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
Rishi K. Vishwakarma, M. Zuhaib Qayyum, Paul Babitzke, Katsuhiko S. Murakami
Summary: NusG is a transcription elongation factor that induces transcription pausing in bacteria by interacting with a specific sequence in the non-template DNA strand. The interaction between NusG and the DNA rearranges the transcription bubble and affects the conformational changes of RNA polymerase, leading to the inhibition of RNA synthesis. This mechanism of pausing is widely conserved in bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(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
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
Multidisciplinary Sciences
Sandra Schilbach, Haibo Wang, Christian Dienemann, Patrick Cramer
Summary: This study presents an atomic model for the yeast preinitiation complex (PIC) with core mediator, revealing the molecular details of RNA polymerase II (Pol II) transcription initiation. The structure of the mediator middle module was optimized, and the missing subunit Med1 was identified. The study found that the flexible C-terminal repeat domain (CTD) of Pol II forms defined interactions with the mediator head and middle modules, as well as other regions of the mediator. The binding mode between the yeast mediator and Pol II differs from the human counterpart.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Liqiang Shen, Giorgio Lai, Linlin You, Jing Shi, Xiaoxian Wu, Maria Puiu, Zhanxi Gu, Yu Feng, Yulia Yuzenkova, Yu Zhang
Summary: This study presents the cryo-EM structures of cyanobacterial transcription initiation complexes, revealing the role of SI3-& sigma; arch interaction in transcription initiation of cyanobacteria. Disruption of this structure affects the growth and stress response of cyanobacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Qiang Lu, Taiyu Chen, Jiening Wang, Feng Wang, Wenlong Ye, Lixin Ma, Shan Wu
Summary: This study presents a cryo-EM structure of an RNA polymerase transcription complex containing a temperature-sensitive bacterial sigma factor, sigma(32) (sigma(32)-RPo). The structure reveals key interactions essential for the assembly of E. coli sigma(32)-RNAP holoenzyme and for promoter recognition and unwinding by sigma(32). These unique structural features advance our understanding of the mechanism of transcription initiation mediated by different sigma factors.
Article
Microbiology
Shuang Han, Zhen Gong, Tian Liang, Yu Chen, Jianping Xie
Summary: Mycobacterium tuberculosis (Mtb) is a pathogen causing tuberculosis, while Mfd, a bacterial DNA translocase, has functions in resolving transcription replication conflicts, mitigating bacterial damage, and promoting bacteria mutagenesis. There are widespread studies on Mfd in bacteria, but limited research has been done on Mtb.
MICROBIOLOGICAL RESEARCH
(2021)
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
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)
Review
Biochemistry & Molecular Biology
Matthew D. Gibbons, Yu Fang, Austin P. Spicola, Niko Linzer, Stephen M. Jones, Breanna R. Johnson, Lu Li, Mingyi Xie, Jorg Bungert
Summary: Enhancers in higher eukaryotes and upstream activating sequences (UASs) in yeast recruit components of the RNA polymerase II transcription machinery. Pol II recruited to enhancers in higher eukaryotes initiates transcription and generates enhancer RNA (eRNA), while UASs in yeast do not recruit the required transcription factor TFIIH. In both systems, Pol II is transferred from enhancers/UASs to promoters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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)
Article
Biochemistry & Molecular Biology
Sandra Schilbach, Shintaro Aibara, Christian Dienemann, Frauke Grabbe, Patrick Cramer
Summary: This study reveals the high-resolution structure of the transcription initiation complex and the mechanism of DNA opening, crucial for promoter-initiated transcription. TFIIE facilitates initiation by supporting the clamp head loop and regulating the TFIIH translocase.
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
Chemistry, Multidisciplinary
Aswathi Chakrapani, Olatz Ruiz-Larrabeiti, Radek Pohl, Martin Svoboda, Libor Krasny, Michal Hocek
Summary: This study investigates the effects of glucosylation on DNA containing modified bases and its impact on transcription activity in bacteriophages or kinetoplastid parasites. The results show that glucosylation fully protects DNA from restriction endonuclease cleavage and while glucosylated 5hmU inhibits transcription, glucosylated 5hmC allows similar levels of transcription as natural DNA. Therefore, enzymatic glucosylation of 5hmC-containing DNA can be used to modulate transcription activity.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Microbiology
Viola Vankova Hausnerova, Olga Marvalova, Michaela Sikova, Mahmoud Shoman, Jarmila Havelkova, Milada Kambova, Martina Janouskova, Dilip Kumar, Petr Halada, Marek Schwarz, Libor Krasny, Jarmila Hnilicova, Josef Panek
Summary: Bacteria use small non-coding RNAs to regulate gene expression. The study identified a specific RNA called Ms1 in Actinobacteria that binds to the core of RNA polymerase and affects its intracellular level. Through computational search and gene synteny approach, the study also found Ms1 RNA candidates in other Actinobacteria, demonstrating the widespread presence of Ms1 RNA as a class of RNAP binding sRNAs.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Simon Pospisil, Alessandro Panattoni, Filip Gracias, Veronika Sykorova, Viola Vankova Hausnerva, Dragana Vitovska, Hana Sanderova, Libor Krasny, Michal Hocek
Summary: By systematically studying five 2'-deoxyribonucleotide triphosphates (dNTPs) derived from epigenetic pyrimidines, it was found that these modified pyrimidine dNTPs can be incorporated into DNA by DNA polymerases. This incorporation of modified nucleotides into DNA could potentially lead to gene silencing and affect the replication of modified bacteriophage genomes.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Medicinal
Duy Dinh Do Pham, Viktor Mojr, Michaela Helusova, Gabriela Mikusova, Radek Pohl, Eva Davidova, Hana Sanderova, Dragana Vitovska, Katerina Bogdanova, Renata Vecerova, Miroslava Htoutou Sedlakova, Radovan Fiser, Petra Sudzinova, Jiri Pospisil, Oldrich Benada, Tomas Krizek, Adela Galandakova, Milan Kolar, Libor Krasny, Dominik Rejman
Summary: The novel antibacterial compounds LEGO-LPPOs were developed based on LPPOs, showing activity against various bacteria with low cytotoxicity and resistance development potential. This new class of compounds demonstrates efficacy against multiresistant strains and persisters, by depleting membrane potential and creating pores in the cytoplasmic membrane.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Cell Biology
Tomas Kouba, Anna Dubankova, Petra Drncova, Elisa Donati, Pietro Vidossich, Valentina Speranzini, Alex Pflug, Johanna Huchting, Chris Meier, Marco De Vivo, Stephen Cusack
Summary: The antiviral pseudo-base T705 and its de-fluoro analog T1106 can compete with adenine or guanine in viral RNA-dependent RNA polymerases. Single incorporation of these analogs is mutagenic, while consecutive incorporation causes polymerase stalling and chain termination. Cryogenic electron microscopy shows that the product-template duplex backtracks after consecutive T1106 incorporation, which sheds light on the mechanism of chain termination by pyrazinecarbox-amide base analogs.
Article
Biochemistry & Molecular Biology
David Tuzincin, Petr Padrta, Hana Sanderova, Alzbeta Rabatinova, Katerina Bendova, Libor Krasny, Lukas Zidek, Pavel Kaderavek
Summary: Sigma factors are essential components of bacterial RNA polymerase and play a crucial role in recognizing promoter sequences and initiating transcription. In this study, it was found that domain 1.1 of Bacillus subtilis sigma(A) exists in structurally distinct variants in equilibrium, and the population of a minor unfolded state increases with temperature. Functional experiments revealed that the full-length sigma(A) increases transcription activity with temperature, while the version lacking domain 1.1 shows constant activity.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Eliska Koutna, Vanda Lux, Tomas Kouba, Jana Skerlova, Jiri Novacek, Pavel Srb, Rozalie Hexnerova, Hana Svachova, Zdenek Kukacka, Petr Novak, Milan Fabry, Simon Poepsel, Vaclav Veverka
Summary: This study reports the ability of the PWWP domain of transcriptional coactivator LEDGF to bind to specific histone modifications and reveals the role of the intrinsically disordered region in nucleosome binding. The interplay between the H3K36 methylation reader and protein binding module of LEDGF facilitates productive transcription elongation.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Microbiology
Petra Sudzinova, Hana Sanderova, Tomas Koval, Tereza Skalova, Nabajyoti Borah, Jarmila Hnilicova, Tomas Kouba, Jan Dohnalek, Libor Krasny
Summary: Rifampicin, a clinically important antibiotic, can bind to and block the DNA/RNA channel of bacterial RNA polymerase. HelR proteins from high G+C Actinobacteria have been found to dissociate rifampicin-stalled RNA polymerases from DNA, providing rifampicin resistance. This discovery provides a blueprint for studying novel mechanisms of bacterial antibiotic resistance.
FEMS MICROBIOLOGY REVIEWS
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
M. Shoman, V. Vankova Hausnerova, L. Krasny, J. Hnilicova
Meeting Abstract
Biochemistry & Molecular Biology
B. Brezovska, M. Sikova, J. Hnilicova, H. Sanderova, S. Narasimhan, L. Zidek, L. Krasny
Article
Biochemistry & Molecular Biology
Filip Gracias, Olatz Ruiz-Larrabeiti, Viola Vankova Hausnerova, Radek Pohl, Blanka Klepetarova, Veronika Sykorova, Libor Krasny, Michal Hocek
Summary: Homologues of natural epigenetic pyrimidine nucleosides and nucleotides were synthesized and used as substrates for transcription, showing different effects on transcription efficiency.
RSC CHEMICAL BIOLOGY
(2022)