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codon bias

Alexei Y Kostygov, Anzhelika Butenko, Anna Nenarokova, Daria Tashyreva, Pavel Flegontov, Julius Lukeš, Vyacheslav Yurchenko
We have sequenced, annotated, and analyzed the genome of Ca. Pandoraea novymonadis, a recently described bacterial endosymbiont of the trypanosomatid Novymonas esmeraldas. When compared with genomes of its free-living relatives, it has all the hallmarks of the endosymbionts' genomes, such as significantly reduced size, extensive gene loss, low GC content, numerous gene rearrangements, and low codon usage bias. In addition, Ca. P. novymonadis lacks mobile elements, has a strikingly low number of pseudogenes, and almost all genes are single copied...
2017: Frontiers in Microbiology
Jonas Kjær, Graham J Belsham
Foot-and-mouth disease virus (FMDV) has a positive-sense ssRNA genome including a single, large, open reading frame. Splitting of the encoded polyprotein at the 2A/2B junction is mediated by the 2A peptide (18 residues long) which induces a non-proteolytic, co-translational, "cleavage" at its own C-terminus. A conserved feature among variants of 2A is the C-terminal motif N16P17G18/P19 where P19 is the first residue of 2B. It has been shown previously that certain amino acid substitutions can be tolerated at residues E14, S15 and N16 within the 2A sequence of infectious FMDVs but no variants at residues P17, G18 or P19 have been identified...
October 17, 2017: RNA
Irepan Salvador-Martínez, Marta Coronado-Zamora, David Castellano, Antonio Barbadilla, Isaac Salazar-Ciudad
We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns and development, with the aim of mapping adaptation over the entire embryo's anatomy. Our adaptation map is based on analyzing spatial gene expression information for 5,969 genes (from text-based annotations of in situ hybridization data directly from the BDGP database, Tomancak et al. 2007) and the polymorphism and divergence in these genes (from the project DGRP, Mackay et al...
October 10, 2017: Molecular Biology and Evolution
Zhenguo Zhang, Gaurav Sablok
One amino acid is added to a growing peptide by a ribosome through reading triple nucleotides, i.e., a codon, each time. Twenty species of amino acids are often coded by 61 codons, so one amino acid can be coded by more than one codon and the codons coding the same amino acid are called synonymous. Intriguingly, synonymous codons' usage is often uneven: some are used more often than their alternatives in a genome. The unevenness of codon usage is termed codon usage bias (CUB). CUB is widespread, and its causes and consequences have been under intensive investigation...
2018: Methods in Molecular Biology
Shao'e Sun, Qi Li, Lingfeng Kong, Hong Yu
Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. The strand-specific bias in the nucleotide composition of the mtDNA has been known to be highly problematic for phylogenetic analyses. Here, the strand asymmetry was compared across 140 mollusc species and analyzed for a mtDNA fragment including twelve protein-coding genes. The analyses show that almost all species in Gastropoda (except Heterobranchia) and all species in Bivalvia present reversals of strand bias...
October 13, 2017: Molecular Phylogenetics and Evolution
Gulshana A Mazumder, Arif Uddin, Supriyo Chakraborty
Schistosoma japonicum and Ascaris suum are considered as the major parasites of human which cause various life threatening diseases such as schistomiasis and ascariasis. The codon usage bias (CUB) is known as the phenomenon of more usage of a specific codon than the other synonymous codons for an amino acid. The factors that influence the codon usage bias are mutation pressure, natural selection, gene expression, gene length, GC content, RNA stability, recombination rates, codon position etc. Here we had used various bioinformatic tools and statistical analyses to understand the compositional features, expression level and codon usage bias in the genes of these two species...
December 20, 2017: Acta Parasitologica
Prosenjit Paul, Arup Kumar Malakar, Supriyo Chakraborty
Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes...
October 14, 2017: Genetica
Daniel M Lyons, Adam S Lauring
The substitution rates of transitions are higher than expected by chance relative to those of transversions. Many have argued that selection disfavors transversions, as nonsynonymous transversions are less likely to conserve biochemical properties of the original amino acid. Only recently has it become feasible to directly test this selective hypothesis by comparing the fitness effects of a large number of transition and transversion mutations. For example, a recent study of six viruses and one beta-lactamase gene did not find evidence supporting the selective hypothesis...
September 25, 2017: Molecular Biology and Evolution
Renhui Bai, Yunbo Zhang, Chundi Wang, Feiyang Zhang, Zhe Zhang, Fubao Sun, Zhenyu Zhang
Deficient activity of endo-1,4-beta-glucanase II (Cel5A) secreted by Trichoderma reesei is one of the challenges involved in effective cellulase saccharification of cellulosic substrates. Therefore, we expressed Cel5A in Pichia pastoris by constructing a recombinant strain. With the gene optimization based on codon bias, and the construction of expression vector pPIC9K-eg2, the optimized gene was electro-transformed into P. pastoris GS115 to form transformants. Then, a high Cel5A activity producing recombinant, namely P...
October 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Kuppusamy Sivasankaran, Pratheesh Mathew, Sekar Anand, Stanislaus Antony Ceasar, Soosaimanikam Mariapackiam, Savarimuthu Ignacimuthu
The complete mitochondrial genome of the fruit piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575 bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), 22 transfer RNA (tRNA) genes and an A + T-rich region (D-loop). The nucleotide composition of the genome is highly A + T biased, accounting for 80.67% of nucleotides...
December 2017: Genomics Data
Sug-Young Yoon, Hyung-Min Lee, Ji-Na Kong, Kwang-Hoon Kong
Agarase catalyzes the hydrolysis of agar, which is primarily used as a medium for microbiology, various food additives, and new biomass materials. In this study, we described the expression of the synthetic gene encoding β-agarase from Agarivorans albus in Escherichia coli. The synthetic β-agarase gene was designed based on the biased codons of E. coli in order to optimize its expression and extracellular secretion in an active, soluble form. The synthesized agarase gene, including its signal sequence, was cloned into the pET-26 expression vector, and the pET-Aaβ-agarase plasmid was introduced into E...
October 11, 2017: Preparative Biochemistry & Biotechnology
Gavin Hanson, Jeff Coller
The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts; this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery...
October 11, 2017: Nature Reviews. Molecular Cell Biology
Hiwa Mohammadi, Mohammad Taghi Joghataei, Zohreh Rahimi, Faezeh Faghihi, Habibolah Khazaie, Hashem Farhangdoost, Masoud Mehrpour
Developmental stuttering is known to be a sexually dimorphic and male-biased speech motor control disorder. In the present case-control study, we investigated the relationship between developmental stuttering and steroid hormones. Serum levels of testosterone, dihydrotestosterone (DHT), dehydroepiandrosterone (DHEA), oestradiol, progesterone, cortisol, and sex hormone binding globulin (SHBG), as well as the 2nd/4th digit ratio (2D:4D), an indicator of prenatal testosterone level, were compared between children who stutter (CWS) and children who do not stutter (CWNS)...
October 6, 2017: Brain and Language
Laura E Kirby, Donna Koslowsky
Trypanosoma brucei is transmitted between mammalian hosts by the tsetse fly. In the mammal, they are exclusively extracellular, continuously replicating within the bloodstream. During this stage, the mitochondrion lacks a functional electron transport chain (ETC). Successful transition to the fly, requires activation of the ETC and ATP synthesis via oxidative phosphorylation. This life cycle leads to a major problem: in the bloodstream, the mitochondrial genes are not under selection and are subject to genetic drift that endangers their integrity...
October 2017: PLoS Neglected Tropical Diseases
Kun Liu, Xuzhong Liu, Shuo Gu, Qing Sun, Yunyan Wang, Junsong Meng, Zongyuan Xu
BACKGROUND: Epidemiological studies have investigated the role of transforming growth factor-β1 (TGF-β1) in chronic allograft dysfunction (CAD) following kidney transplantation. TGFB1 gene polymorphisms (SNP rs1800470 and rs1800471) may be associated with the risk of CAD. In this meta-analysis, the relationship between these two variations and the risk of CAD was explored. MATERIALS AND METHODS: MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), Embase, the Chinese CNKI and WANFANG databases were searched...
September 22, 2017: Oncotarget
Li-Shang Dai, Saima Kausar, Muhammad Nadeem Abbas, Tian-Tian Wang
In the present study, we sequenced the entire mitochondrial genome (mitogenome) of Ectropis oblique using PCR amplification and sequencing methods The entire mitogenome is 15,356bp long, including 13 protein coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and A+T rich element. The base composition and gene arrangement are identical to those of other lepidopterans. Of these 37 genes, twenty three are resided on heavy strand, while fourteen located on light strand. The newly sequenced mitogenome displayed a biased Adenine/thymine 84...
September 26, 2017: International Journal of Biological Macromolecules
Siyu Chen, Ke Li, Wenqing Cao, Jia Wang, Tong Zhao, Qing Huan, Yu-Fei Yang, Shaohuan Wu, Wenfeng Qian
Codon usage bias (CUB) refers to the observation that synonymous codons are not used equally frequently in a genome. CUB is stronger in more highly expressed genes, a phenomenon commonly explained by stronger natural selection on translational accuracy and/or efficiency among these genes. Nevertheless, this phenomenon could also occur if CUB regulates gene expression at the mRNA level, a hypothesis that has not been tested until recently. Here, we attempt to quantify the impact of synonymous mutations on mRNA level in yeast using 3,556 synonymous variants of a heterologous gene encoding green fluorescent protein (GFP) and 523 synonymous variants of an endogenous gene TDH3...
August 24, 2017: Molecular Biology and Evolution
Supriyo Chakraborty, Arif Uddin, Monisha Nath Choudhury
No abstract text is available yet for this article.
November 30, 2017: Gene
Ye Chen, Quanming Xu, Chen Tan, Xinxin Li, Xiaojuan Chi, Binxiang Cai, Ziding Yu, Yanmei Ma, Ji-Long Chen
Senecavirus A (SVA) infection was recently confirmed in pigs in Brazil, United States of America and Canada. To better understand the molecular characteristics of isolated SVA genomes, we first reported genome-wide comprehensive analyses of codon usage and various factors that have contribute to the molecular evolution in SVA. The effective number of codons (ENC) ranged from 54.51 to 55.54 with an average of 54.87 ± 0.285, which reveals a relatively stable nucleotide composition. We found that codon usage bias of the SVA was low...
September 22, 2017: Microbial Pathogenesis
Ying Li, Xue-Jun Kuang, Xiao-Xuan Zhu, Ying-Jie Zhu, Chao Sun
This study aimed to provide guidance for the heterogenous gene expression, gene prediction and species evolution by analyzing codon usage bias of Catharanthus roseus.The codon composition and usage bias of 30 437 high-confidence coding sequences from C.roseus were analyzed and the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 25 genes involved in the biosynthesis of terpenoid indole alkaloids (TIAs) in C.roseus were calculated.The results showed that the average GC content of the genes was 42...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
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