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https://www.readbyqxmd.com/read/28209199/making-life-difficult-for-clostridium-difficile-augmenting-the-pathogen-s-metabolic-model-with-transcriptomic-and-codon-usage-data-for-better-therapeutic-target-characterization
#1
Sara Saheb Kashaf, Claudio Angione, Pietro Lió
BACKGROUND: Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better understanding of this organism and the relationship between its genotype and phenotype is essential to the search for an effective treatment. Genome-scale metabolic models contain all known biochemical reactions of a microorganism and can be used to investigate this relationship. RESULTS: We present icdf834, an updated metabolic network of C...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28198504/complete-mitochondrial-genome-of-the-amur-hedgehog-erinaceus-amurensis-erinaceidae-and-higher-phylogeny-of-the-family-erinaceidae
#2
N H Kim, S J Lim, H M Chae, Y C Park
We sequenced and characterized the complete mitogenome (KX964606) of the Amur hedgehog Erinaceus amurensis to provide more data for comparative mitogenomics of the genus Erinaceus (Erinaceidae). The mitogenome of E. amurensis is a circular molecule 16,941 bp long, consisting of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes, and two rRNA genes (12S rRNA and 16S rRNA). The mitogenome of E. amurensis is AT-biased, with a nucleotide composition of 33.9% A, 21...
February 8, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28187713/novel-methods-to-optimize-gene-and-statistic-test-for-evaluation-an-application-for-escherichia-coli
#3
Tran Tuan-Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao
BACKGROUND: Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host's expression system, so the yields can fall down significantly...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28185367/codon-degeneracy-and-amino-acid-abundance-influence-the-measures-of-codon-usage-bias-improved-nc-n%C3%AC-c-and-encprime-n%C3%AC-c-measures
#4
Siddhartha Sankar Satapathy, Ajit Kumar Sahoo, Suvendra Kumar Ray, Tapash Chandra Ghosh
Effective number of codons (N^c) and its variant N^'c (effective number of codons prime) are the two widely used methods for measuring unequal usage of synonymous codons in coding sequences, known as the codon usage bias (CUB). The mathematical formula used in calculating N^c and N^'c values is giving inappropriate measures of CUB in case of low abundance of amino acids. In addition, the magnitude of error also varies according to codon degeneracy. In this study, a modified formula for N^c and N^'c has been developed to measure the CUB more accurately...
February 10, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28177830/analysis-of-codon-usage-patterns-in-morus-notabilis-based-on-genome-and-transcriptome-data
#5
Yan Wen, Ziliang Zou, Hongshun Li, Zhonghuai Xiang, Ningjia He
Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tree), and analyze genome-wide codon usage in 12 other Rosales species. The codon usage of M. notabilis was affected by nucleotide composition, mutation pressure, nature selection, and gene expression level...
January 3, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28168289/ribo-seq-enlightens-codon-usage-bias
#6
Damien Paulet, Alexandre David, Eric Rivals
No abstract text is available yet for this article.
February 7, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28157073/codon-optimization-underpins-generalist-parasitism-in-fungi
#7
Thomas Badet, Remi Peyraud, Malick Mbengue, Olivier Navaud, Mark Derbyshire, Richard P Oliver, Adelin Barbacci, Sylvain Raffaele
The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom...
February 3, 2017: ELife
https://www.readbyqxmd.com/read/28124482/nucleotide-composition-and-codon-usage-bias-of-sry-gene
#8
M N Choudhury, A Uddin, S Chakraborty
The SRY gene is present within the sex-determining region of the Y chromosome which is responsible for maleness in mammals. The nonuniform usage of synonymous codons in the mRNA transcript for encoding a particular amino acid is the codon usage bias (CUB). Analysis of codon usage pattern is important to understand the genetic and molecular organisation of a gene. It also helps in heterologous gene expression, design of primer and synthetic gene. However, the analysis of codon usage bias of SRY gene was not yet studied...
January 26, 2017: Andrologia
https://www.readbyqxmd.com/read/28122952/the-impact-of-selection-at-the-amino-acid-level-on-the-usage-of-synonymous-codons
#9
Paweł Błažej, Dorota Mackiewicz, Małgorzata Wnętrzak, Paweł Mackiewicz
There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, the biased codon usage can be also a by-product of a general selection at the amino acid level interacting with nucleotide replacements. To evaluate the validity and strength of such effect, we superimposed more than 3.5 billion unrestricted mutational processes on the selection of non-synonymous substitutions based on the differences in physicochemical properties of the coded amino acids...
January 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28113866/codon-context-optimization-in-synthetic-gene-design
#10
Dimitris Papamichail, Hongmei Liu, Vitor Machado, Nathan Gould, J Robert Coleman, Georgios Papamichail
Advances in de novo synthesis of DNA and computational gene design methods make possible the customization of genes by direct manipulation of features such as codon bias and mRNA secondary structure. Codon context is another feature significantly affecting mRNA translational efficiency, but existing methods and tools for evaluating and designing novel optimized protein coding sequences utilize untested heuristics and do not provide quantifiable guarantees on design quality. In this study we examine statistical properties of codon context measures in an effort to better understand the phenomenon...
March 23, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28102546/ataluren-and-similar-compounds-specific-therapies-for-premature-termination-codon-class-i-mutations-for-cystic-fibrosis
#11
REVIEW
Aisha A Aslam, Colin Higgins, Ian P Sinha, Kevin W Southern
BACKGROUND: Cystic fibrosis is a common life-shortening genetic disorder in the Caucasian population (less common in other ethnic groups) caused by the mutation of a single gene that codes for the production of the cystic fibrosis transmembrane conductance regulator protein. This protein coordinates the transport of salt (and bicarbonate) across cell surfaces and the mutation most notably affects the airways. In the lungs of people with cystic fibrosis, defective protein results in a dehydrated surface liquid and compromised mucociliary clearance...
January 19, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28095667/sequence-analysis-of-mitochondrial-genome-of-toxascaris-leonina-from-a-south-china-tiger
#12
Kangxin Li, Fang Yang, A Y Abdullahi, Meiran Song, Xianli Shi, Minwei Wang, Yeqi Fu, Weida Pan, Fang Shan, Wu Chen, Guoqing Li
Toxascaris leonina is a common parasitic nematode of wild mammals and has significant impacts on the protection of rare wild animals. To analyze population genetic characteristics of T. leonina from South China tiger, its mitochondrial (mt) genome was sequenced. Its complete circular mt genome was 14,277 bp in length, including 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The nucleotide composition was biased toward A and T. The most common start codon and stop codon were TTG and TAG, and 4 genes ended with an incomplete stop codon...
December 2016: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28086981/does-antiretroviral-treatment-change-hiv-1-codon-usage-patterns-in-its-genes-a-preliminary-bioinformatics-study
#13
Navaneethan Palanisamy, Nathan Osman, Frédéric Ohnona, Hong-Tao Xu, Bluma Brenner, Thibault Mesplède, Mark A Wainberg
BACKGROUND: Codon usage bias has been described for various organisms and is thought to contribute to the regulation of numerous biological processes including viral infections. HIV-1 codon usage has been previously shown to be different from that of other viruses and man. It is evident that the antiretroviral drugs used to restrict HIV-1 replication also select for resistance variants. We wanted to test whether codon frequencies in HIV-1 sequences from treatment-experienced patients differ from those of treatment-naive individuals due to drug pressure affecting codon usage bias...
January 7, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28077169/distinct-5-methylcytosine-profiles-in-poly-a-rna-from-mouse-embryonic-stem-cells-and-brain
#14
Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura, Alexandra Lusser
BACKGROUND: Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes...
January 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28068395/correction-analysis-of-synonymous-codon-usage-bias-of-zika-virus-and-its-adaption-to-the-hosts
#15
Hongju Wang, Siqing Liu, Bo Zhang, Wenqiang Wei
[This corrects the article DOI: 10.1371/journal.pone.0166260.].
2017: PloS One
https://www.readbyqxmd.com/read/28062753/standard-codon-substitution-models-overestimate-purifying-selection-for-non-stationary-data
#16
Benjamin D Kaehler, Von Bing Yap, Gavin A Huttley
Estimation of natural selection on protein-coding sequences is a key comparative genomics approach for de novo prediction of lineage-specific adaptations. Selective pressure is measured on a per-gene basis by comparing the rate of non-synonymous substitutions to the rate of synonymous substitutions. All published codon substitution models have been time-reversible and thus assume that sequence composition does not change over time. We previously demonstrated that if time-reversible DNA substitution models are applied in the presence of changing sequence composition, the number of substitutions is systematically biased towards overestimation...
January 5, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28045602/simplified-method-to-obtain-enhanced-expression-of-tau-protein-from-e-coli-and-one-step-purification-by-direct-boiling
#17
V Guru KrishnaKumar, Sharad Gupta
Tau is an intrinsically disordered protein responsible for maintaining the structure and stability of axonal microtubules. However, in certain disease conditions including Alzheimer's disease, tau protein may undergo biochemical and structural changes to form intracellular aggregates. Since tau is a proline- and arginine-rich eukaryotic protein, heterologous expression in Escherichia coli often results in poor yield and has been a major technical challenge. In the current work, we have improved the expressed yield of tau by overcoming codon bias problem and established a simplified protocol for efficient extraction...
January 3, 2017: Preparative Biochemistry & Biotechnology
https://www.readbyqxmd.com/read/27992716/fidelity-of-the-dna-ligase-catalyzed-scaffolding-of-peptide-fragments-on-nucleic-acid-polymers
#18
Chun Guo, Ryan Hili
We describe the development and analysis of the T4 DNA ligase-catalyzed DNA templated polymerization of pentanucleotides modified with peptide fragments toward the generation of ssDNA-scaffolded peptides. A high-throughput duplex DNA sequencing method was developed to facilitate the determination of fidelity for various codon sets and library sizes used during the polymerization process. With this process, we identified several codon sets that enable the efficient and sequence-specific incorporation of peptide fragments along a ssDNA template at fidelities up to 99% and with low sequence bias...
December 28, 2016: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/27964762/new-tools-to-analyze-overlapping-coding-regions
#19
Amir H Bayegan, Juan Antonio Garcia-Martin, Peter Clote
BACKGROUND: Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement)...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27935840/a-stress-induced-bias-in-the-reading-of-the-genetic-code-in-escherichia-coli
#20
Adi Oron-Gottesman, Martina Sauert, Isabella Moll, Hanna Engelberg-Kulka
: Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM), composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant...
November 15, 2016: MBio
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