Article
Biochemical Research Methods
Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchene
Summary: This article introduces a new pipeline for designing searchable databases on the 2D and 3D structures of protein-bound nucleic acids (NA), selecting context-specific NA structures, and creating corresponding fragment libraries. The strength of this pipeline lies in its modularity, allowing it to be adapted to various specific modeling problems.
Article
Medicine, Research & Experimental
Romualdo Troisi, Claudia Riccardi, Kevan Perez de Carvasal, Michael Smietana, Francois Morvan, Pompea Del Vecchio, Daniela Montesarchio, Filomena Sica
Summary: This article discusses the advantages and disadvantages of oligonucleotide aptamers and proposes strategies for improvement. Crystallographic analysis of an engineered oligonucleotide in complex with thrombin reveals that terminal modifications enhance the interaction with thrombin, thereby expanding its potential.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Biochemistry & Molecular Biology
Caterina Ciani, Anna Perez-Rafols, Isabelle Bonomo, Mariachiara Micaelli, Alfonso Esposito, Chiara Zucal, Romina Belli, Vito Giuseppe D'Agostino, Irene Bianconi, Vito Calderone, Linda Cerofolini, Orietta Massidda, Michael Bernard Whalen, Marco Fragai, Alessandro Provenzani
Summary: This study identified an RNA-binding protein, AB-Elavl, in the Gram-negative pathogen Acinetobacter baumannii. The protein contains a single RNA Recognition Motif (RRM) and exhibits structural similarities to the human HuR protein. Despite some differences in binding specificity and affinity, AB-Elavl can bind to AU-rich regions similar to HuR. This finding expands our understanding of RNA-binding proteins in A. baumannii and their potential role in antibiotic resistance.
Article
Biochemistry & Molecular Biology
Xiaomin Ni, Andreas C. Joerger, Apirat Chaikuad, Stefan Knapp
Summary: FUBP-interacting repressor (FIR) is a suppressor of the proto-oncogene MYC's transcription, by binding to the far upstream element (FUSE) of the MYC promoter. Competition with FUSE-binding protein 1 (FUBP1) is a crucial mechanism for MYC transcriptional regulation.
Article
Biochemistry & Molecular Biology
Olivier Finet, Carlo Yague-Sanz, Lara Katharina Kruger, Phong Tran, Valerie Migeot, Max Louski, Alicia Nevers, Mathieu Rougemaille, Jingjing Sun, Felix G. M. Ernst, Ludivine Wacheul, Maxime Wery, Antonin Morillon, Peter Dedon, Denis L. J. Lafontaine, Damien Hermand
Summary: This study reveals the importance of RNA modifications in gene expression control, and develops a new integrated pipeline to detect modifications in a transcriptome-wide manner. The researchers identify a novel RNA modification and demonstrate its biological function in mRNA of fission yeast. They also find that the modification is evolutionarily conserved in human cells.
Article
Microbiology
Franziska Schramm, Andreas Borst, Uwe Linne, Joerg Soppa
Summary: Translation is an essential step in gene expression, with initiation of translation playing a crucial role and displaying more diversity phylogenetically compared to elongation or termination. While bacteria have only three initiation factors, eukaryotes possess over 10, and archaea also contain genes encoding archaeal homologs of eukaryotic initiation factors, albeit with limited experimental characterization. By studying the protein-protein interaction network of aIFs in Haloferax volcanii, it was found that aIF5B and aIF2B alpha are not only central hubs in the translation initiation network, but also play key roles in coupling transcription and translation.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Emma Minnee, William James Faller
Summary: Protein synthesis is crucial in all kingdoms of life, and dysregulation can drive cancer development, as seen in colorectal cancer with translational reprogramming. Multiple signaling pathways impact the translation initiation machinery, playing a critical role in regulating gene expression differentially.
Article
Biology
Komal Soni, Georg Kempf, Karen Manalastas-Cantos, Astrid Hendricks, Dirk Flemming, Julien Guizetti, Bernd Simon, Friedrich Frischknecht, Dmitri I. Svergun, Klemens Wild, Irmgard Sinning
Summary: The study investigates the Alu domain of Plasmodium falciparum, a divergent apicomplexan protozoan that causes human malaria, and reveals that it adopts an 'open' Y-shaped conformation unlike its prokaryotic and eukaryotic counterparts. The analysis extends the structural database of Alu domains to protozoan species and shows species-specific differences in the recognition of SRP Alu domains by ribosomes.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ying Luo, Yirong Wang, Ying Huang
Summary: PPR protein Ppr10 and translational activator Mpa1 may function together to mediate the assembly of mitochondrial translational initiation complex, and disruption of Ppr10 impairs mitochondrial protein synthesis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Pooja Kumari, Neel Sarovar Bhavesh
Summary: RNA recognition motif (RRM) is a commonly found RNA binding domain in eukaryotes, playing a crucial role in cellular regulation. The crystal structure of human DND1-RRM2 domain revealed a non-canonical fold maintained by a 3D domain swapped dimer between beta(1) and beta(4) strands. Structural and dynamics studies highlighted key determinants and molecular basis for the domain swapped dimerization observed in the RRM domain.
Article
Genetics & Heredity
Xuan He, Sai Zhang, Yanqing Zhang, Zhixin Lei, Tao Jiang, Jianyang Zeng
Summary: The study introduced a model named PULSE based on convolutional neural network for analyzing large-scale Psi site data and characterizing the sequence features of pseudouridylation. The validation tests showed that PULSE outperformed other prediction methods, providing novel insights into the functional roles of pseudouridylation and enabling further research on the transcriptome-wide landscape of Psi sites.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Review
Microbiology
James Chen, Hande Boyaci, Elizabeth A. Campbell
Summary: This review examines universal pathways and diverse regulatory mechanisms in transcription initiation in evolutionarily divergent bacteria, as well as the mechanisms by which antimicrobials inhibit transcription initiation. The study highlights the simplicity of mechanistic studies in transcription initiation in bacteria and the importance of bacteria in human health.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiongwen Cao, Alexandra Khitun, Cecelia M. Harold, Carson J. Bryant, Shu-Jian Zheng, Susan J. Baserga, Sarah A. Slavoff
Summary: This study discovered unannotated alt-proteins that play important roles in DNA damage stress and cell cycle regulation. One of these alt-proteins, MINAS-60, was found to negatively regulate assembly of the pre-60S ribosomal subunit. Depletion of MINAS-60 increases cytoplasmic 60S ribosomal subunit, leading to upregulated protein synthesis and cell proliferation.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sashank Agrawal, Monika Jain, Wei-Zen Yang, Hanna S. Yuan
Summary: This study compared the biochemical and biophysical properties of TDP-43 truncated proteins with and without the P112H mutation, revealing that the mutated proteins have higher thermal stability, impaired RNA-binding activity, and reduced aggregation propensity. The P112H mutation causes local conformational changes in TDP-43, disrupting interactions with nucleic acids. These findings suggest that the P112H mutation contributes to frontotemporal dementia through functional impairment of RNA metabolism and changes in protein clearance mechanisms.
Article
Microbiology
Maikke B. Ohlson, Jennifer L. Eitson, Alexandra I. Wells, Ashwani Kumar, Seoyeon Jang, Chunyang Ni, Chao Xing, Michael Buszczak, John W. Schoggins
Summary: Viruses rely on host ribosomes for protein synthesis, but the specific factors involved in translation of viral RNAs are not fully understood. Through a CRISPR screen, researchers identified multiple host factors, including 60S ribosome biogenesis proteins, that are required for viral protein synthesis. In addition, the study revealed the importance of SBDS and SPATA5 in viral replication for a wide range of viruses.