In plants, the 5S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35S rDNA units (L-type). The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5S genes in several species from family Asteraceae known to contain linked 35S-5S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays.
We found that homogenization of L-type units went to completion in most (4/6) but not all species. Two species contained major L-type and minor S-type units (termed Ls-type). The linked genes dominate 5S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5’-RGSWTGGGTG-3’) is proposed. The 5S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35S-5S arrays with nucleolar periphery indicating that transcription of 5S genes may occur in this territory.
We show that the unusual linked arrangement of 5S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs.
Keywords: 5S expression, Artemisia, Asteraceae, C-box, DNA methylation, Pol III promoter divergence, rDNA organization