Occurrence of plastid RNA editing in all major lineages of land plants.

RNA editing changes posttranscriptionally single nucleotides in chloroplast-encoded transcripts. Although much work has been done on mechanistic and functional aspects of plastid editing, little is known about evolutionary aspects of this RNA processing step. To gain a better understanding of the evolution of RNA editing in plastids, we have investigated the editing patterns in ndhB and rbcL transcripts from various species comprising all major groups of land plants. Our results indicate that RNA editing occurs in plastids of bryophytes, fern allies, true ferns, gymnosperms, and angiosperms. Both editing frequencies and editing patterns show a remarkable degree of interspecies variation. Furthermore, we have found that neither plastid editing frequencies nor the editing pattern of a specific transcript correlate with the phylogenetic tree of the plant kingdom. The poor evolutionary conservation of editing sites among closely related species as well as the occurrence of single species-specific editing sites suggest that the differences in the editing patterns and editing frequencies are probably due both to independent loss and to gain of editing sites. In addition, our results indicate that RNA editing is a relatively ancient process that probably predates the evolution of land plants. This supposition is in good agreement with the phylogenetic data obtained for plant mitochondrial RNA editing, thus providing additional evidence for common evolutionary roots of the two plant organellar editing systems.

Cloning and sequence analysis of laccase-encoding cDNA clones from tobacco.

Three laccase-encoding cDNAs were cloned from a tobacco stem cDNA library. One of them contains a full length sequence coding for a cationic laccase. The predicted polypeptide sequence shows 48% identity with sycamore laccase. Amino acid comparisons with other laccases and ascorbate oxidases have shown that this new plant laccase sequence also contains four potential copper binding regions which are highly conserved among the blue copper oxidases.

Complex arrangement of dispersed repeated DNA sequences in Oryza officinalis.

A 525-bp BglII fragment was isolated from Oryza officinalis DNA (accession W1278) and shown to correspond to a new dispersed repetitive DNA sequence with specificity restricted to a subset of the wild rice with a C genome. The sequence of the fragment was determined but it does not correspond to any sequence already present in databases. It contains several imperfect palindromes. Larger genomic clones (12-18 kbp) were isolated and all contain sequences homologous to the BglII element. Analysis of these clones confirms that the BglII element is dispersed in the O. officinalis genome. From one genomic clone, the sequences adjacent to the BglII element were subcloned and used as probes to demonstrate that the sequences flanking the BglII element are variable in different genomic clones and that some of them are also dispersed repetitive sequences. The genomic specificity of two of these dispersed repeats was evaluated and shown to be different from that of the initial BglII element. This analysis revealed a complex arrangement of various dispersed repeated sequences.

Characterization of a dispersed repetitive DNA sequence associated with the CCDD genome of wild rice.

A HindII repetitive fragment (pOD3) was isolated and cloned from the genomic DNA of an accession of Oryza latifolia, a wild rice species that possesses a tetraploid CCDD genome. Southern blot analysis using this clone as a probe demonstrated that this repetitive DNA sequence had a dispersed organization in the CCDD genome and seemed to be highly specific for this genome type. This fragment is the first CCDD-specific repeated DNA sequence to be described. The hybridization pattern is similar for most CCDD accessions tested, although a few showed no hybridization signal. The nucleotide sequence of the element cloned in pOD3 was determined and analysed. The 1783 base pair long repeated sequence shows no homology with other known nucleotide sequences. In addition, none of the amino acid sequences deduced from the potential open reading frames contained in the pOD3 repeat is homologous to any known protein. The nucleotide sequence presents several internal repeats, direct or inverted, but their significance remains unknown.

Characterization of new variants of a satellite DNA from Oryza officinalis, specific for the CC genome of wild rice.

Two groups of tandemly repeated DNA fragments have been isolated and cloned from the Oryza officinalis genome (W 1278). These fragments have been sequenced and are 374 and 367 bp long. They were compared with an element previously isolated from another O. officinalis accession. They are 76 and 92% homologous to the latter and show 78% homology between themselves. The two types of elements are interspersed within large blocks of tandemly organized units. Their copy number is in the range of 200,000 units. This sequence was present only in wild rice accessions with a CC genome. However, this apparent specificity is even more restricted, since it was absent from some O. officinalis accessions and from the allotetraploid species of the CCDD type. Use of digestions with 4-bp restriction enzyme cutters and analysis on denaturing polyacrylamide gels revealed polymorphism that might be used to map the repeats in the genome as well as to establish the relationship between accessions. Finally, hybridization of the repeated sequence to DNA prepared from the eight available O. sativa-O. officinalis monosomic addition lines revealed that the elements are located on two alien chromosomes. This suggests that these elements have at least some restricted chromosome specificity.