22 papers · ranked by Valyu relevance
Sarah L. Gillen, Joseph A. Waldron, Martin Bushell
A key characteristic of cancer cells is their increased proliferative capacity, which requires elevated levels of protein synthesis. The process of protein synthesis involves the translation of codons within the mRNA coding sequence into a string of amino acids to form a polypeptide chain. As most amino acids are…
Michelle L DeVore, Ariel A Bazzini, M Arbeitman
The ribosome plays a crucial role in translating mRNA into protein; however, the genetic code extends beyond merely specifying amino acids. Upon translation, codons, the 3-nucleotide sequences interpreted by ribosomes, have regulatory properties affecting mRNA stability, a phenomenon known as codon optimality. Codon…
Santiago Gerardo Medina-Muñoz, Michay Diez, Luciana Andrea Castellano, Gabriel da Silva Pescador + 2 more
Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability, in turn, is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon optimality. We have developed iCodon (www.iCodon.org), an algorithm…
Chotiwat Seephetdee, Nada Bejar, Eric Chau, Thy Y. Nguyen + 2 more
Despite advancements in RNA sequence design, evidence regarding the preferential use of synonymous codons on cellular stress and innate immune responses is lacking. To this end, we developed a new codon optimality formula to re-engineer the coding sequences of three luciferase reporters. We demonstrate that mRNAs…
Chloe L. Barrington, Amanda L. Koch, Gabriel Galindo, Emma Larkin-Gero + 4 more
Synonymous codon usage regulates gene expression such that transcripts rich in optimal codons produce significantly more protein than their nonoptimal counterparts. A major unresolved issue has been understanding the mechanisms by which synonymous codons regulate gene expression. We and others have previously shown…
Anastasiia Iu Paremskaia, Anna A. Kogan, Anastasiia Murashkina, Daria A. Naumova + 6 more
'Daria A. Naumova' 'Anakha Satish' 'Ivan S. Abramov' 'Sofya G. Feoktistova' 'Olga N. Mityaeva' 'Andrei A. Deviatkin' 'Pavel Yu Volchkov'] Codon optimization has evolved to enhance protein expression efficiency by exploiting the genetic code’s redundancy, allowing for multiple codon options for a single amino acid.…
Miquel Àngel Schikora-Tamarit, Lucas B. Carey
Living organisms are error-prone. Every second a single human cell produces over 100 transcripts with a substitution, frameshift or splicing error. Multiple mRNA quality control pathways exist to degrade these transcripts. Many of these pathways involve co-translational regulation of mRNA stability, such as nonsense…
Jiawei Li, Xinxiu Dong, Jie Liu
High-Codon is a deep learning-based codon optimization tool designed to enhance the expression levels of heterologous proteins in Escherichia coli. This approach employs a BERT pre-trained model to construct a sequence labeling framework for predicting optimal codons. Additionally, an expression-level weighted loss…
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…
Luciana A Castellano, Ryan J McNamara, Horacio M Pallares, Andrea V Gamarnik + 2 more
Codon optimality refers to the effect codon composition has on messenger RNA (mRNA) stability and translation level and implies that synonymous codons are not silent from a regulatory point of view. Here, we investigated the adaptation of virus genomes to the host optimality code using mosquito-borne dengue virus…
Stark, Hannes, Padia, Umesh + 6 more
Generating protein sequences conditioned on protein structures is an impactful technique for protein engineering. When synthesizing engineered proteins, they are commonly translated into DNA and expressed in an organism such as yeast. One difficulty in this process is that the expression rates can be low due to…
Paweł Błażej, Małgorzata Wnętrzak, Dorota Mackiewicz, Paweł Mackiewicz + 1 more
'Paweł Mackiewicz' 'Alexandre G. de Brevern'] Many biological systems are typically examined from the point of view of adaptation to certain conditions or requirements. One such system is the standard genetic code (SGC), which generally minimizes the cost of amino acid replacements resulting from mutations or…
José Santos, Ángel Monteagudo
Background As the canonical code is not universal, different theories about its origin and organization have appeared. The optimization or level of adaptation of the canonical genetic code was measured taking into account the harmful consequences resulting from point mutations leading to the replacement of one amino…
Dimitris Papamichail, Hongmei Liu, Vitor Machado, Nathan C. Gould + 2 more
'J. Robert Coleman' 'Georgios Papamichail'] Abstract—Advances in de novo synthesis of DNA and computational gene design methods make possible the customization of genes by direct manipulation of features such as codon bias and mRNA secondary structure. Codon context is another feature significantly affecting mRNA…
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…
Emily A. Seward, Steven Kelly
Background Most amino acids are encoded by multiple synonymous codons. However, synonymous codons are not used equally, and this biased codon use varies between different organisms. It has previously been shown that both selection acting to increase codon translational efficiency and selection acting to decrease codon…
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…
Emily A. Seward, Steven Kelly
Most amino acids are encoded by multiple synonymous codons. However synonymous codons are not used equally and this biased codon use varies between different organisms. It has previously been shown that both selection acting to increase codon translational efficiency and selection acting to decrease codon biosynthetic…
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…
Harry Buhrman, Peter T. S. van der Gulik, Gunnar W. Klau, Christian Schaffner + 2 more
'Christian Schaffner' 'Dave Speijer' 'Leen Stougie'] Abstract The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic code which…
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…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…