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Codon usage

Otgontuya Tsogbadrakh, Ah Reum Choi, Kwang-Hwan Jung
Microbial rhodopsins are well-known seven-transmembrane proteins that have been extensively studied for their structure and function. These retinal-binding proteins can be divided into two types. Type I is microbial rhodopsin, and type II (visual pigment) is expressed mostly in mammalian eyes. The two primary functions of type I rhodopsin are ion pumping activity and sensory transduction. Anabaena sensory rhodopsin (ASR) is a microbial rhodopsin with a specific function of photosensory transduction. ASR is expressed at moderate levels in Escherichia coli, but its expression level is lower compared to the general green light absorbing proteorhodopsin (GPR)...
May 21, 2018: Protein Expression and Purification
Marielton Dos Passos Cunha, Ayda Susana Ortiz-Baez, Caio César de Melo Freire, Paolo Marinho de Andrade Zanotto
Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. Herein, we sought evidence for fine-tuning in viral codon usage, possibly due to viral adaptation to human transmission. We compared the codon adaptation of DENV serotype 2 (DENV-2) genotypes from urban and sylvatic habitats and tried to correlate the findings with key evolutionary determinants...
May 21, 2018: Infection, Genetics and Evolution
Sudipa Das, Arif Uddin, Debjyoti Bhattacharyya, Supriyo Chakraborty
The present study attempts to focus on the pattern of codon usage bias (CUB) in mitochondrial genes among four species of Calypogeia viz. C. arguta, C. integristipula, C. neogaea and C. suecica along with the factors influencing their CUB as no work was reported yet. The four taxa exhibit noticeable difference in their morphological features, habitat preference and growth forms. To understand the patterns of codon usage in Calypogeia mitochondrial genomes, we used bioinformatic tools to analyze the mitochondrial protein-coding sequences of four Calypogeia...
May 17, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Caio César de Melo Freire, Giuseppe Palmisano, Carla T Braconi, Fernanda R Cugola, Fabiele B Russo, Patricia Cb Beltrão-Braga, Atila Iamarino, Daniel Ferreira de Lima Neto, Amadou Alpha Sall, Livia Rosa-Fernandes, Martin R Larsen, Paolo Marinho de Andrade Zanotto
BACKGROUND: Zika virus (ZIKV) was recognised as a zoonotic pathogen in Africa and southeastern Asia. Human infections were infrequently reported until 2007, when the first known epidemic occurred in Micronesia. After 2013, the Asian lineage of ZIKV spread along the Pacific Islands and Americas, causing severe outbreaks with millions of human infections. The recent human infections of ZIKV were also associated with severe complications, such as an increase in cases of Guillain-Barre syndrome and the emergence of congenital Zika syndrome...
May 10, 2018: Memórias do Instituto Oswaldo Cruz
Daniel M Chodur, Dean A Rowe-Magnus
V. vulnificus is a potent opportunistic human pathogen that contaminates the human food-chain by asymptomatically colonizing seafood. Expression of the 9-gene brp exopolysaccharide locus mediates surface adherence and is controlled by the secondary signaling molecule c-di-GMP and the regulator BrpT. Here, we show that c-di-GMP and BrpT also regulate the expression of an adjacent 5-gene cluster that includes the cabABC operon, brpT and another VpsT-like transcriptional regulator, brpS The expression of the 14 genes spanning the region increased with elevated intracellular c -di-GMP levels in a BrpT-dependent manner, save brpS , which was positively regulated by c-di-GMP and repressed by BrpT...
May 14, 2018: Journal of Bacteriology
Gur Pines, Ryan T Gill
Saturation mutagenesis is conveniently located between the two extremes of protein engineering, namely random mutagenesis, and rational design. It involves mutating a confined number of target residues to other amino acids, and hence requires knowledge regarding the sites for mutagenesis, but not their final identity. There are many different strategies for performing and designing such experiments, ranging from simple single degenerate codons to codon collections that code for distinct sets of amino acids...
2018: Methods in Molecular Biology
Andrew Hart, María Paz Cortés, Mauricio Latorre, Servet Martinez
The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships...
2018: PloS One
Priyanka Kumari, Subodh Kumar Singh, Rajiva Raman
OBJECTIVE: To evaluate the association of transforming growth factor β3 ( TGFβ3), muscle segment homeobox 1 ( MSX1), Metalloproteinases 3 ( MMP3), and MMP9 genes as candidates for nonsyndromic cleft lip and/or palate in an Indian population. DESIGN: Case-control association study, mutational screening, and functional evaluation of obtained mutations. SETTING: Mutational screening of the developmental genes, TGFβ3 and MSX1, along with functional evaluation and association of promoter region SNPs-one each in MMP3 and MMP9...
January 1, 2018: Cleft Palate-craniofacial Journal
Idan Frumkin, Marc J Lajoie, Christopher J Gregg, Gil Hornung, George M Church, Yitzhak Pilpel
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 significant cis effects 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 counterpart in several highly expressed genes in Escherichia coli This perturbation reduces both the cellular fitness and the translation efficiency of genes that have high initiation rates and are naturally enriched with the manipulated codon, in agreement with theoretical predictions...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
Tatsuhiro Nomaguchi, Yoshiaki Maeda, Tomoko Yoshino, Toru Asahi, Leila Tirichine, Chris Bowler, Tsuyoshi Tanaka
BACKGROUND: Allopolyploidy is a genomic structure wherein two or more sets of chromosomes derived from divergent parental species coexist within an organism. It is a prevalent genomic configuration in plants, as an important source of genetic variation, and also frequently confers environmental adaptability and increased crop productivity. We previously reported the oleaginous marine diatom Fistulifera solaris JPCC DA0580 to be a promising host for biofuel production and that its genome is allopolyploid, which had never previously been reported in eukaryotic microalgae...
May 4, 2018: BMC Genomics
Fernando Puente-Sánchez, Silvia Díaz, Vanessa Penacho, Angeles Aguilera, Sanna Olsson
To better understand heavy metal tolerance in Chlamydomonas acidophila, an extremophilic green alga, we assembled its transcriptome and measured transcriptomic expression before and after Cd exposure in this and the neutrophilic model microalga Chlamydomonas reinhardtii. Genes possibly related to heavy metal tolerance and detoxification were identified and analyzed as potential key innovations that enable this species to live in an extremely acid habitat with high levels of heavy metals. In addition we provide a data set of single orthologous genes from eight green algal species as a valuable resource for comparative studies including eukaryotic extremophiles...
April 27, 2018: Aquatic Toxicology
Yao Tan, Bing Jia, Yuan-Ming Chi, Hai-Bin Han, Xiao-Rong Zhou, Bao-Ping Pang
Lygus pratensis is a phytophagous pest responsible for yield losses in Bt alfalfa and other economic crops in Northwestern China. To better characterize Miridae at the genomic level, the complete mitochondrial (mt) genome of L. pratensis was sequenced and analyzed in this study. The mt genome was amplified via the polymerase chain reaction to generate overlapping fragments. These fragments were then sequenced, spliced, and analyzed to include the examination of nucleotide composition, codon usage, compositional biases, protein-coding genes (PCGs), and RNA secondary structures...
March 1, 2018: Journal of Insect Science
Eli Goz, Zohar Zafrir, Tamir Tuller
Motivation: Understanding how viruses co-evolve with their hosts and adapt various genomic level strategies in order to ensure their fitness may have essential implications in unveiling the secrets of viral evolution, and in developing new vaccines and therapeutic approaches. Here, based on a novel genomic analysis of 2,625 different viruses and 439 corresponding host organisms, we provide evidence of universal evolutionary selection for high dimensional 'silent' patterns of information hidden in the redundancy of viral genetic code...
April 30, 2018: Bioinformatics
Jing Meng, Xuepei Li, Hongtao Li, Junbo Yang, Hong Wang, Jun He
Aconitum (Ranunculaceae) consists of approximately 400 species distributed in the temperate regions of the northern hemisphere. Many species are well-known herbs, mainly used for analgesia and anti-inflammatory purposes. This genus is well represented in China and has gained widespread attention for its toxicity and detoxification properties. In southwestern China, several Aconitum species, called ‘Dula’ in the Yi Nationality, were often used to control the poisonous effects of other Aconitum plants...
April 26, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
J Jansing, J F Buyel
The yield of recombinant proteins in plants determines their economic competitiveness as a production platform compared to microbes and mammalian cells. The promoter, untranslated regions (UTRs) and codon usage can all contribute to the yield, but potential interactions among these components have not been examined in detail. Here we investigated the effect of two promoters (35SS and nos) and four 5'UTRs on the spatiotemporal expression of DsRed mRNA and the accumulation of DsRed protein during transient expression in tobacco (Nicotiana tabacum) mediated by Agrobacterium tumefaciens...
April 27, 2018: Biotechnology Journal
Ting Fang, Zhenghong Tao, Yanhong Liu, Changming Yu, Ruizhi Zhi, Rui Yu
CRM197 (cross-reacting material 197), a non-toxic mutant of diphtheria toxin, has wide application potential in biopharmaceuticals. However, it is difficult to express CRM197 in bacteria other than Corynebacterium diphtheriae. Here we proposed a new alternative method to produce soluble CRM197 without label in Escherichia coli. In particular, a synthetic gene coding for CRM197, optimized for E. coli codon usage, was cloned in the pET32a (+) vector. Accordingly, the over-expression of the protein was simply induced with IPTG in E...
April 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Rafael J Argüello, Marisa Reverendo Simoes, Andreia Mendes, Voahirana Camosseto, Adrian G Torres, Lluis Ribas de Pouplana, Serge A van de Pavert, Evelina Gatti, Philippe Pierre
The processing rate of translating ribosomes along mRNAs regulates gene expression by controling co-translational protein folding and mRNA stability. Many factors regulate translation elongation, including tRNA levels, codon usage, or phosphorylation of eukaryotic Elongation Factor 2 ( eEF2 ). Current methods to measure translation elongation lack single cell resolution, require expression of multiple transgenes and have never been successfully applied ex-vivo. Here, we show by using a combination of puromycilation detection and flow cytometry (SunRiSE), that translation elongation can be measured accurately in primary cells in pure or heterogenous populations isolated from blood or tissues...
April 26, 2018: Journal of Cell Science
Gairu Li, Ruyi Wang, Cheng Zhang, Shilei Wang, Wanting He, Junyan Zhang, Jie Liu, Yuchen Cai, Jiyong Zhou, Shuo Su
The H3N2 canine influenza virus (CIV) originated from an avian species. Since its emergence, it has circulated in multiple states and has caused pandemics among dog populations; however, no comprehensive studies have explored the causes driving these ongoing cases. The study of the codon usage patterns of viruses can reveal the genetic changes required for the viruses to adapt to new hosts and the external environment. Here we performed a thorough genetic, evolutionary, and codon usage analysis. We identified three evolutionary H3N2 CIV clades from a timescaled phylogenetic tree, namely, Origin, China, and Korea/USA, by principal component analysis (PCA)...
April 25, 2018: Emerging Microbes & Infections
Adi Yannai, Sophia Katz, Ruth Hershberg
Codon usage bias affects the genomes of organisms from all kingdoms of life, and results from both background substitution biases and natural selection. Natural selection on codon usage to increase translation accuracy and efficiency has long been known to affect gene sequences. Such selection is stronger on highly, compared to lowly expressed genes, resulting in higher levels of codon bias within genes with higher expression levels. Additionally, selection on translation accuracy affects more strongly codons encoding conserved amino acids, since these will more often affect protein folding and/or function...
April 23, 2018: Genome Biology and Evolution
Le-Ping Zhang, Yin-Yin Cai, Dan-Na Yu, Kenneth B Storey, Jia-Yong Zhang
The family Toxoderidae (Mantodea) contains an ecologically diverse group of praying mantis species that have in common greatly elongated bodies. In this study, we sequenced and compared the complete mitochondrial genomes of two Toxoderidae species, Paratoxodera polyacantha and Toxodera hauseri , and compared their mitochondrial genome characteristics with another member of the Toxoderidae, Stenotoxodera porioni (KY689118) . The lengths of the mitogenomes of T. hauseri and P. polyacantha were 15,616 bp and 15,999 bp, respectively, which is similar to that of S...
2018: PeerJ
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