Presence of a transposon-like element in the promoter region of an inactive patatin gene in Solanum tuberosum L

Identification of Active Transposon dTok , a Member of the hAT Family, in Rice

Recent completion of the sequencing of the rice genome has revealed that it contains >40% repetitive sequences, most of which are related to inactive transposable elements. During the molecular analysis of the floral organ number 1/multiple pistil 2 (fon1/mp2) mutant, we identified an active transposable element dTok0 that was inserted at the kinase domain of FON1, a homolog of CLAVATA1. Insertion of the element into FON1 generated an 8 bp duplication of its target sites, which is one of the major characteristics of the hAT family of transposons. The dTok0 element was actively transposed out of the FON1 gene, leaving 5-8 bp footprints. Reinsertion into a new location was observed at a low frequency. Analysis of the genome sequence showed that the rice cultivar 'Nipponbare' contains 25 copies of dTok elements; similar numbers were present in all the Oryza species examined. Because dTok0 does not encode a transposase, enzyme activity should be provided in trans. We identified a putative autonomous transposon, Tok1 that contains an intact open reading frame of the Ac-like transposase.

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.

Circadian expression of the maize catalase Cat3 gene is highly conserved among diverse maize genotypes with structurally different promoters

The Cat3 gene of maize exhibits a transcriptionally regulated circadian rhythm. In the present study we examined the following: (1) the extent of the circadian Cat3 expression between maize genotypes of diverse origin; (2) the functional significance of a Tourist transposable element located in the Cat3 promoter of the inbred line W64A, which harbors putative regulatory elements (GATA repeat, CCAAT boxes) shown to be involved in the light induction and circadian regulation of the Arabidopsis CAB2, as well as other plant genes; and (3) aspects of the physiological role of CAT-3 in maize metabolism. Results confirm that the circadian Cat3 expression is a general phenomenon in maize. Regulation of Cat3 gene expression is not dependent on the presence of the Tourist element in the promoter of the gene nor on the presence of motifs similar to those found significant in the circadian expression of the Arabidopsis CAB2 gene. Structural diversity was revealed in the Cat3 promoters of maize genotypes of diverse origins. However, highly conserved regions with putative regulatory motifs were identified. Relevance of the conserved regions to the circadian regulation of the gene is discussed. Possible physiological roles of CAT-3 are suggested.

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.

Nonautonomous inverted repeat Alien transposable elements are associated with genes of both monocotyledonous and dicotyledonous plants

Alien are highly repeated plant transposable elements characterized by their small size (approx. 400 bp), high A + T content, target site specificity, potential to form stable secondary structures and possession of a conserved 28-bp terminal inverted repeat (TIR). Besides the TIR, they contain subterminal inverted repeat motifs (SIRM), as well as the 5'-CATGCAT domain which has been reported to be a cis-acting regulatory element of gene expression in some plant species. Although they were first identified in the intron of the bell pepper (Capsicum annuum) Sn-2 gene and in the promoter region of the potato starch phosphorylase-encoding gene, Alien arranged in tandem are present in the promoter of patatin class-II genes. PCR on the bell pepper genomic DNA using the Alien TIR consensus sequence as primer yielded DNA fragments of nearly 400 bp. These fragments have characteristics of transposable elements and contain numerous motifs reminiscent of Alien elements. Importantly, PCR on genomic DNA extracts from various monocotyledonous and dicotyledonous plants using the TIR consensus sequence as primer and subsequent hybridization with different Alien probes revealed that these elements are ubiquitously present and highly repeated in the genomes of higher plants.

Guest: a 98 bp inverted repeat transposable element in Neurospora crassa

The region immediately 3' of histidine-3 has been cloned and sequenced from two laboratory strains of the ascomycete fungus Neurospora crassa; St Lawrence 74A and Lindegren, which have different derivations from wild collections. Amongst the differences distinguishing these sequences are insertions ranging in size from 20 to 101 bp present only in St Lawrence. The largest of these is flanked by a 3 bp direct repeat, has terminal inverted repeats (TIR) and shares features with several known transposable elements. At 98 bp, it may be the smallest transposable element yet found in eukaryotes. There are multiple copies of the TIR in the Neurospora genome, similar but not identical to the one sequenced. PCR amplification of Neurospora genomic DNA, using 26 bp of the TIR as a single primer, gave products of discrete sizes ranging from 100 bp to about 1.3 kb, suggesting that the element isolated (Guest) may be a deletion derivative of a family of larger transposable elements. Guest appears to be the first transposable element reported in fungi that is not a retrotransposon.

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

By Northern blot analysis of nitrate reductase-deficient mutants of Nicotiana plumbaginifolia, we identified a mutant (mutant D65), obtained after gamma-ray irradiation of protoplasts, which contained an insertion sequence in the nitrate reductase (NR) mRNA. This insertion sequence was localized by polymerase chain reaction (PCR) in the first exon of NR and was also shown to be present in the NR gene. The mutant gene contained a 565 bp insertion sequence that exhibits the sequence characteristics of a transposable element, which was thus named dTnp1. The dTnp1 element has 14 bp terminal inverted repeats and is flanked by an 8-bp target site duplication generated upon transposition. These inverted repeats have significant sequence homology with those of other transposable elements. Judging by its size and the absence of a long open reading frame, dTnp1 appears to represent a defective, although mobile, transposable element. The octamer motif TTTAGGCC was found several times in direct orientation near the 5' and 3' ends of dTnp1 together with a perfect palindrome located after the 5' inverted repeat. Southern blot analysis using an internal probe of dTnp1 suggested that this element occurs as a single copy in the genome of N. plumbaginifolia. It is also present in N. tabacum, but absent in tomato or petunia. The dTnp1 element is therefore of potential use for gene tagging in Nicotiana species.

A new middle repetitive sequence of Nicotiana plumbaginifolia genome

A middle repetitive sequence NPR18 was isolated from Nicotiana plumbaginifolia nuclear genome [8]. Sequences homologous to the repeat are dispersed through genomes of several Nicotiana species. Computer-assisted data analysis of NPR18 primary sequence reveals several features attributed to mobile genetic elements: an AT content higher than average for nuclear DNA of genus Nicotiana plants; a number of direct and inverted repeats. Some of the repeats displayed homology to the terminal and subterminal repeats of Ac/Ds-like plant elements.

Structural and functional analysis of the Bz2 locus of Zea mays: characterization of overlapping transcripts

Analysis of the transcription pattern of the Bz2 locus revealed that overlapping transcripts are derived from opposite DNA strands. The most abundant transcript (sense transcript) has an open reading frame coding for a protein of 241 amino acids, whilst in the antisense orientation no open reading frame has been detected; the antisense transcripts are detected only in those tissues that show high levels of sense transcript. Particle gun experiments indicate that the sense transcript is sufficient to provide the Bz2 function. The promoter driving the sense transcript contains the elements usually found in front of eukaryotic genes. In addition an element with similarity to the C1 and R binding sites identified in the Bz1 promoter is found. Further upstream in the promoter region a transposon-like insertion has been identified. This element has features similar to members of the Ac/Ds transposable element family. The putative Bz2 protein shows similarity to various other plant proteins and to an Escherichia coli protein. All related proteins have in common the fact that they are involved in stress responses.

Identification and structural characterization of further DNA elements in the potato and pepper genomes homologous to the transposable element-like insertion Tst1

The molecular cloning and nucleotide sequence of elements from potato and pepper that are related to the recently identified Tst1 element are described. Sequence analysis reveals considerable conservation of sequences internal to both the Tst1 element and two of the related elements identified here. In six potato clones analysed, the 11 bp inverted repeat first identified in the Tst1 element is conserved. Several of the elements are flanked by an 8 bp direct repeat. DNA fragments which were amplified from several pepper genomes by polymerase chain reaction (PCR) amplification using the inverted repeat as sequence primers also display considerable conservation of sequences internal to the Tst1 element. These data further support the possibility that Tst1 is a non-autonomous transposable element and that Tst1 might be the first example of a transposable element which occurs in several genera of solanaceous plants.

Molecular analysis of the Bg-rbg transposable element system of Zea mays L

The two components of the Bg-rbg transposable element system of maize have been cloned. The Bg element, isolated from the mutable allele wx-m32:: Bg is inserted in the intron of the Waxy (Wx) gene between exons 12 and 13. The length of the element is of 4869 bp. Bg has 5 bp terminal inverted repeats, and generates upon insertion an 8 bp direct duplication of the target sequence. Both ends of the Bg element contain a 76 bp direct repeat adjacent to the terminal inverted repeats. The hexamer motif TATCGGC is here repeated several times in direct or inverse orientation. The rbg element was isolated from the mutable allele o2m(r) where it is located in the promoter region of the Opaque-2 (O2) gene. rbg is approximately 4.5 kb in length, has terminal inverted repeats identical to those of the Bg element, and is also flanked by an 8 bp direct duplication at the target site. Like Bg, rbg carries the 76 bp direct repeats. Restriction enzyme analysis reveals that, compared to Bg, the receptor element is distinguishable by small deletion and insertion events. Sequence data indicate that not more than 75% homology exists at the DNA level between the rbg element and the autonomous Bg element.