Influence of codon usage bias on FGLamide-allatostatin mRNA secondary structure.
The FGLamide allatostatins (ASTs) are invertebrate neuropeptides which inhibit juvenile hormone biosynthesis in Dictyoptera and related orders. They also show myomodulatory activity. FGLamide AST nucleotide frequencies and codon bias were investigated with respect to possible effects on mRNA secondary structure. 367 putative FGLamide ASTs and their potential endoproteolytic cleavage sites were identified from 40 species of crustaceans, chelicerates and insects. Among these, 55% comprised only 11 amino acids. An FGLamide AST consensus was identified to be (X)(1→16)Y(S/A/N/G)FGLGKR, with a strong bias for the codons UUU encoding for Phe and AAA for Lys, which can form strong Watson-Crick pairing in all peptides analyzed. The physical distance between these codons favor a loop structure from Ser/Ala-Phe to Lys-Arg. Other loop and hairpin loops were also inferred from the codon frequencies in the N-terminal motif, and the first amino acids from the C-terminal motif, or the dibasic potential endoproteolytic cleavage site. Our results indicate that nucleotide frequencies and codon usage bias in FGLamide ASTs tend to favor mRNA folds in the codon sequence in the C-terminal active peptide core and at the dibasic potential endoproteolytic cleavage site.
Martínez-Pérez
Francisco
F
Department of Cell and Systems Biology, University of Toronto, 110 St. George St., Toronto, ON M5S 3G5, Canada.
Bendena
William G
WG
Chang
Belinda S W
BS
Tobe
Stephen S
SS
D000818:Animals; D003058:Cockroaches / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D009479:Neuropeptides / Q000235:genetics*; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000235:genetics*
D003062:Codon; D009479:Neuropeptides; D012333:RNA, Messenger; C076523:allatostatin