Review
Biochemistry & Molecular Biology
Paul R. Copeland, Michael T. Howard
Summary: This passage discusses the decoding of genetic information into polypeptides during translation, as well as the reassignment of UGA codons in selenoprotein mRNAs to encode for selenocysteine. It also examines the fate of ribosomes that fail to incorporate selenocysteine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Towako Taguchi, Morito Kurata, Iichiroh Onishi, Yuko Kinowako, Yunosuke Sato, Sayuri Shiono, Sachiko Ishibashi, Masumi Ikeda, Masahide Yamamoto, Masanobu Kitagawa, Kouhei Yamamoto
Summary: SECISBP2 overexpression is associated with poor prognosis in diffuse large B-cell lymphoma, potentially through downregulation of selenoproteins and increased oxidative stress. The interaction between SECISBP2 and GPX4 may play a critical role in mediating cell death in malignant lymphoma.
LABORATORY INVESTIGATION
(2021)
Review
Virology
John F. Atkins, Kate M. O'Connor, Pramod R. Bhatt, Gary Loughran
Summary: Many viruses use recoding strategies to increase coding capacity and generate protein products with different functions; sacrificing accuracy for speed in viral expression can create opportunities for host immune defense; some viruses utilize recoding to evade immune responses or specific drugs.
Article
Microbiology
Adair L. Borges, Yue Clare Lou, Rohan Sachdeva, Basem Al-Shayeb, Petar Penev, Alexander L. Jaffe, Shufei Lei, Joanne M. Santini, Jillian F. Banfield
Summary: Computational analyses have revealed widespread recoding in gut phages, which is believed to control the timing of lysis. This study found that stop-codon recoding has evolved in diverse clades of phages that infect both human and animal gut microbiota. The recoded stop codons are over-represented in phage structural and lysis genes, suggesting that they might prevent premature protein production.
NATURE MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Laure Bidou, Olivier Bugaud, Goulven Merer, Matthieu Coupet, Isabelle Hatin, Egor Chirkin, Sabrina Karri, Stephane Demais, Pauline Francois, Jean-Christophe Cintrat, Olivier Namy
Summary: In this study, a new drug was developed and evaluated for its clinical potential in treating genetic diseases caused by premature termination codons (PTCs). The drug, TLN468, was found to be more effective than the currently used gentamicin and acted on a broader range of sequences without affecting normal stop codon readthrough.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Olga A. Postnikova, Sheetal Uppal, Weiliang Huang, Maureen A. Kane, Rafael Villasmil, Igor B. Rogozin, Eugenia Poliakov, T. Michael Redmond
Summary: The SARS-CoV-2 Spike glycoprotein has acquired a unique insert sequence that could affect virus spread and infection mechanisms, prompting further investigation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Anamika Avni, Ashish Joshi, Anuja Walimbe, Swastik G. Pattanashetty, Samrat Mukhopadhyay
Summary: The authors introduced a unique single-droplet surface-enhanced Raman scattering (SERS) methodology to investigate molecular information within the mesoscopic liquid condensed phase. This study sheds light on the formation and regulation mechanism of biomolecular condensates. The highly sensitive measurements enable the capture of crucial interactions, conformational heterogeneity, and structural distributions.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Eva Kummer, Katharina Noel Schubert, Tanja Schoenhut, Alain Scaiola, Nenad Ban
Summary: The mitochondrial translation system, derived from a bacterial ancestor, has diverged significantly during evolution. Using single-particle cryo-electron microscopy, researchers identified mitochondrial translation termination mechanisms in molecular detail. Mitochondrial release factor 1a and peptidyl-tRNA hydrolase ICT1 play crucial roles in mitochondrial protein synthesis.
Article
Biochemical Research Methods
Stefanie Muhlhausen, Laurence D. Hurst
Summary: Transgene-design is a web application that assists in designing transgenes for mammalian studies. It utilizes the discovery that transgenes without introns and native retrogenes can be highly expressed if the GC content at exonic synonymous sites is high. The application allows for the manipulation of exonic splice enhancers and the option to retain the first intron and protect or avoid specific motifs.
Article
Biochemistry & Molecular Biology
Soumyanetra Chandra, Kritika Gupta, Shruti Khare, Pehu Kohli, Aparna Asok, Sonali Vishwa Mohan, Harsha Gowda, Raghavan Varadarajan
Summary: Deep mutational scanning studies suggest that genes in an operonic context are more sensitive to both synonymous and nonsynonymous point mutations than previously inferred.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Genetics & Heredity
Rachel McNamar, Katrina Rothblum, Lawrence Rothblum
Summary: Pol I is responsible for transcribing ribosomal DNA genes in eukaryotes, and abnormalities in its activity are linked to cancer and genetic diseases. Studies show differences in Pol I transcription between yeast and mammals, which may affect the function and regulation of PAFs.
Article
Cell Biology
Yoshitaka Matsuo, Toshifumi Inada
Summary: The study finds that Hel2 preferentially binds to pre-engaged secretory ribosome-nascent chain complexes, especially under signal recognition particle (SRP) deficient conditions. Deletion of Hel2 exacerbates mitochondrial defects caused by insufficient SRP, leading to mistargeting of secretory proteins into mitochondria. These insights shed light on risk management in the secretory pathway for maintaining cellular protein homeostasis.
Article
Biochemistry & Molecular Biology
David E. Wright, Tarana Siddika, Ilka U. Heinemann, Patrick O'Donoghue
Summary: This study developed a new mammalian cell-based model to investigate TrxR1 activity. By combining genetically encoded selenocysteine and TAT peptide, efficient cellular uptake of TrxR1 was achieved, and its robust activity in live cells was demonstrated. This provides a novel platform to study TrxR1 biology in human cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Plant Sciences
Ricardo Colon, Michelle Wheater, Emily J. Joyce, Emma J. Ste Marie, Robert J. Hondal, Kathleen S. Rein
Summary: The research reveals that brevetoxins produced by Karenia brevis not only harm fish and wildlife, but may also play a role in the endogenous function of K. brevis. The most common brevetoxin, PbTx-2, also inhibits a key enzyme TrxR, affecting cellular redox homeostasis.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Cell Biology
Ahmad Jomaa, Simon Eitzinger, Zikun Zhu, Sowmya Chandrasekar, Kan Kobayashi, Shu-ou Shan, Nenad Ban
Summary: Protein targeting to membranes by the signal recognition particle (SRP) is a conserved pathway from bacteria to humans, but the mechanism in mammals is not well understood. Electron cryo-microscopy structures reveal specific molecular interactions between SRP, signal sequences, and the regulation of GTPase activity by SRP.SR in the early and late stages of protein targeting.
Article
Biochemical Research Methods
Nicole Dimos, Carl P. O. Helmer, Andrea M. Chanique, Markus C. Wahl, Robert Kourist, Tarek Hilal, Bernhard Loll
Summary: Enzyme catalysis is a crucial technology for developing efficient and sustainable processes. Plants provide diverse enzymes that facilitate complex reactions. Cryo-electron microscopy can reveal the structures of plant enzymes, providing a pathway for developing new biocatalysts.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Alexandra Bergfort, Marco Preussner, Benno Kuropka, Ibrahim Avsar Ilik, Tarek Hilal, Gert Weber, Christian Freund, Tugce Aktas, Florian Heyd, Markus C. Wahl
Summary: The intrinsically unstructured protein C9ORF78 interacts tightly with the spliceosome remodeling factor BRR2, and its knockout leads to changes in splice site usage and exon skipping, dependent on BRR2.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Sumangala P. Shetty, Nora T. Kiledjian, Paul R. Copeland
Summary: Selenoproteins contain selenocysteine and their mRNA 3'UTRs are not conserved, while the 3'UTR of a given selenoprotein is often conserved across species. We identified PTBP1 as a RNA binding protein that interacts specifically with the sequence between two SECIS elements. Deletion of regions surrounding the first SECIS element affects SELENOP mRNA and protein levels in response to selenium concentrations.
Article
Chemistry, Multidisciplinary
Philip Nickl, Tarek Hilal, Daniel Olal, Ievgen Sergeevitch Donskyi, Jorg Radnik, Kai Ludwig, Rainer Haag
Summary: This study presents a method for preparing a graphene-based modified support film to address the problem of protein adsorption at the air-water interface in cryoEM. The chemical modification of graphene sheets allows for the covalent anchoring of unmodified proteins, which improves particle orientations and prevents protein denaturation. The application of the modified support film in single particle analysis demonstrates its potential for high resolution structure determination.
Article
Biochemistry & Molecular Biology
Vu Thuy Khanh Le-Trilling, Sofia Banchenko, Darius Paydar, Pia Madeleine Leipe, Lukas Binting, Simon Lauer, Andrea Graziadei, Robin Klingen, Christine Gotthold, Joerg Buerger, Thilo Bracht, Barbara Sitek, Robert Jan Lebbink, Anna Malyshkina, Thorsten Mielke, Juri Rappsilber, Christian M. T. Spahn, Sebastian Voigt, Mirko Trilling, David Schwefel
Summary: This study revealed that rat cytomegalovirus infection induces the loss of transcription factor STAT2, which is crucial for antiviral interferon signaling. It was found that viral protein E27 exploits the host-cell CRL4 complexes to degrade STAT2 through poly-ubiquitylation. Furthermore, structural analyses showed that E27 recruits STAT2 through a bipartite binding interface, partially overlapping with the IRF9 binding site.
Article
Multidisciplinary Sciences
Bo Qin, Simon M. M. Lauer, Annika Balke, Carlos H. H. Vieira-Vieira, Jorg Buerger, Thorsten Mielke, Matthias Selbach, Patrick Scheerer, Christian M. T. Spahn, Rainer Nikolay
Summary: Ribosome biogenesis is a multi-step cellular process that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal proteins. By using a minimal in vitro reconstitution system, researchers studied the early assembly phase of the bacterial 50S subunit and found that it occurs in a domain-wise fashion, with late assembly proceeding incrementally. The study also showed that ribosomal proteins and folded rRNA helices induce or stabilize rRNA folds within adjacent regions, creating cooperativity.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Junqiao Jia, Tarek Hilal, Katherine E. Bohnsack, Aleksandar Chernev, Ning Tsao, Juliane Bethmann, Aruna Arumugam, Lane Parmely, Nicole Holton, Bernhard Loll, Nima Mosammaparast, Markus T. Bohnsack, Henning Urlaub, Markus C. Wahl
Summary: The study reveals that ASCC3, with the assistance of TRIP4 protein, can unwind DNA by threading one strand of the substrate duplex through both helicase units.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Julia Smirnova, Justus Loerke, Gunnar Kleinau, Andrea Schmidt, Joerg Buerger, Etienne H. Meyer, Thorsten Mielke, Patrick Scheerer, Ralph Bock, Christian M. T. Spahn, Reimo Zoschke
Summary: Translation in plant cells occurs in three compartments, and this study focuses on the structure of the 80S ribosomes in the cytosol. By using cryo-electron microscopy, the researchers solved the structure of translating tobacco ribosomes and gained insights into the molecular underpinnings of cytosolic translation in plants.