Article
Multidisciplinary Sciences
Sayanur Rahaman, Simone Faravelli, Sylvia Voegeli, Attila Becskei
Summary: The stability gain of mRNA in yeast depends on the mRNA coding sequence length. Codon optimality affects mRNA stability and polysome propensity above a threshold length. The untranslated regions (UTR) can tune this threshold length and some UTRs can destabilize mRNAs without reducing translation, which is important for controlling the oscillatory expression of cell cycle genes.
Article
Multidisciplinary Sciences
Yavuz T. Durmaz, Alankrit Shatadal, Kyle Friend
Summary: Messenger RNA translation and the presence of certain codons can affect mRNA stability and protein folding, with ribosomes playing a role in mRNA decay and ribosomal collisions potentially promoting mRNA decay and protein misfolding.
Article
Neurosciences
Sherif Rashad, Shane R. Byrne, Daisuke Saigusa, Jingdong Xiang, Yuan Zhou, Liyin Zhang, Thomas J. Begley, Teiji Tominaga, Kuniyasu Niizuma
Summary: This study investigated the impact of blocking transcription or translation on Erastin (Class I) or RSL3 (Class II) induced ferroptosis. It was found that blocking transcription or translation protected cells against Erastin but was detrimental against RSL3. The study also revealed divergent mRNA stability changes and codon usage biases in cellular response to Erastin or RSL3. Additionally, the role of a tRNA modifying enzyme in the ferroptosis stress response was evaluated.
Article
Multidisciplinary Sciences
Fangzhou Zhao, Zhipeng Zhou, Yunkun Dang, Hyunsoo Na, Catherine Adam, Anna Lipzen, Vivian Ng, Igor Grigoriev, Yi Liu
Summary: Codon usage bias plays a critical role in regulating gene expression levels, not only through translation but also through transcription in fungal and mammalian genes. In Neurospora, the correlation between codon usage and RNA levels is maintained both genome-wide and in the nucleus, suggesting a broad influence of codon usage on mRNA levels through transcription in a translation-independent manner. A large-scale genetic screen identified multiple chromatin regulators and transcription factors as mediators of the transcriptional effect of codon usage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Qiushuang Wu, Ariel A. Bazzini
Summary: Messenger RNA (mRNA) stability and translational efficiency play crucial roles in protein production. Recent studies have shown that ribosomes, in addition to protein synthesis, also control mRNA stability in a codon-dependent manner known as codon optimality. Codons have a significant impact on mRNA stability and provide cis-regulatory information beyond their encoding amino acids. The molecular mechanism of codon optimality is still not fully understood, but it appears that the translation elongation rate triggers mRNA decay, where transfer RNAs may serve as master gene regulators influencing mRNA stability. This article discusses the findings of codon optimality and gene regulation related to codon composition in different eukaryotic species.
ANNUAL REVIEW OF BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Janaina Lima de Oliveira, Atahualpa Castillo Morales, Laurence D. Hurst, Araxi O. Urrutia, Christopher R. L. Thompson, Jason B. Wolf
Summary: Studies have found that synonymous codons are used at different frequencies due to the effects of neutral and selective forces. Selection in highly expressed genes remains to be extensively studied, with some evidence suggesting that certain factors do not impact codon preference.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Christine Mordstein, Laura Cano, Atahualpa Castillo Morales, Bethan Young, Alexander T. Ho, Alan M. Rice, Michael Liss, Laurence D. Hurst, Grzegorz Kudla
Summary: The codon usage of viruses is influenced by various selective and mutational pressures, including GC content, dinucleotide content, and sequence motifs related to gene regulation. The effects of these factors on gene expression vary depending on whether the genetic material is DNA or RNA, how it is transcribed, and where transcription occurs.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Agathe Gilbert, Cosmin Saveanu
Summary: New findings challenge models for NMD mechanisms and suggest that the imbalance between active and inactive states of NMD complexes may contribute to RNA degradation defects.
Article
Biochemistry & Molecular Biology
Ronit Nir, Thomas Philipp Hoernes, Hiromi Muramatsu, Klaus Faserl, Katalin Kariko, Matthias David Erlacher, Aldema Sas-Chen, Schraga Schwartz
Summary: RNA can be modified post-transcriptionally with various modifications, including pseudouridine (psi), which has been found in mRNA molecules. This study investigates the possibility of snoRNA-guided pseudouridylation of mRNA targets and provides insights into the factors affecting the efficiency of this modification. The study also explores the potential therapeutic application of pseudouridylation in suppressing translational termination.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Evolutionary Biology
Rosa M. Pinto, Albert Bosch
Summary: Codon bias, a common phenomenon in all organisms, is influenced by mutation, drift, and selection. While selection for translation efficiency and accuracy is well recognized, fewer studies have explored the impact of translation rate control on codon usage. Experimental molecular evolution using RNA virus populations is a powerful tool in understanding the mechanisms behind codon bias. Furthermore, experimental studies are encouraged to define the role of selection in codon evolution, as most studies on virus codon usage rely on computational analyses.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Krishnamurthy Subramanian, Bryan Payne, Felix Feyertag, David Alvarez-Ponce
Summary: This is an online database that provides codon usage statistics for all species in RefSeq, allowing users to search for specific species or taxonomic groups and access relevant statistical tables.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Yi Liu, Qian Yang, Fangzhou Zhao
Summary: Codon usage bias affects gene expression levels and protein structures, influencing translation speed, accuracy, and the protein folding process. It also plays a key role in determining the proteome landscape. Furthermore, codon usage impacts mRNA levels through various effects on transcription and translation processes.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
Article
Immunology
Xuhua Xia
Summary: The design of Pfizer/BioNTech and Moderna mRNA vaccines involves various optimizations such as enhancing translation efficiency and improving mRNA stability. Different optimizations may conflict with each other, requiring compromises to be made.
Article
Biotechnology & Applied Microbiology
Xavier Hernandez-Alias, Hannah Benisty, Leandro G. Radusky, Luis Serrano, Martin H. Schaefer
Summary: The study reveals tissue-specific codon preferences and their impact on protein synthesis. A machine learning model identifies clusters of tissues with different codon usage patterns. The developed algorithm, CUSTOM, optimizes protein production by suggesting synonymous codon design. This research has implications in gene design and biotechnological applications.
Article
Forestry
Yajun Zeng, Lianwen Shen, Shengqun Chen, Shuang Qu, Na Hou
Summary: This study analyzed the codon usage patterns of 26 Juglandaceae chloroplast genomes and found that chloroplast codons tend to exhibit conserved GC content and are primarily altered by natural selection.