Influence of codon usage and translation initiation codon context in theAcNPV-based expression system: Computer analysis using homologous and heterologous genes

Codon usage by all the known gene sequences fromAutographa californica nuclear polyhedrosis virus (AcNPV) was compared with that of firefly luciferase (luc) and the beta subunit of human chorionic gonadotropin (hCG) expressed to contrasting levels in the baculovirus system. The highly expressedluc gene showed a codon usage similar toAcNPV 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 hCG gene displayed a high D-squared value (7.3) and G/C usage (82.5%) at the wobble base positions. Alignment of the 20 nucleotides around the initiation codon of 23AcNPV 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.