AI Article Synopsis
- An outbreak of atypical pneumonia caused by a new Betacoronavirus, SARS-CoV-2, has been declared a public health emergency by the WHO.
- A detailed analysis of the virus's genome and codon usage showed a biased nucleotide composition unique to SARS-CoV-2.
- This bias mainly favors A- and U-ending codons, indicating that mutational influences shape its codon usage, with notable differences compared to human cells.
Article Abstract
An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152894 | PMC |
| http://dx.doi.org/10.1016/j.virusres.2020.197976 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Improving the generalization of protein expression models with mechanistic sequence information.
Nucleic Acids Res
January 2025
School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, United Kingdom.
The growing demand for biological products drives many efforts to maximize expression of heterologous proteins. Advances in high-throughput sequencing can produce data suitable for building sequence-to-expression models with machine learning. The most accurate models have been trained on one-hot encodings, a mechanism-agnostic representation of nucleotide sequences.
View Article and Find Full Text PDFFitness and adaptive evolution of a Rhodococcus sp. harboring dioxin-catabolic plasmids.
World J Microbiol Biotechnol
January 2025
Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, 72 Binhai Road, Jimo, Qingdao, 266237, China.
Catabolic plasmids are critical factors in the degradation of recalcitrant xenobiotics, such as dioxins. Understanding the persistence and evolution of native catabolic plasmids is pivotal for controlling their function in microbial remediation. Here, we track the fitness and evolution of Rhodococcus sp.
View Article and Find Full Text PDFDecoding Codon Bias: The Role of tRNA Modifications in Tissue-Specific Translation.
Int J Mol Sci
January 2025
Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan.
The tRNA epitranscriptome has been recognized as an important player in mRNA translation regulation. Our knowledge of the role of the tRNA epitranscriptome in fine-tuning translation via codon decoding at tissue or cell levels remains incomplete. We analyzed tRNA expression and modifications as well as codon optimality across seven mouse tissues.
View Article and Find Full Text PDFMitochondrial Genome Characteristics Reveal Evolution of and Phylogenetic Relationships.
Int J Mol Sci
January 2025
School of Life Sciences, Nanchang University, Nanchang 330031, China.
is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS).
View Article and Find Full Text PDFComparative Analysis of Complete Chloroplast Genomes and Phylogenetic Relationships of 21 Sect. ( L.) Plants.
Genes (Basel)
January 2025
College of Forestry, Guizhou University, Guiyang 550025, China.
: Section is the most diverse group in the genus L., and this group of plants has a long history of cultivation in China as popular ornamental flowers and oil plants. Sect.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!