Review
Cell Biology
Mathias Girbig, Agata D. Misiaszek, Christoph W. Mueller
Summary: The transcription of RNA is mainly conducted by three RNA polymerases, which have similarities and differences in structure and function. Each RNA polymerase is responsible for synthesizing different types of RNA molecules, and the transcription process consists of three stages: initiation, elongation, and termination.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Review
Microbiology
Aartjan J. W. te Velthuis, Jonathan M. Grimes, Ervin Fodor
Summary: RNA viruses, including important human and animal pathogens, have genomes consisting of single or multiple RNA segments. Replication and transcription are performed by RNA-dependent RNA polymerases, and recent high-resolution studies have provided insights into the structures of these enzymes and their roles in viral transcription and replication, offering potential targets for antiviral drug design.
NATURE REVIEWS MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ana I. Garrido-Godino, Francisco Gutierrez-Santiago, Francisco Navarro
Summary: Despite the specificity in the synthesis of different RNA types by three RNA polymerases in eukaryotes, the biogenesis process is proposed to be similar to that of bacteria, requiring the formation of subassembly complexes in the cytoplasm before nuclear import. Recent studies in Saccharomyces cerevisiae have shed light on the biogenesis of RNA polymerases by characterizing elements involved in the assembly of these complexes, some of which are conserved in humans.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Physical
Inacrist Geronimo, Pietro Vidossich, Marco De Vivo
Summary: The fidelity of DNA polymerases is influenced by the metal-mediated dynamics of local structural features at the catalytic center, which determines whether the nucleotide is correctly inserted.
Review
Biochemistry & Molecular Biology
Marina Barba-Aliaga, Paula Alepuz, Jose E. Perez-Ortin
Summary: In eukaryotic cells, three nuclear RNA polymerases may have evolved from a single enzyme in a common ancestor with archaea. This diversity allows each polymerase to specialize in synthesizing different types of transcripts, potentially influencing the evolution of regulatory mechanisms to adapt to environmental changes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Jiqin Wu, Xinyu Wang, Qiaojie Liu, Guoliang Lu, Peng Gong
Summary: This study presents crystal structures of the RNA-dependent RNA polymerase complex from dengue virus serotype 2, revealing a dramatic refolding of the priming element during elongation and confirming its essential interactions with the RNA duplex backbone for enzyme stability. Enzymology data further suggest that the critical refolding transition of the priming element likely occurs after the synthesis of a 4- to 5-nucleotide product.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Dong-Lei Yang, Kun Huang, Deyin Deng, Yuan Zeng, Zhenxing Wang, Yu Zhang
Summary: DNA-dependent RNA polymerases (Pols) transfer genetic information from genomic DNA to RNA in all organisms. Plants have two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs respectively, for silencing transposable elements. The distinct functions of the five plant Pols arise from unique subunits interacting with specific regulatory factors. This review summarizes recent advances in understanding the evolution, function, structure, and transcription cycles of nucleus-localized Pols in plants.
Article
Biotechnology & Applied Microbiology
Yongpeng Jiang, Jie Huang, Kai Tian, Xiao Yi, Haonan Zheng, Yi Zhu, Tiannan Guo, Xiong Ji
Summary: This study reveals the cross-regulatory effects between RNA polymerases, showing that depletion of Pol III affects the transcription of Pol II and regulates the local chromatin structures and the FACT-Pol II axis, thereby affecting Pol II transcription rate.
Article
Multidisciplinary Sciences
John H. Shin, Steve L. Bonilla, Sarah K. Denny, William J. Greenleaf, Daniel Herschlag
Summary: Structured RNAs and RNA/protein complexes play critical roles in cellular functions. This study focuses on dissecting the 11nt receptor (11ntR) motif to understand its energetic architecture by measuring the binding of single and double mutants to tetraloops. The findings reveal a gradient of cooperativity and exceptions to the stability-abundance relationship, highlighting the power of high-throughput approaches.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Tomasz W. Turowski, Magdalena Boguta
Summary: RNAPI and RNAPIII are multi-heterogenic protein complexes specialized in transcribing highly abundant non-coding RNAs, more complex than RNAPII synthesizing mRNAs. They share associated subcomplexes formed by specific subunits in yeast and establish an assembly platform co-translationally during the synthesis of the Rpb10 subunit.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Rodrigo Jacome, Jose Alberto Campillo-Balderas, Arturo Becerra, Antonio Lazcano
Summary: Our understanding of the RNA virosphere has changed significantly in recent years due to metagenomics, allowing for a greater understanding of potential hosts and the identification of conserved proteins, such as the RNA-dependent RNA polymerase. Structural comparisons have revealed multiple evolutionary routes for these polymerases, and the inclusion of DNA polymerases in the analysis suggests a divergence from B-family polymerases.
JOURNAL OF MOLECULAR EVOLUTION
(2022)
Review
Virology
Kavitha Ramaswamy, Mariya Rashid, Selvarajan Ramasamy, Tamilselvan Jayavelu, Sangita Venkataraman
Summary: This review explores the structural differences of RdRPs in RNA binding and polymerization mechanisms, based on recent studies of RdRP complexes with various cofactors, RNA moieties, analogs, and inhibitors.
Article
Biochemistry & Molecular Biology
Bo Yan, George Tzertzinis, Ira Schildkraut, Laurence Ettwiller
Summary: ReCappable-seq is a new method that allows the identification of transcription start sites (TSSs) for both Pol II and non-Pol II transcripts at single-nucleotide resolution. It provides a comprehensive understanding of various cell functions involved in eukaryotic transcription.
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
Chemistry, Multidisciplinary
Pulak Ghosh, Heike M. Kropp, Karin Betz, Samra Ludmann, Kay Diederichs, Andreas Marx, Seergazhi G. Srivatsan
Summary: This study demonstrates the use of environment-sensitive heterocycle-modified fluorescent nucleotide substrates to probe the incorporation mechanism of DNA polymerases in real-time and at the atomic level. The results show that different nucleotide analogs have varying incorporation efficiencies in different DNA polymerase families, and some modified nucleotides can serve as reporters for monitoring enzyme activity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Mark A. Farrugia, Beibei Wang, Michael Feig, Robert P. Hausinger
Meeting Abstract
Biophysics
Patrick O. Ochieng, Beibei Wang, Michael Feig, Charles G. Hoogstraten
BIOPHYSICAL JOURNAL
(2015)
Article
Multidisciplinary Sciences
Zhicheng Zuo, Beibei Wang, Jingwei Weng, Wenning Wang
SCIENTIFIC REPORTS
(2015)
Article
Microbiology
Beibei Wang, Jingwei Weng, Wenning Wang
FRONTIERS IN MICROBIOLOGY
(2015)
Meeting Abstract
Biophysics
Michael Feig, Beibei Wang, Joshua Francis
BIOPHYSICAL JOURNAL
(2016)
Article
Biochemical Research Methods
Beibei Wang, Joshua Francis, Monika Sharma, Sean M. Law, Alexander V. Predeus, Michael Feig
PLOS COMPUTATIONAL BIOLOGY
(2016)
Article
Biophysics
Beibei Wang, Alexander V. Predeus, Zachary F. Burton, Michael Feig
BIOPHYSICAL JOURNAL
(2013)
Review
Chemistry, Multidisciplinary
Beibei Wang, Michael Feig, Robert I. Cukier, Zachary F. Burton
Article
Chemistry, Physical
Beibei Wang, Jingwei Weng, Kangnian Fan, Wenning Wang
JOURNAL OF PHYSICAL CHEMISTRY B
(2012)
Article
Biochemistry & Molecular Biology
Beibei Wang, Jingwei Weng, Kangnian Fan, Wenning Wang
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2011)
Article
Biochemistry & Molecular Biology
Beibei Wang, Jingwei Weng, Wenning Wang
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2014)
Letter
Hematology
Ting Wang, Ying Shen, Yuanyuan Li, Beibei Wang, Benfang Wang, Depei Wu, Changgeng Ruan, Yiqiang Wang
Article
Microbiology
Beibei Wang, Huayi Yang, Jianan Sun, Chuhao Dou, Jian Huang, Feng-Biao Guo
Summary: Synthetic biology aims to create new biological parts, devices, and systems, and reconfigure existing natural biological systems. The development of the BioMaster database complements information about BioBrick parts extensively and provides a user-friendly platform for retrieval and analysis.
FRONTIERS IN MICROBIOLOGY
(2021)
Meeting Abstract
Biophysics
Beibei Wang, Peter Tieleman
BIOPHYSICAL JOURNAL
(2018)