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Codon usage

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https://www.readbyqxmd.com/read/27905914/development-of-a-gene-synthesis-platform-for-the-efficient-large-scale-production-of-small-genes-encoding-animal-toxins
#1
Ana Filipa Sequeira, Joana L A Brás, Catarina I P D Guerreiro, Renaud Vincentelli, Carlos M G A Fontes
BACKGROUND: Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. In addition, when coupled with efficient gene design algorithms that optimize codon usage, it leads to high levels of recombinant protein expression. RESULTS: Here, we describe the development of an optimized gene synthesis platform that was applied to the large scale production of small genes encoding venom peptides...
December 1, 2016: BMC Biotechnology
https://www.readbyqxmd.com/read/27903612/the-role-of-4u-as-an-extended-translation-termination-signal-in-bacteria
#2
Yulong Wei, Xuhua Xia
Termination efficiency of stop codons depends on the first 3' flanking (+4) base in bacteria and eukaryotes. In both Escherichia coli and Saccharomyces cerevisiae, termination read-through is reduced in the presence of +4U; however, the molecular mechanism underlying +4U function is poorly understood. Here, we perform comparative genomics analysis on 25 bacterial species (covering Actinobacteria, Bacteriodetes, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Proteobacteria and Spirochaetae) with bioinformatics approaches to examine the influence of +4U in bacterial translation termination by contrasting between highly and lowly expressed genes (HEGs and LEGs)...
November 30, 2016: Genetics
https://www.readbyqxmd.com/read/27897254/high-level-expression-of-improved-thermo-stable-alkaline-xylanase-variant-in-pichia-pastoris-through-codon-optimization-multiple-gene-insertion-and-high-density-fermentation
#3
Yihong Lu, Cheng Fang, Qinhong Wang, Yuling Zhou, Guimin Zhang, Yanhe Ma
In paper industry, xylanases are used to increase the pulp properties in bleaching process as its eco-friendly nature. The xylanases activity is hindered by high temperature and alkaline conditions with high enzyme production cost in the paper industry. Here, XynHB, an alkaline stable xylanase from Bacillus pumilus HBP8 was mutated at N188A to XynHBN188A. Expressed mutant in E. coli showed 1.5-fold higher xylanase activity than XynHB at 60 °C. The mutant expressed in Pichia pastoris was glycosylated, remained stable for 30 min at 60 °C...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27895624/visualizing-evolutionary-relationships-of-multidomain-proteins-an-example-from-receiver-rec-domains-of-sensor-histidine-kinases-in-the-candidatus-maribeggiatoa-str-orange-guaymas-draft-genome
#4
Barbara J MacGregor
For multidomain proteins, evolutionary changes may occur at the domain as well as the whole-protein level. An example is presented here, with suggestions for how such complicated relationships might be visualized. Earlier analysis of the Candidatus Maribeggiatoa str. Orange Guaymas (BOGUAY; Gammaproteobacteria) single-filament draft genome found evidence of gene exchange with the phylogenetically distant Cyanobacteria, particularly for sensory and signal transduction proteins. Because these are modular proteins, known to undergo frequent duplication, domain swapping, and horizontal gene transfer, a single domain was chosen for analysis...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27893824/analysis-of-synonymous-codon-usage-bias-of-zika-virus-and-its-adaption-to-the-hosts
#5
Hongju Wang, Siqing Liu, Bo Zhang, Wenqiang Wei
Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators...
2016: PloS One
https://www.readbyqxmd.com/read/27889062/monoallelic-mutations-in-the-translation-initiation-codon-of-klhl24-cause-skin-fragility
#6
Yinghong He, Kristin Maier, Juna Leppert, Ingrid Hausser, Agnes Schwieger-Briel, Lisa Weibel, Martin Theiler, Dimitra Kiritsi, Hauke Busch, Melanie Boerries, Katariina Hannula-Jouppi, Hannele Heikkilä, Kaisa Tasanen, Daniele Castiglia, Giovanna Zambruno, Cristina Has
The genetic basis of epidermolysis bullosa, a group of genetic disorders characterized by the mechanically induced formation of skin blisters, is largely known, but a number of cases still remain genetically unsolved. Here, we used whole-exome and targeted sequencing to identify monoallelic mutations, c.1A>G and c.2T>C, in the translation initiation codon of the gene encoding kelch-like protein 24 (KLHL24) in 14 individuals with a distinct skin-fragility phenotype and skin cleavage within basal keratinocytes...
November 21, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27882066/bioinformatic-analysis-of-codon-usage-and-phylogenetic-relationships-in-different-genotypes-of-the-hepatitis-c-virus
#7
Mojtaba Mortazavi, Mohammad Zarenezhad, Seyed Moayed Alavian, Saeed Gholamzadeh, Abdorrasoul Malekpour, Mohammad Ghorbani, Masoud Torkzadeh Mahani, Safa Lotfi, Ali Fakhrzad
BACKGROUND: The hepatitis C virus (HCV) has six major genotypes. The purpose of this study was to phylogenetically investigate the differences between the genotypes of HCV, and to determine the types of amino acid codon usage in the structure of the virus in order to discover new methods for treatment regimes. METHODS: The codon usage of the six genotypes of the HCV nucleotide sequence was investigated through the online application available on the website Gene Infinity...
October 2016: Hepatitis Monthly
https://www.readbyqxmd.com/read/27876621/translational-resistivity-conductivity-of-coding-sequences-during-exponential-growth-of-escherichia-coli
#8
Kazuyuki Takai
Codon adaptation index (CAI) has been widely used for prediction of expression of recombinant genes in Escherichia coli and other organisms. However, CAI has no mechanistic basis that rationalizes its application to estimation of translational efficiency. Here, I propose a model based on which we could consider how codon usage is related to the level of expression during exponential growth of bacteria. In this model, translation of a gene is considered as an analog of electric current, and an analog of electric resistance corresponding to each gene is considered...
November 19, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27845207/codon-usage-pattern-and-prediction-of-gene-expression-level-in-bungarus-species
#9
Supriyo Chakraborty, Debojyoti Nag, Tarikul Huda Mazumder, Arif Uddin
Codon bias study in an organism gains significance in understanding the molecular mechanism as well as the functional conservation of gene expression during the course of evolution. The prime focus in this study is to compare the codon usage patterns among the four species belonging to the genus Bungarus (B. multicinctus, B. fasciatus, B. candidus and B. flaviceps) using several codon bias parameters. Our results suggested that relatively low codon bias exists in the coding sequences of the selected species...
November 11, 2016: Gene
https://www.readbyqxmd.com/read/27842546/optimization-of-construct-design-and-fermentation-strategy-for-the-production-of-bioactive-atf-sap-a-saporin-based-anti-tumoral-upar-targeted-chimera
#10
Alfredo Errico Provenzano, Riccardo Posteri, Francesco Giansanti, Francesco Angelucci, Sopsamorn U Flavell, David J Flavell, Maria Serena Fabbrini, Danilo Porro, Rodolfo Ippoliti, Aldo Ceriotti, Paola Branduardi, Riccardo Vago
BACKGROUND: The big challenge in any anti-tumor therapeutic approach is represented by the development of drugs selectively acting on the target with limited side effects, that exploit the unique characteristics of malignant cells. The urokinase (urokinase-type plasminogen activator, uPA) and its receptor uPAR have been identified as preferential target candidates since they play a key role in the evolution of neoplasms and are associated with neoplasm aggressiveness and poor clinical outcome in several different tumor types...
November 14, 2016: Microbial Cell Factories
https://www.readbyqxmd.com/read/27822527/differential-functional-constraints-cause-strain-level-endemism-in-polynucleobacter-populations
#11
Naseer Sangwan, Iratxe Zarraonaindia, Jarrad T Hampton-Marcell, Herbert Ssegane, Tifani W Eshoo, Geeta Rijal, M Cristina Negri, Jack A Gilbert
The adaptation of bacterial lineages to local environmental conditions creates the potential for broader genotypic diversity within a species, which can enable a species to dominate across ecological gradients because of niche flexibility. The genus Polynucleobacter maintains both free-living and symbiotic ecotypes and maintains an apparently ubiquitous distribution in freshwater ecosystems. Subspecies-level resolution supplemented with metagenome-derived genotype analysis revealed that differential functional constraints, not geographic distance, produce and maintain strain-level genetic conservation in Polynucleobacter populations across three geographically proximal riverine environments...
May 2016: MSystems
https://www.readbyqxmd.com/read/27817871/co-translational-folding-a-novel-modulator-of-local-protein-expression-in-mammalian-neurons
#12
REVIEW
Rico Schieweck, Bastian Popper, Michael A Kiebler
Local protein expression at synapses is a prerequisite for learning in mammalian neurons. It has been shown that a subset of RNAs is localized in dendrites. These transcripts are first assembled into ribonucleoprotein particles in the cell body and are then transported along the cytoskeleton to or near synapses in a translationally repressed state. However, we know very little about the underlying mechanisms of local translation as well as potential protein degradation. Research in the last years showed many features of general translation...
December 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27808241/analysis-of-codon-usage-patterns-in-ginkgo-biloba-reveals-codon-usage-tendency-from-a-u-ending-to-g-c-ending
#13
Bing He, Hui Dong, Cong Jiang, Fuliang Cao, Shentong Tao, Li-An Xu
As one of the most ancient tree species, the codon usage pattern analysis of Ginkgo biloba is a useful way to understand its evolutionary and genetic mechanisms. Several studies have been conducted on angiosperms, but seldom on gymnosperms. Based on RNA-Seq data of the G. biloba transcriptome, amount to 17,579 unigenes longer than 300 bp were selected and analyzed from 68,547 candidates. The codon usage pattern tended towards more frequently use of A/U-ending codons, which showed an obvious gradient progressing from gymnosperms to dicots to monocots...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27788395/in-silico-investigation-of-the-impact-of-synonymous-variants-in-abcb4-gene-on-mrna-stability-structure-splicing-accuracy-and-codon-usage-potential-contribution-to-pfic3-disease
#14
Boudour Khabou, Olfa Siala-Sahnoun, Lamia Gargouri, Emna Mkaouar-Rebai, Leila Keskes, Mongia Hachicha, Faiza Fakhfakh
Progressive Familial Intrahepatic Cholestasis type 3 (PFIC3) is an autosomal-recessive liver disease due to mutations in the ABCB4 gene encoding for the MDR3 protein. In the present study, we performed molecular and bioinformatic analyses in PFIC3 patients in order to understand the molecular basis of the disease. The three studied patients with PFIC3 were screened by PCR amplification followed by direct sequencing of the 27 coding exons of ABCB4. In silico analysis was performed by bioinformatic programs. We revealed three synonymous polymorphisms c...
October 22, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27783132/orthogonal-protein-translation-using-pyrrolysyl-trna-synthetases-for-single-and-multiple-noncanonical-amino-acid-mutagenesis
#15
Tobias Baumann, Matthias Exner, Nediljko Budisa
To date, the two systems most extensively used for noncanonical amino acid (ncAA) incorporation via orthogonal translation are based on the Methanococcus jannaschii TyrRS/tRNA CUA(Tyr) and the Methanosarcina barkeri/Methanosarcina mazei PylRS/tRNA CUA(Pyl) pairs. Here, we summarize the development and usage of the pyrrolysine-based system for orthogonal translation, a process that allows for the recombinant production of site-specifically labeled proteins and peptides. Via stop codon suppression in Escherichia coli and mammalian cells, genetically encoded biomolecules can be equipped with a great diversity of chemical functionalities including click chemistry handles, post-translational modifications, and photocaged sidechains...
October 26, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27782154/expression-of-varied-gfps-in-saccharomyces-cerevisiae-codon-optimization-yields-stronger-than-expected-expression-and-fluorescence-intensity
#16
Misato Kaishima, Jun Ishii, Toshihide Matsuno, Nobuo Fukuda, Akihiko Kondo
Green fluorescent protein (GFP), which was originally isolated from jellyfish, is a widely used tool in biological research, and homologs from other organisms are available. However, researchers must determine which GFP is the most suitable for a specific host. Here, we expressed GFPs from several sources in codon-optimized and non-codon-optimized forms in the yeast Saccharomyces cerevisiae, which represents an ideal eukaryotic model. Surprisingly, codon-optimized mWasabi and mNeonGreen, which are typically the brightest GFPs, emitted less green fluorescence than did the other five codon-optimized GFPs tested in S...
October 26, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27777018/successful-derivation-of-xeno-free-mesenchymal-stem-cell-lines-from-endometrium-of-infertile-women
#17
Tatsanee Phermthai, Kittima Tungprasertpol, Suphakde Julavijitphong, Puttachart Pokathikorn, Sasiprapa Thongbopit, Suparat Wichitwiengrat
Transplantation of mesenchymal stem cells (MSC) can effectively repair endometrial deficiencies, including infertile patients with a problem of inadequate endometrium thickness. Although, MSC derived from different organ sources have a similarity of MSC specific characteristics, endometrial stem cells (EMSC) are temporally regulated throughout the menstrual cycle in a micro-environmental niche found only in endometrial tissue. Given the micro-environment niche, developing treatments for endometrial disorders with EMSC should be a top priority...
December 2016: Reproductive Biology
https://www.readbyqxmd.com/read/27776434/codon-usage-bias-and-phylogenetic-analysis-of-mitochondrial-nd1-gene-in-pisces-aves-and-mammals
#18
Arif Uddin, Monisha Nath Choudhury, Supriyo Chakraborty
The mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) gene is a subunit of the respiratory chain complex I and involved in the first step of the electron transport chain of oxidative phosphorylation (OXPHOS). To understand the pattern of compositional properties, codon usage and expression level of mitochondrial ND1 genes in pisces, aves, and mammals, we used bioinformatic approaches as no work was reported earlier. In this study, a perl script was used for calculating nucleotide contents and different codon usage bias parameters...
October 24, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/27776193/the-role-of-the-5-terminal-region-of-p53-mrna-in-the-p53-gene-expression
#19
Agata Swiatkowska, Paulina Zydowicz, Joanna Sroka, Jerzy Ciesiołka
The p53 tumour suppressor protein is one of the major factors responsible for cell cycle regulation and protection against cancer development. This is why it is often referred to as "the guardian of the genome". On the other hand, mutations in the p53 gene are connected with more than 50% of tumours of various types. The thirty-six years of extensive research on the p53 gene and its protein products have shown how sophisticated the p53-based cell system control is. An additional level of complexity of the p53 research is connected with at least twelve p53 isoforms which have been identified in the cell...
October 25, 2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27766939/phylogenetic-tree-construction-using-trinucleotide-usage-profile-tup
#20
Si Chen, Lih-Yuan Deng, Dale Bowman, Jyh-Jen Horng Shiau, Tit-Yee Wong, Behrouz Madahian, Henry Horng-Shing Lu
BACKGROUND: It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length. For a satisfactory result, the recommended word length (k) ranges from 6 to 15 and it may not be a multiple of 3 (codon length)...
October 6, 2016: BMC Bioinformatics
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