20 papers · ranked by Valyu relevance
Michay Diez, Santiago Gerardo Medina-Muñoz, Luciana Andrea Castellano, Gabriel da Silva Pescador + 2 more
'Gabriel da Silva Pescador' 'Qiushuang Wu' 'Ariel Alejandro Bazzini'] Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon…
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…
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.…
Smitha Soman, Somdeb Chattopadhyay, Siya Ram, Vinay Kumar Nandicoori + 1 more
'G. Aneeshkumar Arimbasseri'] Mycobacterium tuberculosis (Mtb) is a slow-growing, intracellular pathogen that exhibits a high GC-rich genome. Several factors, including the GC content of the genome, influence the evolution of specific codon usage biases in genomes. As a result, the Mtb genome exhibits strong biases for…
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…
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…
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…
Reed S. Sorenson, Leslie E. Sieburth
Degeneracy in the genetic code has been shown to play a major role in yeast mRNA stability; differences in optimality (charged tRNA supply vs demand) among synonymous codons were revealed as a determinant of mRNA decay rates. However, whether and how much this mechanism determines mRNA decay rates in plants is…
Loveday E. Lewin, Kate G. Daniels, Laurence D. Hurst, Marc Robinson-Rechavi
'Marc Robinson-Rechavi'] In many species highly expressed genes (HEGs) over-employ the synonymous codons that match the more abundant iso-acceptor tRNAs. Bacterial transgene codon randomization experiments report, however, that enrichment with such “translationally optimal” codons has little to no effect on the…
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…
Rodolfo L. Carneiro, Fernando L. Palhano
Synonymous codon usage is a major determinant of mRNA half-life in yeast, functioning as a second layer of genetic information during translation. In this system, the CCR4-NOT complex plays a key role by interacting with the ribosome when both its A and E sites are vacant—a state that typically occurs when a…
Shashank Pathak, Guohui Lin
Motivation Codon optimization of Open Reading Frame (ORF) sequences is essential for enhancing mRNA stability and expression in applications like mRNA vaccines, where codon choice can significantly impact protein yield which directly impacts immune strength. In this work, we investigate the use of a pre-trained protein…
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…
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…
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…
Subhash Kak
We investigate the large-scale geometry of the DNA-protein complex of chromatin using a generalized optimality principle, which requires that not only should all sub-parts of a natural process be optimal but also the unfolding of higher recursive levels. It was shown previously that an information-theoretic geometry of…