Article
Biochemistry & Molecular Biology
Maria Claudia Villegas Kcam, Annette J. Tsong, James Chappell
Summary: CRISPR-Cas activator systems have the potential to selectively activate target genes, but face limitations in bacteria due to strict distance-dependent target binding requirements. By utilizing rational protein engineering, a new CRISPRa platform has been developed with increased modularity and targeting flexibility. This approach allows for easy customization and expanded target range through harnessing engineered Cas proteins.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Franziska Guenl, Tim Krischuns, Julian A. Schreiber, Lea Henschel, Marius Wahrenburg, Hannes C. A. Drexler, Sebastian A. Leidel, Vlad Cojocaru, Guiscard Seebohm, Alexander Mellmann, Martin Schwemmle, Stephan Ludwig, Linda Brunotte
Summary: The replication of influenza A virus relies on ubiquitination of the viral polymerase derived from host cells. This study reveals that site-specific ubiquitination of PB1-K578 is acquired during infection and regulates the dimerization of polymerase and the binding of NP. Mass spectrometry analysis has identified 59 modified lysines across the three subunits of the viral polymerase, which affect mRNA transcription, vRNA replication, and the generation of recombinant viruses via non-proteolytic mechanisms.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Fluids & Plasmas
Jin Qian, David Dunlap, Laura Finzi
Summary: In this study, a thermodynamic model of transcriptional pausing is proposed to describe the kinetics of different types of pauses based on the thermal energy of transcription bubbles and nascent RNA structures. The model can accurately predict experimentally detected pauses and the effects of tension and transcription factors on pausing.
Review
Microbiology
Robert Landick
Summary: RNA polymerase plays a crucial role in expressing genetic information through transcription of DNA, and has evolved to sense and process environmental information. Transcriptional pauses, which occur during transcript elongation, play a key role in regulatory decisions. After decades of study, four classes of transcriptional pause signals have been identified, raising numerous questions about how RNA polymerase responds to these signals and the broader regulation of transcript elongation.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
(2021)
Article
Biochemistry & Molecular Biology
Juha Kurkela, Julia Fredman, Tiina A. Salminen, Taina Tyystjarvi
Summary: The omega subunit of RNA polymerase is the only nonessential subunit in the core of bacterial RNAP. It stabilizes correct folding, interacts with the beta ' subunit, and plays a crucial role in core assembly and promoter selection. Omega-less strains exhibit pleiotropic phenotypes and interactions with other subunits differ between bacterial taxa.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Oliver M. Stockert, Chandra M. Gravel, Katherine E. Berry
Summary: This protocol introduces a three-hybrid system and a forward genetics screen to analyze RNA-protein interactions in live bacteria. The system connects the strength of an RNA-protein interaction to the transcription of a reporter gene in Escherichia coli cells. It provides a powerful complement to traditional biochemical methods for studying RNA-protein interactions.
Article
Multidisciplinary Sciences
Kai Sheng, Ning Li, Jessica N. Rabuck-Gibbons, Xiyu Dong, Dmitry Lyumkis, James R. Williamson
Summary: In this study, cryo-electron microscopy and subclassification were used to identify intermediates in the assembly of the 50S ribosomal subunit from E. coli. The study reveals a complete assembly map for all RNA and protein components, and shows that assembly generally proceeds co-transcriptionally.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Xinyun Cao, Hande Boyaci, James Chen, Yu Bao, Robert Landick, Elizabeth A. Campbell
Summary: Fidaxomicin is effective in treating Cdiff infections with minimal impact on gut commensals, and its activity is determined by a specific binding determinant in Cdiff RNA polymerase.
Article
Biochemistry & Molecular Biology
Daniel S. Wenholz, Michael Miller, Catherine Dawson, Mohan Bhadbhade, David StC Black, Renate Griffith, Hue Dinh, Amy Cain, Peter Lewis, Naresh Kumar
Summary: A series of hybrid compounds incorporating anthranilic acid and activated 1H-indoles were designed to target bacterial RNA polymerase holoenzyme formation using computational docking. Experimental results showed that these compounds demonstrated activity against a range of pathogenic bacteria, potentially serving as new antibacterial drugs.
BIOORGANIC CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Marie Delaby, Lydia M. Varesio, Laurence Degeorges, Sean Crosson, Patrick H. Viollier
Summary: TrcR, an uncharacterized protein, has been identified as a potential antibiotic target and the founding member of the DUF1013 family. It interacts with RNAP to promote transcription during the cell cycle, showing conservation in different bacteria species such as Sinorhizobium sp. and Brucella spp.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Hana Veler, Haitian Fan, Jeremy R. Keown, Jane Sharps, Marjorie Fournier, Jonathan M. Grimes, Ervin Fodor
Summary: This study characterizes the interaction between the viral polymerase and Rab11a and identifies the important domains involved in this interaction. The findings provide insights into the cytoplasmic transport of vRNPs and suggest a potential target site for the development of influenza antiviral drugs.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wenjie Cai, Huimin Liao, Mingqi Lu, Xiangting Zhou, Xiaoyan Cheng, Christian Staehelin, Weijun Dai
Summary: This study developed an experimental evolutionary approach to identify additional determinants for quorum-sensing (QS) reprogramming in Pseudomonas aeruginosa. The study revealed a new functional role for RpoA in regulating QS activity and identified a RpoA-dependent regulatory circuit critical for QS-reprogramming.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Maura Mittermeier, Bing Wang, Nelly Said, Daniela Gjorgjevikj, Markus C. Wahl, Irina Artsimovitch
Summary: Escherichia coli RfaH plays a role in abolishing Rho-mediated polarity in lipopolysaccharide core biosynthesis operons. A temperature-sensitive mutant rpoC397* was identified as a suppressor of SDS sensitivity, with 46 C-terminal residues of the RNA polymerase beta' subunit replaced by 23 residues carrying a net positive charge. The rpoC397* mutant mimics RfaH's resistance to Rho and exhibits similar responses to pause signals and Nus factors, while still binding to Rho and Nus factors in vivo.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biology
Abhishek Mazumder, Richard H. Ebright, Achillefs N. Kapanidis
Summary: This study used single-molecule techniques to investigate the unwinding process of bacterial promoters, and found that the RNAP clamp remains closed during binding to the promoter, continues to stay closed during unwinding, and further closes after unwinding, locking the DNA in the active center cleft of the RNAP.
Article
Multidisciplinary Sciences
Zuanning Yuan, Roxana Georgescu, Huilin Li, Michael E. E. O'Donnell
Summary: DNA polymerase α has separate RNA and DNA polymerase subunits to form a unique-length RNA-DNA primer. Cryo-EM structures of each stage in primer synthesis reveal large conformational changes among the four subunits and explain how primer length is limited.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Vadim Molodtsov, Paul R. Fleming, Charles J. Eyermann, Andrew D. Ferguson, Melinda A. Foulk, David C. McKinney, Craig E. Masse, Ed T. Buurman, Katsuhiko S. Murakami
JOURNAL OF MEDICINAL CHEMISTRY
(2015)
Article
Biochemistry & Molecular Biology
Alexander V. Yakhnin, Katsuhiko S. Murakami, Paul Babitzke
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Biochemistry & Molecular Biology
Huiqiong Gu, Shigeo Yoshinari, Raka Ghosh, Anna V. Ignatochkina, Paul D. Gollnick, Katsuhiko S. Murakami, C. Kiong Ho
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Vadim Molodtsov, Nathan T. Scharf, Maxwell A. Stefan, George A. Garcia, Katsuhiko S. Murakami
MOLECULAR MICROBIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Vadim Molodtsov, Katsuhiko S. Murakami
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Yeonoh Shin, Mark Hedglin, Katsuhiko S. Murakami
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Yeonoh Shin, M. Zuhaib Qayyum, Danil Pupov, Daria Esyunina, Andrey Kulbachinskiy, Katsuhiko S. Murakami
Summary: The study reveals the cryo-EM structures of E. coli RNA polymerase and rRNA promoter complex with DksA/ppGpp during open complex formation, providing insights into the key steps of promoter recognition and opening.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Janne J. Makinen, Yeonoh Shin, Eeva Vieras, Pasi Virta, Mikko Metsa-Ketel, Katsuhiko S. Murakami, Georgiy A. Belogurov
Summary: In multi-subunit RNA polymerases, a conserved Arg residue plays a major role in selecting against deoxyribonucleoside substrates.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
M. Zuhaib Qayyum, Vadim Molodtsov, Andrew Renda, Katsuhiko S. Murakami
Summary: In Escherichia coli, the ATPase RapA from the Swi2/Snf2 family has been found to enhance RNAP recycling by binding to RNAP away from the DNA-binding main channel and allosterically closing the RNAP clamp, thereby preventing nonspecific DNA binding and hindering PTC formation. This mechanism allows RapA to act as a guardian of RNAP, enhancing transcription efficiency without affecting the binding of promoter DNA recognition factors.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biology
Anoop Narayanan, Manju Narwal, Sydney A. Majowicz, Carmine Varricchio, Shay A. Toner, Carlo Ballatore, Andrea Brancale, Katsuhiko S. Murakami, Joyce Jose
Summary: In this study, a screening strategy for antiviral drugs against SARS-CoV-2 was developed, which involves in-cell protease assay, antiviral and biochemical activity assessments, as well as structural determinations. Several protease inhibitors with low cytotoxicity were identified and their mechanisms of action were examined.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
James R. Portman, M. Zuhaib Qayyum, Katsuhiko S. Murakami, Terence R. Strick
Summary: It has been found that the RapA protein can dislodge stalled RNA polymerase from DNA via backtracking, and this process is influenced by supercoiling and torque, inhibited by GreB, and depends on the length of RNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Lidiya Lisitskaya, Yeonoh Shin, Aleksei Agapov, Anna Olina, Ekaterina Kropocheva, Sergei Ryazansky, Alexei A. Aravin, Daria Esyunina, Katsuhiko S. Murakami, Andrey Kulbachinskiy
Summary: This study identifies a new class of pAgos that use DNA guides to process RNA targets and can sense mismatches and modifications in the target. The findings broaden our understanding of prokaryotic defense systems and expand the potential application of programmable nucleases in RNA technology.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
Lidiya Lisitskaya, Yeonoh Shin, Aleksei Agapov, Anna Olina, Ekaterina Kropocheva, Sergei Ryazansky, Alexei A. Aravin, Daria Esyunina, Katsuhiko S. Murakami, Andrey Kulbachinskiy
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Zachary F. Mandell, Rishi K. Vishwakarma, Helen Yakhnin, Katsuhiko S. Murakami, Mikhail Kashlev, Paul Babitzke
Summary: The contributions of Rho-dependent and intrinsic transcription termination mechanisms in bacteria were investigated. It was found that NusA and NusG stimulate a significant portion of intrinsic terminators and participate in Rho-dependent termination. Rho was also found to stimulate termination at some intrinsic terminators in vivo. Computational analyses and in vitro experiments provided insights into how Rho stimulates intrinsic terminators.
NATURE MICROBIOLOGY
(2022)
Meeting Abstract
Chemistry, Multidisciplinary
K. Murakami
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2020)