Article
Biochemistry & Molecular Biology
Dustin Niblett, Charlotte Nelson, Calvin S. Leung, Gillian Rexroad, Jake Cozy, Jie Zhou, Laura Lancaster, Harry F. Noller
Summary: Recent studies have shown that the ribosome complex undergoes partial translocation without elongation factor EF-G can disrupt codon-anticodon pairing, leading to frame slippage, implicating EF-G in maintaining translational reading frame. Mutations in EF-G, particularly in domain IV, were found to increase -1 frameshifting during protein synthesis, slow down mRNA translocation rates, and inhibit rotational movement of the 30S ribosomal subunit. These interactions with the translocating tRNA backbone may help EF-G prevent uncoupled tRNA movement and stabilize the anticodon conformation for better base-pairing with the codon.
Article
Biochemistry & Molecular Biology
Ananya Das, Chen Bao, Dmitri N. Ermolenko
Summary: In this study, two independent FRET assays were used to confirm that pre-translocation ribosomes without EF-G can undergo spontaneous intersubunit rotations between non-rotated and rotated conformations. The fraction of spontaneously fluctuating molecules changes depending on experimental conditions, highlighting the importance of using multiple FRET assays in studies of ribosome dynamics and emphasizing the role of thermally-driven large-scale ribosome rearrangements in translation.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Maximiliane Wieland, Mikael Holm, Emily J. Rundlet, Martino Morici, Timm O. Koller, Tinashe P. Maviza, Domen Pogorevc, Ilya A. Osterman, Rolf Muller, Scott C. Blanchard, Daniel N. Wilson
Summary: In this study, the inhibition mechanism of ArgB on EF-G was investigated using cryo-EM and smFRET techniques. It was found that ArgB inhibits intermediate steps of the translocation mechanism by binding specifically to EF-G on the ribosome without interfering with ribosome binding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Riccardo Belardinelli, Heena Sharma, Frank Peske, Marina Rodnina
Summary: This study demonstrates how translocation inhibitors affect the principal motions of the small ribosomal subunits during EF-G-promoted translocation. The antibiotics mainly inhibit backward movements of the SSU body and/or the head domains, with some completely inhibiting these movements. These findings highlight the importance of ribosome dynamics in tRNA-mRNA translocation and provide insights into antibiotic mechanisms.
Article
Biochemistry & Molecular Biology
Wataru Nishima, Dylan Girodat, Mikael Holm, Emily J. Rundlet, Jose L. Alejo, Kara Fischer, Scott C. Blanchard, Karissa Y. Sanbonmatsu
Summary: This study combines molecular simulations with single-molecule fluorescence resonance energy transfer imaging to uncover the key steps of ribosome completion and resetting during translocation. Diffusive motions of the ribosomal small subunit head domain and the role of ribosomal RNA enable mRNA and tRNA to achieve full translocation, while the engagement of peptidyl-tRNA and disengagement of deacyl-tRNA facilitate the ribosome resetting mechanism.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jing Wang, Yuka Yashiro, Yuriko Sakaguchi, Tsutomu Suzuki, Kozo Tomita
Summary: CdiA-CTEC869 cleaves specific tRNAs by interacting with translation factors Tu and Ts, and interacts with domain II of Tu to affect the structure and cleavage efficiency of tRNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Christine E. Carbone, Anna B. Loveland, Howard B. Gamper, Ya-Ming Hou, Gabriel Demo, Andrei A. Korostelev
Summary: This study visualized the structures of ribosome-EF-G intermediates at near-atomic resolution using time-resolved cryo-EM, revealing how EF-G rectifies ribosomal dynamics into tRNA-mRNA translocation. The mechanism of EF-G in translocating tRNA and mRNA through the ribosome involves a combination of motor- and pawl-like mechanisms, with GTP hydrolysis and Pi release driving EF-G dissociation.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Panagiotis Poulis, Anoshi Patel, Marina V. Rodnina, Sarah Adio
Summary: Slippery sequences in mRNA can cause the ribosome to change its reading frame, affecting the translation process. Research has shown that during translocation on slippery sequences, the ribosome switches from a fast and accurate translation mode to a slow and frameshifting-prone mode, reducing translation fidelity.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Asem Hassan, Sandra Byju, Frederico Campos Freitas, Claude Roc, Nisaa Pender, Kien Nguyen, Evelyn M. Kimbrough, Jacob M. Mattingly, Ruben L. Gonzalez, Ronaldo Junio de Oliveira, Christine M. Dunham, Paul C. Whitford
Summary: Protein synthesis requires large-scale rearrangements of the ribosome. By analyzing the RCSB PDB database, we describe the structures of ribosome complexes and subunits from various species. We found universal and organism/domain-specific aspects of subunit rearrangements. This study provides a foundation for further research on the dynamics of this molecular machine.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Changil Kim, Mikael Holm, Chandra Sekhar Mandava, Suparna Sanyal
Summary: This study optimized a popular fluorescent-mRNA based translocation assay for studying ribosomal translocation kinetics and found that a 10-base fluorescently labelled mRNA is best suited for the assay. Comparisons between a commonly used peptidyl tRNA analog and a natural dipeptidyl tRNA showed that the analog translocates slower and produces biphasic kinetics.
Article
Multidisciplinary Sciences
Chen Bao, Mingyi Zhu, Inna Nykonchuk, Hironao Wakabayashi, David H. Mathews, Dmitri N. Ermolenko
Summary: This study demonstrates that specific length and structure, rather than high thermodynamic stability, are crucial for regulatory mRNA stem-loops to pause translation. These findings provide insights into the identification of new regulatory mRNA stem-loops.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Qiongzheng Hu, Haina Jia, Yuhong Wang, Shoujun Xu
Summary: This paper reports a method for determining the functional positions of nucleic acids using mechanical force with single-nucleotide resolution. The method overcomes the variations in analyte concentration and buffer conditions commonly encountered in biological settings. Two examples are provided to validate the effectiveness of the method.
Article
Biochemistry & Molecular Biology
Soneya Majumdar, Andrew Emmerich, Sascha Krakovka, Chandra Sekhar Mandava, Staffan G. Svard, Suparna Sanyal
Summary: Using cryo-electron microscopy, we have determined high-resolution structures of six translocation intermediates from Giardia ribosomes. These ribosomes possess eukaryotic rRNAs and proteins, but also retain some bacterial features. The study elucidates the mechanism of translocation in protists and sheds light on the evolution of translation machinery.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Shijie Huang, Arpan Bhattacharya, Mikel D. Ghelfi, Hong Li, Clark Fritsch, David M. Chenoweth, Yale E. Goldman, Barry S. Cooperman
Summary: This study identifies the binding sites of the translation readthrough inducing drug (TRID) ataluren on the ribosome, and reveals how it inhibits termination at nonsense codons.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
En Li, Jin-Xin Hu, Xuemeng Feng, Zishu Zhou, Liheng An, Kam Tuen Law, Ning Wang, Nian Lin
Summary: The authors demonstrate the emergence of multiple ultra-flat electronic bands in twisted bilayer WSe2 using scanning tunneling microscopy and spectroscopy, indicating the potential for further study of exotic correlated phases in TB-TMDs.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Albena Draycheva, Sejeong Lee, Wolfgang Wintermeyer
SCIENTIFIC REPORTS
(2018)
Article
Biology
Sarah Adio, Heena Sharma, Tamara Senyushkina, Prajwal Karki, Cristina Maracci, Ingo Wohlgemuth, Wolf Holtkamp, Frank Peske, Marina V. Rodnina
Article
Chemistry, Organic
Mehdi Zaghouani, Lena A. K. Boegeholz, Evan Mercier, Wolfgang Wintermeyer, Stephane P. Roche
Review
Biochemistry & Molecular Biology
Marina V. Rodnina, Frank Peske, Bee-Zen Peng, Riccardo Belardinelli, Wolfgang Wintermeyer
BIOLOGICAL CHEMISTRY
(2020)
Review
Biochemistry & Molecular Biology
Marija Liutkute, Ekaterina Samatova, Marina V. Rodnina
Article
Biochemistry & Molecular Biology
Evan Mercier, Wolfgang Wintermeyer, Marina Rodnina
Article
Multidisciplinary Sciences
Ka Man Yip, Niels Fischer, Elham Paknia, Ashwin Chari, Holger Stark
Article
Multidisciplinary Sciences
Kai-Hsin Chan, Valentyn Petrychenko, Claudia Mueller, Cristina Maracci, Wolf Holtkamp, Daniel N. Wilson, Niels Fischer, Marina V. Rodnina
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Evan Mercier, Xiaolin Wang, Manisankar Maiti, Wolfgang Wintermeyer, Marina Rodnina
Summary: The study reveals that during the synthesis of membrane proteins, the lateral gate fluctuations are highly dynamic, continuously sampling between open and closed states even without ligands. Ribosome binding and transmembrane segment insertion do not stop the gate fluctuations but tend to increase sampling of the open state. Binding of YidC facilitates substantial opening of the gate, aiding in the folding of YidC-dependent polytopic membrane proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Sung-Hui Yi, Valentyn Petrychenko, Jan Erik Schliep, Akanksha Goyal, Andreas Linden, Ashwin Chari, Henning Urlaub, Holger Stark, Marina Rodnina, Sarah Adio, Niels Fischer
Summary: This study reveals key intermediates during translation initiation in human cells using cryo-EM structures and kinetic methods. The results show the formation of two distinct ribosome populations, representing stages before and after codon recognition in the presence of specific initiation factors. The study also highlights differences in the start codon selection mechanism between humans and yeast.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Panagiotis Poulis, Anoshi Patel, Marina V. Rodnina, Sarah Adio
Summary: Slippery sequences in mRNA can cause the ribosome to change its reading frame, affecting the translation process. Research has shown that during translocation on slippery sequences, the ribosome switches from a fast and accurate translation mode to a slow and frameshifting-prone mode, reducing translation fidelity.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Marieke Enders, Ralf Ficner, Sarah Adio
Summary: The DEAH/RHA helicase Prp43 plays an important role in RNA splicing and ribosome biogenesis. Using single-molecule Forster Resonance Energy Transfer (smFRET) technology, we discovered that the RecA domains in Prp43 undergo conformational changes during catalysis, and Pfa1(gp) can induce alternating between open and closed states. Additionally, Pfa1(gp) enables Prp43 to switch between RNA-bound and RNA-unbound states, instead of dissociating from the RNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Marieke Enders, Ralf Ficner, Sarah Adio
Summary: The DEAH-box helicase Prp43 plays a crucial role in pre-mRNA splicing and ribosome biogenesis by remodeling structured RNAs. It is activated by G-patch (gp) factors in the presence of ATP, which enhances its ATPase and RNA unwinding activity. However, the mechanism of RNA loading and the regulation by its substrates and G-patch partners remain unclear.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Valentyn Petrychenko, Bee-Zen Peng, Ana C. de A. P. Schwarzer, Frank Peske, Marina V. Rodnina, Niels Fischer
Summary: In this study, the researchers visualized the mechanism of EF-G in the ribosome translocation process using time-resolved cryo-EM, revealing the crucial role of GTP hydrolysis in promoting the movement of the ribosome along mRNA.
NATURE COMMUNICATIONS
(2021)