Abstract
Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context.
Highlights
Nuclear ribosomal RNA genes represent the oldest repetitive fraction universal to all eukaryotic genomes
Ribosome biogenesis consumes a tremendous amount of cellular energy and ribosomal RNA (rRNA) synthesis is tightly linked to cell growth and proliferation, and as such, it is responsive to general metabolism and environmental challenges [4]
Ribosomopathies are diseases caused by abnormalities in the structure or function of ribosomal component proteins or rRNA genes, or other genes whose products are involved in ribosome biogenesis [107]
Summary
RNA is essential for information flow from DNA to protein being the dominant macromolecule in protein synthesis [1]. Beside two mitochondrial rRNAs, i.e., the 12S and 16S rRNA in eukaryotes, there are two fractions of nuclear rDNAs—a large, nucleolus-forming 45/47S rDNA unit and a substantially smaller extra-nucleolar 5S rDNA (Figure 1). Both the 45S and 5S rDNAs are organized into clusters of repeats often enabling their cytogenetic visualization on chromosomes [5]. Strains with artificially reduced rDNA copy numbers became sensitive to DNA damage by chemicals and ultraviolet light This sensitivity further increased as the number of rDNA repeats decreased [7]. Intergenic transcripts originating from a promoter located approximately 2 kb upstream from the pre-rRNA start site are processed into a heterogeneous population of 150–250 nucleotide RNAs, dubbed promoter RNA (pRNA) as their sequence matches the rDNA promoter [6,8,9,11]
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