Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes

Abstract

A new group of long terminal repeats (LTR) retrotransposons, termed terminal-repeat retrotransposons in miniature (TRIM), are described that are present in both monocotyledonous and dicotyledonous plant. TRIM elements have terminal direct repeat sequences between approximately 100 and 250 bp in length that encompass an internal domain of approximately 100-300 bp. The internal domain contains primer binding site and polypurine tract motifs but lacks the coding domains required for mobility. Thus TRIM elements are not capable of autonomous transposition and probably require the help of mobility-related proteins encoded by other retrotransposons. The structural organization of TRIM elements suggests an evolutionary relationship to either LTR retrotransposons or retroviruses. The past mobility of TRIM elements is indicated by the presence of flanking 5-bp direct repeats found typically at LTR retrotransposon insertion sites, the high degree of sequence conservation between elements from different genomic locations, and the identification of related to empty sites (RESites). TRIM elements seem to be involved actively in the restructuring of plant genomes, affecting the promoter, coding region and intron-exon structure of genes. In solanaceous species and maize, TRIM elements provided target sites for further retrotransposon insertions. In Arabidopsis, evidence is provided that the TRIM element also can be involved in the transduction of host genes.

Figure 1

Schematic diagram of the general structure of TRIM elements. (A) The archetypal TRIM contains the following sequence features: TSD, TDRs (flanking shaded boxes), PBS, and PPT. Start and end bases of TDRs are given in the flanking boxes. The possible length of different elements is given underneath (maximum length <540 bp). (B) Multiple alignment of selected TRIM elements (Katydid-At1) elements from A. thaliana. The alignment was created with CLUSTALW by using default parameters. The BOXSHADE program was used for shading. Structural features (abbreviations as described for A) are marked underneath. The elements in chromosomes II (Chr. II, gi 6598569, position 33,850–33,481), III (Chr. III, gi 7629988, position 45,624–45,993), and IV (Chr. IV, gi 3309259, position 95,888–95,519) are shown. (C) Multiple alignment of selected TRIM elements from rice (Oryza sativa). Alignment and abbreviations are as described above. The elements from chromosomes I (Chr. I(a), gi 10800055, position 29,385–29,802), I (Chr. I (b), gi 9711848, position 74,966–74,558), and IV (Chr. IV, gi 5777612, position 77,595–77,183) are shown.

Figure 2

Multiple alignment of selected 5′ TDR sequences of TRIM elements from different species. Sequences from Nicotiana tabacum (gi 9392606, position 3,821–3,947), Lycopersicon esculentum (gi 4220970, position 38–157), S. tuberosum (gi14599414, position 1,522–1,651), M. sativa (gi 19642, position 8,088–8,204), P. vulgaris (gi 2576326, position 1,878–1,761), O. sativa (gi 10800055, position 29,390–29506), A. thaliana Katydid-At2 (gi 7649355, position 68,877–68,994), and A. thaliana Katydid-At1 (gi 6598490, position 7722–7607) are shown. The alignment was created with CLUSTALW (gap opening parameter, 10; gap extension parameter, 1). The program BOXSHADE was used for the shading.

Figure 3

Identification of RESites for TRIM elements (Katydid-At1). Sequences harboring the Katydid-At1 insertion (depicted by the black boxes with arrowheads) are shown above the corresponding RESites. The positions on clone and gi numbers are indicated. Target sequences and TSDs are underlined. Insertion in gi 3702730 is a solo LTR.

Figure 4

Examples of TRIM (Katydid-At1) contributions to gene structures. The gray boxes with white arrowheads depict Katydid-At1 elements. Open boxes represent exons. The predicted start of translation (ATG) and TATA box are indicated. (A) The Katydid-At1 element in gi 3510340 (position 22,673–22,946) contributes sequences for the promoter, first exon, and first exon-intron boundary of a gene encoding a cytochrome P450-like gene. This insertion is truncated. Corresponding identical EST sequences (gi 5841198 and gi 1053954) are represented by thick black bars. Thin lines connecting thick black bars represent a putative intron that is not found in the EST. (B) The Katydid-At1 found on gi 7209738 contributes a splice site to a predicted cytochrome P450 gene. The scale is as described for A. (C) Sequence alignment of Katydid-At1 from A showing the putative translation start codon (boxed) and exon boundaries.

Figure 5

TRIM (Katydid-At1) involvement in the transduction of a cellular gene. (A) Diagram illustrating the region of similarity (93%) between the cellular NMD gene (c-NMD) and the transduced version (r-NMD). The intron sequences on c-NMD (bent thin lines) are absent in r-NMD. Exons are represented by black boxes, and Katydid-At1 sequences and LTRs are represented by gray boxes and arrowheads, respectively. The gi numbers and positions on clones are indicated. (B) Amino acid sequence alignment of r-NMD and c-NMD. Identical residues are shaded in gray.