Article
Multidisciplinary Sciences
Yu Liu, Libing Yu, Chirangini Pukhrambam, Jared T. Winkelman, Emre Firlar, Jason T. Kaelber, Yu Zhang, Bryce E. Nickels, Richard H. Ebright
Summary: This study reveals the mechanism of RNA extension in reiterative transcription initiation, showing that it differs from the mechanism of RNA extension in standard transcription initiation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Xizi Chen, Yilun Qi, Zihan Wu, Xinxin Wang, Jiabei Li, Dan Zhao, Haifeng Hou, Yan Li, Zishuo Yu, Weida Liu, Mo Wang, Yulei Ren, Ze Li, Huirong Yang, Yanhui Xu
Summary: This study elucidates the assembly mechanism of human TFIID-based PIC, showing two tracks for modular reorganization and direct promoter deposition, converging at a holo PIC with around 50 subunits. TFIID stabilizes PIC organization and supports CAK-mediated phosphorylation of Pol II.
Article
Cell Biology
Kevin M. Andre, Nathalie Giordanengo Aiach, Veronica Martinez-Fernandez, Leo Zeitler, Adriana Alberti, Arach Goldar, Michel Werner, Cyril Denby Wilkes, Julie Soutourina
Summary: Chromatin organization is crucial for transcriptional regulation. Mediator and RSC contribute to chromatin remodeling and transcriptional regulation by establishing physical contact and coordinating their functions.
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
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
Biochemistry & Molecular Biology
Mahamaya Biswal, Stephen Diggs, Duo Xu, Nelli Khudaverdyan, Jiuwei Lu, Jian Fang, Gregor Blaha, Rong Hai, Jikui Song
Summary: The replication of the coronavirus genome is regulated by a complex of non-structural proteins, with NSP7 and NSP8 playing key roles. The crystal structure of the NSP7-NSP8 complex reveals a heterotetrameric form, and mutations in interface I and II affect the stability and activity of the complex. This study provides insights into the dynamic assembly of NSP7 and NSP8 in regulating viral genome replication, with implications for antiviral drug development.
NUCLEIC ACIDS RESEARCH
(2021)
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
Chirangini Pukhrambam, Vadim Molodtsov, Mahdi Kooshkbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko, Min Su, Zhou Yin, Jared T. Winkelman, Justin B. Kinney, Richard H. Ebright, Bryce E. Nickels
Summary: In sigma-dependent transcriptional pausing, the presence or absence of GreB determines whether the paused state involves backtracking or scrunched by 2-4 base pairs or 2-3 base pairs respectively. The consensus sequence T(-3)N(-2)Y(-1)G(+1) is associated with pausing in both initial transcription and transcription elongation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Raphael Forquet, William Nasser, Sylvie Reverchon, Sam Meyer
Summary: DNA supercoiling acts as a global transcriptional regulator in bacteria. A thermodynamic model based on DNA elasticity is developed to predict the relative activation of promoters with different spacer lengths. The model is validated through in vitro and in vivo expression assays and genome-scale analysis in Escherichia coli, demonstrating the significant effect of spacer length on genomic expression after superhelical variations.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Mirjana Lilic, Neil A. Holmes, Matthew J. Bush, Alexandra K. Marti, David A. Widdick, Kim C. Findlay, Young Joo Choi, Ruby Froom, Steven Koh, Mark J. Buttner, Elizabeth A. Campbell
Summary: Studies have revealed diverse molecular mechanisms regulating transcriptional initiation in different bacterial clades, including the essential role of WhiA and WhiB factors in cell division gene expression. Cryoelectron microscopy structures of Sven transcriptional regulatory complexes have provided insights into the molecular interactions of WhiA and WhiB with RNA polymerase and DNA, shedding light on their significance in developmental cell division.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Belen Chaves-Arquero, Santiago Martinez-Lumbreras, Sergio Camero, Clara M. Santiveri, Yasmina Mirassou, Ramon Campos-Olivas, Maria Angeles Jimenez, Olga Calvo, Jose Manuel Perez-Canadillas
Summary: Heterodimerization of RNA binding proteins Nrd1 and Nab3 is crucial for yeast cell fitness, and the structure of Nrd1-Nab3 resembles that of Rna14/Rna15 despite sequence and evolutionary differences.
LIFE SCIENCE ALLIANCE
(2022)
Review
Biochemistry & Molecular Biology
Chengli Fang, Yu Zhang
Summary: MerR family transcription factors modulate gene expression in bacteria, functioning as transcription repressors under normal circumstances but rapidly transforming to transcription activators under cellular triggers. They bind in a unique mechanism in the long spacer of the promoter region, regulating transcription activity.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2022)
Article
Multidisciplinary Sciences
Beth A. Shen, Christine M. Hustmyer, Daniel Roston, Michael B. Wolfe, Robert Landick
Summary: Gene silencing in bacteria is controlled by chromatin proteins, such as H-NS in Escherichia coli. The exact structures and DNA-binding mechanisms of H-NS are not well understood. Through a combination of techniques, researchers found that the DNA-binding domains of H-NS contact DNA at consistent positions in both linear and bridged filaments. The orientation and spacing of these domains vary, suggesting a model of switching between different filament structures.
Article
Multidisciplinary Sciences
Ilona Christy Unarta, Siqin Cao, Shintaroh Kubo, Wei Wang, Peter Pak-Hang Cheung, Xin Gao, Shoji Takada, Xuhui Huang
Summary: The study elucidated the dynamics of Thermus aquaticus holoenzyme's gate opening using a quasi-Markov State Model, revealing the differential roles of beta-lobe and clamp in DNA loading and the mechanism by which Myxopyronin inhibits clamp opening. Additionally, a critical role of beta-lobe in DNA loading was uncovered, presenting an opportunity for the development of antibiotics targeting this region of RNAP. The study also demonstrated the potential of quasi-Markov State Models in studying biomolecular dynamics based on generalized master equation formalism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Moustafa M. Saleh, Celia Jeronimo, Francois Robert, Gabriel E. Zentner
Summary: The Mediator coactivator complex is divided into four modules, with deletion of Med16 affecting genes dependent on the SAGA complex and TFIID complex. Altering the balance of transcription pre-initiation complex formation can partially restore normal transcription activity.
Article
Multidisciplinary Sciences
Yun Yang, Vidya C. Darbari, Nan Zhang, Duo Lu, Robert Glyde, Yi-Ping Wang, Jared T. Winkelman, Richard L. Gourse, Katsuhiko S. Murakami, Martin Buck, Xiaodong Zhang
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
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)