Ribosomes, rRNA structure

This definition expands our earlier thoughts in two ways. First, we have included specification of RNA molecules as well as proteins. As noted above, many RNA molecules serve a role as message carrier from DNA to the protein-synthesizing machinery (mRNA) and are translated into protein structures. Other RNA molecules serve other functions as components of the ribosome, rRNA, or as an interface between mRNA and amino acids in protein synthesis, tRNA. Finally, we have the very small RNA molecules known as siRNA. These species of RNA are not translated into proteins and this requires that the definition of a gene include the specification of their structure. 

Fig. 3 Secondary structure of the ribosomal rRNA of Saccharomyces cerevisiae. http //www.ma.icmb.utexas. edu (Cannone et al. 2002). The numbering of nucleotides is according to E. coli. Helices H) discussed in the text are highlighted and localization of yeast rdn mutations are indicated, a Secondary structure of the small subunit 18S rRNA. Helices discussed in the text are labeled in red. b Secondary structure of the 25 rRNA. Helices discussed in the text are labeled in blue. Helix 44 is part of the L7/L12 stalk hehx 95 contains the sarcin-ricin loop. For details, see text...

All ribosomes have two subunits, and each subunit contains several protein chains and one or more chains of RNA (ribosomal RNA, or rRNA). In the ribosome from E. coli, the smaller of the two subunits is known as the 30S subunit and the larger is referred to as the 50S subunit. (The unit S stands for Svedberg, a measure of how rapidly a particle sediments in a centrifuge.) The two subunits combine to form the active 70S ribosomal assembly. The special RNA molecules that are a part of the ribosome are quite distinct from messenger or transfer RNA molecules, and they play important roles in forming the overall ribosomal quaternary structure and in aligning mRNA and tRNA molecules during protein biosynthesis. 

FIGURE 1 The 50S subunit of a bacterial ribosome (PDB ID 1 NKW). The protein backbones are shown as blue wormlike structures the rRNA components are transparent. The unstructured extensions of many of the ribosomal proteins snake into the rRNA structures, helping to stabilize them. 

Besides having a much lower molar mass than DNA, RNA generally forms only single-strand helices. RNA is often found associated with proteins inside cells. The most prevalent bases in RNA are the same as those in DNA, except that uracil is present instead of thymine. Three common types of RNA are ribosomal (rRNA), transfer (tRNA), and messenger RNA (mRNA). They are all involved in protein synthesis, controlling the sequence of amino acids that make up the primary structure. Thus the base sequence in RNA is related to the amino acid sequence in the protein that is made from it. 

It is likely that protein binding and other macromolecular interactions also play a role in stabilizing the rRNA structures. A recent analysis12 reveals that the binding of specific ribosomal protein to rRNA in vitro results in changes within the rRNA modification patterns. Because the experiments detailed herein examine a population of rRNA within the cell, and thus may be analyzing a variety of RNA conformations, it is remarkable that very consistent results are observed. However, the consequence of polysome assembly and translation on the structure of the rRNA and how these structures might be distinct are not addressed in this analysis. In vitro DMS modification of soybean RNA has revealed some differences in base reactivity relative to that observed on RNA modified in vivo as described herein.36 ... 

Translation is the process by which an mRNA is read by tRNAs, ribosomes (complex structures consisting of rRNAs and ribosomal proteins), and numerous other enzymes. Each type of cell is programmed to synthesize only those proteins necessary for its particular cellular functions (Chapter 26). The difference between a neuron and a liver cell is the kind of proteins that are synthesized even though both cells contain exactly the same genetic information. Cellular differentiation is due to differential gene expression a tumor cell invariably is a cell that has lost the ability to regulate and express its genetic information... 

These findings are interpreted to indicate that erythromycin resistance mutation in domain II caused an increase in the peptide and disrupted an indirectly functional interaction between domains II and V, because such a mutation could affect alteration of the stability of a secondary rRNA structure (hairpin sequence structure) in domain II. In addition, the Shine-Dalgamo (SD) sequence of the rRNA-encoded E-peptide ORE is sequestered in the hairpin structure. Thereby, SD and E-peptide codon are not accessible to ribosomes of wild-type E. coli. The conformational change of the hairpin structure by erythromycin resistance mutation can be recognized by ribosomes for the initiation of translation of E-peptide. Thus, the increase of the peptide is expected to show resistance to macrolide antibiotics such as erythromycin, oleandomycin, and spiramycin but not clindamycin and chloramphenicol without preventing their binding to the target. 

RNA is now known to be much more than just an intermediary between DNA and protein. RNA can act as a catalyst (mRNA), a binding site for small molecules (tRNA), a regulator of geue expression (RNAi and siRNA), a structural component of ribosomes (rRNA), and perhaps much more. 

This work is aimed to clarify some aspects of the role played by Mg " ions in the E. coli ribosomes, i.e. to which extent the rRNA structure, both inside and outside the ribosome, is determined by the interaction with the Mg ions. 

More sequence conservation is observed for ribosomal proteins than for rRNA. Structural similarities are significant enough that cross-species RNA interactions were shown possible for proteins LI, LI 1, and SI5. At a minimum, then, the RNA-binding features of these proteins are conserved. 

Ribosomes, the supramolecular assemblies where protein synthesis occurs, are about 65% RNA of the ribosomal RNA type. Ribosomal RNA (rRNA) molecules fold into characteristic secondary structures as a consequence of intramolecular hydrogen bond interactions (marginal figure). The different species of rRNA are generally referred to according to their sedimentation coefficients (see the Appendix to Chapter 5), which are a rough measure of their relative size (Table 11.2 and Figure 11.25). 

Despite the unity in secondary structural patterns, little is known about the three-dimensional, or tertiary, structure of rRNAs. Even less is known about the quaternary interactions that occur when ribosomal proteins combine with rRNAs and when the ensuing ribonucleoprotein complexes, the small and large subunits, come together to form the complete ribosome. Furthermore, assignments of functional roles to rRNA molecules are still tentative and approximate. (We return to these topics in Chapter 33.)... 

Ribosomal Protein Synthesis Inhibitors. Figure 3 The chemical structure of tetracycline and possible interactions with 16S rRNA in the primary binding site. Arrows with numbers indicate distances (in A) between functional groups. There are no interactions obseived between the upper portion of the molecule and 16S rRNA consistent with data that these positions can be modified without affecting inhibitory action (from Brodersen et al. [4] with copynght permission). 

Ribosomal Protein Synthesis Inhibitors. Figure 5 Nucleotides at the binding sites of chloramphenicol, erythromycin and clindamycin at the peptidyl transferase center. The nucleotides that are within 4.4 A of the antibiotics chloramphenicol, erythromycin and clindamycin in 50S-antibiotic complexes are indicated with the letters C, E, and L, respectively, on the secondary structure of the peptidyl transferase loop region of 23S rRNA (the sequence shown is that of E. coll). The sites of drug resistance in one or more peptidyl transferase antibiotics due to base changes (solid circles) and lack of modification (solid square) are indicated. Nucleotides that display altered chemical reactivity in the presence of one or more peptidyl transferase antibiotics are boxed. 

The atomic structure of this subunit and its complexes with substrate analogs revealed the enzymatic activity of the rRNA backbone. Thus, the ribosome is in fact a ribozyme P Nissen, J Hansen, N Ban, PB Moore, TA Steitz. Science 289 920-930, 2000. Atomic structure of the ribosome s small 30S subunit, resolved at 5 A WM Clemons Jr, JL May, BT Wimberly, JP McCutcheon, MS Capel, V Ramakrishnan. Nature 400 833-840, 1999. The 8-A crystal structure of the 70S ribosome reveals a double-helical RNA bridge between the 50S and the 30S subunit GM Culver, JH Cate, GZ Yusupova, MM Yusupov, HF Noller. Science 285 2133-2136, 1999. 

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. 

Fig. 1.1. The phylogenetic structure of the Nematoda revealed by small subunit ribosomal RNA analysis. (A) Neighbour-joining (NJ) analysis of aligned ssu rRNA genes from nematodes. The alignment is based on that of Blaxter etal. (1998), with the addition of sequences from Aleshin etal. (1998), Nadler (1998)...

The ribosome is a ribozyme this is how Cech (2000) commented on the report by Nissen et al. (2000) in Science on the successful proof of ribozyme action in the formation of the peptide bond at the ribosome. It has been known for more than 30 years that in the living cell, the peptidyl transferase activity of the ribosome is responsible for the formation of the peptide bond. This process, which takes place at the large ribosome subunit, is the most important reaction of protein biosynthesis. The determination of the molecular mechanism required more than 20 years of intensive work in several research laboratories. The key components in the ribosomes of all life forms on Earth are almost the same. It thus seems justified to assume that protein synthesis in a (still unknown) common ancestor of all living systems was catalysed by a similarly structured unit. For example, in the case of the bacterium E. coli, the two subunits which form the ribosome consist of 3 rRNA strands and 57 polypeptides. Until the beginning of the 1980s it was considered certain that the formation of the peptide bond at the ribozyme could only be carried out by ri-bosomal proteins. However, doubts were expressed soon after the discovery of the ribozymes, and the possibility of the participation of ribozymes in peptide formation was discussed. 

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