25 papers · ranked by Valyu relevance
Gareth A. Palidwor, Theodore J. Perkins, Xuhua Xia, Dov Joseph Stekel
'Dov Joseph Stekel'] Background In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position, the overall GC bias…
Adam Hilterbrand, Joseph Saelens, Catherine Putonti
Background In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift. Furthermore, correlations between codon usage within host genomes and their…
Prashant Mainali, Sobita Pathak
Codon usage bias is the preferential use of the subset of synonymous codons during translation. In this paper, the comparisons of normalized entropy and GC content between the sequence of coding regions of Escherichia coli k12 and noncoding regions (ncRNA, rRNA) of various organisms were done to shed light on the…
Matthew W Hodgman, Justin B Miller, Taylor E Meurs, John S K Kauwe
Synonymous codon usage significantly impacts translational and transcriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has been implicated in various diseases. However, population-specific differences in codon usage biases remain largely unexplored. Here, we present a web…
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…
Paweł Błażej, Dorota Mackiewicz, Małgorzata Wnętrzak, Paweł Mackiewicz
'Paweł Mackiewicz'] There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, biased codon usage can also be a byproduct of a general selection at the amino acid…
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…
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…
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…
Bohdan B. Khomtchouk, Wolfgang Nonner
DNA encodes protein primary structure using 64 different codons to specify 20 different amino acids and a stop signal. Frequencies of codon occurrence when ordered in descending sequence provide a global characterization of a genome’s preference (bias) for using the different codons of the redundant genetic code.…
Hui Song, Jing Liu, Qiuyan Song, Qingping Zhang + 2 more
'Zhibiao Nan'] Codon usage bias plays an important role in shaping genomes and genes in unicellular species and multicellular species. Here, we first analyzed codon usage bias in seven Epichloë species and their peramine-coding genes. Our results showed that both natural selection and mutation pressure played a role in…
Sergio Forcelloni, Andrea Giansanti
The codon usage bias is the well-known phenomenon of an unequal use of synonymous codons in coding DNA. These patterns reflect the action of weak selection working at the molecular level and allows to quantify the effects of natural selection, which tend to increase the fitness of the organisms. The prevailing…
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…
A. Sciarrino, P. Sorba
The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has been proposed a few years ago. The present paper is a review of the model, of…
Ruth Hershberg, Dmitri A. Petrov, Ahmed Moustafa
In a recent paper published in PLOS ONE, Wang et al. challenge our finding that the identity of optimal codons in different genomes follows a set of clear rules. Here we provide a rebuttal of their paper and demonstrate that the results of our original PLOS Genetics paper stand. This provides us with an opportunity to…
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…
Zhiwen Chen, Jianguo Zhao, Jun Qiao, Weijia Li + 7 more
'Haiyan Wang' 'Zehui Liu' 'Baoyan Xing' 'Jonathan F. Wendel' 'Corrinne E. Grover'] Title: Abstract Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically…
Maddalena Dilucca, Giulio Cimini, Andrea Semmoloni, Antonio Deiana + 1 more
'Andrea Giansanti'] Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon…
Reginald Smith
Codon usage bias is a well recognized phenomenon but the relative influence of its major causes: G+C content, mutational biases, and selection, are often difficult to disentangle. This paper presents methods to calculate modified effective codon numbers that allow the investigation of the sources of codon bias and how…
Maddalena Dilucca, Giulio Cimini, Andrea Giansanti
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species.…
Diego Cocurullo, A. Sciarrino
The usage frequencies for codons belonging to quartets are analized, over the whole exonic region, for 92 biological species. Correlation is put into evidence, between the usage frequencies of synonymous codons with third nucleotide A and C and between the usage frequencies of non synonymous codons, belonging to…
Namiko Mitarai, Steen B. Pedersen
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the…
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…
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…