Eukaryotes rRNA structure

Fig. 4.9. Diagrammatic representations of the secondary structures of the nSSU (left) and mtSSU (right) rRNAs. Universal helices are shown in solid black. Helices present in eukaryotic expansion segments of neodermatans are not shaded. Expansion segments are numbered as V1 to V9, following De Rijk et al. (1992). The equivalent numbering scheme used by Gerbi (1996) is indicated in parentheses. Note that the V7 region adjacent to helix 43 might have a different, as yet unknown, structure in cestodes. The mtSSU rRNA structure is based on that for Fasciola hepatica (Le ef al., 2001). Diagram modified from one supplied by Dr Jan Wuyts.

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. 

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. 

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. 

If a phylogenetic comparison is made of the 16S-Iike rRNAs from an archae-bacterium Halobacterium volcanii), a eubacterium E. coli), and a eukaryote (the yeast Saccharomyces cerevisiae), a striking similarity in secondary structure emerges (Figure 12.40). Remarkably, these secondary structures are similar despite the fact that the nucleotide sequences of these rRNAs themselves exhibit a low degree of similarity. Apparently, evolution is acting at the level of rRNA secondary structure, not rRNA nucleotide sequence. Similar conserved folding patterns are seen for the 23S-Iike and 5S-Iike rRNAs that reside in the... 

FIGURE 12.40 Phylogenetic comparison of secondary structures of 16S-Uke rRNAs from (a) a eubacterium (E. coli), (b) an archaebacterium (H. volcanii), (c) a eukaryote S. cerevisiae, a yeast). 

Other antibiotics inhibit protein synthesis on all ribosomes (puromycin) or only on those of eukaryotic cells (cycloheximide). Puromycin (Figure 38—11) is a structural analog of tyrosinyl-tRNA. Puromycin is incorporated via the A site on the ribosome into the carboxyl terminal position of a peptide but causes the premature release of the polypeptide. Puromycin, as a tyrosinyl-tRNA analog, effectively inhibits protein synthesis in both prokaryotes and eukaryotes. Cycloheximide inhibits peptidyltransferase in the 60S ribosomal subunit in eukaryotes, presumably by binding to an rRNA component. 

The small ribosomal subunit binds to the mRNA. In prokaryotes, the 16S rRNA of the small subunit binds to the Shine-Dalgamo sequence in the 5 untranslated region of the niRNA. In eukaryotes, the small subunit binds to the 5 cap structure and slides down the message to the first AUG. 

Ribosomal RNAs (rRNAs) are found in association with several proteins as components of the ribosomes—the complex structures that serve as the sites for protein synthesis (see p. 433). There are three distinct size species of rRNA (23S, 16S, and 5S) in prokaryotic cells (Figure 30.2). In the eukaryotic cytosol, there are four rRNA size species (28S, 18S, 5.8S, and 5S). [Note "S" is the Svedberg unit, which is related to the jnolecular weight and shape of the compound.] Together, rRNAs make up eighty percent of the total RNA in the cell. 

Ribosomes are large complexes of protein and rRNA (Figure 31.8). They consist of two subunits—one large and one small—whose relative sizes are generally given in terms of their sedimentation coefficients, or S (Svedberg) values. [Note Because the S values are determined both by shape as well as molecular mass, their numeric values are not strictly additive. For example, the prokaryotic 50S and 30S ribosomal subunits together form a ribosome with an S value of 70. The eukaryotic 60S and 40S subunits form an 80S ribosome.] Prokaryotic and eukaryotic ribosomes are similar in structure, and serve the same function, namely, as the "factories" in which the synthesis of proteins occurs. 

Ribosomal RNA (rRNA) As discussed on p. 414, prokaryotic ribosomes contain three molecules of rRNA, whereas eukaryotic ribosomes contain four molecules of rRNA (see Figure 31.8). The rRNAs have extensive regions of secondary structure arising from the base-pairing of complementary sequences of nucleotides in different portions of the molecule. The formation of intramolecular, double-stranded regions is comparable to that found in tRNA. 

Initiation The components of the translation system are assembled, and mRNA associates with the small ribosomal subunit. The process requires initiation factors. In prokaryotes,a purine-rich region (the Shine-Dalgarno sequence) of the mRNA base-pairs with a complementary sequence on 16S rRNA, resulting in the positioning of the mRNA so that translation can begin. The 5 -cap on eukaryotic mRNA is used to position that structure on the ribosome. The initiation codon is 5 -AUG-3. ... 

The sequences of all three pieces of RNA in the E. coli ribosomes are known as are those from many other species. These include eukaryotic mitochondrial, plas-tid, and cytosolic rRNA. From the sequences alone, it was clear that these long molecules could fold into a complex series of hairpin loops resembling those in tRNA. For example, the 16S rRNA of E. coli can fold as in Fig. 29-2A and eukaryotic 18S RNA in a similar way (Fig. 29-4).38/39/67 69 The actual secondary structures of 16S and 18S RNAs, within the folded molecules revealed by X-ray crystallography, are very similar to that shown in Fig. 29-2A. Ribosomal RNAs undergo many posttranscriptional alterations. Methylation of 2 -hydroxyls and of the nucleic acid bases as well as conversion to pseudouridines (pp. 1638-1641) predominate over 200 modifications, principally in functionally important locations that have been found in human rRNA.69a... 

The bulk of the cellular RNA is ribosomal RNA. Although seven genes exist in E. coli for rRNA, they all lead to essentially the same three ribosomal RNA molecules (see table 28.1) which differ substantially in size. The three rRNAs are always found in a complex with proteins in a functional component known as the ribosome. The ribosome is the site where mRNA and tRNAs meet to engage in protein synthesis. In E. coli, ribosomes are referred to as 70S particles, a measure of their rate of sedimentation and hence their size (S refers to Svedberg units, which are defined in chapter 6). A 70S ribosome consists of two dissociable subunits A 50S subunit and a 30S subunit. Each of these contains both RNA and protein. The 50S subunit contains 23S and 5S rRNAs. The 30S subunit contains a single 16S rRNA (fig. 28.5). Eukaryotic ribosomes are similar in structure, although they are somewhat larger (80S) and con-... 

Removal of internal sequences in eukaryotes is not restricted to mRNA processing. It also occurs in the processing of rRNA and some tRNAs. In tRNAs the mechanism appears to be different in that the signal for splicing originates not from the primary sequence but from the secondary or tertiary structure of the pre-tRNA. 

Ribosomes, the intracellular particles on which proteins are assembled, are highly complex and dynamic entities. The structural framework of ribosomes is provided by ribosomal RNA (rRNA) molecules with which many proteins are associated (summarized in Capowski and Tracy, 2003). Homologous rRNA genes occur in all prokaryotes and eukaryotes. The mitochondrial and chloroplast rRNA genes in eukaryotes clearly have prokaryote affinities (Pace et ai, 1986). The genomic DNA from which ribosomal genes are transcribed, along with any associated spacers, is collectively termed ribosomal DNA (rDNA). Sequences and other data from rDNA and its products,... 

Michot, B., Hassouna, N. and Bachellerie, J.P. (1984) Secondary structure of mouse 28S rRNA and general model for the folding of the large rRNA in eukaryotes. Nucleic Acids Research 12, 4259 t279. 

Ribosomal RNAs (rRNAs) play an active structural role in ribosomes that are essential components of the cellular protein synthesis machinery. rRNAs are also believed to participate in tRNA binding, ribosomal subunit association, and antibiotic interactions. In a typical eukaryotic cell, there are four types of rRNA (28S, 18S, 5.8S, and 5S) that vary in size and sequence,... 

No. Eukaryotic RNA polymerases have been isolated from many tissues, and in all cases, three distinct enzymes have been found in the nucleus. All contain a number of polypeptide subunits and are complex in structure, RNA polymerase I is known to be involved specifically in the transcription of rRNA genes. RNA polymerase II gives rise to transcripts that are subsequently processed to yield mRNA. RNA polymerase 111 is responsible for the transcription of the tRNA genes and a small ribosomal RNA gene that yields a species called 55 RNA. The three polymerases are distinguishable from one another by their differential sensitivity to the drug a-amanitin (the toxic principle of the mushroom Amanita phalloides), which does not affect bacterial RNA polymerase. RNA polymerase... 

The mRNA transcript is a linear molecule but can have secondary structure through autocomplementarity as indicated above. In addition to mRNA there are other types of RNA, notably ribosomal RNA (rRNA) and transfer RNA (tRNA). The rRNAs in eukaryotes include 18S, 5.8S, 28S and 5S rRNAs (S, the Svedberg, being a measure of rate of sedimentation in ultracentrifugation and hence of relative size). The rRNAs have extensive secondary structure. The rRNAs and a number of proteins make up the ribosome upon which translation occurs. 

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