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https://www.readbyqxmd.com/read/29678658/essentiality-conservation-evolutionary-pressure-and-codon-bias-in-bacterial-genomes
#1
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. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias...
April 17, 2018: Gene
https://www.readbyqxmd.com/read/29669515/compositional-and-mutational-rate-heterogeneity-in-mitochondrial-genomes-and-its-effect-on-the-phylogenetic-inferences-of-cimicomorpha-hemiptera-heteroptera
#2
Huanhuan Yang, Teng Li, Kai Dang, Wenjun Bu
BACKGROUND: Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets...
April 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29666329/codon-usage-vis-a-vis-start-and-stop-codon-context-analysis-of-three-dicot-species
#3
Prosenjit Paul, Arup Kumar Malakar, Supriyo Chakraborty
To understand the variation in genomic composition and its effect on codon usage, we performed the comparative analysis of codon usage and nucleotide usage in the genes of three dicots, Glycine max, Arabidopsis thaliana and Medicago truncatula. The dicot genes were found to be A/T rich and have predominantly A-ending and/or T-ending codons. GC3s directly mimic theusage pattern of global GC content. Relative synonymous codon usage analysis suggests that the high usage frequency of A/T over G/C mononucleotide containing codons in AT-rich dicot genome is due to compositional constraint as a factor of codon usage bias...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29660556/comparative-analysis-of-ancylostoma-ceylanicum-mitochondrial-genome-with-other-ancylostoma-species
#4
Xianli Shi, Mingwei Wang, A Y Abdullahi, Yeqi Fu, Fang Yang, Xingang Yu, Weida Pan, Xinxin Yan, Jianxiong Hang, Pan Zhang, Guoqing Li
Ancylostoma ceylanicum may inhabit the small intestine of canids, felids and humans, can pose a potential risk to public health. This study is the first time to amplify complete mitochondrial genome sequence of A. ceylanicum from dog and to compare it with Ancylostoma tubaeforme, Ancylostoma duodenale and Ancylostoma caninum. The results showed that the complete mitochondrial genome of A. ceylanicum was 13,660 bp in length, including 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes and 3 non-coding regions (AT-rich region, SNCR and LNCR)...
April 13, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29651700/engineering-pichia-pastoris-for-efficient-production-of-a-novel-bifunctional-strongylocentrotus-purpuratus-invertebrate-type-lysozyme
#5
Peng Huang, Jinlei Shi, Qingwen Sun, Xianping Dong, Ning Zhang
Lysozymes are known as ubiquitously distributed immune effectors with hydrolytic activity against peptidoglycan, the major bacterial cell wall polymer, to trigger cell lysis. In the present study, the full-length cDNA sequence of a novel sea urchin Strongylocentrotus purpuratus invertebrate-type lysozyme (sp-iLys) was synthesized according to the codon usage bias of Pichia pastoris and was cloned into a constitutive expression plasmid pPIC9K. The resulting plasmid, pPIC9K-sp-iLys, was integrated into the genome of P...
April 13, 2018: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29621569/alignment-based-and-alignment-free-methods-converge-with-experimental-data-on-amino-acids-coded-by-stop-codons-at-split-between-nuclear-and-mitochondrial-genetic-codes
#6
Hervé Seligmann
Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data...
April 2, 2018: Bio Systems
https://www.readbyqxmd.com/read/29617800/plastid-transcript-editing-across-dinoflagellate-lineages-shows-lineage-specific-application-but-conserved-trends
#7
Christen M Klinger, Lucas Paoli, Robert J Newby, Matthew Yu-Wei Wang, Hyrum D Carroll, Jeffrey D Leblond, Christopher J Howe, Joel B Dacks, Chris Bowler, Aubery Bruce Cahoon, Richard G Dorrell, Elisabeth Richardson
Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29617761/refining-the-ambush-hypothesis-evidence-that-gc-and-at-rich-bacteria-employ-different-frameshift-defence-strategies
#8
Liam Abrahams, Laurence D Hurst
Stop codons are frequently selected for beyond their regular termination function for error control. The 'ambush hypothesis' proposes out of frame stop codons (OSCs) terminating frameshifted translations are selected for. Although early indirect evidence was partially supportive, recent evidence suggests OSC frequencies are not exceptional when considering underlying nucleotide content. However, prior null tests fail to control amino acid/codon usages or possible local mutational biases. We therefore return to the issue using bacterial genomes, considering several tests defining and testing against a null...
April 2, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29608728/insights-into-an-extensively-fragmented-eukaryotic-genome-de-novo-genome-sequencing-of-the-multinuclear-ciliate-uroleptopsis-citrina
#9
Weibo Zheng, Chundi Wang, Ying Yan, Feng Gao, Thomas G Doak, Weibo Song
Ciliated protists are a large group of single-celled eukaryotes with separate germline and somatic nuclei in each cell. The somatic genome is developed from the zygotic nucleus through a series of chromosomal rearrangements, including fragmentation, DNA elimination, de novo telomere addition, and DNA amplification. This unique feature makes them perfect models for research in genome biology and evolution. However, genomic research of ciliates has been limited to a few species, owing to problems with DNA contamination and obstacles in cultivation...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29596640/multiple-factors-confounding-phylogenetic-detection-of-selection-on-codon-usage
#10
Simon Laurin-Lemay, Hervé Philippe, Nicolas Rodrigue
Detecting selection on codon usage (CU) is a difficult task, since CU can be shaped by both the mutational process and selective constraints operating at the DNA, RNA and protein levels. Yang and Nielsen (2008) developed a test (which we call CUYN) for detecting selection on CU using two competing mutation-selection models of codon substitution. The null model assumes that CU is determined by the mutation bias alone, whereas the alternative model assumes that both mutation bias and/or selection act on CU. In applications on mammalian-scale alignments, the CUYN test detects selection on CU for numerous genes...
March 27, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29584741/genome-wide-analysis-of-codon-usage-bias-in-four-sequenced-cotton-species
#11
Liyuan Wang, Huixian Xing, Yanchao Yuan, Xianlin Wang, Muhammad Saeed, Jincai Tao, Wei Feng, Guihua Zhang, Xianliang Song, Xuezhen Sun
Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids...
2018: PloS One
https://www.readbyqxmd.com/read/29575916/factors-affecting-synonymous-codon-usage-of-housekeeping-genes-in-drosophila-melanogaster
#12
Yi Wen Lu, Tai Sheng Chiu
Housekeeping genes (HK genes) are required for cell survival and the maintenance of basic cellular functions. The investigation of factors affecting codon usage patterns in HK genes of insects can help in understanding the molecular evolution of insects and aid the development of insect pest management strategies. In this study, we employed bioinformatics approaches to analyze the codon usage bias (CUB) of HK genes in the insect model organism, Drosophila melanogaster. A comparison of CUB between 1107 HK genes and 1084 high tissue specificity genes suggested that HK genes have higher CUB in D...
March 2018: Acta Biologica Hungarica
https://www.readbyqxmd.com/read/29551886/evolution-of-synonymous-codon-usage-bias-in-west-african-and-central-african-strains-of-monkeypox-virus
#13
Sudeesh Karumathil, Nimal T Raveendran, Doss Ganesh, Sampath Kumar Ns, Rahul R Nair, Vijaya R Dirisala
The evolution of bias in synonymous codon usage in chosen monkeypox viral genomes and the factors influencing its diversification have not been reported so far. In this study, various trends associated with synonymous codon usage in chosen monkeypox viral genomes were investigated, and the results are reported. Identification of factors that influence codon usage in chosen monkeypox viral genomes was done using various codon usage indices, such as the relative synonymous codon usage, the effective number of codons, and the codon adaptation index...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29548178/determinants-of-translation-speed-are-randomly-distributed-across-transcripts-resulting-in-a-universal-scaling-of-protein-synthesis-times
#14
Ajeet K Sharma, Nabeel Ahmed, Edward P O'Brien
Ribosome profiling experiments have found greater than 100-fold variation in ribosome density along mRNA transcripts, indicating that individual codon elongation rates can vary to a similar degree. This wide range of elongation times, coupled with differences in codon usage between transcripts, suggests that the average codon translation-rate per gene can vary widely. Yet, ribosome run-off experiments have found that the average codon translation rate for different groups of transcripts in mouse stem cells is constant at 5...
February 2018: Physical Review. E
https://www.readbyqxmd.com/read/29547124/codon-usage-biases-co-evolve-with-transcription-termination-machinery-to-suppress-premature-cleavage-and-polyadenylation
#15
Zhipeng Zhou, Yunkun Dang, Mian Zhou, Haiyan Yuan, Yi Liu
Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons results in premature transcription termination (PTT) within open reading frames and the abolishment of full-length mRNA...
March 16, 2018: ELife
https://www.readbyqxmd.com/read/29543155/codon-usage-bias-controls-mrna-and-protein-abundance-in-trypanosomatids
#16
Laura Jeacock, Joana Faria, David Horn
Protein abundance differs from a few to millions of copies per cell. Trypanosoma brucei presents an excellent model for studies on codon bias and differential gene expression because transcription is broadly unregulated and uniform across the genome. T. brucei is also a major human and animal protozoal pathogen. Here, an experimental assessment, using synthetic reporter genes, revealed that GC3 codons have a major positive impact on both mRNA and protein abundance. Our estimates of relative expression, based on coding sequences alone (codon usage and sequence length), are within 2-fold of the observed values for the majority of measured cellular mRNAs (n>7000) and proteins (n>2000)...
March 15, 2018: ELife
https://www.readbyqxmd.com/read/29540301/complete-mitochondrial-genome-of-the-soybean-leaffolder-omiodes-indicata-lepidoptera-pyraloidea-crambidae-and-phylogenetic-analysis-for-pyraloidea
#17
Mingsheng Yang, Lu Song, Jianhang Mao, Yuxia Shi, Changjing Wu, Yunxia Zhang, Li Huang, Weifeng Peng, Xiaomeng Liu
Complete mitochondrial genome (mitogenome) of the Omiodes indicata was sequenced and characterized. The circular mitogenome is 15,367 bp long, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (81.6%). All 13 PCGs initiate with canonical start codon (ATN), except for cox1 that initiates with CGA. All tRNAs have a typical clover-leaf structure, except for trnS1 (AGN) in which the base pairs of the dihydrouridine (DHU) arm are reduced...
March 11, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29535392/prevalence-of-the-single-nucleotide-polymorphism-rs11554137-idh1-105ggt-in-brain-tumors-of-a-cohort-of-italian-patients
#18
Giorgia Acquaviva, Michela Visani, Dario de Biase, Gianluca Marucci, Enrico Franceschi, Alicia Tosoni, Alba A Brandes, Kerry J Rhoden, Annalisa Pession, Giovanni Tallini
IDH mutational status is required for proper diagnosis according to the WHO criteria revised in 2016. The single nucleotide polymorphism (SNP) rs11554137 (IDH1105GGT ) at codon 105 of IDH1 has been reported in patients with several tumor types, including those with glioma. The aim of this study is to investigate the prevalence of IDH1105GGT in a cohort of brain tumors, and its association with clinicopathologic features and IDH1 and IDH2 missense mutations. Exon 4 of IDH1 and IDH2 was analyzed in a series of brain tumors classified according to current WHO criteria...
March 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29534300/adaptation-of-borrelia-burgdorferi-to-its-natural-hosts-by-synonymous-codon-and-amino-acid-usage
#19
Xiao-Xia Ma, Peng Ma, Qiu-Yan Chang, Zhen-Bin Liu, Derong Zhang, Xiao-Kai Zhou, Zhong-Ren Ma, Xin Cao
Lyme disease, caused by Borrelia burgdorferi, is a focally endemic tick-transmitted zoonotic infection. In this study, the major factors underlying synonymous codon-related amino acid usage in the B. burgdorferi genome and bias in synonymous codon usage of the translation initiation region of coding sequences were analyzed. Additionally, adaptation of B. burgdorferi to several of its hosts was analyzed in the context of synonymous codon usage. Principal component analysis (PCA) revealed that nucleotide content at the third synonymous position of a codon influenced the synonymous codon usage pattern, but the strand-specific factor did not influence the synonymous codon usage pattern of B...
March 13, 2018: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/29530949/hepatitis-a-virus-codon-usage-implications-for-translation-kinetics-and-capsid-folding
#20
Rosa M Pintó, Francisco-Javier Pérez-Rodríguez, Lucia D' Andrea, Montserrat de Castellarnau, Susana Guix, Albert Bosch
Codon usage bias is universal to all genomes. Hepatitis A virus (HAV) codon usage is highly biased and deoptimized with respect to its host. Accordingly, HAV is unable to induce cellular translational shutoff and its internal ribosome entry site (IRES) is inefficient. Codon usage deoptimization may be seen as a hawk (host cell) versus dove (HAV) game strategy for accessing transfer RNA (tRNA). HAV avoids use of abundant host cell codons and thereby eludes competition for the corresponding tRNAs. Instead, codons that are abundant or rare in cellular messenger RNAs (mRNAs) are used relatively rarely in its genome, although intermediately abundant host cell codons are abundant in the viral genome...
March 12, 2018: Cold Spring Harbor Perspectives in Medicine
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