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Codon usage

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https://www.readbyqxmd.com/read/28545122/spot-a-novel-and-streamlined-microarray-platform-for-observing-cellular-trna-levels
#1
Simon Grelet, Ariel McShane, Eveline Hok, Jensen Tomberlin, Philip H Howe, Renaud Geslain
Recent studies have placed transfer RNA (tRNA), a housekeeping molecule, in the heart of fundamental cellular processes such as embryonic development and tumor progression. Such discoveries were contingent on the concomitant development of methods able to deliver high-quality tRNA profiles. The present study describes the proof of concept obtained in Escherichia coli (E. coli) for an original tRNA analysis platform named SPOt (Streamlined Platform for Observing tRNA). This approach comprises three steps. First, E...
2017: PloS One
https://www.readbyqxmd.com/read/28539444/improved-prefusion-stability-optimized-codon-usage-and-augmented-virion-packaging-enhance-the-immunogenicity-of-respiratory-syncytial-virus-rsv-fusion-protein-in-a-vectored-vaccine-candidate
#2
Bo Liang, Joan O Ngwuta, Sonja Surman, Barbora Kabatova, Xiang Liu, Matthias Lingemann, Xueqiao Liu, Lijuan Yang, Richard Herbert, Joanna Swerczek, Man Chen, Syed M Moin, Azad Kumar, Jason S McLellan, Peter D Kwong, Barney S Graham, Peter L Collins, Shirin Munir
Respiratory syncytial virus (RSV) is the most important viral agent of severe pediatric respiratory tract disease worldwide, but lacks a licensed vaccine or suitable antiviral drug. A live-attenuated chimeric bovine/human parainfluenza virus type-3 (rB/HPIV3) was developed previously as a vector expressing RSV fusion (F) protein to confer bivalent protection against RSV and HPIV3. In a previous clinical trial in virus-naïve children, rB/HPIV3 was well-tolerated but the immunogenicity of wildtype RSV F was unsatisfactory...
May 24, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28537425/differential-codon-usage-pattern-of-hiv-1-tat-gene-in-those-with-slower-and-faster-rates-of-disease-progression
#3
K K Vidyavijayan, Brahmaiah Anangi, Brindha B, Kannan T, Hassan S, Luke Elizabeth Hanna
Codon usage has been identified as one of the most important factors that influence gene expression. The frequencies with which the different codons are used vary significantly between different organisms and also between the genes within the same organism. Human immunodeficiency virus (HIV) has a remarkable nucleotide composition with an above average percentage of 'A' nucleotides resulting in a codon usage pattern different from that of the human host. Here we compared the codon usage pattern of HIV-1 genes among different groups of HIV disease progressors to understand the influence of differential codon usage pattern on the pathogenic manifestation in the host...
May 24, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28537229/-genomics-and-transcriptomics-of-the-chinese-liver-fluke-clonorchis-sinensis-opisthorchiidae-trematoda
#4
G N Chelomina
The review summarizes the results of first genomic and transcriptomic investigations of the liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda). The studies mark the dawn of the genomic era for opisthorchiids, which cause severe hepatobiliary diseases in humans and animals. Their results aided in understanding the molecular mechanisms of adaptation to parasitism, parasite survival in mammalian biliary tracts, and genome dynamics in the individual development and the development of parasite-host relationships...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28531201/evolutionary-forces-affecting-synonymous-variations-in-plant-genomes
#5
Yves Clément, Gautier Sarah, Yan Holtz, Felix Homa, Stéphanie Pointet, Sandy Contreras, Benoit Nabholz, François Sabot, Laure Sauné, Morgane Ardisson, Roberto Bacilieri, Guillaume Besnard, Angélique Berger, Céline Cardi, Fabien De Bellis, Olivier Fouet, Cyril Jourda, Bouchaib Khadari, Claire Lanaud, Thierry Leroy, David Pot, Christopher Sauvage, Nora Scarcelli, James Tregear, Yves Vigouroux, Nabila Yahiaoui, Manuel Ruiz, Sylvain Santoni, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin
Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28515770/high-level-expression-of-recombinant-human-growth-hormone-in-escherichia-coli-crucial-role-of-translation-initiation-region
#6
Mahsa Ghavim, Khalil Abnous, Fatemeh Arasteh, Sahar Taghavi, Maryam Sadat Nabavinia, Mona Alibolandi, Mohammad Ramezani
For high-throughput production of recombinant protein in Escherichia coli (E. coli), besides important parameters such as efficient vector with strong promoter and compatible host, other important issues including codon usage, rare codons, and GC content specially at N-terminal region should be considered. In the current study, the effect of decreasing the percentage of GC nucleotides and optimizing codon usage at N-terminal region of human growth hormone (hGH) cDNA on the level of its expression in E. coli were investigated...
April 2017: Research in Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28506040/codon-usage-patterns-of-tyrosinase-genes-in-clonorchis-sinensis
#7
Young-An Bae
Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined...
April 2017: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28486986/the-link-between-adjacent-codon-pairs-and-mrna-stability
#8
Yuriko Harigaya, Roy Parker
BACKGROUND: Evidence in diverse organisms suggests that codon optimality is a major determinant of mRNA translation and degradation. Codon optimality is thought to act by modulating the efficiency of ribosome elongation. In Saccharomyces cerevisiae, a recent study has identified 17 adjacent codon pairs that mediate strong inhibition of translation elongation. However, relationships between the inhibitory codon pairs and other aspects of gene expression are unknown. RESULTS: To gain insights into how the inhibitory codon pairs may affect aspects of gene expression, we utilized existing datasets to conduct genome-scale analyses in S...
May 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28475588/widespread-position-specific-conservation-of-synonymous-rare-codons-within-coding-sequences
#9
Julie L Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T Specht, Kim Ngo, Jun Li, Scott Emrich, Patricia L Clark
Synonymous rare codons are considered to be sub-optimal for gene expression because they are translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous rare codons. Rare codons at the 5' terminus of coding sequences have been shown to increase translational efficiency. Although a general functional role for synonymous rare codons farther within coding sequences has not yet been established, several recent reports have identified rare-to-common synonymous codon substitutions that impair folding of the encoded protein...
May 5, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28469144/a-deep-intronic-clrn1-ush3a-founder-mutation-generates-an-aberrant-exon-and-underlies-severe-usher-syndrome-on-the-arabian-peninsula
#10
Arif O Khan, Elvir Becirovic, Christian Betz, Christine Neuhaus, Janine Altmüller, Lisa Maria Riedmayr, Susanne Motameny, Gudrun Nürnberg, Peter Nürnberg, Hanno J Bolz
Deafblindness is mostly due to Usher syndrome caused by recessive mutations in the known genes. Mutation-negative patients therefore either have distinct diseases, mutations in yet unknown Usher genes or in extra-exonic parts of the known genes - to date a largely unexplored possibility. In a consanguineous Saudi family segregating Usher syndrome type 1 (USH1), NGS of genes for Usher syndrome, deafness and retinal dystrophy and subsequent whole-exome sequencing each failed to identify a mutation. Genome-wide linkage analysis revealed two small candidate regions on chromosome 3, one containing the USH3A gene CLRN1, which has never been associated with Usher syndrome in Saudi Arabia...
May 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28468662/heterologous-expression-of-abaecin-peptide-from-apis-mellifera-in-pichia-pastoris
#11
Denis Prudencio Luiz, Juliana Franco Almeida, Luiz Ricardo Goulart, Nilson Nicolau-Junior, Carlos Ueira-Vieira
BACKGROUND: Antimicrobial peptides (AMPs) are the first line of host immune defense against pathogens. Among AMPs from the honeybee Apis mellifera, abaecin is a major broad-spectrum antibacterial proline-enriched cationic peptide. RESULTS: For heterologous expression of abaecin in Pichia pastoris, we designed an ORF with HisTag, and the codon usage was optimized. The gene was chemically synthetized and cloned in the pUC57 vector. The new ORF was sub-cloned in the pPIC9 expression vector and transformed into P...
May 3, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28449100/integrated-analysis-of-individual-codon-contribution-to-protein-biosynthesis-reveals-a-new-approach-to-improving-the-basis-of-rational-gene-design
#12
Juan C Villada, Otávio José Bernardes Brustolini, Wendel Batista da Silveira
Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as frequency, optimality and positional dependency should be combined to unveil individual codon contribution for protein biosynthesis...
April 24, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28448468/transcriptome-analysis-of-core-dinoflagellates-reveals-a-universal-bias-towards-gc-rich-codons
#13
Ernest Williams, Allen Place, Tsvetan Bachvaroff
Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-documented mechanism for controlling gene expression during translation is codon bias, whereby specific codons slow or even terminate protein synthesis. Approximately 10,000 annotatable genes from fifteen "core" dinoflagellate transcriptomes along a range of overall guanine and cytosine (GC) content were used for codonW analysis to determine the relative synonymous codon usage (RSCU) and the GC content at each codon position...
April 27, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28446664/analysis-of-competing-hiv-1-splice-donor-sites-uncovers-a-tight-cluster-of-splicing-regulatory-elements-within-exon-2-2b
#14
Anna-Lena Brillen, Lara Walotka, Frank Hillebrand, Lisa Müller, Marek Widera, Stephan Theiss, Heiner Schaal
The HIV-1 accessory protein Vif is essential for viral replication by counteracting the host restriction factor APOBEC3G (A3G), and balanced levels of both proteins are required for efficient viral replication. Non-coding exons 2/2b contain the Vif start codon between their alternatively used splice donors 2 and 2b (D2 and D2b). For the vif mRNA, intron 1 must be removed, while intron 2 must be retained. Thus, splice acceptor 1 (A1) must be activated by U1 snRNP binding to either D2 or D2b, while splicing at D2 or D2b must be prevented...
April 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28442431/reducing-isoform-complexity-of-human-tetraspanins-by-optimized-expression-in-dictyostelium-discoideum-enables-high-throughput-functional-read-out
#15
Tineke Scheltz, Julia von Bülow, Eric Beitz
The human tetraspanin family of scaffold proteins comprises 33 isoforms. Being integral membrane proteins, they organize a so-called tetraspanin web via homomeric and heteromeric protein-protein interactions with integrins, immunoglobulins, growth factors, receptor tyrosine kinases, proteases, signaling proteins, and viral capsid proteins. Tetraspanins promote cellular effects, such as adhesion, migration, invasion, signaling, membrane fusion, protein trafficking, cancer progression, and infections. The ubiquitous expression of multiple tetraspanin isoforms and partner proteins hampers specific interaction studies...
April 22, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28441787/codon-usage-optimization-and-construction-of-plasmid-encoding-iranian-human-papillomavirus-type-16-e7-oncogene-for-lactococcus-lactis-subsp-cremoris-mg1363
#16
Amir Hossein Mohseni, Vadood Razavilar, Hossein Keyvani, Mohammad Reza Razavi, Ramazan Ali Khavari Nejad
HPV 16 intratypic sequence variations has been recognized in association with oncogenic potential diverge and geographic distribution. This study aimed to investigate nucleotide modifications and optimization of HPV 16 E7 regions from Iranian infected women. Cervical biopsies from 79/163 HPV 16 positive cancer patients detected in our study were analyzed by PCR in a couple of cloning of a complete ORF of the E7 gene, and sequencing. The most frequently observed variant was C196T in E7 which led to an amino acid change of R66W...
March 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28437229/quinolone-resistance-determinants-of-clinical-salmonella-enteritidis-in-thailand
#17
Fuangfa Utrarachkij, Chie Nakajima, Ruchirada Changkwanyeun, Kanokrat Siripanichgon, Siriporn Kongsoi, Srirat Pornruangwong, Kanjana Changkaew, Risa Tsunoda, Yutaka Tamura, Orasa Suthienkul, Yasuhiko Suzuki
Salmonella Enteritidis has emerged as a global concern regarding quinolone resistance and invasive potential. Although quinolone-resistant S. Enteritidis has been observed with high frequency in Thailand, information on the mechanism of resistance acquisition is limited. To elucidate the mechanism, a total of 158 clinical isolates of nalidixic acid (NAL)-resistant S. Enteritidis were collected throughout Thailand, and the quinolone resistance determinants were investigated in the context of resistance levels to NAL, norfloxacin (NOR), and ciprofloxacin (CIP)...
February 23, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28431284/mitovirus-uga-trp-codon-usage-parallels-that-of-host-mitochondria
#18
Max L Nibert
Mitoviruses replicate in mitochondria of their host fungi. They have small RNA genomes that encompass a single ORF encoding the viral RdRp. Since UGA codons encode Trp in fungal mitochondria, the RdRp ORF of a typical mitovirus includes multiple UGA codons. In some mitoviruses, however, the ORF has no such codons, suggesting that these particular viruses may be under selective pressure to exclude them. In this report, new evidence is presented that host fungi whose mitoviruses have no or few UGA codons are distinctive in also having no or few UGA codons in their core mitochondrial genes...
April 18, 2017: Virology
https://www.readbyqxmd.com/read/28428795/non-canonical-translation-in-plant-rna-viruses
#19
REVIEW
Manuel Miras, W Allen Miller, Verónica Truniger, Miguel A Aranda
Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5' cap structure and/or the 3' poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28427327/analysis-of-transcriptome-data-reveals-multifactor-constraint-on-codon-usage-in-taenia-multiceps
#20
Xing Huang, Jing Xu, Lin Chen, Yu Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang
BACKGROUND: Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. RESULTS: Analysis of a total of 8,620 annotated mRNA sequences from T...
April 20, 2017: BMC Genomics
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