To see the effect of temperature on the codon and amino acid usage in phages, codon and amino acid usage of 13 phages of extremely thermophilic prokaryotes were compared with that of 14 phages of mesophilic prokaryotes. Correspondence analysis on RSCU values of two groups of phage genomes clearly shows that phages are separated along the second major axis according to their growth temperature, whereas, they are separated along the first major axis according to their GC content. Correspondence analysis on RAAU values of two groups of phages clearly shows that protein encoding genes of the phages along the second major axis are highly correlated with the GRAVY, aromaticity and cysteine content. Moreover, correspondence analysis on the regular and irregular structures of proteins of phages infecting extremely thermophilic prokaryotes reveals that temperature is one of the factors responsible for most significant differentiation of codon and amino acid usages variation in these phages. KEYWORDS:Relative synonymous codon usage (RSCU), relative amino acid usage (RAAU), correspondence analysis (CA), frequency of G+C at the synonymous third codon positions (GC3s), covalently closed circular (ccc) DNA, GRAVY, aromaticity, cysteine content, thermophilic prokaryotes, mesophilic prokaryotes

Viral protein U (Vpu) is a type-III integral membrane protein encoded by Human Immunodeficiency Virus-1 (HIV- 1). It is expressed in infected host cells and plays several roles in viral progeny escape from infected cells, including down-regulation of CD4 receptors. But key structure/function questions remain regarding the mechanisms by which the Vpu protein contributes to HIV-1 pathogenesis. Here we describe expression of Vpu in bacteria, its purification and characterization. We report the successful expression of PelB-Vpu in Escherichia coli using the leader peptide pectate lyase B (PelB) from Erwinia carotovora. The protein was detergent extractable and could be isolated in a very pure form. We demonstrate that the PelB signal peptide successfully targets Vpu to the cell membranes and inserts it as a type I membrane protein. PelB-Vpu was biophysically characterized by circular dichroism and dynamic light scattering experiments and was shown to be an excellent candidate for elucidating structural models.

Femtosecond X-ray crystallography allows structural analysis of a difficult-to-crystallize fusion protein that is a potential component of a candidate HIV-1 subunit vaccine.

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