Abstract
BackgroundThe nonautonomous maize Ds transposons can only move in the presence of the autonomous element Ac. They comprise a heterogeneous group that share 11-bp terminal inverted repeats (TIRs) and some subterminal repeats, but vary greatly in size and composition. Three classes of Ds elements can cause mutations: Ds-del, internal deletions of the 4.6-kb Ac element; Ds1, ~400-bp in size and sharing little homology with Ac, and Ds2, variably-sized elements containing about 0.5 kb from the Ac termini and unrelated internal sequences. Here, we analyze the entire complement of Ds-related sequences in the genome of the inbred B73 and ask whether additional classes of Ds-like (Ds-l) elements, not uncovered genetically, are mobilized by Ac. We also compare the makeup of Ds-related sequences in two maize inbreds of different origin.ResultsWe found 903 elements with 11-bp Ac/Ds TIRs flanked by 8-bp target site duplications. Three resemble Ac, but carry small rearrangements. The others are much shorter, once extraneous insertions are removed. There are 331 Ds1 and 39 Ds2 elements, many of which are likely mobilized by Ac, and two novel classes of Ds-l elements. Ds-l3 elements lack subterminal homology with Ac, but carry transposase gene fragments, and represent decaying Ac elements. There are 44 such elements in B73. Ds-l4 elements share little similarity with Ac outside of the 11-bp TIR, have a modal length of ~1 kb, and carry filler DNA which, in a few cases, could be matched to gene fragments. Most Ds-related elements in B73 (486/903) fall in this class. None of the Ds-l elements tested responded to Ac. Only half of Ds insertion sites examined are shared between the inbreds B73 and W22.ConclusionsThe majority of Ds-related sequences in maize correspond to Ds-l elements that do not transpose in the presence of Ac. Unlike actively transposing elements, many Ds-l elements are inserted in repetitive DNA, where they probably become methylated and begin to decay. The filler DNA present in most elements is occasionally captured from genes, a rare feature in transposons of the hAT superfamily to which Ds belongs. Maize inbreds of different origin are highly polymorphic in their DNA transposon makeup.
Highlights
The nonautonomous maize Ds transposons can only move in the presence of the autonomous element Ac
Unlike the 11-bp terminal inverted repeats (TIRs), the 8-bp target site duplication (TSD) is not a specific sequence. Because it is the site where the Ds element inserted into the genome, the TSD can be almost any combination of 8 bp
Based on the sequence characteristics of Ac and Ds elements, we developed a data mining algorithm, written in PERL, to search through the maize pseudomolecules for Ds sequences and found sequences with perfect TIRs and identical TSD sequences and with TIRs and TSD sequences differing by up to 2 bp
Summary
The nonautonomous maize Ds transposons can only move in the presence of the autonomous element Ac. Ds could break chromosomes at its site of insertion and could move in response to another factor, which she named Ac (Activator) and showed to be self-mobilizing or autonomous [2]. After this discovery, McClintock established that there were two types of Ac-responsive Ds elements: those that caused chromosome breaks at high frequency and those that did not. McClintock established that there were two types of Ac-responsive Ds elements: those that caused chromosome breaks at high frequency and those that did not She named the former state I Ds and the latter, state II Ds [3].
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