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https://www.readbyqxmd.com/read/28334743/comparative-genomic-analysis-of-translation-initiation-mechanisms-for-genes-lacking-the-shine-dalgarno-sequence-in-prokaryotes
#1
So Nakagawa, Yoshihito Niimura, Takashi Gojobori
In prokaryotes, translation initiation is believed to occur through an interaction between the 3΄ tail of a 16S rRNA and a corresponding Shine-Dalgarno (SD) sequence in the 5΄ untranslated region (UTR) of an mRNA. However, some genes lack SD sequences (non-SD genes), and the fraction of non-SD genes in a genome varies depending on the prokaryotic species. To elucidate non-SD translation initiation mechanisms in prokaryotes from an evolutionary perspective, we statistically examined the nucleotide frequencies around the initiation codons in non-SD genes from 260 prokaryotes (235 bacteria and 25 archaea)...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28332757/selective-modes-determine-evolutionary-rates-gene-compactness-and-expression-patterns-in-brassica
#2
Yue Guo, Jing Liu, Jiefu Zhang, Shengyi Liu, Jianchang Du
It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories, i.e., positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (Ka) and the synonymous substitution (Ks) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa, and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs...
March 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28324177/a-detailed-analysis-of-codon-usage-patterns-and-influencing-factors-in-zika-virus
#3
Niraj K Singh, Anuj Tyagi
Recent outbreaks of Zika virus (ZIKV) in Africa, Latin America, Europe, and Southeast Asia have resulted in serious health concerns. To understand more about evolution and transmission of ZIKV, detailed codon usage analysis was performed for all available strains. A high effective number of codons (ENC) value indicated the presence of low codon usage bias in ZIKV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations between nucleotide compositions at third codon positions and ENCs...
March 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28321010/discovery-and-complete-genome-sequence-of-a-bacteriophage-from-an-obligate-intracellular-symbiont-of-a-cellulolytic-protist-in-the-termite-gut
#4
Ajeng K Pramono, Hirokazu Kuwahara, Takehiko Itoh, Atsushi Toyoda, Akinori Yamada, Yuichi Hongoh
Termites depend nutritionally on their gut microbes, and protistan, bacterial, and archaeal gut communities have been extensively studied. However, limited information is available on viruses in the termite gut. We herein report the complete genome sequence (99,517 bp) of a phage obtained during a genome analysis of "Candidatus Azobacteroides pseudotrichonymphae" phylotype ProJPt-1, which is an obligate intracellular symbiont of the cellulolytic protist Pseudotrichonympha sp. in the gut of the termite Prorhinotermes japonicus...
March 17, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28315836/a-phylogenetic-codon-substitution-model-for-antibody-lineages
#5
Kenneth B Hoehn, Gerton Lunter, Oliver G Pybus
Phylogenetic methods have shown promise in understanding the development of broadly neutralizing antibody lineages (bNAbs). However, the mutational process that generates these lineages -- somatic hypermutation -- is biased by hotspot motifs, which violates important assumptions in most phylogenetic substitution models. Here, we develop a modified GY94-type substitution model that partially accounts for this context-dependency while preserving independence of sites during calculation. This model shows a substantially better fit to three well-characterized bNAb lineages than the standard GY94 model...
March 17, 2017: Genetics
https://www.readbyqxmd.com/read/28289571/differential-bicodon-usage-in-lowly-and-highly-abundant-proteins
#6
Luis A Diambra
Degeneracy in the genetic code implies that different codons can encode the same amino acid. Usage preference of synonymous codons has been observed in all domains of life. There is much evidence suggesting that this bias has a major role on protein elongation rate, contributing to differential expression and to co-translational folding. In addition to codon usage bias, other preference variations have been observed such as codon pairs. In this paper, I report that codon pairs have significant different frequency usage for coding either lowly or highly abundant proteins...
2017: PeerJ
https://www.readbyqxmd.com/read/28288557/bicodon-bias-can-determine-the-role-of-synonymous-snps-in-human-diseases
#7
Christina McCarthy, Alejandra Carrea, Luis Diambra
BACKGROUND: For a long time synonymous single nucleotide polymorphisms were considered as silent mutations. However, nowadays it is well known that they can affect protein conformation and function, leading to altered disease susceptibilities, differential prognosis and/or drug responses, among other clinically relevant genetic traits. This occurs through different mechanisms: by disrupting the splicing signals of precursor mRNAs, affecting regulatory binding-sites of transcription factors and miRNAs, or by modifying the secondary structure of mRNAs...
March 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28287622/a-codon-shuffling-method-to-prevent-reversion-during-production-of-replication-defective-herpesvirus-stocks-implications-for-herpesvirus-vaccines
#8
Gang Li, Charles Ward, Rukhsana Yeasmin, Steven Skiena, Laurie T Krug, J Craig Forrest
Herpesviruses establish life-long chronic infections that place infected hosts at risk for severe disease. Herpesvirus genomes readily undergo homologous recombination (HR) during productive replication, often leading to wild-type (WT) reversion during complementation of replication-defective and attenuated viruses via HR with the helper gene provided in trans. To overcome this barrier, we developed a synthetic-biology approach based on a technique known as codon shuffling. Computer-assisted algorithms redistribute codons in a helper gene, thereby eliminating regions of homology, while enabling manipulation of factors such as codon-pair bias and CpG content to effectively titrate helper-gene protein levels...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28286710/the-complete-chloroplast-genome-sequence-of-morus-cathayana-and-morus-multicaulis-and-comparative-analysis-within-genus-morus-l
#9
Wei Qing Kong, Jin Hong Yang
Trees in the Morus genera belong to the Moraceae family. To better understand the species status of genus Morus and to provide information for studies on evolutionary biology within the genus, the complete chloroplast (cp) genomes of M. cathayana and M. multicaulis were sequenced. The plastomes of the two species are 159,265 bp and 159,103 bp, respectively, with corresponding 83 and 82 simple sequence repeats (SSRs). Similar to the SSRs of M. mongolica and M. indica cp genomes, more than 70% are mononucleotides, ten are in coding regions, and one exhibits nucleotide content polymorphism...
2017: PeerJ
https://www.readbyqxmd.com/read/28282871/factors%C3%A2-that%C3%A2-shape%C3%A2-eukaryotic%C3%A2-trnaomes-%C3%A2-processing-%C3%A2-modification%C3%A2-and%C3%A2-anticodon-codon%C3%A2-use
#10
REVIEW
Richard J Maraia, Aneeshkumar G Arimbasseri
Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias...
March 8, 2017: Biomolecules
https://www.readbyqxmd.com/read/28265498/digging-deeper-new-gene-order-rearrangements-and-distinct-patterns-of-codons-usage-in-mitochondrial-genomes-among-shrimps-from-the-axiidea-gebiidea-and-caridea-crustacea-decapoda
#11
Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Gary C B Poore, Christopher M Austin
BACKGROUND: Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information...
2017: PeerJ
https://www.readbyqxmd.com/read/28264512/rapid-sampling-of-escherichia-coli-after-changing-oxygen-conditions-reveals-transcriptional-dynamics
#12
Joachim von Wulffen, Andreas Ulmer, Günter Jäger, Oliver Sawodny, Ronny Feuer
Escherichia coli is able to shift between anaerobic and aerobic metabolism by adapting its gene expression, e.g., of metabolic genes, to the new environment. The dynamics of gene expression that result from environmental shifts are limited, amongst others, by the time needed for regulation and transcription elongation. In this study, we examined gene expression dynamics after an anaerobic-to-aerobic shift on a short time scale (0.5, 1, 2, 5, and 10 min) by RNA sequencing with emphasis on delay times and transcriptional elongation rates (TER)...
February 28, 2017: Genes
https://www.readbyqxmd.com/read/28261263/analytical-biases-associated-with-gc-content-in-molecular-evolution
#13
Jonathan Romiguier, Camille Roux
Molecular evolution is being revolutionized by high-throughput sequencing allowing an increased amount of genome-wide data available for multiple species. While base composition summarized by GC-content is one of the first metrics measured in genomes, its genomic distribution is a frequently neglected feature in downstream analyses based on DNA sequence comparisons. Here, we show how base composition heterogeneity among loci and taxa can bias common molecular evolution analyses such as phylogenetic tree reconstruction, detection of natural selection and estimation of codon usage...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28254474/new-insights-on-the-sister-lineage-of-percomorph-fishes-with-an-anchored-hybrid-enrichment-dataset
#14
Alex Dornburg, Jeffrey P Townsend, Willa Brooks, Elizabeth Spriggs, Ron I Eytan, Jon A Moore, Peter C Wainwright, Alan Lemmon, Emily Moriarty Lemmon, Thomas J Near
Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias)...
February 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28254397/high-level-expression-of-two-thermophilic-%C3%AE-mannanases-in-yarrowialipolytica
#15
Wang YaPing, Rao Ben, Zhang Ling, Ma Lixin
Two thermophilic β-mannanases (ManA and ManB)were successfully expressed in Yarrowialipolytica using vector pINA1296I. The sequences of manA from Aspergillus niger CBS 513.88 and manB from Bacillus subtilis BCC41051 were optimized based on codon-usage bias in Y.lipolytica and synthesized by overlapping polymerase chain reaction (PCR). We utilized the pINA1296I vector, which allows inserting and expression of multiple copies of an expression cassette, to engineer recombinant strains containing multiple copies of manA or manB...
February 22, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28230975/tuning-of-recombinant-protein-expression-in-escherichia-coli-by-manipulating-transcription-translation-initiation-rates-and-incorporation-of-noncanonical-amino-acids
#16
Orr Schlesinger, Yonatan Chemla, Mathias Heltberg, Eden Ozer, Ryan Marshall, Vincent Noireaux, Mogens Høgh Jensen, Lital Alfonta
Protein synthesis in cells has been thoroughly investigated and characterized over the past 60 years. However, some fundamental issues remain unresolved, including the reasons for genetic code redundancy and codon bias. In this study, we changed the kinetics of the Eschrichia coli transcription and translation processes by mutating the promoter and ribosome binding domains and by using genetic code expansion. The results expose a counterintuitive phenomenon, whereby an increase in the initiation rates of transcription and translation lead to a decrease in protein expression...
March 9, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28215215/the-mitochondrial-genome-of-ancylostoma-tubaeforme-from-cats-in-china
#17
X L Shi, Y Q Fu, A Y Abdullahi, M W Wang, F Yang, X G Yu, W D Pan, X X Yan, J X Hang, P Zhang, G Q Li
Ancylostoma tubaeforme may infect canids, felids and humans, and pose a potential risk to public health. Polymerase chain reaction (PCR) techniques were used to amplify the complete mitochondrial (mt) genome sequence of A. tubaeforme from cats and to analyse its sequence characteristics after molecular identification based on the internal transcribed spacer ITS1+ sequence. The results show that the complete mt genome sequence (GenBank accession number KY070315) of A. tubaeforme from cats was 13,730 bp in length, including 12 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, two non-coding regions and an AT-rich region...
February 20, 2017: Journal of Helminthology
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
#18
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
#19
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
#20
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
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