A research article published in the journal PloS Pathogens could lead to improvements in the production of vaccines for hepatitis A, the most widespread viral disease in the world.
The study reported in the article was carried out by a team of experts from the University of Barcelona Enteric Viruses Group, a leading international group in the genomic study of the hepatitis A virus, directed by Rosa M. Pintó and Albert Bosch, lecturers for the Department of Microbiology and members of the Institute for Nutrition and Food Safety Research (INSA-UB).
According to the World Health Organization, there are more than 1.4 million new cases of hepatitis A in the world every year. The disease is caused by the hepatitis A virus (HAV) and is most commonly transmitted by the fecal-oral route via contaminated food or drinking water. The HAV is a member of the family Picornaviridae (which have RNA as their genetic material) with an icosahedral capsid that is highly resistant to environmental conditions, and exists as a single serotype. "This virus has a number of highly specific characteristics, is difficult to study and difficult to process in the laboratory setting. There are still many aspects of its biology about which very little is known: it has a very low replication rate, which means that the process for obtaining a vaccine antigen is also slow and very expensive", explains Albert Bosch.
The study looked at the mechanism for the translation of the genetic message and at protein synthesis in the HAV: complex biological machinery involving ribosomes, transfer RNA (tRNA), messenger RNA (mRNA) and the amino acids that will combine to form the polypeptide chains. The specific genetic information is transmitted via mRNA codons, the triplets of nitrogen bases that encode the information for each amino acid. tRNAs, which contain the anticodon, or complementary fragment to the mRNA codon, are the molecules which adapt the chemical information of the mRNA to the amino acid sequence in protein synthesis.
According to the authors, understanding the codon usage signature of the HAV is one of the keys to improving control of HAV replication. "Every organism has a unique codon usage signature. In the case of viruses, which are strict intracellular parasites, codon usage is usually adapted to that of the host cell. This usage strategy is linked to the tRNA pool available to the virus during its life cycle and which will be translated by the cellular", says Rosa M. Pintó.
From an evolutionary perspective, this mechanism corresponds to translational selection, a process with high biological efficiency in which codon usage bias favours paring with abundant tRNAs. However, the hepatitis A virus displays a contrasting pattern, in which selection of codon usage to optimize translation kinetics causes some codons to pair with common tRNAs and others to pair with rare tRNAs. The HAV is also a highly unique virus that demonstrates different codon usage to that of the host cell, exhibiting a deoptimized strategy. Rosa M. Pintó explains that in this scenario, "Finding a rare tRNA is much more difficult - really just a question of luck. At this point, translation on the ribosome slows and protein folding in synthesis pathways is more controlled".
One of the questions commonly asked by researchers is whether, under optimum conditions, it would be possible to optimize the HAV codon usage strategy. To find an answer, the group designed a protocol using the dug actinomycin D, which inhibits cellular transcription, increasing the available tRNA pool and allowing the virus codon usage to readapt. Surprisingly, under optimal tRNA pool availability, the virus response was to further de-optimize its codon usage to favour rare tRNAs, thus suggesting a preference for a slow translation rate. The virus adapts to the new conditions by altering its codon usage, which is made possible by the replication dynamics of RAN virus quasi-species. The evolution of the viral population reflects the famous paradox of the Red Queen effect (Leigh van Valen, 1973), inspired by the tales of Lewis Carroll, in which living beings evolve constantly to maintain their position in a constantly-changing environment. According to experts, the strategic usage of rarer codons favours the virus' survival by enhancing protein folding in the capsid, the protein shell which remains highly stable in the external environment.
The research community is interested in how the translation rate of HAV can be accelerated and whether other viruses show similar codon usage biases. The UB's Enteric Virus Group, a pioneering group in international research into codon usage in picornaviruses, aims to answer these questions and to pursue important goals such as determining whether the underlying mechanism of the usage bias is unique to the hepatitus A virus, designing genomic strategies for optimizing codon usage and the viral replication rate, obtaining more efficient strains of the virus, and lowering the costs of producing the vaccine against this common liver disease.