20 papers · ranked by Valyu relevance
Brian Dehlinger, Jared Jurss, Karson Lychuk, Catherine Putonti
Bacterial genomes often reflect a bias in the usage of codons. These biases are often most notable within highly expressed genes. While deviations in codon usage can be attributed to selection or mutational biases, they can also be functional, for example controlling gene expression or guiding protein structure.…
Arthur J Jallet, Antonin Demange, Fiona Leblay, Mathilde Decourcelle + 3 more
The frequency of synonymous codons in protein coding genes is non-random and varies both between species and between genes within species. Whether this codon usage bias (CUBias) reflects underlying neutral mutational processes or is instead shaped by selection remains an open debate, especially regarding the role of…
Maahil Arshad, Matthew Uchmanowicz, Vanshika Rana, Brett Trost + 2 more
Although the genetic code is degenerate, codon selection is non-random and reflects significant functional constraints. Codon usage bias (CUB) acts as a layer of post-transcriptional regulation, influencing mRNA stability, translation kinetics, and co-translational protein folding. While CUB is well-characterized in…
Maahil Arshad, Matthew Uchmanowicz, Vanshika Rana, Brett Trost + 2 more
The redundancy of the genetic code permits multiple codons to specify a single amino acid, but codon selection is far from random and reflects underlying functional significance. Most lifeforms exhibit codon bias, where the usage of certain codons is favored over others that code for the same amino acid and hence used…
Ana Filipa Moutinho, Adam Eyre-Walker
Bias in synonymous codon usage has been reported across all kingdoms of life. Evidence across species suggests that codon usage bias is often driven by selective pressures, typically for translational efficiency. These selective pressures have been shown to depress the rate at which synonymous sites evolve. We…
Tapan Kumar Mohanta
Codon usage bias is a fundamental genomic characteristic that prefers non-random preferential use of synonymous codons. It is a major determinant of translational efficiency, gene regulation, and molecular evolution. However, the evolutionary bias and functional relevance of codon usage bias across the plant lineage is…
Alexander L. Cope, Michael A. Gilchrist
Background Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given…
Qiang Li, Yingyong Luo, Ajia Sha, Wenqi Xiao + 5 more
'Xiaodie Chen' 'Jing He' 'Lianxin Peng' 'Liang Zou'] Introduction Codon basis is a common and complex natural phenomenon observed in many kinds of organisms. Methods In the present study, we analyzed the base bias of 12 mitochondrial core protein-coding genes (PCGs) shared by nine Amanita species. Results The results…
Kerui Huang, Wenyan Zhao, Huan Li, Ningyun Zhang + 14 more
Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon usage bias (CUB) to override phylogenetic history remains a fundamental…
You Kyoung Chung, Dongkeun Lee, Junho Lee, Jaehee Kim + 2 more
Codon optimization is crucial for gene expression in heterologous hosts with varying genetic codes and codon usage, potentially resulting in enhanced protein expression and stability. Traditionally, the codon optimization problem has been solved using classical numerical techniques; however, with recent advancements…
Patrick Eldin, Alexandre David, Christophe Hirtz, Jean-Luc Battini + 2 more
Codon bias analysis of SARS-CoV-2 reveals suboptimal adaptation for translation in human cells it infects. The detailed examination of the codons preferentially used by SARS-CoV-2 shows a strong preference for LysAAA, GlnCAA, GluGAA, and ArgAGA, which are infrequently used in human genes. In the absence of an adapted…
Maxime Fages‐Lartaud, Kristoffer Hundvin, Martin Frank Hohmann‐Marriott
'Martin Frank Hohmann‐Marriott'] Title: SUMMARY Chloroplasts possess a considerably reduced genome that is decoded via an almost minimal set of tRNAs. These features make an excellent platform for gaining insights into fundamental mechanisms that govern protein expression. Here, we present a comprehensive and revised…
A. Sciarrino, P. Sorba
Analyzing the codon usage frequencies of a specimen of 20 plants, for which the codon-anticodon pattern is known, we have remarked that the hierarchy of the usage frequencies present an almost "universal" behavior. Searching to explain this behavior, we assume that the codon usage probability results from the sum of…
Baoling Yang, Ziwen Cheng, Like Luo, Kuo Cheng + 4 more
Proteins are the primary bearers of life activities, composed of codons made up of nucleotides that are translated into amino acids. Therefore, the final function of a protein is influenced by the usage of its codons. Proteins are primarily composed of 20 standard amino acids, and different species use various…
Kun Zhang, Yiheng Wang, Yue Zhang, Xiaofei Shan
Background Hemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and ornamental value. The phenomenon of codon usage bias (CUB) is prevalent in various genomes and provides excellent clues for gaining insight into organism evolution and phylogeny.…
Yoonho Jeong, Hyunwoo Choi, Ryan Fernandez Medina Hariri, Eok Kyun Lee + 2 more
Codon harmonization aims to adapt the coding sequences for heterologous expression while preserving the native-like patterns of frequent and rare codons that may influence local translation dynamics and co-translational protein folding. However, widely used harmonization metrics, such as $\%$MinMax, are defined on…
Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Özlem Özmen Garibay
The growing importance of mRNA therapeutics and synthetic biology highlights the need for models that capture the latent structure of synonymous codon (different triplets encoding the same amino acid) usage, which subtly modulates translation efficiency and gene expression. While recent efforts incorporate codon-level…
Yuji Omachi, Nen Saito, Chikara Furusawa
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen and been maintained during evolution, it may have been preserved under selection…
Seo, Yudam, Tlusty, Tsvi + 2 more
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure is a solution optimized for robustness against mutations and translational…
Josh Smith, Sara Carillo, Aditya Kulkarni, Erin Redman + 2 more
Adeno-associated viruses (AAVs) are viral vectors used as delivery systems for gene therapies. Intact protein characterization of AAV viral capsid proteins (VPs) and their post-translational modifications is critical to ensuring product quality. In this study, microchip based ZipChip capillary electrophoresis-mass…