Article
Biochemical Research Methods
Artyom A. Egorov, Gemma C. Atkinson
Summary: This article presents a tool for annotating conserved uORFs, which can predict functional ORFs in the upstream sequences of a user-defined protein or a set of protein homologs. It generates publication-quality figures with multiple sequence alignments, sequence logos, and locus annotation of the predicted conserved uORFs in graphical vector format.
Article
Biology
Eriko Matsuura-Suzuki, Tadahiro Shimazu, Mari Takahashi, Kaoru Kotoshiba, Takehiro Suzuki, Kazuhiro Kashiwagi, Yoshihiro Sohtome, Mai Akakabe, Mikiko Sodeoka, Naoshi Dohmae, Takuhiro Ito, Yoichi Shinkai, Shintaro Iwasaki, Qing Zhang
Summary: In this study, it was discovered that human METTL18 acts as a histidine methyltransferase for the ribosomal protein RPL3. The methylation of RPL3 at His245 position slows ribosome traversal on Tyr codons, allowing proper protein folding and preventing cellular aggregation of Tyr-rich proteins.
Article
Multidisciplinary Sciences
Yan Zhang, Nikolay A. Aleksashin, Dorota Klepacki, Caleb Anderson, Nora Vazquez-Laslop, Carol A. Gross, Alexander S. Mankin
Summary: Kasugamycin (KSG) is a small ribosomal subunit-targeting antibiotic that interferes with translation in different stages. It inhibits protein synthesis by blocking the binding of canonical messenger RNA (mRNA) and initiator transfer RNA (tRNA) to the small ribosomal subunit. Even after the formation of the 70S initiation complex, KSG can still interfere with translation to a certain extent. However, it does not completely abolish translation and allows for the expression of certain proteins. The effectiveness of KSG depends on the nature of the mRNA residue preceding the start codon and is attenuated by translational coupling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Zachary D. Aron, Atousa Mehrani, Eric D. Hoffer, Kristie L. Connolly, Pooja Srinivas, Matthew C. Torhan, John N. Alumasa, Mynthia Cabrera, Divya Hosangadi, Jay S. Barbor, Steven C. Cardinale, Steven M. Kwasny, Lucas R. Morin, Michelle M. Butler, Timothy J. Opperman, Terry L. Bowlin, Ann Jerse, Scott M. Stagg, Christine M. Dunham, Kenneth C. Keiler
Summary: Bacterial ribosome rescue pathways are potential antibiotic targets that selectively inhibit the main ribosome rescue pathway trans-translation. Optimization of pharmacokinetic and antibiotic properties of acylaminooxadiazoles produced MBX-4132, effective in clearing multi-drug resistant Neisseria gonorrhoeae infection in mice. Structural analyses reveal a new mechanism for specific inhibition of trans-translation and a novel conformation within the bacterial ribosome critical for ribosome rescue pathways.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Viswanathan Chandrasekaran, Nirupa Desai, Nicholas O. Burton, Hanting Yang, Jon Price, Eric A. Miska, V Ramakrishnan
Summary: This study elucidates the crucial role of GTPBP7 in the assembly of human mitochondrial ribosomes and highlights its interactions with RNA methyltransferase NSUN4 and MTERF4. Mutations disrupting the binding of their Caenorhabditis elegans orthologs activate mitochondrial stress response and induce gene expression changes related to mitochondrial protein synthesis.
Review
Biochemistry & Molecular Biology
Panagiotis Poulis, Frank Peske, Marina V. Rodnina
Summary: During translation elongation, the ribosome moves along the mRNA by a codon with the assistance of elongation factor G (EF-G). This process involves precise structural rearrangements and maintains the correct codon-wise step size. However, mRNA signals and environmental cues can alter the timing and dynamics of these rearrangements, leading to recoding and the production of trans-frame peptides. In this review, recent advances in the mechanics of translocation and reading frame maintenance are discussed, as well as the mechanisms and biological relevance of non-canonical translocation pathways and their relationship to disease and infection.
BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Madhurima Datta, Maalavika Pillai, Mamata Jayant Modak, Aivar Liiv, Faisal Tarique Khaja, Tanweer Hussain, Jaanus Remme, Umesh Varshney
Summary: The study demonstrates that the L48K mutation in uS12 leads to a cold-sensitive phenotype and ribosome biogenesis defect in E. coli, affecting initiation and elongation translation steps, and interacting genetically with RRF and Pth, revealing a novel role of the PNSA loop in ribosome recycling.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Madhurima Datta, Jitendra Singh, Mamata Jayant Modak, Maalavika Pillai, Umesh Varshney
Summary: The structure of the anticodon stem of initiator tRNA (i-tRNA) plays a crucial role in translation initiation, with specific GC base pairs affecting the accuracy of translation. Studies on gene mutations in Escherichia coli reveal that IF3 and uS12 are key players in i-tRNA selection and translation accuracy.
MOLECULAR MICROBIOLOGY
(2022)
Article
Virology
Chris H. Hill, Ian Brierley
Summary: Protein synthesis is a crucial process for gene expression, and programmed ribosomal frameshifting is a strategy used by RNA viruses to control the levels of viral proteins. Recent studies have revealed the structural diversity and complexity of this mechanism.
ANNUAL REVIEW OF VIROLOGY
(2023)
Editorial Material
Biology
Martina M. Yordanova, Pavel Baranov
Summary: The efficiency of ribosomes in shifting reading frames when decoding viral RNA may vary during an infection.
Article
Virology
Xinying Wang, Marli Vlok, Stephane Flibotte, Eric Jan
Summary: The study explores a novel viral translational mechanism, uncovering the IGR IRES sequence from ancient Northwest territories cripavirus dating back 700 years. The research demonstrates that aNCV IRES can bind to ribosomes and drive translation, supporting the historical significance of this viral translational mechanism.
Article
Virology
Sawsan Napthine, Chris H. Hill, Holly C. M. Nugent, Ian Brierley
Summary: The study demonstrates that SHFL can inhibit ribosomal frameshifting of various viruses in vitro, including coronaviruses and cardioviruses, by RNA binding activity.
Article
Biochemistry & Molecular Biology
Ka-Weng Ieong, Gabriele Indrisiunaite, Arjun Prabhakar, Joseph D. Puglisi, Mans Ehrenberg
Summary: The study revealed that m(6)A decreases the accuracy of reading sense and stop codons by reducing k(a) significantly more in cognate than near-cognate cases, leading to a significant increase in amino acid substitution errors in the process.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Yuzuru Itoh, Anas Khawaja, Ivan Laptev, Miriam Cipullo, Ilian Atanassov, Petr Sergiev, Joanna Rorbach, Alexey Amunts
Summary: This study reveals the sequential assembly mechanism of the small mitoribosomal subunit (SSU) using cryo-electron microscopy. The results demonstrate the role of auxiliary factors in promoting rRNA maturation and conformational changes, leading to the formation of the catalytic human mitoribosome.
Article
Microbiology
Eunna Choi, Yoontak Han, Shinae Park, Hyojeong Koo, Jung-Shin Lee, Eun-Jin Lee
Summary: Translation of the mgtQ ORF in Salmonella enhances the expression of the downstream MgtB Mg2+ transporter by releasing a translation-inhibitory structure, showing a unique mechanism of uORF-mediated gene regulation.
Article
Biochemistry & Molecular Biology
Annika Soderholm, Xiaohu Guo, Matilda S. Newton, Gary B. Evans, Joakim Nasvall, Wayne M. Patrick, Maria Selmer
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Cell Biology
Dan I. Andersson, Jon Jerlstrom-Hultqvist, Joakim Nasvall
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2015)
Article
Biochemical Research Methods
Yang Chen, Joakim Nasvall, Shiying Wu, Dan I. Andersson, Maria Selmer
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Anna Knoppel, Joakim Nasvall, Dan I. Andersson
MOLECULAR BIOLOGY AND EVOLUTION
(2016)
Article
Biochemistry & Molecular Biology
Joakim Nasvall, Anna Knoppel, Dan I. Andersson
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Erik Lundin, Po-Cheng Tang, Lionel Guy, Joakim Nasvall, Dan I. Andersson
MOLECULAR BIOLOGY AND EVOLUTION
(2018)
Article
Multidisciplinary Sciences
Matilda S. Newton, Xiaohu Guo, Annika Soderholm, Joakim Nasvall, Patrik Lundstrom, Dan I. Andersson, Maria Selmer, Wayne M. Patrick
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Biochemistry & Molecular Biology
Ana Laura Stern, Sander Egbert Van der Verren, Sandesh P. Kanchugal, Joakim Nasvall, Hugo Gutierrez-de-Teran, Maria Selmer
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Microbiology
Anna Knoppel, Michael Knopp, Lisa M. Albrecht, Erik Lundin, Ulrika Lustig, Joakim Nasvall, Dan I. Andersson
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Multidisciplinary Sciences
Joakim Nasvall
Article
Ecology
Omar Warsi, Erik Lundin, Ulrika Lustig, Joakim Naesvall, Dan I. Andersson
Article
Microbiology
Anna Knoppel, Dan I. Andersson, Joakim Nasvall
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Hind Abdalaal, Shreya Pundir, Xueliang Ge, Suparna Sanyal, Joakim Nasvall
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Microbiology
Erik Lundin, Joakim Nasvall, Dan Andersson
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Microbiology
Anna Knoppel, Joakim Nasvall, Dan I. Andersson
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2017)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)