Isolation and molecular characterization of dTnp1, a mobile and defective transposable element of Nicotiana plumbaginifolia

A review of strategies used to identify transposition events in plant genomes

Transposable elements (TEs) were initially considered redundant and dubbed 'junk DNA'. However, more recently they were recognized as an essential element of genome plasticity. In nature, they frequently become active upon exposition of the host to stress conditions. Even though most transposition events are neutral or even deleterious, occasionally they may happen to be beneficial, resulting in genetic novelty providing better fitness to the host. Hence, TE mobilization may promote adaptability and, in the long run, act as a significant evolutionary force. There are many examples of TE insertions resulting in increased tolerance to stresses or in novel features of crops which are appealing to the consumer. Possibly, TE-driven de novo variability could be utilized for crop improvement. However, in order to systematically study the mechanisms of TE/host interactions, it is necessary to have suitable tools to globally monitor any ongoing TE mobilization. With the development of novel potent technologies, new high-throughput strategies for studying TE dynamics are emerging. Here, we present currently available methods applied to monitor the activity of TEs in plants. We divide them on the basis of their operational principles, the position of target molecules in the process of transposition and their ability to capture real cases of actively transposing elements. Their possible theoretical and practical drawbacks are also discussed. Finally, conceivable strategies and combinations of methods resulting in an improved performance are proposed.

A flax transposon identified in two spontaneous mutant alleles of the L6 rust resistance gene

Two spontaneous mutant alleles of the L6 flax rust resistance gene, 16-X3A and 16-X117, contain the same transposable element designated dLute (defective Linum usitatissimum transposable element). The element is 314 bp long, 70% AT-rich and, because it contains no extended open reading frame, is probably non-autonomous. It has 14 bp imperfect terminal inverted repeats related to those in the Ac family of plant transposons and, like Ac, causes 8 bp target site duplications upon insertion. Multiple copies of dLute-related sequences exist in the flax genome. Rust resistant revertants were recovered amongst the progeny of both mutants and reversion was associated with excision of dLute. Excision either restored the wild-type L6 sequence or was imprecise, leaving sequence alterations ('footprints') resulting in one to three amino acid alterations in the L6 protein. No phenotypic differences were discerned between plants containing the standard and revertant L6 alleles.

Analysis of flower pigmentation mutants generated by random transposon mutagenesis in Petunia hybrida

Fifty new flower pigmentation mutants in Petunia hybrida using endogenous transposable elements (TEs) as a mutagen were generated. Forty-six mutants displayed somatic and sporogenic instability indicating that they were caused by a TE. Phenotypic analysis showed that the mutation altered either anthocyanin biosynthesis (40 alleles for seven loci), the intracellular pH of petals (six alleles for three loci) or the shape of petal cells (two alleles for two loci). To identify the TEs responsible for the mutations, the authors subjected 16 alleles of the anthocyanin-3 (an3) locus, encoding flavanone 3 beta-hydroxylase, to molecular analysis. This showed that 11 out of 12 unstable an3 alleles harboured TE insertions of a single family, dTph1, while one allele harboured a new 177 bp TE designated dTph2. In addition, the authors found one an3 allele (an3-W138A) in which a dTph1 element had inserted 30 bp upstream the translation start, without inactivating the gene. This 'cryptic' element was responsible for the creation of a stable recessive (untagged) an3 allele, where a large rearrangement inactivated the gene. These findings indicate that mutants for novel loci are most likely tagged by dTph1 elements opening the way for their isolation.

Characterization of the Sol3 family of nonautonomous transposable elements in tomato and potato

Sol3 transposons are mobile elements defined by long terminal inverted repeats which are found in tomato and potato. Members of the Sol3 family have been isolated from a variety of solanaceous species including Solanum tuberosum (potato), S. demissum, S. chacoense, Lycopersicon esculentum (tomato), and L. hirsutum. While highly conserved elements are found within different species, Sol3 terminal inverted repeats can also flank unrelated sequences. Southern blot analysis indicates that Sol3 elements are less prevalent in the potato (approximately 50 copies) than in the tomato (>100 copies) genome. No Sol3-hybridizing sequences were observed in tobacco. While a number of Sol3 elements ranging in size from 500 bp to 2 kbp were sequenced, no transposase coding domains could be identified within the internal regions of the elements. The data suggest that the Sol3 represent a heterogeneous family of nonautonomous transposable elements associated with an as-yet-unidentified autonomous transposon.

Molecular and functional characterization of Slide, an Ac-like autonomous transposable element from tobacco

A new transposable element of tobacco, Slide, was isolated from the tl mutant line, which shows somatic instability, after its transposition into a locus encoding nitrate reductase (NR). The Slide-124 element is 3733 bp long and its coding sequences show similarities with conserved domains of the transposases of Ac, Tam3 and hobo. Excision from the NR locus is detectable in somatic leaf tissues and Slide mobility is triggered by in vitro tissue culture. Slide excision events create footprints similar to those left by Ac and Tam3. Tobacco lines derived from the tl mutant line seem characterized by unmethylated copies of a few members of the highly repetitive Slide family. Slide mobility was monitored in transient expression assays. In wild-type tobacco protoplasts, the complete Slide element, as well as a defective copy, is able to excise. The complete Slide element, but not the defective version, is able to excise in protoplasts of the heterologous species lettuce (Lactuca sativa). These results show that Slide carries the functions required for its own mobility, and represents the first autonomous Ac-like element characterized in Solanaceae species.

The phytochrome gene family in tomato includes a novel subfamily

Data presented here define five tomato phytochrome genes (PHY) and indicate the existence of additional PHY in the tomato genome. Portions of each gene, encoding amino acids 203 through 315 in a consensus amino acid sequence, were amplified by polymerase chain reaction. Four of these genes, PHYA, PHYB1, PHYB2 and PHYE, are members of previously identified PHY subfamilies, while the fifth, PHYF, is identified as a member of a new PHY subfamily. PHYA, PHYB1, PHYB2 and PHYE fragments encode amino acid sequences that share 88% to 98% sequence identity with their Arabidopsis counterparts. The PHYF fragment, however, encodes a polypeptide that shares only 65% to 74% sequence identity with previously identified Arabidopsis phytochromes. A phylogenetic analysis suggests that PHYF arose soon after, or perhaps prior to, the origin of angiosperms. This analysis leads to the prediction that PHYF might be widespread among angiosperms, including both monocotyledons and dicotyledons. Each of the five tomato PHY is expressed as a transcript of sufficient size to encode a full-length phytochrome apoprotein. Two PHYF transcripts, 4.4 and 4.7 kb in length, have been detected in 9-day-old light-grown seedlings, consistent with either multiple transcription start sites or differential processing. Analyses of genomic Southern blots hybridized with radiolabelled RNA probes derived from the five tomato PHY, as well as Arabidopsis PHYC, indicate that the tomato genome contains as many as 9 to 13 PHY. The tomato PHY family is apparently not only different from, but also larger than, the PHY family presently described for Arabidopsis.

Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgaris L.): LINEs and Ty1-copia-like elements as major components of the genome

DNA sequences of the reverse transcriptase gene of long terminal repeat (LTR) and non-LTR (non-viral) retrotransposons have been isolated and cloned from the genome of sugar beet (Beta vulgaris). Both retrotransposon types are highly amplified in sugar beet and may account for 2-5% of the genome. The BNR1 family, representing the first non-viral retrotransposon reported from a dicotyledonous species, shows homology to the mammalian L1 family of long interspersed repeated sequences (LINEs) and to retrotransposable elements from maize and lily. Sequences of the Tbv family are homologous to the Ty1-copia class of LTR retrotransposons. The BNR1 and Tbv retrotransposon families are characterized by sequence heterogeneity and are probably defective. The deduced peptide sequences were used to investigate the relation to other retroelements from plants, insects and mammals. Fluorescence in situ hybridization was used to investigate the physical distribution and revealed that both retrotransposon families are present on all sugar beet chromosomes and largely excluded from chromosomal regions harbouring the 18S-5.8S-25S rRNA genes. The BNR1 family is organized in discrete clusters, while the Tbv family of Ty1-copia-like retrotransposons shows a more uniform distribution along chromosome arms and is absent from some chromosomal regions. These contrasting distributions emphasize the differences in evolutionary amplification and dispersion mechanisms between the two types of retrotransposons. The in situ results of both elements reflect significant features of a higher order structure of the genome, as it is known for both short interspersed repeated sequences (SINEs) and LINEs in human.

Identification by mutational analysis of four critical residues in the molybdenum cofactor domain of eukaryotic nitrate reductase

The nucleotide sequence of the nitrate reductase (NR) molybdenum cofactor (MoCo) domain was determined in four Nicotiana plumbaginifolia mutants affected in the NR apoenzyme gene. In each case, missense mutations were found in the MoCo domain which affected amino acids that were conserved not only among eukaryotic NRs but also in animal sulfite oxidase sequences. Moreover an abnormal NR molecular mass was observed in three mutants, suggesting that the integrity of the MoCo domain is essential for a proper assembly of holo-NR. These data allowed to pinpoint critical residues in the NR MoCo domain necessary for the enzyme activity but also important for its quaternary structure.

Functional analysis of the tobacco Tnt1 retrotransposon

Retroelements represent by far the largest and most widespread class of mobile genetic elements. Representative of several classes of retrotransposons have been characterized in a broad range of plant species, but only a few of them have been shown to be active. Among these, the tobacco Tnt1 retrotransposon has been isolated after insertion mutagenesis and is one of the very few to be transcriptionally active. Tnt1 expression is strongly regulated in a tissue-specific and developmental manner. Moreover, Tnt1 expression is induced by a range of biotic or abiotic elicitors, which all have in common the ability to induce the plant defense response. Regulatory sequences involved in this elicitor-mediated induction have been located in the LTR U3 region. The link between Tnt1 activation and the plant defense response might represent an example of the involvement of transposable elements in genome restructurations needed in response to environmental fluctuations such as pathogen attacks.