Article
Biotechnology & Applied Microbiology
Joss D. Leehan, Wayne L. Nicholson
Summary: RNA polymerase is an important machine for genetic information processing, and mutations in the rpoB gene in Bacillus subtilis can lead to changes in multiple phenotypes and rifampin resistance depending on the environment. Different rpoB alleles have different competitive advantages in different growth environments.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zhaozhu Lin, Fulin Wang, Zhuo Shang, Wei Lin
Summary: The delta subunit of bacterial RNA polymerase from low-G+C-content Gram-positive strains like Staphylococcus aureus is essential for transcription regulation. Through structural analyses and biochemical assays, interactions between the delta subunit and RNAP core enzyme as well as DNA were uncovered, shedding light on its unique regulatory role in transcription in Gram-positive bacteria.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Paula Clemente, Javier Calvo-Garrido, Sarah F. Pearce, Florian A. Schober, Megumi Shigematsu, Stefan J. Siira, Isabelle Laine, Henrik Spahr, Christian Steinmetzger, Katja Petzold, Yohei Kirino, Rolf Wibom, Oliver Rackham, Aleksandra Filipovska, Joanna Rorbach, Christoph Freyer, Anna Wredenberg
Summary: Using Drosophila and mouse models, this study demonstrates that non-canonical RNA processing in mammalian mitochondria results in the formation of 3' phosphates, which are hydrolyzed by the phosphatase activity of the carbon catabolite repressor 4 domain-containing family member ANGEL2. The findings also suggest the involvement of the FAST kinase domain-containing protein family in the generation of these 3' phosphates.
NATURE COMMUNICATIONS
(2022)
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
Biochemistry & Molecular Biology
Yuan Lou, Sarah A. Woodson
Summary: This study shows that self-cleavage of the glmS ribozyme riboswitch can occur during transcription before the ribozyme is fully synthesized. Co-transcriptional folding of the RNA allows the ribozyme catalytic core to react without the downstream stability domain. Slow sequential folding promotes the formation of the native core structure. Ribozyme self-cleavage at an early stage of transcription is important for the regulation of glmS in B. subtilis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Hannah Spitzer, Scott Berry, Mark Donoghoe, Lucas Pelkmans, Fabian J. Theis
Summary: CAMPA is a deep learning framework that learns representations of molecular pixel profiles from multiplexed images. It clusters these representations to quantify subcellular landmarks and captures interpretable cellular phenotypes. Using this framework, the study reveals the changes in subcellular organization upon perturbation of RNA synthesis, RNA processing, or cell size, and uncovers the links between the molecular composition of membraneless organelles and cell-to-cell variability in bulk RNA synthesis rates.
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
Biology
Jasmin van den Heuvel, Caroline Ashiono, Ludovic C. Gillet, Kerstin Dorner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay
Summary: In this study, it was found that the ribosomal protein eS30 is synthesized with the ubiquitin-like protein FUBI in human cells, but FUBI is cleaved off during ribosomal subunit maturation. Deubiquitinase USP36 was identified as an enzyme involved in FUBI-eS30 processing, demonstrating its functional importance in ribosomal subunit maturation and identifying a novel protease in the process.
Article
Cell Biology
Lin Wang, Mande Xue, Huairen Zhang, Lijun Ma, Danhua Jiang
Summary: Plant TONSOKU (TSK) and its animal ortholog TON-SOKU-like (TONSL) play a crucial role in maintaining chromatin stability during DNA replication. TSK interacts with histone modifiers and Polycomb proteins to preserve repressive chromatin modifications. TSK is specifically involved in a critical period of time following DNA replication to ensure the preservation of chromatin states.
Article
Multidisciplinary Sciences
Cedric Debes, Antonios Papadakis, Sebastian Groenke, Oezlem Karalay, Luke S. Tain, Athanasia Mizi, Shuhei Nakamura, Oliver Hahn, Carina Weigelt, Natasa Josipovic, Anne Zirkel, Isabell Brusius, Konstantinos Sofiadis, Mantha Lamprousi, Yu-Xuan Lu, Wenming Huang, Reza Esmaillie, Torsten Kubacki, Martin R. Spaeth, Bernhard Schermer, Thomas Benzing, Roman-Ulrich Mueller, Adam Antebi, Linda Partridge, Argyris Papantonis, Andreas Beyer
Summary: During ageing, impairment of cellular processes such as transcription and RNA splicing compromises physiological homeostasis. This study reveals that transcriptional elongation speed and RNA splicing are correlated with age across different species, and lifespan-extending interventions can reverse these changes. These findings uncover fundamental molecular mechanisms underlying animal ageing and lifespan extension.
Article
Multidisciplinary Sciences
Mahmoud M. Elguindy, Joshua T. Mendell
Summary: Liquid-liquid phase separation is a key mechanism through which long noncoding RNA controls RNA-binding proteins and maintains genomic stability in mammalian cells. The study shows that RNA-driven phase separation competitively sequesters RNA-binding proteins by nucleating the formation of phase-separated condensates, influencing RBP activity and genome maintenance. The repetitive sequence architecture of lncRNAs suggests that phase separation may be a widely used mechanism of lncRNA-mediated regulation.
Article
Multidisciplinary Sciences
Carlo Yague-Sanz, Valerie Migeot, Marc Larochelle, Francois Bachand, Maxime Wery, Antonin Morillon, Damien Hermand
Summary: Transcription of RNA polymerase II is coupled with remodeling of chromatin, and this study reveals that transcription of RNA polymerase II is also required to maintain nucleosome depletion at RNA polymerase III loci. The mechanism involves the involvement of the Pcr1 transcription factor, which affects local histone occupancy through the associated SAGA complex and a Pol II phospho-S2 CTD / Mst2 pathway. These findings expand our understanding of the role of RNA polymerase II in gene expression.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Izabela Rudzinska, Malgorzata Ciesla, Tomasz W. Turowski, Alicja Armatowska, Ewa Lesniewska, Magdalena Boguta
Summary: The study showed that the rpc128-1007 mutant disrupts Pol III assembly, affecting mRNA expression levels, particularly through modulation of the general transcription factor Gcn4. Additionally, regardless of suppressor genes, the rpc128-1007 mutation leads to a slight increase in the expression of ribosome biogenesis genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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)
Review
Multidisciplinary Sciences
Jana Wiedermannova, Christina Julius, Yulia Yuzenkova
Summary: Recent discoveries have shown the existence of diverse non-canonical 5'-end RNA cap-like modifications in prokaryotes and eukaryotes, including metabolic cofactors and cell wall precursors, installed by specific enzymes. The emerging variety of capping molecules and enzymes reveals an unrecognized level of complexity in RNA metabolism.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Review
Chemistry, Multidisciplinary
Aldo R. Camacho-Zarco, Vincent Schnapka, Serafima Guseva, Anton Abyzov, Wiktor Adamski, Sigrid Milles, Malene Ringkjobing Jensen, Lukas Zidek, Nicola Salvi, Martin Blackledge
Summary: This review introduces the applications of nuclear magnetic resonance (NMR) in understanding the structure, dynamic behavior, and interaction trajectories of intrinsically disordered proteins. NMR provides ensemble averaged structural and dynamic parameters for each assigned resonance, revealing the importance of these parameters in the kinetics and thermodynamics of cellular and extracellular reactions. Furthermore, NMR can uncover the mechanistic basis of functional disordered molecular assemblies that are crucial for human health.
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
Biochemistry & Molecular Biology
Jitka Plucarova, Severine Jansen, Subhash Narasimhan, Alice Lanikova, Marc Lewitzky, Stephan M. Feller, Lukas Zidek
Summary: This study used NMR spectroscopy to investigate the phosphorylation kinetics of MAP2c and discovered important phosphorylation sites. Comparison with phosphorylation of other proteins revealed differences in phosphorylation profiles of MAP2c and Tau, providing insights into their specific biological functions. Furthermore, the study elucidated the effect of ERK2 phosphorylation on the binding of MAP2c with other proteins.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
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)
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)
Review
Chemistry, Multidisciplinary
Aldo R. Camacho-Zarco, Vincent Schnapka, Serafima Guseva, Anton Abyzov, Wiktor Adamski, Sigrid Milles, Malene Ringkjobing Jensen, Lukas Zidek, Nicola Salvi, Martin Blackledge
Summary: Intrinsically disordered proteins play essential roles in cellular and extracellular biochemistry. Nuclear magnetic resonance is a powerful tool for studying their structural and dynamic behavior, providing insights into reaction kinetics and thermodynamics essential for function. Recent applications of NMR have helped uncover the mechanistic basis of functional disordered molecular assemblies important for human health.