Deletions in a dspm insert in a maize bronze-1 allele alter RNA processing and gene expression

Abstract

The bz-m13 allele of the bronze-1 (bz) locus in maize contains a 2.2-kb defective Suppressor-mutator (dSpm) transposable element inserted in the second exon. We compared bz expression in bz-m13 and five derivatives in which the dSpm insertion had sustained deletions ranging from 2 to 1300 bp. Tissues homozygous for bz-m13 in the absence of Spm-s activity were found to contain from 5 to 13% of the enzymatic activity conditioned by a wild-type allele at the bz locus. Tissues homozygous for the deletion derivatives contained enzymatic activities ranging from less than 1% to 67%. These differences are closely correlated with the steady-state level of one of two alternatively spliced transcripts. In all alleles bz transcription proceeds through the dSpm insert. Subsequent RNA processing uses the donor site of the single bz intron and either one of two alternative acceptor splice sites (AS1 and AS2) located within the dSpm sequence. Use of the AS1 removes all but 2 bp of dSpm sequence and produces the 1.8-kb transcript whose level corresponds closely to the level of enzymatic activity. Use of AS2 produces a transcript which retains more than 600 bp of dSpm sequence. Those derivatives in which AS2 is either deleted or inactivated have substantially increased levels of both the 1.8-kb transcript and enzymatic activity. We therefore document one sequence of events which began with the insertion of a transposable element and resulted in novel and stable introns which retain element-derived sequence and which in certain cases permit substantial host-gene expression.