Summary: The study reveals a key role of the G2BR region of the ERAD accessory protein AUP1 in maintaining stability of the ERAD ubiquitin-conjugating enzyme UBE2G2. Additionally, G2BR(AUP1) is essential for both recruiting and activating UBE2G2 at the ER membrane during ERAD.
Article
Biochemistry & Molecular Biology
Sudhaker Dharavath, Gary X. Shaw, Xinhua Ji
Summary: RNase III family is a class of dsRNA-specific endonucleases that recognizes substrates in a sequence-specific manner. This study reveals the reaction trajectory of two-Mg2+-ion catalysis by prokaryotic and eukaryotic RNase III enzymes and identifies the functional role of a third Mg2+ ion in bacterial RNase III.
Article
Biochemistry & Molecular Biology
Hyun Kyung Lee, Yun-Tzai Lee, Lixin Fan, Haley M. Wilt, Chelsie E. Conrad, Ping Yu, Jinwei Zhang, Genbin Shi, Xinhua Ji, Yun-Xing Wang, Jason R. Stagno
Summary: The thiamine pyrophosphate (TPP)-sensing riboswitch is a widely studied riboswitch. This study presents the crystal structure of the Escherichia coli TPP riboswitch in its ligand-free state, revealing an extended Y-shaped conformation. The loss of ligand interactions disrupts key tertiary interactions and generates conformational flexibility necessary for gene regulation. The ligand-binding site remains partially preformed. Overall, this study provides insights into the ligand-induced conformational changes in TPP riboswitches and their role in gene regulation.
Article
Biochemistry & Molecular Biology
Gary X. Shaw, Lixin Fan, Scott Cherry, Genbin Shi, Joseph E. Tropea, Xinhua Ji
Summary: Dihydroneopterin aldolase (DHNA) is an essential enzyme for folate biosynthesis in microorganisms and a potential target for antimicrobial agents. The crystal structure of Helicobacter pylori DHNA (HpDHNA) in complex with a pterin molecule has been determined, showing a tetrameric form. This tetrameric complex has well-formed active sites with the exit blocked by two amino acid residues, suggesting a characteristic feature of DHNA active sites. Comparative analysis with Staphylococcus aureus DHNA (SaDHNA) structures suggests a fragment-based strategy for the development of isozyme-specific inhibitors.
CURRENT RESEARCH IN STRUCTURAL BIOLOGY
(2023)
Article
Microbiology
Fei Yu, He Song, Yanling Wu, So Young Chang, Lili Wang, Wei Li, Binbin Hong, Shuai Xia, Chunyu Wang, Surender Khurana, Yang Feng, Yanping Wang, Zhiwu Sun, Biao He, Dongni Hou, Jody Manischewitz, Lisa R. King, Yuanlin Song, Ji-Young Min, Hana Golding, Xinhua Ji, Lu Lu, Shibo Jiang, Dimiter S. Dimitrov, Tianlei Ying
CELL HOST & MICROBE
(2017)