Eukaryotic rRNA

Pseudouridine is formed by enzymatic rearrangement of uridine in the original transcript (Eq. 28-3). It can form a base pair with adenine in the same manner as does uracil. Pseudouridine is found not only in tRNA but also in several places in both large and small ribo-somal RNA subunits. For example, it is present at position 516 in the E. coli 16S RNA,364 at a specific position in the 23S RNA, and at many more locations in eukaryotic rRNA. 

The primary eukaryotic rRNA transcripts extend several hundred nucleotides past the 3 termini of the... 

The cap protects the 5 end of the primary transcript against attack by ribonu-cleases that have specificity for 3 5 phosphodiester bonds and so cannot hydrolyze the 5 5 bond in the cap structure. In addition, the cap plays a role in the initiation step of protein synthesis in eukaryotes. Only RNA transcripts from eukaryotic protein-coding genes become capped prokaryotic mRNA and eukaryotic rRNA and tRNAs are uncapped. 

Eukaryotic cells contain multiple copies of the 5S rRNA gene. Unlike other eukaryotic rRNA genes, the 5S rRNA genes are transcribed by RNA Pol III. Two control elements, an A box and a C box, lie downstream of the transcriptional start site. The C box binds TFIIIA which then recruits TFIIIC. TFIIIB now binds and interacts with RNA Pol III to form the transcription initiation complex. Transcription produces a mature 5S rRNA that requires no processing. 

Eukaryotic rRNA molecules are generally larger and there are four eukaryotic rRNA molecules. Rat liver rRNA molecules are used as standards the S values and the average number of nucleotides are 5S (120), 5.8S (150), 18S (2100), and 28S (5050), respectively. The eukaryotic 5.8S species corresponds functionally to the prokaryotic... 

There are four major classes of RNA in cells messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). The relative abundance, and complexity (number of distinct types), of these RNA molecules is quite different. About 80% of RNA in a cell consists of rRNA, the RNA component of ribosomes. There are only four types of eukaryotic rRNA (28S, 18S, 5.8S, and 5S) and, therefore, the sequence complexity of this class is actually quite low. In contrast, mRNA constitutes just 5% of total cellular RNA, yet it is the most diverse, with an estimated 104105 different species which correspond to the same number of protein coding genes. Both tRNA and snRNA (in eukaryotes) make up the remaining fraction of RNA in a cell (-15%), with -50 different types of tRNA and -10 different snRNAs. The total number of molecules per cell of each class of RNA is therefore based on the relationship between the total mass of each RNA class, the average length of RNA molecules in that class, and the sequence complexity. 

Figure 25.7 shows the processing pathway of human 45S rRNA into the two functional 28S rRNA and 18S rRNA products. As described in Chapter 24, eukaryotic rRNA genes are transcribed by RNA pol I. Less is known about the enzymology of eukaryotic rRNA processing than that of bacteria however, it is presumed that site-specific RNases are also involved in the cleavage reactions. 

The processing of rRNAs is primarily a matter of methylation and of trimming to the proper size. In prokaryotes, there are three rRNAs in an intact ribosome, which has a sedimentation coefficient of 70S. (Sedimentation coefficients and some aspects of ribosomal structure are reviewed in the discussion of ribosomal RNA in Section 9.5.) In the smaller subunit, which has a sedimentation coefficient of SOS, one RNA molecule has a sedimentation coefficient of 16S. The BOS subunit contains two kinds of RNA, with sedimentation coefficients of 5S and 23S. The ribosomes of eukaryotes have a sedimentation coefficient of SOS, with 40S and 60S subunits. The 40S subunit contains an 18S RNA, and the 60S subunit contains a 5S RNA, a 5.8S RNA, and a 28S RNA. Base modifications in both prokaryotic and eukaryotic rRNA are accomplished primarily by methylation. 

Splicing of some eukaryotic pre-rRNA Only a few eukaryotic rRNA transcripts contain introns, which are excised and self-spliced (subsection 11.7.2). 

Mougey, E O Reilly, M Osheim, Y. N Miller, O. L.. Jr.. Beyer, A. L., and Sollner-Webb, B. (1993). The terminal balls characteristic of eukaryotic rRNA transcription units in chromatin spreads are rRNA processing complexes. Genes Dev. 7, 1609-1619. 

Ribosomal RNAs constitute 80—90% of total cellular RNAs and are the essential components (50—60%) of ribosome structure. Ribosomes (70S in prokaryotes, SOS in eukaryotes) provide the platform for translation of the genetic code and the link between genotype and phenotype. Ribosomal RNAs have the most extensive secondary structure of all RNAs and, by cooperative interactions with associated proteins, fold into complex tertiary structures within the ribosome (156,157). In contrast to the prokaryotic and eukaryotic rRNAs, protozoan rRNAs are derived by self-splicing (see Section II,D,4,b, this chapter). 

Eukaryotic rRNAs include 18S (1.8 kb), 5.8S, and 28S (4.7 kb) molecules. They are derived from the nucleolytic processing of a single precursor molecule (pre-rRNA) which is transcribed by RNA polymerase I. The 5.8S RNA remains attached to the 28S RNA by H-bonds. In humans, the pre-rRNA is 13 kb (45S) long and has a structure in which three exons are separated by both internal and external RNA spacers (total length of 31 kb). The fourth component of rRNA is 5S RNA which is transcribed by RNA polymerase III. The 5S rRNA gene is not normally linked to that of other rRNAs. Together with ribosomal proteins, the 18S rRNA constitutes the small 40S ribosomal subunit 5S, 5.8S, and 28S rRNAs make up the large 60S subunit. 

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