Isolation and characterization of an unusual repeated sequence from the ribosomal intergenic spacer of the crucifer Sisymbrium irio

Abstract

A recombinant plasmid containing a 433 base pair (bp) Bam HI fragment from Sisymbrium irio genomic DNA was isolated and characterized. This fragment was shown to be a ribosomal intergenic spacer (IGS) sequence which is reiterated up to six times in the IGS and extends close to the 5' end of the 18S rRNA gene. The nucleotide sequence of the cloned element is composed of 10-11 40 bp blocks that are probably derived from a common ancestor. The presence of a similar sequence can be detected in the DNA of another Sisymbrium species and in Matthiola incana. Homology was also found with the last 43 nucleotides of the radish IGS 3' end, suggesting that there is possibly a common ancestral nucleotide motif in cruciferous IGS sequences. The cloned element hybridises to RNA transcripts, indicating that the S. irio IGS repetitive sequence is at least partially transcribed during the pre-rRNA transcription process.

Characterization of the nuclear ribosomal DNA unit in Oxalis tuberosa Oxalidacea and related species

“…In agreement with published data from other plant species, the length of IGS sub-repeats, within most individual species, does not seem to differ by more than a few base pairs and their sequences show a high degree of similarity. Among these differences, one of the sub-repeat types showed a variable EcoRI recognition sequence; similarly to the previously described BamHI site found in Sisymbrium irio (Grellet et al 1989). Although not thoroughly analyzed here, it is likely that rDNA unit heterogeneity and polymorphism is due to variation in the number of subrepeats within an rDNA repeat, as happens at different NOR loci between and within individual species and sometimes at the same NOR locus in different individuals of the same species.…”

“…40 bp in Sisymbrium irio, Grellet et al 1989; 115 bp in barley Saghai-Maroof et al 1984;Gupta et al 2002;130 bp in wheat, Appels and Dvorak, 1982;May and Appels, 1987; 340 bp in alfalfa Cluster et al 1996; 460 bp in carrot Taira et al 1988). The length and sequence of subrepeats within most individual species are quite conserved.…”

“…enzyme digestion coupled whit Southern hybridization (Appels et al 1980;Appels and Dvorack, 1982;Grellet et al 1989;Sano and Sano, 1990;Clegg, 1990;Maggini et al 1992;Lakshmikumaran et al 1994;Cluster et al 1996;Jeandroz et al 1996;Gupta et al 2002 and reference there are in; Skalická et al 2003;Lim et al 2004;Kovarik et al 2005).…”

A R2R3-MYB gene, AtMYB30 , acts as a positive regulator of the hypersensitive cell death program in plants in response to pathogen attack

“…Total RNA was isolated from leaves and Northern analysis was performed as described by Lummerzheim et al (23). DNA fragments corresponding to the full-length cDNA clones of hypersensitivity-related gene 203 (hsr203), hsr515, PR-1a, and PR-5 in the case of tobacco, Athsr3 and PR-1 in the case of Arabidopsis, or the ribosomal intergenic spacer (24) of rDNA, were used as probes. Transcript levels for each gene were quantified by scanning the RNA gel blot and measuring the relative intensity of the corresponding bands with IMAGEQUANT software (Molecular Dynamics).…”

A Rapeseed Cold-Inducible Transcript Encodes a Phosphoenolpyruvate Carboxykinase

“…The filters were washed twice for 30 min in 0.2X SSC, 0.1% SDS at room temperature (980-bp probe) or 30 min in 2X SSC, 0.1% SDS at 65°C (270-bp probe) and autoradiographed at -80°C. After hybridization the filters were hybridized with the radish 18s rRNA probe, pRG3 (Grellet et al, 1989), as an interna1 standard.…”