Plant & Animal Genome VI Conference

P4

CONSENSUS SEQUENCES FLANKING THE TRANSLATION INITIATION CODON MAY BE USEFUL IN GENOME SEQUENCING OF PLANTS

1. Plant Biotechnology Research Center, Institute of Wood Research, School of Forestry and Wood Products, Michigan Technological University, Houghton, MI 49931, USA
2. Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA

Recent initiative of genome sequencing of plants such as Arabidopsis involves a large scale sequencing of many overlapping genomic clones and identification of coding regions among these millions of basepairs will be a formidable task. The information regarding the consensus sequences flanking the translation start codon in plants could be very useful in identifying the putative coding regions of the unidentified genes. We have, therefore, designed new computer programs that retrieved the information regarding the translation start codons from thousands of plant genes and performed a systematic analysis of nucleotide frequencies in the region flanking the AUG codons. In this survey of 5074 plant genes for their AUG context sequences, purines are present at the -3 and +4 positions in about 80 % of the sequences. The number of plant mRNAs with purines at the -3 position is significantly lower and at the +4 position is remarkably higher than reported for vertebrate mRNAs. Higher plants have an AC rich consensus sequence, caA(A/C)aAUGGCg as a context of translation initiator codon that is similar to earlier observation (Joshi CP, NAR 15: 6643-6653, 1987). Between the two major groups of angiosperms, the context of the AUG codon in dicot mRNAs is aaA(A/C)aAUGGCu which is similar to the higher plant consensus but monocot mRNAs have c(a/c)(A/G)(A/C)cAUGGCG as a consensus which exhibits an overall similarity with the vertebrate consensus. The experimental evidence regarding the functional importance of the AUG context in plants will also be discussed.