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
Dermatology
Angelique N. Voorberg, Hanna Niehues, Jart A. F. Oosterhaven, Geertruida L. E. Romeijn, Ivonne M. J. J. Vlijmen-Willems, Piet E. J. Erp, Thomas H. A. Ederveen, Patrick L. J. M. Zeeuwen, Marie L. A. Schuttelaar
Summary: Hand eczema is a common inflammatory skin condition of the hands with unknown pathogenesis. Through RNA-sequencing analysis, this study found significantly elevated expression of genes/proteins related to keratinocyte host defense and inflammation in lesional skin of patients with vesicular hand eczema.
EXPERIMENTAL DERMATOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Qianmin Wang, Ming Lei, Jian Wu
Summary: RNA polymerase III (Pol III) is a complex protein complex that plays an important role in producing various short non-coding RNAs in all eukaryotes. Recent advances in cryogenic electron microscopy have allowed us to gain insights into the structure of human Pol III.
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
Biochemistry & Molecular Biology
Qianqian Wang, Xueliang Lyu, Jiasen Cheng, Yanping Fu, Yang Lin, Assane Hamidou Abdoulaye, Daohong Jiang, Jiatao Xie
Summary: This study analyzed the codon usage patterns of mycoviruses that infect plant pathogenic fungi. The results showed that mycoviral codon usage is influenced by natural selection and similar to that of host genes, indicating that CUB is a potential evolutionary mechanism for mycoviruses to adapt to their hosts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Gianluca Prezza, Daniel Ryan, Gohar Maedler, Sarah Reichardt, Lars Barquist, Alexander J. Westermann
Summary: This study investigates the functional roles of noncoding RNA in gut bacteria through comparative genomics, focusing on Bacteroides thetaiotaomicron as a representative member. While technical hurdles hinder analogous analyses in anaerobic gut microbiota, computational tools and comparative genomics can provide insight into RNA biology. The research demonstrates the power of RNA informatics in studying anaerobic microbiota members.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Qianmin Wang, Shaobai Li, Futang Wan, Youwei Xu, Zhenfang Wu, Mi Cao, Pengfei Lan, Ming Lei, Jian Wu
Summary: The study provides insights into the structure of human Pol III in different states, highlighting the important roles of RPC7 and RPC10 subunits in Pol III transcription, and offers a comprehensive understanding of the regulation mechanism of Pol III transcription.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zhijun Wang, Yanjun Li, Qianhao Zhu, Liwen Tian, Feng Liu, Xinyu Zhang, Jie Sun
Summary: In this study, the molecular mechanisms underlying the varietal difference in Mepiquat chloride (MC) sensitivity in cotton plants were investigated using transcriptome analysis. The results revealed that signal transduction of phytohormones, biosynthesis of gibberellins (GAs) and brassinosteroids (BRs), and profiles of transcription factors (TFs) were differentially affected by MC in the two cotton varieties. These findings indicate that although the same or similar biological pathways are influenced by MC treatment in cotton plants, the extent of effect varies, leading to different phenotypic outcomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Masahiko Okuda, Toru Ekimoto, Jun-ichi Kurita, Mitsunori Ikeguchi, Yoshifumi Nishimura
Summary: TFIIH is a crucial factor in transcription and DNA repair, with the p62 subunit containing a flexible PH-D domain that plays a key role in TFIIH localization and function. By establishing the solution structure of p62 PH-D and modeling its dynamic position in TFIIH, researchers have gained insights into the interaction mechanism between TFIIH and its binding partners. The study also showed that the binding partners use their intrinsically disordered acidic regions for TFIIH recruitment, providing a deeper understanding of the molecular mechanisms involved.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Wolfram Seifert-Davila, Mathias Girbig, Luis Hauptmann, Thomas Hoffmann, Sebastian Eustermann, Christoph W. Mueller
Summary: Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to target genes by recognizing intragenic A- and B-box motifs. Cryo-electron microscopy structures revealed that the tau B module of TFIIIC recognizes the B-box through DNA shape and sequence readout. TFIIIC220 acts as a linker connecting the tau A and tau B subcomplexes, facilitating scanning for A-boxes and Pol III activation by TFIIIB.
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
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
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
Multidisciplinary Sciences
Pietro Fontana, Sara C. Buch-Larsen, Osamu Suyari, Rebecca Smith, Marcin J. Suskiewicz, Kira Schutzenhofer, Antonio Ariza, Johannes Gregor Matthias Rack, Michael L. Nielsen, Ivan Ahel
Summary: ADP-ribosylation signalling plays a crucial role in the DNA damage response of mammals, and its mechanism in fruit flies has been established using a multidisciplinary approach. Ser-ADPr is the major form of ADP-ribosylation in the DNA damage response of Drosophila melanogaster, and its formation depends on the dParp1:dHpf1 complex. The findings suggest that fruit flies are valuable model organisms to study the physiological role of Ser-ADPr signalling.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Emmanuel Compe, Jean-Marc Egly
Summary: In eukaryotes, transcription of protein-coding genes requires the assembly of a preinitiation machinery at core promoters containing RNAPII and GTFs. Transcription is enhanced by regulatory elements called enhancers, recognized by specific DNA-binding transcription factors. Understanding the transcription initiation mechanism has benefited from the study of altered transcription components associated with human diseases.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
Correction
Ecology
Nicolas Gallois, Beatrice Alpha-Bazin, Nicolas Bremond, Philippe Ortet, Mohamed Barakat, Laurie Piette, Abbas Mohamad Ali, David Lemaire, Pierre Legrand, Nicolas Theodorakopoulos, Magali Floriani, Laureline Fevrier, Christophe Den Auwer, Pascal Arnoux, Catherine Berthomieu, Jean Armengaud, Virginie Chapon
Article
Multidisciplinary Sciences
Cameron D. Fyfe, Noelia Bernardo-Garcia, Laura Fradale, Stephane Grimaldi, Alain Guillot, Clemence Brewee, Leonard M. G. Chavas, Pierre Legrand, Alhosna Benjdia, Olivier Berteau
Summary: Methyl-coenzyme M reductase plays a central role in regulating global methane levels. The study of Methanosarcina acetivorans' Mmp10 provides insights into its unique enzyme structure and catalytic control mechanism, as well as the structural changes prior to catalysis. This research is important for understanding the catalytic mechanism of the emerging superfamily of B-12-dependent radical SAM enzymes.
Article
Multidisciplinary Sciences
Laura Pieri, Fengbin Wang, Ana-Andreea Arteni, Matthijn Vos, Jean-Marie Winter, Marie-Helene Le Du, Franck Artzner, Frederic Gobeaux, Pierre Legrand, Yves Boulard, Stephane Bressanelli, Edward H. Egelman, Maite Paternostre
Summary: Functional nano- and microassemblies formed by biological molecules can be found at all levels of life, with Lanreotide being one of the best characterized synthetic peptides forming well-defined nanostructures. The atomic structure of Lanreotide nanotubes, determined through cryoelectron microscopy, revealed surprising differences compared to the molecular model. This work highlights the challenge of predicting higher-order assemblies formed by even well-characterized small peptides.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Medicine, Research & Experimental
Justyna Ciolek, Claude Zoukimian, Justine Dhot, Melanie Burban, Mathilde Triquigneaux, Benjamin Lauzier, Christelle Guimbert, Didier Boturyn, Marine Ferron, Lidia Ciccone, Livia Tepshi, Enrico Stura, Pierre Legrand, Philippe Robin, Gilles Mourier, Beatrice Schaack, Imen Fellah, Guillaume Blanchet, Chantal Gauthier-Erfanian, Remy Beroud, Denis Servent, Michel De Waard, Nicolas Gilles
Summary: This study identified a selective M2R ligand, MT9, from mamba snake venom and investigated its contribution to arterial contractions. MT9 exhibited a 100 times stronger affinity for M2R compared to other muscarinic receptors, and antagonized the M2R/Gi pathways in cell tests. It also acted as a non-competitive antagonist with low nM potency against acetylcholine or arecaine in isolated arteries.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Audrey Lavielle, Fabien Boux, Justine Deborne, Noel Pinaud, Sandrine Dufort, Camille Verry, Sylvie Grand, Irene Tropres, Clement Vecco-Garda, Geraldine Le Duc, Stephane Mornet, Yannick Cremillieux
Summary: This study aims to generate T1 maps from MR images using the MPRAGE sequence and evaluate its feasibility in phantoms, animal models, and patients with brain metastases. The results demonstrate that the MPRAGE sequence can be used as a method to measure the concentration of Gd-based theranostic agents within a standard clinical imaging protocol.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Biochemistry & Molecular Biology
Giovanna Cesaro, Heloisa Tramontin da Soler, Eloise Pavao Guerra-Slompo, Ahmed Haouz, Pierre Legrand, Nilson Ivo Tonin Zanchin, Beatriz Gomes Guimaraes
Summary: Rrp44/Dis3 is a conserved eukaryotic ribonuclease that plays a role in processing and degradation of almost all types of RNA. Depletion of Rrp44 in Trypanosoma brucei blocks maturation of ribosomal RNA, leading to disruption of ribosome synthesis and inhibition of cell proliferation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Claire Cargemel, Stephanie Marsin, Magali Noiray, Pierre Legrand, Halil Bounoua, Ines Li De la Sierra-Gallay, Helene Walbott, Sophie Quevillon-Cheruel
Summary: During bacterial genome replication initiation, replicative helicases rely on specialized proteins for their loading onto oriC. DnaC and DnaI were the first loaders to be characterized. However, many bacteria do not have these genes and instead have domesticated phage elements that have replaced the original loader gene dciA. A crystal structure study of the complex from Vibrio cholerae revealed that two VcDciA molecules interact with a dimer of VcDnaB without altering its canonical structure, providing insights into how DciA assists in DnaB loading. Surprisingly, DnaC from Escherichia coli also targets the same module on EcDnaB, suggesting functional interchangeability between VcDciA and EcDnaC despite their lack of structural similarity. This study represents a significant advancement in understanding the mechanism by which phage helicase loaders hijack bacterial replicative helicases during evolution.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Marco Vezzoli, Lara Isabel de Llobet Cucalon, Chiara Di Vona, Marco Morselli, Barbara Montanini, Susana de la Luna, Martin Teichmann, Giorgio Dieci, Roberto Ferrari
Summary: Regulation of histone acetylation plays a crucial role in gene expression patterns. The study uncovered a more complex picture of histone acetyltransferases (HATs) responsible for histone acetylation in hESCs. Specifically, p300 is only partially involved in acetylation of H3K18 and H3K27 in stem cells, while TFIIIC is associated with H3K18ac in stemness genes and is found near genes related to neuronal biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Dariusz Czernecki, Antonin Nourisson, Pierre Legrand, Marc Delarue
Summary: Family A DNA polymerases (PolAs) are important enzymes involved in DNA replication and repair. This study re-examines all available PolA sequences and classifies them into 19 major clusters. In addition to characterizing known subfamilies, this study identifies eight new subfamilies and analyzes their general characteristics, phylogenetic relationships, and conservation in sequence motifs. The study also uses AlphaFold2 to generate prediction models for clusters lacking experimentally determined structures and identifies new features in PolAs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Clement Madru, Markel Martinez-Carranza, Sebastien Laurent, Alessandra C. Alberti, Maelenn Chevreuil, Bertrand Raynal, Ahmed Haouz, Remy A. Le Meur, Marc Delarue, Ghislaine Henneke, Didier Flament, Mart Krupovic, Pierre Legrand, Ludovic Sauguet
Summary: Using an integrative approach, the authors characterized the structure of RPA in Archaea, revealing shared features with eukaryotes, as well as the formation of a tetrameric supercomplex in the absence of DNA. This supercomplex provides protection for ssDNA during replication. These findings contribute to our understanding of the evolution of replication factors in eukaryotes.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Ornella Bimai, Pierre Legrand, Jean-Luc Ravanat, Nadia Touati, Jingjing Zhou, Nisha He, Marine Lenon, Frederic Barras, Marc Fontecave, Beatrice Golinelli-Pimpaneau
Summary: Thiolation of uridine 34 in tRNAs is conserved in all three domains of life and is essential for accurate protein translation. The mechanism of U34-tRNA thiolation involves a [4Fe-4S] cluster, which is coordinated by conserved cysteine residues. The enzyme NcsA in archaea and the Ctu1/Ctu2 complex in eukaryotes play a crucial role in catalyzing U34-tRNA thiolation. The crystal structure of NcsA from Methanococcus maripaludis reveals the coordination of the [4Fe-4S] cluster and provides insights into the binding and activation of the sulfur donor.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Antonia Kefala Stavridi, Amandine Gontier, Vincent Morin, Philippe Frit, Virginie Ropars, Nadia Barboule, Carine Racca, Sagun Jonchhe, Michael J. Morten, Jessica Andreani, Alexey Rak, Pierre Legrand, Alexa Bourand-Plantefol, Steven W. Hardwick, Dimitri Y. Chirgadze, Paul Davey, Taiana Maia De Oliveira, Eli Rothenberg, Sebastien Britton, Patrick Calsou, Tom L. Blundell, Paloma F. Varela, Amanda K. Chaplin, Jean-Baptiste Charbonnier
Summary: This study reveals the molecular mechanism by which the interaction between the Ku70-Ku80 heterodimer and inositol-hexaphosphate (IP6) enhances the activity of classical Non-Homologous End Joining (c-NHEJ) pathway for DNA repair.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Organic
Jean Guillon, Solene Savrimoutou, Sandra Albenque-Rubio, Noel Pinaud, Nina Fillova, Stephane Moreau, Virginie Baylot, Vanessa Desplat
Summary: A new substituted pyrroloquinoxaline compound was designed, synthesized, and characterized in this study. The compound showed interesting cytotoxic potential against different human leukemia cell lines.
Article
Chemistry, Multidisciplinary
Marie E. Perrin, Bo Li, Johanne Mbianda, May Bakail, Christophe Andre, Gwenaelle Moal, Pierre Legrand, Virginie Ropars, Celine Douat, Francoise Ochsenbein, Gilles Guichard
Summary: In this study, we investigated the substitution of 4 α-residues with 3-urea segments in a short α-helical peptide known to bind ASF1. By analyzing the effects of different foldamer replacements, we discovered new binding modes for the peptide-urea chimeras with ASF1.
CHEMICAL COMMUNICATIONS
(2023)
Article
Endocrinology & Metabolism
Carole Fruchart Gaillard, Ali Ben Djoudi Ouadda, Lidia Ciccone, Emmanuelle Girard, Sepideh Mikaeeli, Alexandra Evagelidis, Mailys Le Devehat, Delia Susan-Resiga, Evelyne Cassar Lajeunesse, Herve Nozach, Oscar Henrique Pereira Ramos, Aurelien Thureau, Pierre Legrand, Annik Prat, Vincent Dive, Nabil G. Seidah
Summary: The liver-derived circulating PCSK9 accelerates the degradation of LDL receptor in endosomes/lysosomes. Inhibition or silencing of PCSK9 is used in clinics to reduce LDL-cholesterol, thereby reducing incidence of cardiovascular disease and possibly cancer/metastasis. The mechanism by which the PCSK9-LDLR complex is sorted to degradation compartments remains unclear. This study investigates the interaction of PCSK9 with nanobody P1.40 and CAP1 to uncover their role in regulating LDLR degradation.
MOLECULAR METABOLISM
(2023)