AI Article Synopsis
- Despite the genetic code's conservation, codon usage varies due to mutational bias and selection pressures, influenced by environmental factors and tRNA concentration.
- tRNA modifications are crucial in determining codon preference in proteobacteria.
- Certain codons, like CGA and AGG, show low variability in usage across different genomes, indicating that codon evolution in proteobacteria may be tied to specific codons affected by tRNA modifications.
Article Abstract
Despite the highly conserved nature of the genetic code, the frequency of usage of each codon can vary significantly. The evolution of codon usage is shaped by two main evolutionary forces: mutational bias and selection pressures. These pressures can be driven by environmental factors, but also by the need for efficient translation, which depends heavily on the concentration of transfer RNAs (tRNAs) within the cell. The data presented here supports the proposal that tRNA modifications play a key role in shaping the overall preference of codon usage in proteobacteria. Interestingly, some codons, such as CGA and AGG (encoding arginine), exhibit a surprisingly low level of variation in their frequency of usage, even across genomes with differing GC content. These findings suggest that the evolution of GC content in proteobacterial genomes might be primarily driven by changes in the usage of a specific subset of codons, whose usage is itself influenced by tRNA modifications.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11332805 | PMC |
| http://dx.doi.org/10.3389/fmicb.2024.1412318 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Complete chloroplast genome of eight Phaius (Orchidaceae) species from China: comparative analysis and phylogenetic relationship.
BMC Plant Biol
January 2025
College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China.
Background: Phaius Lour. (Collabieae, Orchidaceae) is a small genus consisting of about 45 species, with highly ornamental and medicinal values. However, the phylogenetic relationship of Phaius among Calanthe s.
View Article and Find Full Text PDFEffective Gene Expression Prediction and Optimization from Protein Sequences.
Adv Sci (Weinh)
January 2025
State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
High soluble protein expression in heterologous hosts is crucial for various research and applications. Despite considerable research on the impact of codon usage on expression levels, the relationship between protein sequence and expression is often overlooked. In this study, a novel connection between protein expression and sequence is uncovered, leading to the development of SRAB (Strength of Relative Amino Acid Bias) based on AEI (Amino Acid Expression Index).
View Article and Find Full Text PDFIn this study, we performed a comparative analysis based on a total of 255 spider mitogenomes and four outgroups, of which the mitogenomes of 39 species were assembled de novo, to explore the phylogenetic relationships and the adaptive evolution of mitogenomes. Results showed that had the longest mitochondrial length and the most pronounced codon preference to be UUA, followed by CCU. Codon usage frequencies were similar between families and codon usage in the mitogenome of spiders was mainly influenced by natural selection pressures rather than G/C mutation bias.
View Article and Find Full Text PDFDefining serine tRNA knockout as a strategy for effective repression of gene expression in organisms with a recoded genome.
Nucleic Acids Res
January 2025
Division of Pharmacoengineering and Molecular Pharmaceutics, The University of North Carolina at Chapel Hill, 125 Mason Farm Rd. Chapel Hill, NC 27599, USA.
Whole genome codon compression-the reassignment of all instances of a specific codon to synonymous codons-can generate organisms capable of tolerating knockout of otherwise essential transfer RNAs (tRNAs). As a result, such knockout strains enable numerous unique applications, such as high-efficiency production of DNA encoding extremely toxic genes or non-canonical proteins. However, achieving stringent control over protein expression in these organisms remains challenging, particularly with proteins where incomplete repression results in deleterious phenotypes.
View Article and Find Full Text PDFTransfer RNA Levels Are Tuned to Support Differentiation During Drosophila Neurogenesis.
Genes (Basel)
December 2024
Quantitative and Systems Biology Graduate Program, Department of Molecular and Cell Biology, University of California, Merced, CA 95343, USA.
Background/objectives: Neural differentiation requires a multifaceted program to alter gene expression along the proliferation to the differentiation axis. While critical changes occur at the level of transcription, post-transcriptional mechanisms allow fine-tuning of protein output. We investigated the role of tRNAs in regulating gene expression during neural differentiation in larval brains.
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!