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Codon usage

Zhipeng Zhou, Yunkun Dang, Mian Zhou, Haiyan Yuan, Yi Liu
Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons results in premature transcription termination (PTT) within open reading frames and the abolishment of full-length mRNA...
March 16, 2018: ELife
Laura Jeacock, Joana Faria, David Horn
Protein abundance differs from a few to millions of copies per cell. Trypanosoma brucei presents an excellent model for studies on codon bias and differential gene expression because transcription is broadly unregulated and uniform across the genome. T. brucei is also a major human and animal protozoal pathogen. Here, an experimental assessment, using synthetic reporter genes, revealed that GC3 codons have a major positive impact on both mRNA and protein abundance. Our estimates of relative expression, based on coding sequences alone (codon usage and sequence length), are within 2-fold of the observed values for the majority of measured cellular mRNAs (n>7000) and proteins (n>2000)...
March 15, 2018: ELife
Janaina de Freitas Nascimento, Steven Kelly, Jack Sunter, Mark Carrington
Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs...
March 15, 2018: ELife
Genki Yoshikawa, Ahmed Askora, Romain Blanc-Mathieu, Takeru Kawasaki, Yanze Li, Miyako Nakano, Hiroyuki Ogata, Takashi Yamada
Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host...
March 14, 2018: Scientific Reports
Xiao-Xia Ma, Xin Cao, Peng Ma, Qiu-Yan Chang, Lin-Jie Li, Xiao-Kai Zhou, De-Rong Zhang, Ming-Sheng Li, Zhong-Ren Ma
The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position...
March 14, 2018: Journal of Basic Microbiology
Xiao-Xia Ma, Peng Ma, Qiu-Yan Chang, Zhen-Bin Liu, Derong Zhang, Xiao-Kai Zhou, Zhong-Ren Ma, Xin Cao
Lyme disease, caused by Borrelia burgdorferi, is a focally endemic tick-transmitted zoonotic infection. In this study, the major factors underlying synonymous codon-related amino acid usage in the B. burgdorferi genome and bias in synonymous codon usage of the translation initiation region of coding sequences were analyzed. Additionally, adaptation of B. burgdorferi to several of its hosts was analyzed in the context of synonymous codon usage. Principal component analysis (PCA) revealed that nucleotide content at the third synonymous position of a codon influenced the synonymous codon usage pattern, but the strand-specific factor did not influence the synonymous codon usage pattern of B...
March 13, 2018: Journal of Basic Microbiology
Rosa M Pintó, Francisco-Javier Pérez-Rodríguez, Lucia D' Andrea, Montserrat de Castellarnau, Susana Guix, Albert Bosch
Codon usage bias is universal to all genomes. Hepatitis A virus (HAV) codon usage is highly biased and deoptimized with respect to its host. Accordingly, HAV is unable to induce cellular translational shutoff and its internal ribosome entry site (IRES) is inefficient. Codon usage deoptimization may be seen as a hawk (host cell) versus dove (HAV) game strategy for accessing transfer RNA (tRNA). HAV avoids use of abundant host cell codons and thereby eludes competition for the corresponding tRNAs. Instead, codons that are abundant or rare in cellular messenger RNAs (mRNAs) are used relatively rarely in its genome, although intermediately abundant host cell codons are abundant in the viral genome...
March 12, 2018: Cold Spring Harbor Perspectives in Medicine
Ruth Suchsland, Bettina Appel, Sabine Müller
The preparation of protein libraries is a key issue in protein engineering and biotechnology. Such libraries can be prepared by a variety of methods, starting from the respective gene library. The challenge in gene library preparation is to achieve controlled total or partial randomization at any predefined number and position of codons of a given gene, in order to obtain a library with a maximum number of potentially successful candidates. This purpose is best achieved by the usage of trinucleotide synthons for codon-based gene synthesis...
2018: Beilstein Journal of Organic Chemistry
Mousumi Sarkar Saha, Shilpee Pal, Indrani Sarkar, Ayan Roy, Pradeep K Das Mohapatra, Arnab Sen
Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done...
February 28, 2018: Genomics
Joy Goffena, Frances Lefcort, Yongqing Zhang, Elin Lehrmann, Marta Chaverra, Jehremy Felig, Joseph Walters, Richard Buksch, Kevin G Becker, Lynn George
Familial dysautonomia (FD) results from mutation in IKBKAP/ELP1, a gene encoding the scaffolding protein for the Elongator complex. This highly conserved complex is required for the translation of codon-biased genes in lower organisms. Here we investigate whether Elongator serves a similar function in mammalian peripheral neurons, the population devastated in FD. Using codon-biased eGFP sensors, and multiplexing of codon usage with transcriptome and proteome analyses of over 6,000 genes, we identify two categories of genes, as well as specific gene identities that depend on Elongator for normal expression...
March 1, 2018: Nature Communications
Hao Zhang, Jian Li, Ruixue Wang, Junkai Zhi, Peng Yin, Jichen Xu
Expansins are essential components of plant cell wall and play an important role in plant growth, development, and stress resistance via loosening function. To understand the codon usage pattern of expansin genes, we gained the sequence data of expansin genes from eight plant species. Statistics analysis showed obvious codon characteristics between monocot and dicot plants. Comparably, expansin genes in monocot plants had really higher GC content, more high frequency codons, and more optimal codons than that in dicot plants...
February 26, 2018: Journal of Biomolecular Structure & Dynamics
Ming-Li Wu, Qing Li, Jiang Xu, Xi-Wen Li
Background: Amomum compactum is one of the basic species of the traditional herbal medicine amomi fructus rotundus, with great pharmacology effect. The system position of A. compactum is not clear yet, and the introduction of this plant has been hindered by many plant diseases. However, the correlational molecular studies are relatively scarce. Methods: The total chloroplast (cp) DNA was extracted according to previous studies, and then sequenced by 454 GS FLX Titanium platform...
2018: Chinese Medicine
Yanci Yang, Juan Zhu, Li Feng, Tao Zhou, Guoqing Bai, Jia Yang, Guifang Zhao
Fagaceae is one of the largest and economically important taxa within Fagales. Considering the incongruence among inferences from plastid and nuclear genes in the previous Fagaceae phylogeny studies, we assess the performance of plastid phylogenomics in this complex family. We sequenced and assembled four complete plastid genomes ( Fagus engleriana, Quercus spinosa, Quercus aquifolioides , and Quercus glauca ) using reference-guided assembly approach. All of the other 12 published plastid genomes in Fagaceae were retrieved for genomic analyses (including repeats, sequence divergence and codon usage) and phylogenetic inference...
2018: Frontiers in Plant Science
Dechun Lin, Liqiang Li, Tian Xie, Qingqing Yin, Nitin Saksena, Rangke Wu, Wanyu Li, Geyang Dai, Jinmin Ma, Xiaohong Zhou, Xiao-Guang Chen
A comprehensive demonstration of Zika virus (ZIKV) molecular evolution is essential for understanding its adaptation and expansion in its recent pandemics. Despite several studies on mutations and codon usage in ZIKVs, the variations in codon usage patterns across individual genes and their biological implication remains unclear. Here, we performed a gene-by-gene comparison of the codon usage variation in ZIKVs of the African and Asian lineages. We found that besides the evidence of positive selection (Ka/Ks > 1) in the Asian lineage of the ZIKV genome, codon usage patterns were gene-specific and codon usage variation of ZIKV genes, was possibly constrained by their individual functional features, such as transmembrane domains, or antigenicity...
February 8, 2018: Virus Research
Rama K Sarvani, Drashti R Parmar, Wajeeda Tabasum, Neelima Thota, Ara Sreenivas, Ajay Gaur
The mitochondrial genome of Indian mouse deer (Moschiola indica) was sequenced, assembled and characterized for the first time using 22 pairs of polymerase chain reaction (PCR) primers. The mitogenome of M. indica which is 16,444 bp in size was found very similar to most vertebrates in organisation that harbours 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and 1A + T-rich region. Its comparison with over 52 mitogenomes of the order Artiodactyla, showed a conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins except that M...
February 9, 2018: Scientific Reports
Andreas Porse, Thea S Schou, Christian Munck, Mostafa M H Ellabaan, Morten O A Sommer
Elucidating the factors governing the functional compatibility of horizontally transferred genes is important to understand bacterial evolution, including the emergence and spread of antibiotic resistance, and to successfully engineer biological systems. In silico efforts and work using single-gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts...
February 6, 2018: Nature Communications
Supriyo Chakraborty, Tarikul Huda Mazumder, Arif Uddin
The BRCA1 gene is located on the human chromosome 17q21.31 and plays important role in biological processes. The aminoacyl-tRNA synthetases (AARS) are a family of heterogenous enzymes responsible protein synthesis and whose secondary functions include a role in autoimmune myositis. Our findings reveal that the compositional constraint and the preference of more A/T -ending codons determine the codon usage patterns in BRCA1 gene while more G/C-ending codons influence the codon usage pattern of AARS gene among mammals...
January 27, 2018: Genomics
Vincent P Mauro
Biotherapeutics are increasingly becoming the mainstay in the treatment of a variety of human conditions, particularly in oncology and hematology. The production of therapeutic antibodies, cytokines, and fusion proteins have markedly accelerated these fields over the past decade and are probably the major contributor to improved patient outcomes. Today, most protein therapeutics are expressed as recombinant proteins in mammalian cell lines. An expression technology commonly used to increase protein levels involves codon optimization...
February 2018: BioDrugs: Clinical Immunotherapeutics, Biopharmaceuticals and Gene Therapy
N Galtier, C Roux, M Rousselle, J Romiguier, E Figuet, S Glémin, N Bierne, L Duret
Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. In animals, the population genetics of codon usage bias has only been studied in a handful of model organisms so far, and can be affected by confounding, non-adaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data we analysed the relationship between codon usage, gene expression, allele frequency distribution and recombination rate in 30 non-model species of animals, each from a different family, covering a wide range of effective population sizes...
January 30, 2018: Molecular Biology and Evolution
Yong Wang, Fang-Chao Zhu, Li-Sheng He, Antoine Danchin
The position 34 of a tRNA is always modified for efficient recognition of codons and accurate integration of amino acids by the translation machinery. Here, we report genomics features of a deep-sea gut symbiotic Spiroplasma, which suggests that the organism does not require tRNA(34) anticodon modifications. In the genome, there is a novel set of tRNA genes composed of 32 species for recognition of the 20 amino acids. Among the anticodons of the tRNAs, we witnessed the presence of both U34- and C34-containing tRNAs required to decode NNR (A/G) 2:2 codons as countermeasure of probable loss of anticodon modification genes...
January 30, 2018: Nucleic Acids Research
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