Functional analysis of the tobacco Tnt1 retrotransposon

MERE1, a low-copy-number copia-type retroelement in Medicago truncatula active during tissue culture

We have identified an active Medicago truncatula copia-like retroelement called Medicago RetroElement1-1 (MERE1-1) as an insertion in the symbiotic NSP2 gene. MERE1-1 belongs to a low-copy-number family in the sequenced Medicago genome. These copies are highly related, but only three of them have a complete coding region and polymorphism exists between the long terminal repeats of these different copies. This retroelement family is present in all M. truncatula ecotypes tested but also in other legume species like Lotus japonicus. It is active only during tissue culture in both R108 and Jemalong Medicago accessions and inserts preferentially in genes.

Involvement of ethylene in stress-induced expression of the TLC1.1 retrotransposon from Lycopersicon chilense Dun

The TLC1 family is one of the four families of long terminal repeat (LTR) retrotransposons identified in the genome of Lycopersicon chilense. Here, we show that this family of retroelements is transcriptionally active and its expression is induced in response to diverse stress conditions such as wounding, protoplast preparation, and high salt concentrations. Several stress-associated signaling molecules, including ethylene, methyl jasmonate, salicylic acid, and 2,4-dichlorophenoxyacetic acid, are capable of inducing TLC1 family expression in vivo. A representative of this family, named TLC1.1, was isolated from a genomic library from L. chilense. Transient expression assays in leaf protoplasts and stably transformed tobacco (Nicotiana tabacum) plants demonstrate that the U3 domain of the 5'-LTR region of this element can drive stress-induced transcriptional activation of the beta-glucuronidase reporter gene. Two 57-bp tandem repeated sequences are found in this region, including an 8-bp motif, ATTTCAAA, previously identified as an ethylene-responsive element box in the promoter region of ethylene-induced genes. Expression analysis of wild-type LTR and single and double ethylene-responsive element box mutants fused to the beta-glucuronidase gene shows that these elements are required for ethylene-responsive gene expression in protoplasts and transgenic plants. We suggest that ethylene-dependent signaling is the main signaling pathway involved in the regulation of the expression of the TLC1.1 element from L. chilense.

OARE-1, a Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses

Transcriptionally active Ty1-copia LTR-retrotransposons were found in oat using RT-PCR for amplifying the reverse transcriptase domain. Sequence analysis of the RT-PCR clones suggested that oat LTR-retrotransposons consist of at least seven groups, which were tentatively designated as Oatrt1 to Oatrt7. A full length copy of Oatrt1 was isolated from an oat genomic library, and was designated OARE-1. OARE-1 was 8,665 bp long and a member of the BARE-1 subgroup. The oat genome carried it in multiple copies (at least 10,000 copies / a hexaploid genome). The expression of OARE-1 was intensively induced by wounding, UV light, jasmonic acid and salicylic acid, and its pattern was very similar to that of the PAL (phenylalanin ammonia lyase) gene. Furthermore, OARE-1 was highly activated by infection with an incompatible race of the crown rust fungus, Puccinia coronata. These results suggest that OARE-1 is highly sensitive to various abiotic and biotic stimuli leading to plant defense responses.

Retrovirus-like end processing of the tobacco Tnt1 retrotransposon linear intermediates of replication

The tobacco retrotransposon Tnt1 can transpose through an RNA intermediate in the heterologous host Arabidopsis thaliana. We report here the identification and characterization of extrachromosomal linear and circular DNA forms of Tnt1 in this heterologous host. Our results demonstrate that Tnt1 linear intermediates possess two extra base pairs at each end compared with Tnt1's integrated forms. Prior to integration into the host genome, the two terminal nucleotides at the 3' end of these linear intermediates are removed, as in the case of the yeast Ty3 retrotransposon and of retroviruses. Our data, together with those from recent studies of Ty3, reinforce the idea that 3' dinucleotide cleavage is not restricted to retroviral integrases and is probably a feature shared by many different retrotransposons' enzymes.

Extrachromosomal circular forms of the tobacco retrotransposon Tto1

Extrachromosomal DNA forms of Drosophila retrotransposons (RTn) and retroviruses have been extensively analyzed. However, no such analysis with plant RTn has been reported. Here, we report the analysis of extrachromosomal forms of the tobacco RTn Tto1. Tto1 is one of a few active RTn of plants and has been shown to be activated in tissue culture. Extrachromosomal circular DNA forms of Tto1, with one or two long terminal repeats (LTR), were found in cultured cells. Sequence analysis of the sites of circularization through joining two LTR showed that the junction between the LTR contains small deletions and/or insertions. The insertions are heterogeneous and do not show any homology to the Tto1 sequence. Similar insertions have been detected in the extrachromosomal circular forms of the copia element of Drosophila and suggested to be the result of excision of genomic copia. The structural features of the junctions found in Tto1 suggest that the insertions are produced by a mechanism other than excision. The potential mechanism of production of the extrachromosomal circular forms of Tto1 is discussed.