10.5: Ribosomal RNA Processing in Eukaryotic Nuclei

In most eukaryotes, a large rRNA gene transcribes a 45S precursor transcript containing (from shortest to longest) 5.8S rRNA, 18S rRNA and 28S rRNA. The S comes from Theodor Svedberg, the biochemist who developed the sedimentation velocity ultra-centrifugation technique to separate molecules like RNA by size. The higher the S value, the larger the molecule and therefore the faster it moves through the viscous sugar gradient during centrifugation. RNA polymerase I transcribes 45S precursor rRNAs (pre-RNAs) from multiple large transcription units in the genome. One such unit is shown in Figure 10.21.

Figure 10.21: The 45S eukaryotic rRNA genes (1) encode the 18S, 5.8S and 28S ribosomal RNAs (2). PrerRNA transcripts contains the rRNAs (3). Hydrolytic cleavage of the pre-rRNA (3) will separate the rRNAs and specific rRNA nucleases will hydrolyze spacer and flanking RNA, leaving behind mature rRNAs (4).

The 45S pre-rRNA is processed by hydrolytic cleavage. The many copies (two hundred to four hundred!) of the 45S gene in eukaryotic cells might be expected, since making proteins (and therefore ribosomes) will be an all-consuming cellular activity. In humans, 45S genes (45S rDNA) are distributed among five acrocentric chromosomes (those that have a centromere very near one end of the chromosome). The 45S rDNA in chromosomes is packed into the nucleolus, inside the nucleus. Because these genes are present in so many copies and are organized into a specific region of chromatin, it is possible to visualize 45S transcription in progress in electron micrographs such as the ones in Figure 10.22.

Figure 10.22: As early as 1906, chromatic fibers were described in light micrographs of stained nucleoli of salamander oocytes. At high power (left) these fibers looked like a bottle brush used for cleaning bottles, or a lamp brush used to clean the chimneys of old-fashioned kerosene lamps. Today we know chromatic fibers as lampbrush chromosomes, and we also know that the bristles are nascent strands of rRNA arranged along transcribed 45S genes.

The term lampbrush comes from the shape of the 45S genes undergoing transcription; the RNAs extending from the DNA template look like an old-fashioned brush used to clean the chimney of a kerosene lamp. For a high-resolution transmission electron micrograph, see High Res Lampbrush Chromosomes.

Multiple gene copies encode 5S rRNAs. However, unlike the 45S rRNA genes, 5S rRNA genes may be spread among many chromosomes (seven in Neurospora crassa, the bread mold). Or in the case of humans, 5S RNA gene copies are found distributed along chromosome 1. The 5S rRNA genes are transcribed by RNA polymerase III with minimal posttranscriptional processing. As we noted, the promoters of the 5S genes are within the transcribed part of the genes, rather than upstream of their 5S transcription units.

199-2 rRNA Transcription & Processing

CHALLENGE

In the same species, rRNA genes can differ in copy number as well as DNA sequence. This might be expected, especially when they are repeated in tandem. Why?