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Codon usage

Shengyan Li, Zeyu Wang, Yiyao Zhou, Changhui Li, Guiping Wang, Hai Wang, Jie Zhang, Gemei Liang, Zhihong Lang
To improve the novel Bacillus thuringiensis insecticidal gene cry2Ah1 toxicity, two mutants cry2Ah1-vp (V354VP) and cry2Ah1-sp (V354SP) were performed. SWISS-MODEL analysis showed two mutants had a longer loop located between β-4 and β-5 of domain II, resulting in higher binding affinity with brush border membrane vesicles (BBMV) of Helicoverpa armigera comparing with Cry2Ah1. The cry2Ah1, cry2Ah1-vp, and cry2Ah1-sp were optimized codon usage according to plant codon bias, and named mcry2Ah1, mcry2Ah1-vp, and mcry2Ah1-sp...
January 11, 2018: Scientific Reports
S J Yoo, T Kwon, K Kang, H Kim, S C Kang, J A Richt, Y S Lyoo
Modified live vaccines (MLVs) based on genotype 1 strains, particularly C-strain, have been used to prevent and control classical swine fever virus (CSFV) worldwide. Nevertheless, a shift in the predominant CSFV strains circulating in the field from genotype 1 or 3 to genotype 2 is seen. Genotype 2 is genetically distant from the vaccine strains and was recently reported during outbreaks after vaccine failure; this has raised concerns that vaccination has influenced viral evolution. In Korea in 2016, there was an unexpected CSF outbreak in a MLV-vaccinated commercial pig herd...
January 10, 2018: Transboundary and Emerging Diseases
Eu-Hyun Im, Sun Shim Choi
Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations...
December 2017: Genomics & Informatics
Danfeng Jin, Xianwen Meng, Yue Wang, Jingjing Wang, Yuhua Zhao, Ming Chen
Many small RNAs have been confirmed to play important roles in the development of root nodules and arbuscular mycorrhiza. In this study, we carried out the identification of certain small RNAs in leguminous plants (Medicago truncatula, soybean, peanut and common bean), such as miRNAs, tRFs and srRNAs, as well as the computational investigation of their regulations. Thirty miRNAs were predicted to be involved in establishing root nodules and mycorrhiza, and 12 of them were novel in common bean and peanut. The generation of tRFs in M...
January 3, 2018: Science China. Life Sciences
Ye Chen, Quanming Xu, Xiaomin Yuan, Xinxin Li, Ting Zhu, Yanmei Ma, Ji-Long Chen
Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which first broken out in Jeddah in 2012, causes a severe acute respiratory illness with a high mortality rate. To better understand the molecular characteristics of isolated MERS-CoV genomes, we first analysed the codon usage pattern of the zoonotic MERS-CoV strains comprehensively to gain an insight into the mechanism of cross-species transmission. We found that MERS human/camel isolates showed a low codon usage bias. Both mutation and nature selection pressure have contributed to this low codon usage bias, with the former being the main determining factor...
December 15, 2017: Oncotarget
Lars B Scharff, Piotr Gawroński, Poul Erik Jensen, Stanislaw Karpinski, Dario Leister
Many mRNAs contain pause sites that briefly interrupt the progress of translation. Specific features that induce ribosome pausing have been described; however, their individual contributions to pause-site formation, and the overall biological significance of ribosome pausing, remain largely unclear. We have taken advantage of the compact genome of chloroplasts to carry out a plastid genome-wide survey of pause sites, as a basis for studying the impact of pausing on post-translational processes. Based on ribosomal profiling of Arabidopsis thaliana chloroplast mRNAs, we demonstrate that a combination of factors - mRNA secondary structure, internal Shine-Dalgarno sequences, and positively charged amino acids in the nascent peptide chain - explains 95% of the major pause sites on plastid mRNAs, while codon usage has little impact...
January 3, 2018: Plant Physiology
Jeff Gauthier, Antony T Vincent, Steve J Charette, Nicolas Derome
Aeromonas sobria is a mesophilic motile aeromonad currently depicted as an opportunistic pathogen, despite increasing evidence of mutualistic interactions in salmonid fish. However, the determinants of its host-microbe associations, either mutualistic or pathogenic, remain less understood than for other aeromonad species. On one side, there is an over-representation of pathogenic interactions in the A. sobria literature, of which only three articles to date report mutualistic interactions; on the other side, genomic characterization of this species is still fairly incomplete as only two draft genomes were published prior to the present work...
2017: Frontiers in Microbiology
Yi-Ning Wang, Wen-Heng Ji, Xue-Rui Li, Yong-Sheng Liu, Jian-Hua Zhou
Currently, the comparison between GC usage pattern at the 3rd codon position and codon usage index is commonly used to estimate the roles of evolutionary forces in shaping synonymous codon usages, however, this kind of analysis often losses the information about the role of A/T usage bias in shaping synonymous codon usage bias. To overcome this limitation and better understand the interplay between nucleotide and codon usages for the evolution of bacteria at gene levels, in this study, we employed the information entropy method with some modification to estimate roles of nucleotide compositions in the overall codon usage bias for 18 mycoplasma species in combination with Davies-Bouldin index...
December 20, 2017: Bio Systems
Iulia Darolti, Alison E Wright, Pascal Pucholt, Sofia Berlin, Judith E Mank
The relative rate of evolution for sex-biased genes has often been used as a measure of the strength of sex-specific selection. In contrast to studies in a wide variety of animals, far less is known about the molecular evolution of sex-biased genes in plants, particularly in dioecious angiosperms. Here, we investigate the gene expression patterns and evolution of sex-biased genes in the dioecious plant Salix viminalis. We observe lower rates of sequence evolution for male-biased genes expressed in the reproductive tissue compared to unbiased and female-biased genes...
December 23, 2017: Molecular Ecology
Liqiang Zhong, Minghua Wang, Daming Li, Shengkai Tang, Tongqing Zhang, Wenji Bian, Xiaohui Chen
Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species...
December 17, 2017: Genomics
Yuan Wang, Peng Jia, Rahat Sharif, Zhengchen Li, Yuhong Li, Peng Chen
Endonuclease I is a widely distributed periplasmic or extracellular enzyme. A method for the high-level production of recombinant AsEndI (endonuclease I from Aliivibrio salmonicida) in Escherichia coli with secretion expression is investigated. The coding sequence of AsEndI gene was assembled according to the E. coli codon usage bias, and AsEndI was expressed in the periplasm of E. coli TOP10 with a C-terminal 6× His-tagged fusion. The recombinant AsEndI (His-AsEndI) was purified by Ni-NTA resin with a yield of 1...
December 18, 2017: Applied Biochemistry and Biotechnology
Lucas D Fernandes, Alessandro P S de Moura, Luca Ciandrini
Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we propose transcript length as a further key determinant of translation efficiency. Based on a physical model that considers the kinetics of ribosomes advancing on the mRNA and diffusing in its surrounding, as well as mRNA circularisation and ribosome drop-off, we explain how the transcript length may play a central role in establishing ribosome recruitment and the overall translation rate of an mRNA...
December 12, 2017: Scientific Reports
Binata Halder, Arup Kumar Malakar, Supriyo Chakraborty
We illustrated the descriptive aspects of codon usage of some important human genes and their expression potential in E. coli. By comparing the results of various codon usage parameters, effects that are due to selection and mutational pressures have been deciphered. The variation in GC3s explains a significant proportion of the variation in codon usage patterns. The codons CGC, CGG, CTG and GCG showed strong positive correlation with GC3, which suggested that codon usage had been influenced by GC bias. We also found that ACC (Thr, RSCU-1...
December 8, 2017: Gene
Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
Genome-scale metabolic models are valuable tools for assessing the metabolic potential of living organisms. Being downstream of gene expression, metabolism is increasingly being used as an indicator of the phenotypic outcome for drugs and therapies. We here present a review of the principal methods used for constraint-based modelling in systems biology, and explore how the integration of multi-omic data can be used to improve phenotypic predictions of genome-scale metabolic models. We believe that the large-scale comparison of the metabolic response of an organism to different environmental conditions will be an important challenge for genome-scale models...
2018: Methods in Molecular Biology
Sergio Calderon-Salais, Prisiliana Velazquez-Bernardino, Victor E Balderas-Hernandez, Ana P Barba-de la Rosa, Antonio De Leon-Rodriguez
Vasostatin 30 (Vs30) is an active fragment derived from the N-terminal region (135-164aa) of human calreticulin (hCALR) and has the ability to inhibit angiogenesis. In this work, the expression of Vs30 was performed using a protease-deficient strain of the methylotrophic yeast Pichia pastoris. The vs30 gene was optimized for P. pastoris preferential codon usage and inserted into constitutive expression vector pGAPZαA. In addition, a multi-copy strain was obtained using an in vitro multimerization approach...
December 5, 2017: Protein Expression and Purification
Yimin Du, Wu Dai, Christopher H Dietrich
The widespread leafhopper genus Scaphoideus Uhler is the most diverse genus in Scaphoideini and includes some species that are serious pests and vectors of plant pathogens. Here the first Scaphoideus mitogenome sequences are provided for three species, S. maai, S. nigrivalveus and S. varius, representing three main species groups in the Oriental region based on color pattern. The lengths of these three mitogenomes were 15,188, 15,235 and 15,207 bp, respectively. Gene order of three mitogenomes is highly conserved and identical to that of the putative ancestral insect...
December 4, 2017: Scientific Reports
Xianhua Sun, Xianli Xue, Mengzhu Li, Fei Gao, Zhenzhen Hao, Huoqing Huang, Huiying Luo, Lina Qin, Bin Yao, Xiaoyun Su
Cellulase and mannase are both important enzyme additives of animal feeds. Expressing the two enzymes simultaneously within one microbial host could potentially lead to cost saving in animal feeding. For this purpose, we codon optimized the Aspergillus niger Man5A gene to the codon usage bias of Trichoderma reesei. By comparing the free energy and the local structure of the nucleotide sequences, one optimized sequence was finally selected and transformed into the T. reesei pyridine auxotrophic strain TU-6. The codon optimized gene was expressed to a higher level than the original one...
December 4, 2017: Journal of Agricultural and Food Chemistry
Siddiq Ur Rahman, Xiaoting Yao, Xiangchen Li, Dekun Chen, Shiheng Tao
Crimean-Congo hemorrhagic fever virus (CCHFV) is a negative-sense, single stranded RNA virus with a three-segmented genome that belongs to the genus Nairovirus within the family Bunyaviridae. CCHFV uses Hyalomma ticks as a vector to infect humans with a wide range of clinical signs, from asymptomatic to Zika-like syndrome. Despite significant progress in genomic analyses, the influences of viral relationships with different hosts on overall viral fitness, survival, and evading the host's immune systems remain unknown...
November 30, 2017: Infection, Genetics and Evolution
Supriyo Chakraborty, Arif Uddin, Tarikul Huda Mazumder, Monisha Nath Choudhury, Arup Kumar Malakar, Prosenjit Paul, Binata Halder, Himangshu Deka, Gulshana Akthar Mazumder, Riazul Ahmed Barbhuiya, Masuk Ahmed Barbhuiya, Warepam Jesmi Devi
The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes...
November 28, 2017: Mitochondrion
Kalia S I Bistolas, Ryan M Besemer, Lars G Rudstam, Ian Hewson
Aquatic invertebrates are common reservoirs of a rapidly expanding group of circular Rep-encoding ssDNA (CRESS-DNA) viruses. This study identified and explored the phylogenetic relationship between novel CRESS-DNA viral genotypes associated with Pacific intertidal isopods Idotea wosnesenskii, Idotea resecata, and Gnorimosphaeroma oregonensis. One genotype associated with I. wosnesenskii, IWaV278, shared sequence similarity and genomic features with Tombusviridae (ssRNA) and Circoviridae (ssDNA) genomes and was putatively assigned to the Cruciviridae clade comprising chimeric viruses...
November 26, 2017: Viruses
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