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Codon usage

Shilpee Pal, Indrani Sarkar, Ayan Roy, Pradeep K Das Mohapatra, Keshab C Mondal, Arnab Sen
The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium...
September 18, 2017: Genetica
Jaitip Tipanee, Thierry VandenDriessche, Marinee K Chuah
Transposons have emerged as promising vectors for gene therapy that can potentially overcome some of the limitations of commonly used viral vectors. Transposons stably integrate into the target cell genome, enabling persistent expression of therapeutic genes. Transposons have evolved from being used as basic tools in biomedical research to bona fide therapeutics. Currently, the most promising transposons for gene therapy applications are derived from Sleeping Beauty (SB) or piggyBac (PB). Stable transposition requires co-delivery of the transposon DNA with the corresponding transposase gene, mRNA, or protein...
August 22, 2017: Human Gene Therapy
Shaokui Yi, Yanhe Li, Weimin Wang
Neutrality plots revealed that selection probably dominates codon bias, whereas mutation plays only a minor role, in shaping the codon bias in three loaches, Misgurnus anguillicaudatus, M. mohoity, and M. bipartitus. These three species also clearly showed similar tendencies in the preferential usage of codons. Nineteen, nine, and 14 preferred codon pairs and 179, 182, and 173 avoided codon pairs were also detected in M. anguillicaudatus, M. bipartitus, and M. mohoity, respectively, and the most frequently avoided type of cP3-cA1 dinucleotide in these species was nnUAnn...
September 11, 2017: Genomics
Nico J Claassens, Melvin F Siliakus, Sebastiaan K Spaans, Sjoerd C A Creutzburg, Bart Nijsse, Peter J Schaap, Tessa E F Quax, John van der Oost
High-level, recombinant production of membrane-integrated proteins in Escherichia coli is extremely relevant for many purposes, but has also been proven challenging. Here we study a combination of transcriptional fine-tuning in E. coli LEMO21(DE3) with different codon usage algorithms for heterologous production of membrane proteins. The overexpression of 6 different membrane proteins is compared for the wild-type gene codon usage variant, a commercially codon-optimized variant, and a codon-harmonized variant...
2017: PloS One
Ye Chen, Xinxin Li, Xiaojuan Chi, Song Wang, Yanmei Ma, Jilong Chen
The classical swine fever virus (CSFV), circulating worldwide, is a highly contagious virus. Since the emergence of CSFV, it has caused great economic loss in swine industry. The envelope glycoprotein E2 gene of the CSFV is an immunoprotective antigen that induces the immune system to produce neutralizing antibodies. Therefore, it is essential to study the codon usage of the E2 gene of the CSFV. In this study, 140 coding sequences of the E2 gene were analyzed. The value of effective number of codons (ENC) showed low codon usage bias in the E2 gene...
2017: PloS One
Àlbert Rafels-Ybern, Adrian Gabriel Torres, Xavier Grau-Bove, Iñaki Ruiz-Trillo, Lluís Ribas de Pouplana
The modification of adenosine to inosine at position 34 of tRNA anticodons has a profound impact upon codon-anticodon recognition. In bacteria, I34 is thought to exist only in tRNA(Arg), while in eukaryotes the modification is present in eight different tRNAs. In eukaryotes, the widespread use of I34 strongly influenced the evolution of genomes in terms of tRNA gene abundance and codon usage. In humans, codon usage indicates that I34 modified tRNAs are preferred for the translation of highly repetitive coding sequences, suggesting that I34 is an important modification for the synthesis of proteins of highly skewed amino acid composition...
September 7, 2017: RNA Biology
Maϊwen Caudron-Herger, Sven Diederichs
As a genetic disease, cancer is caused by the activation of oncogenes and the inhibition of tumor suppressor genes via genetic and epigenetic mechanisms. Given the important role of energy metabolism in tumors, we analyzed the cancer-derived mutations occurring in the DNA of the mitochondrion. Mutations in the mitochondrial DNA (mtDNA) compared to nuclear DNA are 62% decreased relative to the coding length per chromosome. We find that the majority of these mutations affects highly conserved nucleotides - significantly exceeding the conservation of the mtDNA - and are devoid of single nucleotide polymorphisms (SNPs)...
September 5, 2017: RNA Biology
John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V Santana-Quintero, Upendra Katneni, Vahan Simonyan, Chava Kimchi-Sarfaty
BACKGROUND: Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codons may affect protein expression, structure, and function. Recombinant gene technologies commonly take advantage of the former effect by implementing a technique termed codon optimization, in which codons are replaced with synonymous ones in order to increase protein expression...
September 2, 2017: BMC Bioinformatics
Ana Subotić, Erwin Swinnen, Liesbeth Demuyser, Herlinde De Keersmaecker, Hideaki Mizuno, Hélène Tournu, Patrick Van Dijck
Investigation of protein-protein interactions (PPI) in Candida albicans is essential for understanding the regulation of the signal transduction network that triggers its pathogenic lifestyle. Unique features of C. albicans, such as the alternative codon usage and incomplete meiosis, have enforced the optimization of standard genetic methods as well as development of novel approaches. Since the existing methods for detection of PPI are limited for direct visualization of the interacting complex in vivo, we have established a bimolecular fluorescence complementation (BiFC) in C...
August 31, 2017: G3: Genes—Genomes—Genetics
Darja Kanduc
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 hypothesis that HCMV usage of rare human codons might hinder HCMV protein synthesis, in this way leading to HCMV latency...
September 1, 2017: Journal of Molecular Microbiology and Biotechnology
Jian Tian, Yaru Yan, Qingxia Yue, Xiaoqing Liu, Xiaoyu Chu, Ningfeng Wu, Yunliu Fan
Of the 20 common amino acids, 18 are encoded by multiple synonymous codons. These synonymous codons are not redundant; in fact, all of codons contribute substantially to protein expression, structure and function. In this study, the codon usage pattern of genes in the E. coli was learned from the sequenced genomes of E. coli. A machine learning based method, Presyncodon was proposed to predict synonymous codon selection in E. coli based on the learned codon usage patterns of the residue in the context of the specific fragment...
August 30, 2017: Scientific Reports
Bin Li, Furong Lin, Ping Huang, Wenying Guo, Yongqi Zheng
Decaisnea insignis is a wild resource plant and is used as an ornamental, medicinal, and fruit plant. High-throughput sequencing of chloroplast genomes has provided insight into the overall evolutionary dynamics of chloroplast genomes and has enhanced our understanding of the evolutionary relationships within plant families. In the present study, we sequenced the complete chloroplast genome of D. insignis and used the data to assess its genomic resources. The D. insignis chloroplast genome is 158,683 bp in length and includes a pair of inverted repeats of 26,167 bp that are separated by small and large single copy regions of 19,162 bp and 87,187 bp, respectively...
August 30, 2017: Scientific Reports
A E Vinogradov, O V Anatskaya
The AT-rich DNA is mostly associated with condensed chromatin, whereas the GC-rich sequence is preferably located in the dispersed chromatin. The AT-rich genes are prone to be tissue-specific (silenced in most tissues), while the GC-rich genes tend to be housekeeping (expressed in many tissues). This paper reports another important property of DNA base composition, which can affect repertoire of genes with high AT content. The GC-rich sequence is more liable to mutation. We found that Spearman correlation between human gene GC content and mutation probability is above 0...
August 23, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
Eva Kaesler, Peter M Kappeler, Markus Brameier, Janina Demeler, Cornelia Kraus, Josué H Rakotoniaina, Anni M Hämäläinen, Elise Huchard
Genes of the Major Histocompatibility Complex (MHC) play a central role in adaptive immune responses of vertebrates. They exhibit remarkable polymorphism, often crossing species boundaries with similar alleles or allelic motifs shared across species. This pattern may reflect parallel parasite-mediated selective pressures, either favouring the long maintenance of ancestral MHC allelic lineages across successive speciation events by balancing selection ('trans-species polymorphism'), or alternatively favouring the independent emergence of functionally similar alleles post-speciation via convergent evolution...
August 21, 2017: Molecular Ecology
Bidhan Ch Bera, Nitin Virmani, Naveen Kumar, Taruna Anand, S Pavulraj, Adam Rash, Debra Elton, Nicola Rash, Sandeep Bhatia, Richa Sood, Raj Kumar Singh, Bhupendra Nath Tripathi
BACKGROUND: Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. RESULTS: The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades...
August 23, 2017: BMC Genomics
Hui Song, Qingping Zhang, Pei Tian, Zhibiao Nan
The patterns of evolution and expression of tissue-specific genes are poorly understood beyond sex-specific genes. Accordingly, we identified 3,191 tissue-specific genes and 38,745 common genes using 22 RNA-seq datasets from cultivated peanut. The expression levels of tissue-specific genes were significantly lower than those of common genes. Further, the expression levels of sex-specific genes were significantly higher than those of somatic tissue-specific genes. Among sex-specific genes, the expression levels of gynoecium-specific genes were significantly higher than those of androecium-specific genes...
August 21, 2017: Scientific Reports
Supriyo Chakraborty, Arif Uddin, Monisha Nath Choudhury
Codon usage bias (CUB) is extensively found in a wide variety genomes and it is mostly affected by mutation pressure and natural selection. Analysis of CUB helps in studying the evolutionary features of a genome. The SRY gene plays an important role in male reproductive organ and a good candidate to study the evolutionary forces, since little work was reported earlier on this gene. We used bioinformatic methods to analyze the protein-coding sequences of SRY gene in 172 different mammalian species to understand the patterns of codon usage and the evolutionary forces acting on it...
September 30, 2017: Gene
Fanny Pouyet, Dominique Mouchiroud, Laurent Duret, Marie Sémon
Synonymous codon usage (SCU) varies widely among human genes. In particular, genes involved in different functional categories display a distinct codon usage, which was interpreted as evidence that SCU is adaptively constrained to optimize translation efficiency in distinct cellular states. We demonstrate here that SCU is not driven by constraints on tRNA abundance, but by large-scale variation in GC-content, caused by meiotic recombination, via the non-adaptive process of GC-biased gene conversion (gBGC). Expression in meiotic cells is associated with a strong decrease in recombination within genes...
August 15, 2017: ELife
Wanting He, Hongyu Zhang, Yuchen Zhang, Ruyi Wang, Sijia Lu, Yanjie Ji, Chang Liu, Pengkun Yuan, Shuo Su
Since its emergence, rabies virus (RABV) has been a major worldwide concern especially in developing countries. The nucleoprotein (N) of RABV is highly conserved and key for genetic typing, thus a better understanding of the N gene evolutionary trajectory can assist the development of control measures. We found that the N gene of RABV has a low codon usage bias with a mean effective number of codons (ENC) value of 56.33 influenced by both mutation pressure and natural selection. However, neutrality analysis indicated that natural selection dominates over mutation pressure...
August 14, 2017: Infection, Genetics and Evolution
Ilya Lapovok, Vita Laga, Elena Kazennova, Marina Bobkova
BACKGROUND: Natural variability of integrase (IN) across HIV-1 variants may influence the emergence of resistant viruses. The most apparent explanation of these fact is the IN polymorphism and the associated differences in codon usage, which, in turn, influence the probability and the terms of DRMs acquisition. Possible mechanisms by which polymorphisms affect DRMs emergence remain disputed and should still be clarified because these substitutions may be associated with a reduced activity of some INSTIs and may impact on ART regimen choice depending of HIV-1 subtype...
August 15, 2017: Current HIV Research
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