scholarly journals Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

2010 ◽  
Vol 6 (3) ◽  
pp. e1000797 ◽  
Author(s):  
Lluís Aragonès ◽  
Susana Guix ◽  
Enric Ribes ◽  
Albert Bosch ◽  
Rosa M. Pintó
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Driving Force ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Fine Tuning ◽  
Virus Capsid

scholarly journals Mapping codon usage in sequence regions flanking cleavage positions in the hepatitis A virus polyprotein

2013 ◽  
Vol 12 (3) ◽  
pp. 2306-2319 ◽  
Author(s):  
X.-X. Ma ◽  
Y.-P. Feng ◽  
L. Chen ◽  
Y.-Q. Zhao ◽  
J.-L. Liu ◽  
...  
Keyword(s):  
Codon Usage ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Virus Polyprotein

scholarly journals Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Wenqi Ran ◽  
David M. Kristensen ◽  
Eugene V. Koonin
Keyword(s):  
Codon Usage ◽  
Protein Level ◽  
Codon Usage Bias ◽  
Protein Sequence ◽  
Gc Content ◽  
Protein Sequences ◽  
Microbial Evolution ◽  
Fine Tuning ◽  
Selection For ◽  
Genomic Gc Content

ABSTRACT The relationship between the selection affecting codon usage and selection on protein sequences of orthologous genes in diverse groups of bacteria and archaea was examined by using the Alignable Tight Genome Clusters database of prokaryote genomes. The codon usage bias is generally low, with 57.5% of the gene-specific optimal codon frequencies (F opt ) being below 0.55. This apparent weak selection on codon usage contrasts with the strong purifying selection on amino acid sequences, with 65.8% of the gene-specific dN/dS ratios being below 0.1. For most of the genomes compared, a limited but statistically significant negative correlation between F opt and dN/dS was observed, which is indicative of a link between selection on protein sequence and selection on codon usage. The strength of the coupling between the protein level selection and codon usage bias showed a strong positive correlation with the genomic GC content. Combined with previous observations on the selection for GC-rich codons in bacteria and archaea with GC-rich genomes, these findings suggest that selection for translational fine-tuning could be an important factor in microbial evolution that drives the evolution of genome GC content away from mutational equilibrium. This type of selection is particularly pronounced in slowly evolving, “high-status” genes. A significantly stronger link between the two aspects of selection is observed in free-living bacteria than in parasitic bacteria and in genes encoding metabolic enzymes and transporters than in informational genes. These differences might reflect the special importance of translational fine-tuning for the adaptability of gene expression to environmental changes. The results of this work establish the coupling between protein level selection and selection for translational optimization as a distinct and potentially important factor in microbial evolution. IMPORTANCE Selection affects the evolution of microbial genomes at many levels, including both the structure of proteins and the regulation of their production. Here we demonstrate the coupling between the selection on protein sequences and the optimization of codon usage in a broad range of bacteria and archaea. The strength of this coupling varies over a wide range and strongly and positively correlates with the genomic GC content. The cause(s) of the evolution of high GC content is a long-standing open question, given the universal mutational bias toward AT. We propose that optimization of codon usage could be one of the key factors that determine the evolution of GC-rich genomes. This work establishes the coupling between selection at the level of protein sequence and at the level of codon choice optimization as a distinct aspect of genome evolution.

scholarly journals Hepatitis A Virus Capsid Structure

2018 ◽  
Vol 9 (5) ◽  
pp. a031807 ◽  
Author(s):  
David I. Stuart ◽  
Jingshan Ren ◽  
Xiangxi Wang ◽  
Zihe Rao ◽  
Elizabeth E. Fry
Keyword(s):  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Virus Capsid

scholarly journals The Critical Role of Codon Composition on the Translation Efficiency Robustness of the Hepatitis A Virus Capsid

2019 ◽  
Vol 11 (9) ◽  
pp. 2439-2456 ◽  
Author(s):  
Lucía D’Andrea ◽  
Francisco-Javier Pérez-Rodríguez ◽  
Montserrat de Castellarnau ◽  
Susana Guix ◽  
Enric Ribes ◽  
...  
Keyword(s):  
Codon Usage ◽  
Sequence Space ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Critical Role ◽  
Translation Efficiency ◽  
Rare Codons ◽  
Codon Composition ◽  
Cellular Genome

AbstractHepatoviruses show an intriguing deviated codon usage, suggesting an evolutionary signature. Abundant and rare codons in the cellular genome are scarce in the human hepatitis A virus (HAV) genome, while intermediately abundant host codons are abundant in the virus. Genotype–phenotype maps, or fitness landscapes, are a means of representing a genotype position in sequence space and uncovering how genotype relates to phenotype and fitness. Using genotype–phenotype maps of the translation efficiency, we have shown the critical role of the HAV capsid codon composition in regulating translation and determining its robustness. Adaptation to an environmental perturbation such as the artificial induction of cellular shutoff—not naturally occurring in HAV infection—involved movements in the sequence space and dramatic changes of the translation efficiency. Capsid rare codons, including abundant and rare codons of the cellular genome, slowed down the translation efficiency in conditions of no cellular shutoff. In contrast, rare capsid codons that are abundant in the cellular genome were efficiently translated in conditions of shutoff. Capsid regions very rich in slowly translated codons adapt to shutoff through sequence space movements from positions with highly robust translation to others with diminished translation robustness. These movements paralleled decreases of the capsid physical and biological robustness, and resulted in the diversification of capsid phenotypes. The deviated codon usage of extant hepatoviruses compared with that of their hosts may suggest the occurrence of a virus ancestor with an optimized codon usage with respect to an unknown ancient host.

scholarly journals Hepatitis A Virus Codon Usage: Implications for Translation Kinetics and Capsid Folding

2018 ◽  
Vol 8 (10) ◽  
pp. a031781 ◽  
Author(s):  
Rosa M. Pintó ◽  
Francisco-Javier Pérez-Rodríguez ◽  
Lucia D’Andrea ◽  
Montserrat de Castellarnau ◽  
Susana Guix ◽  
...  
Keyword(s):  
Codon Usage ◽  
Hepatitis A ◽  
Hepatitis A Virus

scholarly journals Genome Variability and Capsid Structural Constraints of Hepatitis A Virus

2003 ◽  
Vol 77 (1) ◽  
pp. 452-459 ◽  
Author(s):  
Glòria Sánchez ◽  
Albert Bosch ◽  
Rosa M. Pintó
Keyword(s):  
Codon Usage ◽  
Rna Structure ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Foot And Mouth Disease ◽  
Structural Constraints ◽  
Translation Speed ◽  
Synonymous Mutations ◽  
Rare Codons ◽  
Mouth Disease Virus

ABSTRACT The number of synonymous mutations per synonymous site (Ks ), the number of nonsynonymous mutations per nonsynonymous site (Ka ), and the codon usage statistic (Nc ) were calculated for several hepatitis A virus (HAV) isolates. While Ks was similar to those of poliovirus (PV) and foot-and-mouth disease virus (FMDV), Ka was 1 order of magnitude lower. The Nc parameter provides information on codon usage bias and decreases when bias increases. The Nc value in HAV was about 38, while in PV and FMDV, it was about 53. The emergence of 22 rare codons in front of 8 in PV and 7 in FMDV was detected. Most of the conserved rare codons of the P1 region were strategically located at the carboxy borders of β barrels and α helices, their potential function being the assurance of proper folding of the capsid proteins through a decrease in the translation speed. This strategic location was not observed for amino acids encoded by the conserved rare codons of the 3D region. The percentage of bases with low pairing number values was higher in the latter region, suggesting a role of the conserved rare codons in the maintenance of RNA structure. Many of the rare codons in HAV are among the most frequent in humans, unlike in PV or in FMDV. This fact may be explained by the lack of cellular shutoff in HAV. One hypothesis is that HAV has evolved in order to avoid competition with its host for cellular tRNAs.

scholarly journals Assessing the risk of a community outbreak of hepatitis A on blood safety in Latvia, 2008

2010 ◽  
Vol 15 (33) ◽  
Author(s):  
J Perevoščikovs ◽  
A Lenglet ◽  
I Lucenko ◽  
A Šteinerte ◽  
L Payne Hallström ◽  
...  
Keyword(s):  
Public Health ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Disease Outbreak ◽  
Capital City ◽  
Fine Tuning ◽  
Risk Assessments ◽  
Blood Safety ◽  
Infectious Disease Outbreak ◽  
Post Transfusion Hepatitis

Post-transfusion hepatitis A virus (HAV) infection worldwide is considered a sporadic event. An outbreak of HAV infection occurred in Latvia between the end of 2007 and throughout 2008 with more than 2,800 confirmed cases reported over a 13-month period (incidence of 123 per 100,000 population). The majority of reported HAV infection cases were in people over 18 years of age and in people living in the capital city, Riga. We estimated that the crude risk for HAV contamination of whole blood supplies in Riga between February and October 2008 ranged from 1.4 to 10.6per 10,000 donated units. In people under 40 years of age, the risk of receiving an infectious blood transfusion was more than 3.0 per 10,000 recipients between August and October 2008 during the peak of the outbreak. We conclude that there is a previously under-recognised impact of HAV on blood safety during widespread outbreaks of this disease. Estimating the risk of contamination of blood supplies during an infectious disease outbreak scenario is important for fine tuning risk assessments and potentially improving public health practices.

scholarly journals Analysis of synonymous codon usage in Hepatitis A virus

2011 ◽  
Vol 8 (1) ◽  
Author(s):  
Yiqiang Zhang ◽  
Yongsheng Liu ◽  
Wenqian Liu ◽  
Jianhua Zhou ◽  
Haotai Chen ◽  
...  
Keyword(s):  
Codon Usage ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Synonymous Codon ◽  
Synonymous Codon Usage
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