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Codon usage

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https://www.readbyqxmd.com/read/28431284/mitovirus-uga-trp-codon-usage-parallels-that-of-host-mitochondria
#1
Max L Nibert
Mitoviruses replicate in mitochondria of their host fungi. They have small RNA genomes that encompass a single ORF encoding the viral RdRp. Since UGA codons encode Trp in fungal mitochondria, the RdRp ORF of a typical mitovirus includes multiple UGA codons. In some mitoviruses, however, the ORF has no such codons, suggesting that these particular viruses may be under selective pressure to exclude them. In this report, new evidence is presented that host fungi whose mitoviruses have no or few UGA codons are distinctive in also having no or few UGA codons in their core mitochondrial genes...
April 18, 2017: Virology
https://www.readbyqxmd.com/read/28428795/non-canonical-translation-in-plant-rna-viruses
#2
REVIEW
Manuel Miras, W Allen Miller, Verónica Truniger, Miguel A Aranda
Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5' cap structure and/or the 3' poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28427327/analysis-of-transcriptome-data-reveals-multifactor-constraint-on-codon-usage-in-taenia-multiceps
#3
Xing Huang, Jing Xu, Lin Chen, Yu Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang
BACKGROUND: Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. RESULTS: Analysis of a total of 8,620 annotated mRNA sequences from T...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28421323/gene-expression-nucleotide-composition-and-codon-usage-bias-of-genes-associated-with-human-y-chromosome
#4
Monisha Nath Choudhury, Arif Uddin, Supriyo Chakraborty
Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position...
April 18, 2017: Genetica
https://www.readbyqxmd.com/read/28420819/synonymous-and-biased-codon-usage-by-mers-cov-papain-like-and-3cl-proteases
#5
Mahmoud Kandeel, Abdallah Altaher
Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias...
April 18, 2017: Biological & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28419256/chloromitocu-codon-patterns-across-organelle-genomes-for-functional-genomics-and-evolutionary-applications
#6
Gaurav Sablok, Ting-Wen Chen, Chi-Ching Lee, Chi Yang, Ruei-Chi Gan, Jill L Wegrzyn, Nicola L Porta, Kinshuk C Nayak, Po-Jung Huang, Claudio Varotto, Petrus Tang
Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes...
April 17, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28416948/comparative-analysis-of-predicted-gene-expression-among-crenarchaeal-genomes
#7
Shibsankar Das, Brajadulal Chottopadhyay, Satyabrata Sahoo
Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416383/comparative-characterization-analysis-of-synonymous-codon-usage-bias-in-classical-swine-fever-virus
#8
Xin Xu, Dongliang Fei, Huansheng Han, Honggui Liu, Jiayong Zhang, Yulong Zhou, Chuang Xu, Hongbin Wang, Hongwei Cao, Hua Zhang
Classical swine fever virus (CSFV) is responsible for the highly contagious viral disease of swine, and causes great economic loss in the swine-raising industry. Considering the significance of CSFV, a systemic analysis was performed to study its codon usage patterns. In this study, using the complete genome sequences of 76 CSFV representing three genotypes, we firstly analyzed the relative nucleotide composition, effective number of codon (ENC) and synonymous codon usage in CSFV genomes. The results showed that CSFV is GC-moderate genome and the third-ended codons are not preferentially used...
April 14, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28406397/evolutionary-changes-in-transcription-factor-coding-sequence-quantitatively-alter-sensory-organ-development-and-function
#9
Simon Weinberger, Matthew P Topping, Jiekun Yan, Annelies Claeys, Natalie De Geest, Duru Ozbay, Talah Hassan, Xiaoli He, Joerg T Albert, Bassem A Hassan, Ariane Ramaekers
'Toolkit' genes are highly conserved developmental regulators. While changes in their regulatory elements contribute to morphological evolution, the role of coding sequence (CDS) evolution remains unresolved. We used CDS-specific knock-ins of the proneural transcription factor Atonal homologs (ATHs) to address this question. Drosophila Atonal CDS was endogenously replaced with that of distant ATHs at key phylogenetic positions, non-ATH proneural genes, and the closest CDS to ancestral proneural genes. ATHs and the ancestral-like gene rescued sensory organ fate in atonal mutants, in contrast to non-ATHs...
April 13, 2017: ELife
https://www.readbyqxmd.com/read/28401291/the-human-retinoblastoma-susceptibility-gene-rb1-an-evolutionary-story-in-primates
#10
Maria C Viana, William C Tavares, Ayslan C Brant, Mariana Boroni, Héctor N Seuánez
The tumor suppressor gene RB1 (Human Retinoblastoma Susceptibility Gene) plays a prominent role in normal development, gene transcription, DNA replication, repair, and mitosis. Its complete biallelic dysfunction in retinoblasts is the main cause of retinoblastoma in the human. Although this gene has been evolutionary conserved, comparisons between the reference and human RB1 coding region with its counterparts in 19 non-human primates showed 359 sites where nucleotide replacements took place during the radiation of these species...
April 11, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28397791/adaptation-and-evolution-of-deep-sea-scale-worms-annelida-polynoidae-insights-from-transcriptome-comparison-with-a-shallow-water-species
#11
Yanjie Zhang, Jin Sun, Chong Chen, Hiromi K Watanabe, Dong Feng, Yu Zhang, Jill M Y Chiu, Pei-Yuan Qian, Jian-Wen Qiu
Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28389662/frequent-gu-wobble-pairings-reduce-translation-efficiency-in-plasmodium-falciparum
#12
Sherwin Chan, Jun-Hong Ch'ng, Mats Wahlgren, Jessada Thutkawkorapin
Plasmodium falciparum genome has 81% A+T content. This nucleotide bias leads to extreme codon usage bias and culminates in frequent insertion of asparagine homorepeats in the proteome. Using recodonized GFP sequences, we show that codons decoded via G:U wobble pairing are suboptimal codons that are negatively associated to protein translation efficiency. Despite this, one third of all codons in the genome are GU wobble codons, suggesting that codon usage in P. falciparum has not been driven to maximize translation efficiency, but may have evolved as translational regulatory mechanism...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28387456/synonymous-codon-usage-of-genes-in-polymerase-complex-of-newcastle-disease-virus
#13
Chandra Shekhar Kumar, Sachin Kumar
Newcastle disease virus (NDV) is pathogenic to both avian and non-avian species but extensively finds poultry as its primary host and causes heavy economic losses in the poultry industry. In this study, a total of 186 polymerase complex comprising of nucleoprotein (N), phosphoprotein (P), and large polymerase (L) genes of NDV was analyzed for synonymous codon usage. The relative synonymous codon usage and effective number of codons (ENC) values were used to estimate codon usage variation in each gene. Correspondence analysis (COA) was used to study the major trend in codon usage variation...
April 7, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28376863/pichia-pastoris-versus-saccharomyces-cerevisiae-a-case-study-on-the-recombinant-production-of-human-granulocyte-macrophage-colony-stimulating-factor
#14
Anh-Minh Tran, Thanh-Thao Nguyen, Cong-Thuan Nguyen, Xuan-Mai Huynh-Thi, Cao-Tri Nguyen, Minh-Thuong Trinh, Linh-Thuoc Tran, Stephanie P Cartwright, Roslyn M Bill, Hieu Tran-Van
BACKGROUND: Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) is a glycoprotein that has been approved by the FDA for the treatment of neutropenia and leukemia in combination with chemotherapies. Recombinant hGM-CSF is produced industrially using the baker's yeast, Saccharomyces cerevisiae, by large-scale fermentation. The methylotrophic yeast, Pichia pastoris, has emerged as an alternative host cell system due to its shorter and less immunogenic glycosylation pattern together with higher cell density growth and higher secreted protein yield than S...
April 4, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28357382/hpv-disease-transmission-protection-and-control
#15
REVIEW
Neil D Christensen
Human papillomaviruses (HPVs) represent a large collection of viral types associated with significant clinical disease of cutaneous and mucosal epithelium. HPV-associated cancers are found in anogenital and oral mucosa, and at various cutaneous sites. Papillomaviruses are highly species and tissue restricted, and these viruses display both mucosotropic, cutaneotropic or dual tropism for epithelial tissues. A subset of HPV types, predominantly mucosal, are also oncogenic and cancers with these HPV types account for more than 200,000 deaths world-wide...
September 5, 2016: Microbial Cell
https://www.readbyqxmd.com/read/28348827/evolutionary-interpretations-of-mycobacteriophage-biodiversity-and-host-range-through-the-analysis-of-codon-usage-bias
#16
Lauren A Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J Dennehy
In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters...
October 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28346360/functional-analysis-of-the-ser149-thr149-variants-of-human-aspartylglucosaminidase-and-optimization-of-the-coding-sequence-for-protein-production
#17
Antje Banning, Jan F König, Steven J Gray, Ritva Tikkanen
Aspartylglucosaminidase (AGA) is a lysosomal hydrolase that participates in the breakdown of glycoproteins. Defects in the AGA gene result in a lysosomal storage disorder, aspartylglucosaminuria (AGU), that manifests mainly as progressive mental retardation. A number of AGU missense mutations have been identified that result in reduced AGA activity. Human variants that contain either Ser or Thr in position 149 have been described, but it is unknown if this affects AGA processing or activity. Here, we have directly compared the Ser149/Thr149 variants of AGA and show that they do not differ in terms of relative specific activity or processing...
March 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28336464/new-insights-into-the-codon-usage-patterns-of-the-bactericidal-permeability-increasing-bpi-gene-across-nine-species
#18
Wei-Yun Qin, Li-Na Gan, Ri-Wei Xia, Shou-Yong Sun, Guo-Qiang Zhu, Sheng-Long Wu, Wen-Bin Bao
Bactericidal/permeability-increasing (BPI) protein is a member of a new generation of proteins known as super-antibiotics that are implicated as endotoxin neutralising agents. Non-uniform usage of synonymous codons for a specific amino acid during translation of a protein is known as codon usage bias (CUB). Analysis of CUB and compositional dynamics of coding sequences could contribute to a better understanding of the molecular mechanism and the evolution of a particular gene. In this study, we performed CUB analysis of the complete coding sequences of the BPI gene from nine different species...
March 20, 2017: Gene
https://www.readbyqxmd.com/read/28326093/the-complete-chloroplast-genome-of-wild-rice-oryza-minuta-and-its-comparison-to-related-species
#19
Sajjad Asaf, Muhammad Waqas, Abdul L Khan, Muhammad A Khan, Sang-Mo Kang, Qari M Imran, Raheem Shahzad, Saqib Bilal, Byung-Wook Yun, In-Jung Lee
Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28324177/a-detailed-analysis-of-codon-usage-patterns-and-influencing-factors-in-zika-virus
#20
Niraj K Singh, Anuj Tyagi
Recent outbreaks of Zika virus (ZIKV) in Africa, Latin America, Europe, and Southeast Asia have resulted in serious health concerns. To understand more about evolution and transmission of ZIKV, detailed codon usage analysis was performed for all available strains. A high effective number of codons (ENC) value indicated the presence of low codon usage bias in ZIKV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations between nucleotide compositions at third codon positions and ENCs...
March 21, 2017: Archives of Virology
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