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Journal articles on the topic 'Rare codon'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Hu, Xiao Huan, Ming Shu Wang, and An Chun Cheng. "Analysis of Synonymous Codon Usage in the US5 Gene of Duck Plague Virus." Advanced Materials Research 641-642 (January 2013): 606–14. http://dx.doi.org/10.4028/www.scientific.net/amr.641-642.606.

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The Duck Plague Virus (DPV) US5 gene was identified by constructing the DPV genomic library, the synonymous codon usage in the US5 gene of DPV and 11 reference herpesviruses have been investigated by using the CodonW 1.4 program, CUSP (create a codon usage table) program and CHIPS (calculated ENC value) of EMBOSS (The European Molecular Biology Open Software Suite). The results reveals that the synonymous codons with A and T at the third codon positon have widely usage in the codon of US5 gene of DPV. G + C compositional constraint is the main factor that determines the codon usage bias in US5

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Yang, Qian, Chien-Hung Yu, Fangzhou Zhao, et al. "eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons." Nucleic Acids Research 47, no. 17 (2019): 9243–58. http://dx.doi.org/10.1093/nar/gkz710.

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Abstract Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and plays an important role in regulating gene expression levels. A major role of codon usage is thought to regulate protein expression levels by affecting mRNA translation efficiency, but the underlying mechanism is unclear. By analyzing ribosome profiling results, here we showed that codon usage regulates translation elongation rate and that rare codons are decoded more slowly than common codons in all codon families in Neurospora. Rare codons resulted in ribosome stalling in manners both dependent and ind

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3

Newaz, Khalique, Gabriel Wright, Jacob Piland, et al. "Network analysis of synonymous codon usage." Bioinformatics 36, no. 19 (2020): 4876–84. http://dx.doi.org/10.1093/bioinformatics/btaa603.

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Abstract Motivation Most amino acids are encoded by multiple synonymous codons, some of which are used more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational protein folding and that positions of some rare codons are evolutionarily conserved. Analyses of their positions in protein 3-dimensional structures, which are richer in biochemical information than sequences alone, might further explain the role of rare codons in protein folding. Results We model protein structures as networks and use network centralit

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Fu, Jingjing, Yunkun Dang, Christopher Counter, and Yi Liu. "Codon usage regulates human KRAS expression at both transcriptional and translational levels." Journal of Biological Chemistry 293, no. 46 (2018): 17929–40. http://dx.doi.org/10.1074/jbc.ra118.004908.

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KRAS and HRAS are highly homologous oncogenic Ras GTPase family members that are mutated in a wide spectrum of human cancers. Despite having high amino acid identity, KRAS and HRAS have very different codon usage biases: the HRAS gene contains many common codons, and KRAS is enriched for rare codons. Rare codons in KRAS suppress its protein expression, which has been shown to affect both normal and cancer biology in mammals. Here, using HRAS or KRAS expression in different human cell lines and in vitro transcription and translation assays, we show that KRAS rare codons inhibit both translation

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D’Andrea, Lucía, Francisco-Javier Pérez-Rodríguez, Montserrat de Castellarnau, et al. "The Critical Role of Codon Composition on the Translation Efficiency Robustness of the Hepatitis A Virus Capsid." Genome Biology and Evolution 11, no. 9 (2019): 2439–56. http://dx.doi.org/10.1093/gbe/evz146.

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AbstractHepatoviruses show an intriguing deviated codon usage, suggesting an evolutionary signature. Abundant and rare codons in the cellular genome are scarce in the human hepatitis A virus (HAV) genome, while intermediately abundant host codons are abundant in the virus. Genotype–phenotype maps, or fitness landscapes, are a means of representing a genotype position in sequence space and uncovering how genotype relates to phenotype and fitness. Using genotype–phenotype maps of the translation efficiency, we have shown the critical role of the HAV capsid codon composition in regulating transla

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Napolitano, Michael G., Matthieu Landon, Christopher J. Gregg, et al. "Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli." Proceedings of the National Academy of Sciences 113, no. 38 (2016): E5588—E5597. http://dx.doi.org/10.1073/pnas.1605856113.

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The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 “recalcitrant” AGRs required

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7

Bakli, Mahfoud, Raul Pascalau, and Laura Smuleac. "Rare Codon Analysis in Rickettsia Affecting Recombinant Protein Expression in Escherichia coli." Advanced Research in Life Sciences 4, no. 1 (2020): 30–35. http://dx.doi.org/10.2478/arls-2020-0015.

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Abstract Rickettsia species are important emerging pathogens causing rickettsial diseases, which are important cause death worldwide. The number of recombinant proteins used for diagnostic and therapeutic applications has increased dramatically, which is important in determination of protein function, structure and antigensity. Although E. coli is widely used expression system, the codon bias can hamper protein expression due to the presence of rare codons in gene sequence coding protein of interest. Using bioinformatics tools, rare codon analysis of rickettsial genes was performed and compare

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8

Kanduc, Darja. "Rare Human Codons and HCMV Translational Regulation." Journal of Molecular Microbiology and Biotechnology 27, no. 4 (2017): 213–16. http://dx.doi.org/10.1159/000478093.

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Restriction of protein synthesis characterizes human cytomegalovirus (HCMV) latency in the human host. In analyzing the molecular factors that hinder HCMV expression, the present study shows that HCMV genes frequently use 6 rare codons, i.e., GCG (Ala), CCG (Pro), CGT (Arg), CGC (Arg), TCG (Ser), and ACG (Thr). In some instances, the rare host codons are clustered along viral nucleotide sequences and represent the majority in sequences encoding short alanine and proline repeats. Given the positive correlation between codon usage, tRNA content, and protein production, the results support the hy

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9

Lee, Song F., Yi-Jing Li, and Scott A. Halperin. "Overcoming codon-usage bias in heterologous protein expression in Streptococcus gordonii." Microbiology 155, no. 11 (2009): 3581–88. http://dx.doi.org/10.1099/mic.0.030064-0.

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One of the limitations facing the development of Streptococcus gordonii into a successful vaccine vector is the inability of this bacterium to express high levels of heterologous proteins. In the present study, we have identified 12 codons deemed as rare codons in S. gordonii and seven other streptococcal species. tRNA genes encoding 10 of the 12 rare codons were cloned into a plasmid. The plasmid was transformed into strains of S. gordonii expressing the fusion protein SpaP/S1, the anti-complement receptor 1 (CR1) single-chain variable fragment (scFv) antibody, or the Toxoplasma gondii cyclop

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10

Frumkin, Idan, Marc J. Lajoie, Christopher J. Gregg, Gil Hornung, George M. Church, and Yitzhak Pilpel. "Codon usage of highly expressed genes affects proteome-wide translation efficiency." Proceedings of the National Academy of Sciences 115, no. 21 (2018): E4940—E4949. http://dx.doi.org/10.1073/pnas.1719375115.

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Although the genetic code is redundant, synonymous codons for the same amino acid are not used with equal frequencies in genomes, a phenomenon termed “codon usage bias.” Previous studies have demonstrated that synonymous changes in a coding sequence can exert significantciseffects on the gene’s expression level. However, whether the codon composition of a gene can also affect the translation efficiency of other genes has not been thoroughly explored. To study how codon usage bias influences the cellular economy of translation, we massively converted abundant codons to their rare synonymous cou

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11

Gurvich, Olga L., Pavel V. Baranov, Raymond F. Gesteland, and John F. Atkins. "Expression Levels Influence Ribosomal Frameshifting at the Tandem Rare Arginine Codons AGG_AGG and AGA_AGA in Escherichia coli." Journal of Bacteriology 187, no. 12 (2005): 4023–32. http://dx.doi.org/10.1128/jb.187.12.4023-4032.2005.

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ABSTRACT The rare codons AGG and AGA comprise 2% and 4%, respectively, of the arginine codons of Escherichia coli K-12, and their cognate tRNAs are sparse. At tandem occurrences of either rare codon, the paucity of cognate aminoacyl tRNAs for the second codon of the pair facilitates peptidyl-tRNA shifting to the +1 frame. However, AGG_AGG and AGA_AGA are not underrepresented and occur 4 and 42 times, respectively, in E. coli genes. Searches for corresponding occurrences in other bacteria provide no strong support for the functional utilization of frameshifting at these sequences. All sequences

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12

Feng, Bin, De Kang Zhu, Xiao Jia Wang, An Chun Cheng, and Ming Shu Wang. "Analysis of Synonymous Codon Usage Bias in D15 Gene Encoded Surface Antigen of Riemerella Anatipestifer." Advanced Materials Research 641-642 (January 2013): 597–605. http://dx.doi.org/10.4028/www.scientific.net/amr.641-642.597.

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In order to provide a basis for understanding the evolutionary relationship and pathogenesis of Riemerella anatipestifer and selecting a appropriate host expression systems to improve the expression of target gene in vivo and in vitro, we identified the codon bias in the newly confirmed D15 gene of Riemerella anatipestifer ATCC 11845 strain and performed comparative analysis of the codon usage bias between D15 gene in R. anatipestifer and the other 10 referenced Flavobacteriaceaes by a series of online bioinformatics softwares. The results revealed that the synonymous codons with A and T at th

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13

He, Yang, An Chun Cheng, Ming Shu Wang, De Kang Zhu, Xiao Jia Wang, and Xin Zhang. "Sequence Analysis of the Cas2 Gene in Riemerella anatipestifer." Advanced Materials Research 647 (January 2013): 570–76. http://dx.doi.org/10.4028/www.scientific.net/amr.647.570.

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Objective: By analyzing the Cas2gene of Riemerella anatipestifer (RA), the aim was to acquire more useful information as a guide of further study. Methods: Using bioinformatics method, sequence analysis of RA Cas2 gene was performed with some databases and software, including homology search, sequence alignment, phylogenetic tree analysis, composition analysis and physicochemical property analysis. Results: Homology search suggested that Cas2 protein sequence of R. anatipestifer showed high similarity to those of strains within Bergeyella zoohelcum and Capnocytophaga canimorsus, consistent wit

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14

Sánchez, Glòria, Albert Bosch, and Rosa M. Pintó. "Genome Variability and Capsid Structural Constraints of Hepatitis A Virus." Journal of Virology 77, no. 1 (2003): 452–59. http://dx.doi.org/10.1128/jvi.77.1.452-459.2003.

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ABSTRACT The number of synonymous mutations per synonymous site (Ks ), the number of nonsynonymous mutations per nonsynonymous site (Ka ), and the codon usage statistic (Nc ) were calculated for several hepatitis A virus (HAV) isolates. While Ks was similar to those of poliovirus (PV) and foot-and-mouth disease virus (FMDV), Ka was 1 order of magnitude lower. The Nc parameter provides information on codon usage bias and decreases when bias increases. The Nc value in HAV was about 38, while in PV and FMDV, it was about 53. The emergence of 22 rare codons in front of 8 in PV and 7 in FMDV was de

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LeMaistre, A., MS Lee, M. Talpaz, et al. "Ras oncogene mutations are rare late stage events in chronic myelogenous leukemia." Blood 73, no. 4 (1989): 889–91. http://dx.doi.org/10.1182/blood.v73.4.889.bloodjournal734889.

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DNA from bone marrow and peripheral blood samples of 44 chronic myelogenous leukemia (CML) patients were analyzed for the presence of mutations of codons 12, 13 or 61 of the N-ras, H-ras, or K-ras genes. In seven patients, samples were available from both their chronic phase and blast crisis. A total of 29 samples examined were at chronic phase and 22 were at blast crisis (eight lymphoid, eight myeloid, and six undifferentiated). No mutations were identified in N-ras or H-ras. Two patients in myeloid blast crisis had K-ras mutations, one patient at codon 12, the other at codon 13. In the forme

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16

Tian, Jian, Qingbin Li, Xiaoyu Chu, and Ningfeng Wu. "Presyncodon, a Web Server for Gene Design with the Evolutionary Information of the Expression Hosts." International Journal of Molecular Sciences 19, no. 12 (2018): 3872. http://dx.doi.org/10.3390/ijms19123872.

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In the natural host, most of the synonymous codons of a gene have been evolutionarily selected and related to protein expression and function. However, for the design of a new gene, most of the existing codon optimization tools select the high-frequency-usage codons and neglect the contribution of the low-frequency-usage codons (rare codons) to the expression of the target gene in the host. In this study, we developed the method Presyncodon, available in a web version, to predict the gene code from a protein sequence, using built-in evolutionary information on a specific expression host. The s

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Clarke, Thomas F., and Patricia L. Clark. "Rare Codon Clustering: Implications for Protein Biogenesis." Biophysical Journal 96, no. 3 (2009): 580a—581a. http://dx.doi.org/10.1016/j.bpj.2008.12.3036.

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18

LeMaistre, A., MS Lee, M. Talpaz, et al. "Ras oncogene mutations are rare late stage events in chronic myelogenous leukemia." Blood 73, no. 4 (1989): 889–91. http://dx.doi.org/10.1182/blood.v73.4.889.889.

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Abstract DNA from bone marrow and peripheral blood samples of 44 chronic myelogenous leukemia (CML) patients were analyzed for the presence of mutations of codons 12, 13 or 61 of the N-ras, H-ras, or K-ras genes. In seven patients, samples were available from both their chronic phase and blast crisis. A total of 29 samples examined were at chronic phase and 22 were at blast crisis (eight lymphoid, eight myeloid, and six undifferentiated). No mutations were identified in N-ras or H-ras. Two patients in myeloid blast crisis had K-ras mutations, one patient at codon 12, the other at codon 13. In

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19

He, Yang, An Chun Cheng, Ming Shu Wang, De Kang Zhu, Xiao Jia Wang, and Xin Zhang. "Sequence Analysis of the Cas1 Gene in Riemerella anatipestifer." Advanced Materials Research 641-642 (January 2013): 797–802. http://dx.doi.org/10.4028/www.scientific.net/amr.641-642.797.

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Objective: The aim was to analyze Riemerella anatipestifer (RA) Cas1 gene and acquire more useful information for guiding the further study of the gene. Methods: Using bioinformatics method, sequence analysis of RA Cas1 gene was carried out with some databases and software. Results: Composition analysis of RA Cas1 gene, and homology search, sequence alignment, phylogenetic tree analysis and physicochemical property analysis of RA Cas1 protein were performed. Homology search revealed that Cas1 protein sequence of R. anatipestifer showed high similarity to those of strains within the Genus Capno

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20

Engel, Anja J., Marina Kithil, Markus Langhans, et al. "Codon Bias Can Determine Sorting of a Potassium Channel Protein." Cells 10, no. 5 (2021): 1128. http://dx.doi.org/10.3390/cells10051128.

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Due to the redundancy of the genetic code most amino acids are encoded by multiple synonymous codons. It has been proposed that a biased frequency of synonymous codons can affect the function of proteins by modulating distinct steps in transcription, translation and folding. Here, we use two similar prototype K+ channels as model systems to examine whether codon choice has an impact on protein sorting. By monitoring transient expression of GFP-tagged channels in mammalian cells, we find that one of the two channels is sorted in a codon and cell cycle-dependent manner either to mitochondria or

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21

Fomina, E. G. "EXPRESSION OF NUCLEOCAPSID VIRAL PROTEINS IN THE BACTERIAL SYSTEM OF Escherichia coli: THE INFLUENCE OF THE CODON COMPOSITION AND THE UNIFORMITY OF ITS DISTRIBUTION WITHIN GENE." Biotechnologia Acta 13, no. 6 (2020): 30–40. http://dx.doi.org/10.15407/biotech13.06.030.

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A heterologous host has got a unique expression ability of each gene. Differences between the synonymous sequences play an important role in regulation of protein expression in organisms from Escherichia coli to human, and many details of this process remain unclear. The work was aimed to study the composition of codons, its distribution over the sequence and the effect of rare codons on the expression of viral nucleocapsid proteins and their fragments in the heterologous system of E.coli. The plasmid vector pJC 40 and the BL 21 (DE 3) E. coli strain were used for protein expression. The codon

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Sauer, Jørgen, and Per Nygaard. "Expression of the Methanobacterium thermoautotrophicum hpt Gene, Encoding Hypoxanthine (Guanine) Phosphoribosyltransferase, in Escherichia coli." Journal of Bacteriology 181, no. 6 (1999): 1958–62. http://dx.doi.org/10.1128/jb.181.6.1958-1962.1999.

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ABSTRACT The hpt gene from the archaeon Methanobacterium thermoautotrophicum, encoding hypoxanthine (guanine) phosphoribosyltransferase, was cloned by functional complementation into Escherichia coli. The hpt-encoded amino acid sequence is most similar to adenine phosphoribosyltransferases, but the encoded enzyme has activity only with hypoxanthine and guanine. The synthesis of the recombinant enzyme is apparently limited by the presence of the rare arginine codons AGA and AGG and the rare isoleucine AUA codon on the hpt gene. The recombinant enzyme was purified to apparent homogeneity.

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Zeng, Yu, Wei Wang, and Wenshe R. Liu. "Towards Reassigning the Rare AGG Codon inEscherichia coli." ChemBioChem 15, no. 12 (2014): 1750–54. http://dx.doi.org/10.1002/cbic.201400075.

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Mortazavi, Mojtaba, Abdolrazagh Barzegar, Abdorrasoul Malekpour, Mohammad Ghorbani, Saeid Gholamzadeh, and Younes Ghasemi. "In Silico Evaluation of the ATP7B Protein: Insights from the Role of Rare Codon Clusters and Mutations that Affect Protein Structure and Function." Current Proteomics 17, no. 3 (2020): 213–26. http://dx.doi.org/10.2174/1570164617666190919114545.

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Background: Wilson’s disease is a rare autosomal recessive genetic disorder of copper metabolism, which is characterized by hepatic and neurological disease. ATP7B encodes a transmembrane protein ATPase (ATP7B), which functions as a copper-dependent P-type ATPase. The mutations in the gene ATP7B (on chromosome 13) lead to Wilson’s disease and is highly expressed in the liver, kidney, and placenta. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web

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Wu, Xianming, Songfeng Wu, Dong Li, et al. "Computational identification of rare codons of Escherichia coli based on codon pairs preference." BMC Bioinformatics 11, no. 1 (2010): 61. http://dx.doi.org/10.1186/1471-2105-11-61.

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26

Sharp, Paul M., and Wen-Hsiung Li. "Codon usage in regulatory genes inEscherichia colidoes not reflect selection for ‘rare’ codons." Nucleic Acids Research 14, no. 19 (1986): 7737–49. http://dx.doi.org/10.1093/nar/14.19.7737.

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27

Osterman, Ilya A., Zoe S. Chervontseva, Sergey A. Evfratov, et al. "Translation at first sight: the influence of leading codons." Nucleic Acids Research 48, no. 12 (2020): 6931–42. http://dx.doi.org/10.1093/nar/gkaa430.

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Abstract First triplets of mRNA coding region affect the yield of translation. We have applied the flowseq method to analyze &gt;30 000 variants of the codons 2–11 of the fluorescent protein reporter to identify factors affecting the protein synthesis. While the negative influence of mRNA secondary structure on translation has been confirmed, a positive role of rare codons at the beginning of a coding sequence for gene expression has not been observed. The identity of triplets proximal to the start codon contributes more to the protein yield then more distant ones. Additional in-frame star

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Postnikova, Olga A., Sheetal Uppal, Weiliang Huang, et al. "The Functional Consequences of the Novel Ribosomal Pausing Site in SARS-CoV-2 Spike Glycoprotein RNA." International Journal of Molecular Sciences 22, no. 12 (2021): 6490. http://dx.doi.org/10.3390/ijms22126490.

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The SARS-CoV-2 Spike glycoprotein (S protein) acquired a unique new 4 amino acid -PRRA- insertion sequence at amino acid residues (aa) 681–684 that forms a new furin cleavage site in S protein as well as several new glycosylation sites. We studied various statistical properties of the -PRRA- insertion at the RNA level (CCUCGGCGGGCA). The nucleotide composition and codon usage of this sequence are different from the rest of the SARS-CoV-2 genome. One of such features is two tandem CGG codons, although the CGG codon is the rarest codon in the SARS-CoV-2 genome. This suggests that the insertion s

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Entius, M. M., A. M. Westerman, F. M. Giardiello, et al. "Peutz-Jeghers polyps, dysplasia, and K-ras codon 12 mutations." Gut 41, no. 3 (1997): 320–22. http://dx.doi.org/10.1136/gut.41.3.320.

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Background—Peutz-Jeghers syndrome (PJS) is a rare, autosomal dominant, polyposis syndrome, associated with an increased risk of gastrointestinal and extragastrointestinal malignancy. Occasionally dysplasia occurs in PJS polyps.Aims—In colorectal carcinomas, mutations in codon 12 of the K-ras oncogene are common and are found at similar frequency in precursor adenomas. Therefore, K-rascodon 12 point mutations in PJS polyps were evaluated.Materials and methods—Fifty two PJS polyps, including four with dysplasia, collected from 19 patients with PJS, were analysed for mutations in the K-ras codon

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Leskiw, B. K., M. J. Bibb, and K. F. Chater. "The use of a rare codon specifically during development?" Molecular Microbiology 5, no. 12 (1991): 2861–67. http://dx.doi.org/10.1111/j.1365-2958.1991.tb01845.x.

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Marin, Monica. "Folding at the rhythm of the rare codon beat." Biotechnology Journal 3, no. 8 (2008): 1047–57. http://dx.doi.org/10.1002/biot.200800089.

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Kobayashi, Hideki. "Inducible Suppression of Global Translation by Overuse of Rare Codons." Applied and Environmental Microbiology 81, no. 7 (2015): 2544–53. http://dx.doi.org/10.1128/aem.03708-14.

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ABSTRACTRecently, artificial gene networks have been developed in synthetic biology to control gene expression and make organisms as controllable as robots. Here, I present an artificial posttranslational gene-silencing system based on the codon usage bias and low tRNA content corresponding to minor codons. I engineered the green fluorescent protein (GFP) gene to inhibit translation indirectly with the lowest-usage codons to monopolize various minor tRNAs (lgfp). The expression oflgfpinterfered nonspecifically with the growth ofEscherichia coli,Saccharomyces cerevisiae, human HeLa cervical can

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Lucaci, Alexander G., Sadie R. Wisotsky, Stephen D. Shank, Steven Weaver, and Sergei L. Kosakovsky Pond. "Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes." PLOS ONE 16, no. 3 (2021): e0248337. http://dx.doi.org/10.1371/journal.pone.0248337.

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Despite many attempts to introduce evolutionary models that permit substitutions to instantly alter more than one nucleotide in a codon, the prevailing wisdom remains that such changes are rare and generally negligible or are reflective of non-biological artifacts, such as alignment errors. Codon models continue to posit that only single nucleotide change have non-zero rates. Here, we develop and test a simple hierarchy of codon-substitution models with non-zero evolutionary rates for only one-nucleotide (1H), one- and two-nucleotide (2H), or any (3H) codon substitutions. Using over 42, 000 em

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Mortazavi, Mojtaba, Masoud Torkzadeh-Mahani, Farzaneh Kargar, Navid Nezafat, and Younes Ghasemi. "In silico analysis of codon usage and rare codon clusters in the halophilic bacteria L-asparaginase." Biologia 75, no. 1 (2019): 151–60. http://dx.doi.org/10.2478/s11756-019-00324-w.

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Gan, Earn H., Katie MacArthur, Anna L. Mitchell, and Simon H. S. Pearce. "The role of functionally defective rare germline variants of sialic acid acetylesterase in autoimmune Addison's disease." European Journal of Endocrinology 167, no. 6 (2012): 825–28. http://dx.doi.org/10.1530/eje-12-0579.

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BackgroundAutoimmune Addison's disease (AAD) is a rare condition with a complex genetic basis. A panel of rare and functionally defective genetic variants in the sialic acid acetylesterase (SIAE) gene has recently been implicated in several common autoimmune conditions. We performed a case–control study to determine whether these rare variants are associated with a rarer condition, AAD.MethodWe analysed nine SIAE gene variants (W48X, M89V, C196F, C226G, R230W, T312M, Y349C, F404S and R479C) in a United Kingdom cohort of 378 AAD subjects and 387 healthy controls. All samples were genotyped usin

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Kawamura, M., A. Kikuchi, S. Kobayashi, et al. "Mutations of the p53 and ras genes in childhood t(1;19)-acute lymphoblastic leukemia." Blood 85, no. 9 (1995): 2546–52. http://dx.doi.org/10.1182/blood.v85.9.2546.bloodjournal8592546.

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We have investigated the alterations of p53 and ras genes including H-, K-, and N-ras genes in 22 acute lymphoblastic leukemia (ALL) cases and five cell lines carrying t(1;19) by use of polymerase chain reaction (PCR)-single-strand conformation polymorphism (SSCP) analysis and direct sequencing. The mutations of the p53 gene were found in 2 of 20 t(1;19)-ALL cases at diagnosis (10%), all of 4 cases at relapse (100%), and 4 of the 5 cell lines (80%). Four of the five patients who died had missense mutations at codons 49, 177, 179, and 248. In cases examined sequentially, one had the same point

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Abrahams, Liam, and Laurence D. Hurst. "A Depletion of Stop Codons in lincRNA is Owing to Transfer of Selective Constraint from Coding Sequences." Molecular Biology and Evolution 37, no. 4 (2019): 1148–64. http://dx.doi.org/10.1093/molbev/msz299.

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Abstract Although the constraints on a gene’s sequence are often assumed to reflect the functioning of that gene, here we propose transfer selection, a constraint operating on one class of genes transferred to another, mediated by shared binding factors. We show that such transfer can explain an otherwise paradoxical depletion of stop codons in long intergenic noncoding RNAs (lincRNAs). Serine/arginine-rich proteins direct the splicing machinery by binding exonic splice enhancers (ESEs) in immature mRNA. As coding exons cannot contain stop codons in one reading frame, stop codons should be rar

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Phoenix, David A., and Eugene Korotkov. "Evidence of rare codon clusters within Escherichia coli coding regions." FEMS Microbiology Letters 155, no. 1 (2006): 63–66. http://dx.doi.org/10.1111/j.1574-6968.1997.tb12686.x.

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Rosano, Germán L., and Eduardo A. Ceccarelli. "Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain." Microbial Cell Factories 8, no. 1 (2009): 41. http://dx.doi.org/10.1186/1475-2859-8-41.

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Kirienko, N. V., K. A. Lepikhov, L. A. Zheleznaya, and N. I. Matvienko. "Significance of Codon Usage and Irregularities of Rare Codon Distribution in Genes for Expression of BspLU11III Methyltransferases." Biochemistry (Moscow) 69, no. 5 (2004): 527–35. http://dx.doi.org/10.1023/b:biry.0000029851.96180.92.

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Nik-Pa, Nik Ida Mardiana, Mohamad Farhan Mohamad Sobri, Suraini Abd-Aziz та ін. "Combined Optimization of Codon Usage and Glycine Supplementation Enhances the Extracellular Production of a β-Cyclodextrin Glycosyltransferase from Bacillus sp. NR5 UPM in Escherichia coli". International Journal of Molecular Sciences 21, № 11 (2020): 3919. http://dx.doi.org/10.3390/ijms21113919.

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Two optimization strategies, codon usage modification and glycine supplementation, were adopted to improve the extracellular production of Bacillus sp. NR5 UPM β-cyclodextrin glycosyltransferase (CGT-BS) in recombinant Escherichia coli. Several rare codons were eliminated and replaced with the ones favored by E. coli cells, resulting in an increased codon adaptation index (CAI) from 0.67 to 0.78. The cultivation of the codon modified recombinant E. coli following optimization of glycine supplementation enhanced the secretion of β-CGTase activity up to 2.2-fold at 12 h of cultivation as compare

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El agy, Fatima, Sanae el Bardai, Ihsane El Otmani, et al. "Mutation status and prognostic value of KRAS and NRAS mutations in Moroccan colon cancer patients: A first report." PLOS ONE 16, no. 3 (2021): e0248522. http://dx.doi.org/10.1371/journal.pone.0248522.

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This study aimed to estimate the incidence of KRAS, NRAS, and BRAF mutations in the Moroccan population, and investigate the associations of KRAS and NRAS gene mutations with clinicopathological characteristics and their prognosis value. To achieve these objectives, we reviewed medical and pathology reports for 210 patients. RAS testing was investigated by Sanger sequencing and Pyrosequencing technology. BRAF (exon 15) status was analyzed by the Sanger method. The expression of MMR proteins was evaluated by Immunohistochemistry. KRAS and NRAS mutations were found in 36.7% and 2.9% of 210 patie

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Hennigan, A. N., and A. Jacobson. "Functional mapping of the translation-dependent instability element of yeast MATalpha1 mRNA." Molecular and Cellular Biology 16, no. 7 (1996): 3833–43. http://dx.doi.org/10.1128/mcb.16.7.3833.

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The determinants of mRNA stability include specific cis-acting destabilizing sequences located within mRNA coding and noncoding regions. We have developed an approach for mapping coding-region instability sequences in unstable yeast mRNAs that exploits the link between mRNA translation and turnover and the dependence of nonsense-mediated mRNA decay on the activity of the UPF1 gene product. This approach, which involves the systematic insertion of in-frame translational termination codons into the coding sequence of a gene of interest in a upf1delta strain, differs significantly from convention

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Edison, Eunice S., Ramachandran V. Shaji, G. D. Sankari та ін. "Analysis of β Globin Mutations in the Indian Population: Presence of Rare and Novel Mutations and Region Wise Heterogeneity." Blood 110, № 11 (2007): 3822. http://dx.doi.org/10.1182/blood.v110.11.3822.3822.

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Abstract β-thalassaemia is a major public health problem in India. A comprehensive data base of the spectrum of mutations causing β thalassaemia in the Indian population is necessary. Each population group in which the disease is prevalent has a different spectrum of β globin mutations and a few mutations account for most of the alleles. From 1997 to 2006, β-Globin gene mutation analysis was carried out in 1030 individuals. The common mutations in the population were screened by reverse dot blot (RDB). Deletion of 619 bp of the β globin gene was detected by gap-PCR. Rare mutations were screene

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Lemm, Ira, and Jeff Ross. "Regulation of c-myc mRNA Decay by Translational Pausing in a Coding Region Instability Determinant." Molecular and Cellular Biology 22, no. 12 (2002): 3959–69. http://dx.doi.org/10.1128/mcb.22.12.3959-3969.2002.

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ABSTRACT A 249-nucleotide coding region instability determinant (CRD) destabilizes c-myc mRNA. Previous experiments identified a CRD-binding protein (CRD-BP) that appears to protect the CRD from endonuclease cleavage. However, it was unclear why a CRD-BP is required to protect a well-translated mRNA whose coding region is covered with ribosomes. We hypothesized that translational pausing in the CRD generates a ribosome-deficient region downstream of the pause site, and this region is exposed to endonuclease attack unless it is shielded by the CRD-BP. Transfection and cell-free translation expe

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Hussain, Hasnain, and Nikson Fatt-Ming Chong. "Combined Overlap Extension PCR Method for Improved Site Directed Mutagenesis." BioMed Research International 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/8041532.

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The combined overlap extension PCR (COE-PCR) method developed in this work combines the strengths of the overlap extension PCR (OE-PCR) method with the speed and ease of the asymmetrical overlap extension (AOE-PCR) method. This combined method allows up to 6 base pairs to be mutated at a time and requires a total of 40–45 PCR cycles. A total of eight mutagenesis experiments were successfully carried out, with each experiment mutating between two to six base pairs. Up to four adjacent codons were changed in a single experiment. This method is especially useful for codon optimization, where doub

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Je, Eun Mi, Chang Hyeok An, Yeun Jun Chung, Nam Jin Yoo, and Sug Hyung Lee. "GNAS Mutation Affecting Codon 201 is Rare in Most Human Tumors." Pathology & Oncology Research 21, no. 3 (2015): 859–60. http://dx.doi.org/10.1007/s12253-015-9919-6.

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Lin, Yizhu, Gemma E. May, Hunter Kready, et al. "Impacts of uORF codon identity and position on translation regulation." Nucleic Acids Research 47, no. 17 (2019): 9358–67. http://dx.doi.org/10.1093/nar/gkz681.

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Abstract Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5′ mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a minority of uORFs encode conserved functional peptides, the coding regions of most uORFs are not conserved. Thus, the importance of uORF coding sequences on their regulatory functions remains largely unknown. We investigated the impact of an uORF coding region on gene regulat

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Murphy, Jo-Ellen, Sara Sadan, Jessica Kim Lee, Jana Pruski-Clark, Rebecca Sutphen, and Kimberly McGregor. "Rare BAP1 variant of unknown significance (VUS) and analysis of BAP1 codon 146 genomics: Potential germline and therapeutic implications." Journal of Clinical Oncology 39, no. 15_suppl (2021): 10533. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.10533.

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10533 Background: The BAP1 gene ( B RCA1-Associated Protein) encodes a protein ubiquitin carboxyl-terminal hydrolase (BAP1), which removes ubiquitin moieties and regulates various cellular functions including DNA repair. This association has driven interest in defining if BAP1 variants confer susceptibility to PARP inhibitors (PARPi). Germline and somatic BAP1 alterations are both rare, mostly unique, often classified as VUS’s, and associated with a broad range of overlapping tumor types. Based on the identification of a BAP1 R146K VUS variant in tumor, also previously identified as germline,

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Schilff, Mirco, Yelena Sargsyan, Julia Hofhuis, and Sven Thoms. "Stop Codon Context-Specific Induction of Translational Readthrough." Biomolecules 11, no. 7 (2021): 1006. http://dx.doi.org/10.3390/biom11071006.

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Premature termination codon (PTC) mutations account for approximately 10% of pathogenic variants in monogenic diseases. Stimulation of translational readthrough, also known as stop codon suppression, using translational readthrough-inducing drugs (TRIDs) may serve as a possible therapeutic strategy for the treatment of genetic PTC diseases. One important parameter governing readthrough is the stop codon context (SCC)—the stop codon itself and the nucleotides in the vicinity of the stop codon on the mRNA. However, the quantitative influence of the SCC on treatment outcome and on appropriate dru

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