CODON USAGE IN PLANT PEROXIDASE GENES

Codon preference and asymmetry in usage in the DNA sequences encoding the mature enzyme protein of 24 plant peroxidases from 12 different sp ecies were examined. Codon usage in highly conserved/non-conserved are as of the sequences was analysed, as well as possible deficiency/exces s in CpG dinucleotides in the pain of codon positions. Sequence relati onships displayed by overall codon usage, dinucleotide frequencies wit hin codons, and amino acid sequences were also studied. The main findi ngs were: (1) Monocots clustered separately from dicots for overall co don usage and dinucleotide frequencies in codon positions 2 and 3, wit h six and seven clusters respectively discernible among these 24 perox idase sequences. The monocot/dicot distinction disappeared in the four clusters among the mature protein amino acid sequences. Overall codon usage in sequences from monocotyledon and dicotyledon species differe d, the monocots favouring codons with C or G in the third position. (2 ) Codon usage was biassed in many sequences; asymmetry was particularl y noticeable in the monocots. (3) For repeated amino acids within cons erved areas, codon preference appeared dependent on the order in which the repeated amino acid occurred, so that its usage of synonymous cod ons frequently balanced out.