Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin(HA)cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes.We have developed a dynamic extended folding strategy to predict RNA secondary structure with RNAstructure 4.1 program in an iterative extension process.Statistical analysis of the sequences showed that the HA cleavage site basic amino acids favor the adenine-rich codons,and the corresponding mRNA fragments are mainly in the folding states of single-stranded loops.Our sequential and structural analyses showed that to prevent and control these highly pathogenic viruses,that is,to inhibit the gene expression of avian influenza virus H5N1 subtypes,we should consider the single-stranded loop regions of the HA cleavage site-coding sequences as the targets of RNA interference.

Genetic insight of the H5N1 hemagglutinin cleavage site

The cleavability of the hemagglutinin (HA) plays a major role in virulence of avian influenza viruses. Detailed analyses of the cleavage sequences and their evolution would give insights into the high pathogenicity of the H5N1 virus. HA segments were visually identifiable in the cellular automata (CA) image, and a feature gene segment (FGS) was only found in H5N1 rather than any other subtype. This FGS is a 30-bp gene segment mainly consisting of ‘A’ and ‘G’. When translated into amino acids the FGS converted into a sequence of mainly basic amino acids with positive charges. This feature amino acid segment (FAAS) was located in the cleavage site loop of HA which was potentially cleavable by various proteases. The 3D structure of H5N1 HA was reconstructed using homology modelling. It was found that the cleavage site loop was well exposed to potential proteases. The molecular surfaces were reconstructed to study how mutation and deletion of some amino acids in the FAAS affected the charge distribution. It was found that some mutations had severely changed the landscape of the charge dis- tribution. Statistical analyses of FAAS were made with respect to when and where the H5N1 viruses were found. In 2005, there were less un-mutated FAAS than the other years according to temporal evolution, and more mutated FAAS appeared in China than other regions according to geographic dis- tribution. These results are helpful for exploring the evolution of virus high pathogenicity.