Codon usage in the prototype baculovirus--Autographa californica nuclear polyhedrosis virus.
Journal - Indian journal of biochemistry & biophysics (INDIA )
The overall codon usage profile of Autographa californica nuclear polyhedrosis virus (AcNPV) was analyzed, using UWGCG sequence analysis software package from the known protein coding gene sequences available in GenBank Release 72. The analysis revealed that although only 45% of the codon used by AcNPV have G/C at wobble base position, 15 out of 20 AcNPV codons over-utilized for their given amino acids has G/C at the wobble position indicating a possible selection of these codons. The differences in codon usage profile were studied using a parameter called D squared value, calculated with the aid of CORRESPOND program of UWGCG software package. While most of the codon usage profile of the individual genes was very similar to the overall AcNPV codon usage profile (D squared value less than 1.5), there were notable differences (D-squared value greater than 1.5). These genes were polh, p10, ub, sod, gp41, core, 25k, 39k, ie-n, etm, ets most of which, interestingly, belonged to late or very late class and were expressed relatively more efficiently. The two highly expressed genes of AcNPV, polh and the p10, differ from the overall AcNPV codon usage profile with respect to at least nine amino acids (Val, Ala, Ser, Lys, Ile, Thr, Leu, Phe, Arg). Our findings that the two highly expressed late genes polh and p10 utilize a codon usage profile different from the early genes have important implications.
|ISSN : ||0301-1208|
|Mesh Heading : ||Animals Base Sequence Molecular Sequence Data Moths Nucleopolyhedrovirus|
|Mesh Heading Relevant : ||Codon genetics|
Influence of codon usage and translational initiation codon context in the AcNPV-based expression system: computer analysis using homologous and heterologous genes.
Journal - Virus genes (UNITED STATES )
Codon usage by all the known gene sequences from Autographa californica nuclear polyhedrosis virus (AcNPV) was compared with that of firefly luciferase (luc) and the beta subunit of human chorionic gonadotropin (beta hCG) expressed to contrasting levels in the baculovirus system. The highly expressed luc gene showed a codon usage similar to AcNPV genes, as reflected by a very low D-squared statistic value (0.78) and a similar G/C usage (45%) at wobble positions. However, the underexpressed beta hCG gene displayed a high D-squared value (7.3) and G/C usage (82.5%) at the wobble base position. Alignment of the 20 nucleotides around the initiation codon of 23 AcNPV genes identified a novel consensus translation initiation sequence aag/ta/tat/aa/cAAaATGaa/ct/ag/aAan, which was quite different from the Kozak consensus sequence (GCC)GCCA/GCCATGG. An extension of these analyses to a sample of other heterologous genes overexpressed and underexpressed in BEVS suggested similar trends. These theoretical analyses have important implications for heterologous gene expression in this system.
|ISSN : ||0920-8569|
|Mesh Heading : ||Animals Automatic Data Processing Base Sequence Chorionic Gonadotropin Chorionic Gonadotropin, beta Subunit, Human DNA, Viral Gene Expression Regulation, Viral Humans Luciferases Molecular Sequence Data Moths Nucleopolyhedrovirus Peptide Fragments Protein Biosynthesis Recombinant Proteins genetics genetics metabolism genetics genetics|
|Mesh Heading Relevant : ||Codon, Initiator genetics|