Chapter 23 : MuDR/Mu Transposable Elements of Maize

Structure of MuDR and the nonautonomous Mu1 element. The shared TIRs are shown in black, and the unrelated internal sequences are crosshatched in Mu1 and open in MuDR. Arrows above the elements indicate the orientation, length, and position of short, conserved repeats found in some Mu elements. MuDR element is composed of two genes, mudrA and mudrB, separated by a repeat-rich intergenic region (hatched box).

Alignment of the TIRs of the mobile Mu elements. Terminal inverted repeat sequences of the autonomous MuDR element are shown on the top. MuDRA is the TIR next to mudrA and MuDRB is the TIR next to mudrB; the few mismatches between these TIRs are shown as shadowed letters. The positions of the presumptive CCAAT and TATA boxes and the transcription initiation start sites for both mudrA and mudrB are indicated with white letters on a black field. In the alignment of TIRs from nonautonomous Mu elements, dots represent matching bases and dashes represent missing bases. Regions with assigned biological function and sequence motifs discussed in the text are boxed.

Phylogenetic analysis of hMuDR elements. Unrooted phylograms were generated by using PAUP to estimate relatedness between the virtual translation of hMUR proteins and the MuDR-encoded proteins. (Left) N-terminal part of hMURA, including exon 2. (Right) Full-length hMURB proteins and their wild-type counterparts.

Major transcripts and predicted proteins encoded by MuDR. (A) Transcriptional units in MuDR. Heavy arrows depict the exon (filled) and intron (open) organization and direction of transcription of the mudrA and mudrB genes. Transcription initiates in the terminal inverted repeats of the element,as indicated by bent arrows above the element diagram, and terminates in the intergenic region. The ATG initiation codons discussed in the text are indicated above the diagram for mudrA and below the diagram for mudrB. The position of the stop codon for the longest transcript from each gene is similarly indicated. (B) Major transcripts. Alternative transcription initiation start sites for mudrA and alternative splicing of the introns in pre-mRNA for both genes generate a variety of transcripts. (C) Major predicted proteins. Alternative splicing and two possible translation initiation start sites in mudrA result in multiple predicted proteins encoded by the known transcripts. MURA proteins contain a region of similarity to bacterial transposases and retroviral integrases,several functional nuclear localization sequences,and a zinc knuckle domain. Alternative splicing results in four predicted MURB proteins encoded by the characterized transcripts of mudrB.

Models for developmental timing and outcome of Mu excision. (A) Double-stranded gap repair masks early and germinal excision. Excision of a Mu element results in a double-stranded gap (1). In germinal and early somatic cells (2), which express abundant MURB protein,the gaps that were generated postreplicatively can be repaired by using the copy of the original locus from the sister chromatid. After insertion of the excised element, there is a net increase in the element copy number and restoration of the original insertion site. Evidence of excision is effectively removed. In late somatic cells (3), which express a low amount of MURB, gap repair does not occur, resulting in a measurable excision event. This is true even when the homologous chromosome contains the identical Mu insertion allele. (B) Competition for binding model to explain developmental timing. MuDR/Mu elements (1) are accessible for MURA transposase (2). In dividing cells, however, abundant transcriptional factors might assemble on specific motifs in the TIRs (3),potentially displacing transposase or affecting the geometry of the transpososome complex (4). Late in development, these transcriptional factors are depleted (5),allowing assembly of the transpositionally active complex, which results in late excision events (6).