A ribonucleoprotein intracellular organelle (about 25–30 nm in diameter) which mediates PROTEIN SYNTHESIS (q.v. for function). Some ribosomes occur in the cytoplasm; others (see e.g. ENDOPLASMIC RETICULUM) are membrane-bound. Ribosomes are usually present in large numbers in the cell.
Each ribosome consists of two subunits—one larger than the other; both subunits contain RNA and protein.
Different types of ribosome are characterized by different sedimentation coefficients (S) on ultracentrifugation (see also SVEDBERG UNIT). Bacterial ribosomes have a sedimentation coefficient of ca. 70S; each consists of one 30S subunit and one 50S subunit. Ribosomes of the eukaryotic cell cytoplasm have a sedimentation coefficient of ca. 80S; each consists of one 40S subunit and one 60S subunit. Other ribosomes reported: those in mammalian mitochondria (ca. 60S), in chloroplasts of plants and algae (ca. 70S), in mitochondria of plants (ca. 78S), and those in the mitochondria of yeasts and other lower eukaryotes (ca. 73S).
Ribosomal RNA (rRNA) comprises ca. 65% (by mass) of the bacterial ribosome, and ca. 50–60% of the eukaryotic 80S ribosome.
The bacterial ribosome contains one molecule of 16S rRNA (in the 30S subunit), and one molecule each of 5S rRNA and 23S rRNA in the 50S subunit; the 16S and 23S rRNA molecules contain modified nucleotides. All three species of bacterial rRNA—together with tRNAs—are transcribed as a single molecule of RNA that is cut at specific sites; in this cutting process the ribozyme RNASE P is required for trimming the 5′ ends of tRNA molecules.
Crystallographic analysis of the 30S subunit from the bacterium Thermus thermophilus has shown that (as predicted) most of the interfacial region of the subunit, i.e. that part in contact with the 50S subunit, consists of RNA [Nature (1999) 400 833–840]. (Results from the study also suggest that some of the proteins may be more directly involved in ribosomal function than has hitherto been assumed.)
The eukaryotic 80S ribosome contains one molecule of 18S rRNA (in the 40S subunit), and one molecule each of 28S, 5.8S and 5S rRNA in the 60S subunit; the 28S and 18S rRNAs contain modified nucleotides (the level of modification being greater than that in bacterial 23S and 16S rRNAs). Genes which encode the 5.8S, 18S and 28S rRNAs occur in the NUCLEOLUS, the gene encoding 5S rRNA being found outside the nucleolus. (For details of rRNA synthesis see entry RRNA.)
Ribosomal proteins (r-proteins). The r-proteins are closely associated with rRNA.
In Escherichia coli the small (30S) ribosomal subunit contains 21 distinct r-proteins which are designated S1–S21 (‘S’ for ‘small’)—according to their electrophoretic mobilities (S1 having the highest MWt). (These proteins were also designated ES1–ES21—‘ES’ for ‘eubacterial small’.) Only one molecule of each type of protein is present in the subunit, and all except S1, S2 and S6 are basic proteins. (S1 is reported to be only loosely associated with the 30S subunit; there is apparently no S1 protein in the ribosomes of Bacillus spp.)
The large (50S) subunit of E. coli was originally reported to contain 34 r-proteins—which were designated L1–L34 (or EL1–EL34). Subsequently, the protein initially designated ‘L8’ was found to be a complex of L7, L10 and L12; ‘L6’ was identified as S20; and L7 and L12 were found to be almost identical—differing only in that L7 is acetylated at the amino terminus. The other L proteins retained their original L numbers. All the L proteins are present in single copy except L7/L12, which is present in four copies; this is the only acidic protein in the 50S subunit.
Eukaryotic 80S ribosomes are more complex; they contain >70 r-proteins.
Archaeal ribosomes resemble (at least superficially) those of bacteria; for example, they contain only three types of rRNA and have a sedimentation coefficient of ca. 70S. However, those of certain archaeans (e.g. Halobacterium cutirubrum and some methanogens) contain many acidic r-proteins which show little or no homology with those of bacteria; moreover, some of the r-proteins from H. cutirubrum appear to share some homology with eukaryotic r-proteins. Furthermore, archaeal ribosomes are insensitive to certain antibiotics (e.g. CHLORAMPHENICOL) which interfere with bacterial ribosome function, while some are sensitive to the 80S (eukaryotic) ribosome inhibitor ANISOMYCIN. [Archaeal (‘archaebacterial’) ribosomes: Book ref. 157, pp 345–377.]
Ribosome structure. The rRNA molecules can adopt complex secondary structures—extensive intramolecular base-pairing resulting in the formation of HAIRPINS and STEM-AND-LOOP STRUCTURES etc. [rRNA structure: ARB (1984) 53 119–162.]
The integrity of a ribosome appears to involve hydrogen-bonding and both ionic and hydrophobic interactions, magnesium ions generally playing an important role in maintaining the structure.
The basic architecture of a ribosome has been strongly conserved during evolution, although ribosomes from e.g. bacteria, the eukaryotic cytoplasm and archaeans appear to show certain distinctive morphological features (cf. PHOTOCYTA.) [Evolving ribosome structure: ARB (1985) 54 507–530. Three-dimensional model of the E. coli ribosome: Prog. Biophys. Mol. Biol. (1986) 48 67–101.]
Taxonomic role of rRNA. Certain regions of rRNA have been very highly conserved during evolution, and sequence homology studies in rRNAs are widely used to indicate evolutionary relationships among organisms. [Evolutionary changes in 5S rRNA higher order structure: NAR (1987) 15 161–179.] (See also RIBOTYPING.)
Biogenesis of ribosomes. Biogenesis appears to involve an assembly process in which, initially, some of the r-proteins bind to particular regions of rRNA; other r-proteins then bind co-operatively to this ‘core’ structure. [Protein–rRNA recognition and ribosome assembly: Book ref. 84, pp 331–352.]
In rapidly growing cells of E. coli the number of ribosomes per cell is essentially proportional to the growth rate; this necessitates control mechanisms for co-ordinated expression of the genes encoding r-proteins and rRNAs.
Genes encoding the r-proteins are grouped into a number of distinct OPERONS. For example, the str operon contains genes for (in order of transcription) S22, S7 and translation elongation factors EF-G and EF-Tu (see PROTEINS SYNTHESIS); the α operon contains genes for S13, S11, S4, RNA polymerase subunit α and L17; the β operon contains genes for L10, L7/12 and RNA polymerase subunits β and β′. Co-ordination of the synthesis of r-proteins involves post-transcriptional AUTOGENOUS REGULATION (translational feedback regulation). One model for the control of these operons postulates that one of the r-proteins encoded by a given operon acts as a regulatory molecule (translational repressor) for that operon by binding to its own (polycistronic) mRNA and blocking translation of some or all of the encoded proteins; thus, for example, in the β operon L10 represses the translation of L10 and L7/L12, but not of the co-transcribed RNA polymerase β and β′ subunits. (See also RPO GENES.) The E. coli IF3–L35–L20 operon contains the genes infC–rpmI–rplT which encode (respectively) initiation factor IF3 (see PROTEIN SYNTHESIS) and the r-proteins L35 (sic) and L20; IF3 acts as a repressor of its own gene, and L20 apparently acts as a translational repressor (in a concentration-dependent way) by binding to a site (a translational operator) upstream of the rpmI sequence in the mRNA, thus blocking translation of both r-proteins. The mechanism of repression by L20 is unknown, but translational control of the operon apparently involves a pseudoknot which affects the control region of rpmI [EMBO (1996) 15 4402–4413].
Some of the operon-regulatory proteins also have binding sites on either 16S or 23S rRNA. It is thought that, if the growth rate decreases, the decreased amount of 16S and 23S rRNA available in nascent ribosomes will leave these proteins free to inhibit translation of their respective transcripts. Note that, in this model, synthesis of ribosomal proteins is linked to the availability of rRNA, regulation of the rRNA genes being the key step in regulating the biogenesis of ribosomes; a ribosome feedback regulation model has been proposed in which rRNA synthesis is repressed (directly or indirectly) by the presence of ‘free’ (i.e. non-translating) ribosomes. [Review of regulation of ribosome biogenesis: Book ref. 188, pp 199–220.]
Synthesis of rRNA is linked to the cell’s translational needs and is thus susceptible to up-regulation or down-regulation according to prevailing conditions. In E. coli the 16S, 23S and 5S rRNAs are co-transcribed (in that order) as a single transcript from the rrn operon; the E. coli chromosome contains seven copies of the rrn operon (designated A–E, G, H), each operon containing one copy each of the three kinds of rRNA—except the D operon, which contains two copies of the 5S gene. If (e.g. through mutation) any reduction occurs in the levels of 16S or 23S rRNA, a compensatory mechanism up-regulates the rrn operons. Interestingly, however, deletion of two or more copies of the 5S rRNA gene in E. coli brings about a sharp drop in growth rate (i.e. there is no compensatory effect)—such a reduction in growth rate being almost reversible by insertion of a plasmid-borne 5S rRNA gene [NAR (1999) 27 637–642].
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