Transposable Elements and Retroelements

Retroelements (class I transposable elements) are discrete components of the plant nuclear genome that replicate and reinsert at multiple sites in a complex process that involves activation of excision, DNA-dependent RNA transcription, translation of the RNA into functional proteins, RNA-dependent DNA synthesis (reverse transcription), and reintegration of newly generated retroelement copies into the genome (reviewed in Kumar and Bennetzen 1999). Major classes of retroelements include LINEs, SINEs, copia- and gypsy-like elements, and retroviruses (Hull and Covey 1996 ; Kumar 1998 ; Harper et al. 1999 ; Jakowitsch et al. 1999 ; Kumar and Bennetzen 1999 ; Schmidt 1999). Retroelements, typically including two or three open reading frames extending over 5 kb, tend to be highly amplified and frequently represent half of the nuclear DNA (Pearce et al. 1996 ; SanMiguel et al. 1996 ; Smit 1996 ).

Retroelements have been found in all plants investigated and are very heterogeneous (Flavell et al. 1992 ), suggesting that they are an ancient component of genomes. They are generally dispersed over plant chromosomes, consistent with their mode of amplification, but may associate with particular genomic regions. Most frequently, the rDNA and centromeric regions, consisting of tandemly repeated DNA elements, show a lower proportion of gypsy- and copia-like retroelements than do other regions (Kamm et al. 1996 ; Heslop-Harrison et al. 1997 ; Kubis et al. 1998a ; Schmidt 1999 ). It is hypothesized that retroelements are more abundant around the centromeres of Arabidopsis chromosomes so as to limit the disruption of genes (Fig 2; Brandes et al. 1997a). Relatively little is known about the chromosomal organization of LINEs (Kubis et al. 1998b). As they insert themselves into the genome, retroelements act as mutagenic agents, thereby providing a putative source of biodiversity (Hirochika et al. 1996 ; Heslop-Harrison et al. 1997 ; Ellis et al. 1998 ; Flavell et al. 1998 ) and serving as markers of diversity. Regulatory mechanisms may act to protect genomes from insertional mutagenesis (Lucas et al. 1995), and it has been suggested that transgene-induced gene silencing reflects mechanisms aiming to prevent genome invasion by retroelements. Plant retrotransposon activity can be regulated at any step of the replication cycle, including transcription, translation, reverse transcription, nuclear import, and integration.

Along with DNA (class II) transposable elements and other elements such as miniature inverted tandem elements (MITES; Wessler et al. 1995 ; Casacuberta et al. 1998), insertion of retrotransposon elements can inactivate or alter gene function (Wessler et al. 1995). Indeed, transposition is estimated to account for 80% of the mutations detected in Drosophila (Capy 1998). Transposons can excise, partially or completely restoring gene function, and can also lead to chromosome rearrangements such as inversions or translocations. Transposable elements can also act to move elements such as exons and promoters into existing sequences so as to create new gene functions and contribute to evolution (Plasterck 1998 ; Moran et al. 1999). Indeed, retroelements are activated under stress conditions (Wessler 1996 ; Grandbastien 1998 ; Kumar and Bennetzen 1999 ; Walbot 1999 ). Alternative splicing of genes caused by transposable elements has been shown in maize (Bureau and Wessler 1994a , Bureau and Wessler 1994b ). Methylation of retroelements can also affect adjacent sequences and lead to transcriptional repression (Yoder et al. 1997 ; Goubely et al. 1999 ).

The sequences of degenerate and potentially active retroelements give valuable data about genome evolution and phylogenetic relationships (Fig 4). In three species in the Vicia genus, copia retroelement copy number varies from 1000 to 1,000,000, with more sequence heterogeneity being present in species with higher copy number (Pearce et al. 1996). Although in part due to random mutation of the high number of copies present in most plant genomes, sequence variability is often nonuniformly distributed along the retroelement: regulatory regions (including the long terminal repeats of copia elements) can evolve faster than coding regions, perhaps enabling elements to coexist with their host genomes without detriment (Vernhettes et al. 1998 ). Although retroelement amplification leads to large genomes (Bennetzen and Kellogg 1997)), it is probable that retroelement turnover and loss can occur in a directed manner (Tatout et al. 1998), leading to different retroelement compositions between species. For example, chromosome sets in the cultivated hexaploid oat, Avena sativa, can be discriminated by the presence of retroelement families (Katsiotis et al. 1996 ).

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