Article
Multidisciplinary Sciences
Ruth M. Saecker, James Chen, Courtney E. Chiu, Brandon Malone, Johanna Sotiris, Mark Ebrahim, Laura Y. Yen, Edward T. Eng, Seth A. Darst
Summary: The initial step in gene expression requires opening the DNA duplex for RNA synthesis. Differences in DNA sequence and length upstream of the start site globally alter interactions between DNA and RNAP, impacting RPo lifetime and subsequent transcription steps. Limited sequence changes can trigger global alterations in the transcription bubble, modulating RPo lifetime and affecting the transcription cycle.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Xiaoxian Wu, Chengzhi Yu, Wenhui Mu, Zhanxi Gu, Yu Feng, Yu Zhang
Summary: Canonical bacterial transcription activators bind to their cognate cis elements at the upstream of transcription start site (TSS) in a form of dimer. Caulobacter crescentus GcrA, a non-canonical transcription activator, can activate transcription from promoters harboring its cis element at the upstream or downstream of TSS in a form of monomer. The cryo-EM structures of C. crescentus GcrA-bound transcription activation complexes, GcrA TAC(U) and GcrA TAC(D), reveal the interactions between GcrA, RNAP, sigma(70), and promoter DNA, as well as the disruption of sequence-specific interaction between GcrA and DNA depending on the location of GcrA cis elements relative to TSS.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jing Lyu, Rui Shao, Philip Yuk Kwong Yung, Simon J. Elsasser
Summary: Recent evidence suggests that G-quadruplex (G4) structures impact gene expression, DNA methylation, replicative processes, and genome stability. The use of CUT&Tag technology allows high-resolution mapping of G4 structures in mammalian cells, revealing widespread presence at active promoters and enhancers in mouse ESCs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Kyle S. Skalenko, Lingting Li, Yuanchao Zhang, Irina O. Vvedenskaya, Jared T. Winkelman, Alexander L. Cope, Deanne M. Taylor, Premal Shah, Richard H. Ebright, Justin B. Kinney, Yu Zhang, Bryce E. Nickels
Summary: Chemical modifications of RNA 5'-ends allow epitranscriptomic regulation, impacting various aspects of RNA fate. In Escherichia coli cells, RNAs with a 5'-end hydroxyl are produced by primer-dependent transcription initiation using dinucleotide RNAs as primers. The study reveals that primer-dependent initiation in E. coli involves different dinucleotide primers and is influenced by promoter sequences surrounding the primer binding site.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Aditi Keshav, Pooja Murarka, Preeti Srivastava
Summary: The TetR family protein DszGR was identified as an activator of the dsz operon responsible for biodesulfurization. It binds to upstream sequences in the promoter, induces a bend in the DNA, and facilitates dsz promoter activity. The presence of an IHF binding site in the promoter, along with reduced desulphurization activity in the absence of IHF subunits, suggests a regulatory role of IHF in the dsz operon.
Article
Chemistry, Analytical
Jia-En Wang, Ying-Chen Zhou, Bi-Han Wu, Xiu-Cai Chen, Junqiu Zhai, Jia-Heng Tan, Zhi-Shu Huang, Shuo-Bin Chen
Summary: Researchers have developed a new immunosorbent assay to monitor the unwinding of various DNA structures by the Werner syndrome (WRN) helicase. This assay is sensitive and can accurately detect substrate-specificity of WRN with a less time-consuming and high throughput process. It can be used as a powerful tool to study helicase functions and discover potent inhibitors.
Article
Multidisciplinary Sciences
Xizi Chen, Xinxin Wang, Weida Liu, Yulei Ren, Xuechun Qu, Jiabei Li, Xiaotong Yin, Yanhui Xu
Summary: RNA polymerase II-mediated eukaryotic transcription begins with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome, positioned about 40 base pairs downstream of the transcription start site (TSS), acts as a barrier to transcription. The study shows that the PIC-Mediator prefers binding to the T40N nucleosome located at the 40 base pairs downstream of the TSS and contacts the T50N nucleosome, but not the T70N nucleosome. The nucleosome facilitates the organization of PIC-Mediator on the promoter and may contribute to transcription initiation. The study reveals the molecular mechanism of PIC-Mediator organization on chromatin and emphasizes the significance of the +1 nucleosome in regulating transcription initiation.
Article
Biochemistry & Molecular Biology
Yehuda M. Danino, Lena Molitor, Tamar Rosenbaum-Cohen, Sebastian Kaiser, Yahel Cohen, Ziv Porat, Hagai Marmor-Kollet, Corine Katina, Alon Savidor, Ron Rotkopf, Eyal Ben-Isaac, Ofra Golani, Yishai Levin, David Monchaud, Ian D. Hickson, Eran Hornstein
Summary: This study reveals a novel role of Bloom's syndrome protein in the regulation of cytoplasmic processes. It demonstrates that BLM can unwind RNA G-quadruplexes and acts as a negative regulator of stress granule formation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Xizi Chen, Xiaotong Yin, Jiabei Li, Zihan Wu, Yilun Qi, Xinxin Wang, Weida Liu, Yanhui Xu
Summary: This study investigates the mechanisms of TFIID and Mediator proteins in regulating transcription initiation and RNA polymerase activity, revealing their interactions and mutual regulation through structural analysis, as well as the phosphorylation process of Pol II CTD by CDK7.
Editorial Material
Biochemistry & Molecular Biology
George Yakoub, Martijn S. Luijsterburg
Summary: A recent study in Nature unveils the mechanism of how transcriptionally active RNA polymerase II clings to the genomic tightrope during replication, enabled by protein-protein interactions between the replication and transcription machineries.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Keyan Bao, Xueli Zhang, Dongyu Li, Wei Sun, Zhenzhao Sun, Jingfei Wang, Ping Zhu
Summary: By studying the structure of reovirus, we have identified the structures of its transcriptase complex in different states and proposed a transcriptional model with five states. Our findings reveal the key regulatory mechanisms during the transcription process of reovirus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Zelin Shan, Niloofar Ghadirian, Dmitry Lyumkis, Nancy C. Horton
Summary: Enzyme filamentation is a widespread phenomenon that accelerates enzyme activity and expands DNA sequence specificity. The study on SgrAI enzyme sheds light on its catalytic function and the mechanism of DNA sequence specificity expansion.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Razvan Cojocaru, Peter J. Unrau
Summary: Early life may have required RNA replication by RNA replicases, with this study focusing on a holopolymerase ribozyme that can selectively polymerize from specific RNA promoters, potentially aiding in distinguishing self from nonself to prevent replicative parasites. Additionally, the clamp-like mechanism of this polymerase could eventually enable strand invasion, a critical requirement for replication in the early evolution of life.
Article
Immunology
Gang Lu, Feiyan Zheng, Jiajun Ou, Xin Yin, Shoujun Li
Summary: In this study, the feline RNA PolI promoter was identified and found to have higher transcriptional activity in feline cells. The equine influenza virus showed higher polymerase activity compared to human and canine influenza viruses. Additionally, the feline myxovirus resistance protein 1 and baloxavir were found to inhibit influenza virus polymerase activity.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Yang Yang, Chang Liu, Wei Zhou, Wei Shi, Ming Chen, Baoyue Zhang, David G. Schatz, Yangbo Hu, Bin Liu
Summary: The MerR family of transcriptional regulators, such as EcmrR, activate promoters with a suboptimal structure for recognition by RNA polymerase holoenzyme. Structural insights into the EcmrR-dependent transcription process elucidate the mechanisms enabling optimal promoter recognition and transition from initiation to elongation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Paul Dominic B. Olinares, Jin Young Kang, Eliza Llewellyn, Courtney Chiu, James Chen, Brandon Malone, Ruth M. Saecker, Elizabeth A. Campbell, Seth A. Darst, Brian T. Chait
Summary: Recent advancements in single-particle cryogenic electron microscopy have allowed for high-resolution structural determination of protein assemblies, although the method remains time-consuming and resource-intensive. The development of a native mass spectrometry platform provides rapid sample quality assessment and streamlined screening before lengthy cryo-EM analyses, enhancing research efficiency.
Article
Multidisciplinary Sciences
Brandon Malone, James Chen, Qi Wang, Eliza Llewellyn, Young Joo Choi, Paul Dominic B. Olinares, Xinyun Cao, Carolina Hernandez, Edward T. Eng, Brian T. Chait, David E. Shaw, Robert Landick, Seth A. Darst, Elizabeth A. Campbell
Summary: Backtracking, a common regulatory feature in transcription, is found in viruses as well, with evidence suggesting that SARS-CoV-2 RdRp may utilize backtracking for viral transcription and replication. The interaction between RdRp and nsp13 helicase facilitates backtracking, which may aid in proofreading and antiviral resistance for SARS-CoV-2.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Cell Biology
Brandon Malone, Nadya Urakova, Eric J. Snijder, Elizabeth A. Campbell
Summary: The molecular basis and complexity of coronavirus RNA-synthesizing machinery is still not fully understood. Recent research has focused on deciphering and understanding the structures, functions, and interactions of the subunits involved in SARS-CoV-2 replication and transcription. Both viral and host factors play a crucial role in coordinating RNA translation, replication, and transcription, making them potential targets for antiviral therapy.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
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
James Chen, Qi Wang, Brandon Malone, Eliza Llewellyn, Yakov Pechersky, Kashyap Maruthi, Ed T. Eng, Jason K. Perry, Elizabeth A. Campbell, David E. Shaw, Seth A. Darst
Summary: In the complex of SARS-CoV-2 nsp13 helicase and RNA polymerase, a mechanism has been revealed through cryo-EM and MD simulations that controls their movement in opposite directions on RNA. This mechanism allows the helicase to drive the polymerase backward on the RNA template and switch between RNA synthesis and backtracking.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Tim Becker, Anna K. Krome, Sahel Vahdati, Andrea Schiefer, Kenneth Pfarr, Alexandra Ehrens, Tilman Aden, Miriam Grosse, Rolf Jansen, Silke Alt, Thomas Hesterkamp, Marc Stadler, Marc P. Huebner, Stefan Kehraus, Gabriele M. Koenig, Achim Hoerauf, Karl G. Wagner
Summary: The in vivo studies in mice are a valuable model for testing new drug ingredients, but the lack of preclinical in vitro evaluations of drug formulations in mice is a gap in research. The development of novel in vitro and in silico models has supported the evaluation of the anti-infective drug CorA. The study found that the solubility of CorA in mice was lower compared to human-specific media, and the solubility was limited by the formulation. The pharmacokinetic studies in mice correlated with the in vitro dissolution prediction and ruled out intestinal efflux transport.
Article
Infectious Diseases
Jan Balansky, Kenneth Pfarr, Christiane Szekat, Stefan Kehraus, Tilman Aden, Miriam Grosse, Rolf Jansen, Thomas Hesterkamp, Andrea Schiefer, Gabriele M. Koenig, Marc Stadler, Achim Hoerauf, Gabriele Bierbaum
Summary: Corallopyronin A (CorA) is an antibiotic that targets the switch region of RNA polymerase and is active against Gram-positive bacteria. It has a lower mutation frequency and mutation rate compared to rifampicin, making it a potential antibiotic for treating S. aureus infections.
Article
Pharmacology & Pharmacy
Katharina Rox, Tim Becker, Andrea Schiefer, Miriam Grosse, Alexandra Ehrens, Rolf Jansen, Tilman Aden, Stefan Kehraus, Gabriele M. Koenig, Anna K. Krome, Marc P. Huebner, Karl G. Wagner, Marc Stadler, Kenneth Pfarr, Achim Hoerauf
Summary: Methicillin-resistant Staphylococcus aureus (MRSA) is a high priority pathogen organism, causing significant global mortality. The natural product CorA, currently in preclinical development, demonstrates effectiveness against MRSA in vitro. This study evaluates the pharmacokinetics and pharmacodynamics of CorA, suggesting its potential for MRSA and MSSA-related infections.
Article
Multidisciplinary Sciences
Andreas U. Mueller, James Chen, Mengyu Wu, Courtney Chiu, B. Tracy Nixon, Elizabeth A. Campbell, Seth A. Darst
Summary: Bacterial transcription initiation requires s factors to induce transcription bubble formation. The canonical s factor sigma(70) enables DNA melting and formation of the transcription bubble by recognizing conserved bases of the promoter -10 motif. However, the mechanism of transcription bubble formation and nucleation during sigma(N)-mediated transcription initiation is still poorly understood. This study shows that sigma(N) captures a flipped, unstacked base between its N-terminal region I (RI) and extra-long helix features, similar to sigma(70). The RI then inserts into the nascent bubble to stabilize it before engagement of the ATPase activator.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Editorial Material
Biochemistry & Molecular Biology
James Chen, Damian C. Ekiert
Summary: This paragraph describes a drug for treating multidrug-resistant tuberculosis, which targets the key enzyme ATP synthase in cellular respiration. A recent study shows that this drug, along with another inhibitor, prevents the enzymatic function by inhibiting the necessary rotational motions.
Article
Biochemistry & Molecular Biology
Gabriel I. Small, Olga Fedorova, Paul Dominic B. Olinares, Joshua Chandanani, Anoosha Banerjee, Young Joo Choi, Henrik Molina, Brian T. Chait, Seth A. Darst, Elizabeth A. Campbell
Summary: The enzymatic activities of the SARS-CoV-2 NiRAN domain, which are essential for viral propagation, have been further elucidated through high-resolution cryo-EM structures. These activities include NMPylation, RNAylation, and deRNAylation/capping reactions, with diverse nucleotide binding poses and metal ion coordination sites promoting their functioning. The structural platform provided by these findings enhances our understanding of this versatile viral domain and can aid drug development.
Article
Multidisciplinary Sciences
James Chen, Alice Fruhauf, Catherine Fan, Jackeline Ponce, Beatrix Ueberheide, Gira Bhabha, Damian C. Ekiert
Summary: To cause tuberculosis, Mycobacterium tuberculosis needs to obtain nutrients from the host cells. The MCE proteins, encoded by gene clusters, play a crucial role in the virulence of M. tuberculosis by transporting fatty acids and cholesterol across the impermeable mycobacterial cell envelope. This study reveals the cryo-EM structure of the Mce1 lipid-import machine in Mycobacterium smegmatis and provides insights into the mechanism of lipid transport across the mycobacterial cell envelope.
Article
Biochemistry & Molecular Biology
Leila T. Alexander, Janani Durairaj, Andriy Kryshtafovych, Luciano A. Abriata, Yusupha Bayo, Gira Bhabha, Cecile Breyton, Simon G. Caulton, James Chen, Seraphine Degroux, Damian C. Ekiert, Benedikte S. Erlandsen, Peter L. Freddolino, Dominic Gilzer, Chris Greening, Jonathan M. Grimes, Rhys Grinter, Manickam Gurusaran, Marcus D. Hartmann, Charlie J. Hitchman, Jeremy R. Keown, Ashleigh Kropp, Petri Kursula, Andrew L. Lovering, Bruno Lemaitre, Andrea Lia, Shiheng Liu, Maria Logotheti, Shuze Lu, Sigurbjorn Markusson, Mitchell D. Miller, George Minasov, Hartmut H. Niemann, Felipe Opazo, George N. N. Phillips Jr, Owen R. Davies, Samuel Rommelaere, Monica Rosas-Lemus, Pietro Roversi, Karla Satchell, Nathan Smith, Mark A. Wilson, Kuan-Lin Wu, Xian Xia, Han Xiao, Wenhua Zhang, Z. Hong Zhou, Krzysztof Fidelis, Maya Topf, John Moult, Torsten Schwede
Summary: We conducted a thorough analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identified and discussed key protein features and evaluated the accuracy of the submitted predictions. While the overall ability to predict protein structures is impressive, reproducing uncommon features remains challenging. The need for novel scoring strategies to emphasize biologically relevant structural regions is highlighted, particularly when dealing with conformational flexibility and large multimeric complexes. Integration of computational and experimental techniques will play a crucial role in unraveling future challenges in structural molecular biology.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
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)