Ribosomal proteins table

In recent years a number of in vitro studies have shown that the presence of Met(O) residues in a wide variety of proteins causes loss of biological activity. Table 2 lists some proteins which have been demonstrated to lose activity when specific Met residues are oxidized in vitro. Two of these proteins, E. coli ribosomal protein LI 2 and mammalian a-1-PI, have been studied extensively and will be discussed in detail. 

Most of the E. coli ribosomal proteins are rather basic with high isoelectric points (Kaltschmidt, 1971) and a high content of basic amino acids (Tables I and II). The complete primary structures of all . coli ribosomal proteins have been determined by Wittmann-Liebold and coworkers (see Table III and Appendix). 

A number of ribosomal proteins contain modihed amino acids at the N terminus or at other positions of the protein chain (Table IV). The N termini of three proteins (S5, S18, and L7) are acetylated, thus they cannot be subjected successfully to manual or automatic Edman degradation because of their blocked N termini. Mutants have been isolated in... 

In addition to the ribosomal proteins, the two initiation factors IF-1 (Pon et ai, 1979) and IF-3 (Brauer and Wittmann-Liebold, 1978), the elongation factor EF-Tu (Arai et ai, 1980), and the two proteins NS-1 and NS-2 (Mende et ai, 1978), which bind to ribosomes and to DNA, have been completely sequenced (Table III). 

IFl-3). In contrast, eukaryotic initiation is a rather complex process involving a large number of initiation factors (elFs, Table 1). This is also the stage of eukaryotic ribosomal protein synthesis, which is most highly regulated to achieve differential protein expression. Elaborating the details of eukaryotic initiation is beyond the scope of this chapter. 

Since numerous DUBs are present in eukaryotic organisms (Table 2), it is probable that they possess substrate specificity. UCHs have been studied in some detail with respect to their substrate specificity. Two major UCHs in mammals are UCH-Ll and UCH-L3. Larsen et al showed that UCH-Ll cleaves linear polyubiquitin molecules more efficiently than UCH-L3. In contrast, UCH-L3 appears to prefer ubiquitin fused to small ribosomal proteins (see Figure 7). The tissue distribution of the two UCHs is indicative of their functional specialization as well. UCH-Ll is a neuronal-specific enzyme whereas UCH-L3 is expressed primarily in hematopoietic tissues. Another UCH called UCH-L2 has wide tissue distribution. ... 

The next victims would be ribosomal proteins. Can we take them out There are some indications that ribosomal proteins may not be essential for protein synthesis (Zhang and Cech, 1998), and there are other suggestions about an ancient and simpler translation system (Nissen et al., 2000 Calderone and Liu, 2004). If we accept this, and take out the 55 genes of the ribosomal proteins and some other enzymes, around 110 genes (second column of Table 11.4) would be obtained. 

Finally, in order to get closer to the real minimal cell, there is the problem of further reduction of the number of genes. In all the systems in Table 11.5, we are still dealing with ribosomal protein biosynthesis and this implies at least 100-200 genes. We are still far from the ideal picture of a minimal cell and can again pose the question of how to reduce this complexity. 

Each E. coli cell contains 15,000 or more ribosomes, making up almost a quarter of the dry weight of the cell. Bacterial ribosomes contain about 65% rRNA and 35% protein they have a diameter of about 18 nm and are composed of two unequal subunits with sedimentation coefficients of 30S and 50S and a combined sedimentation coefficient of 70S. Both subunits contain dozens of ribosomal proteins and at least one large rRNA (Table 27-6). 

Eukaryotic ribosomes are not only larger but also (Table 29-1) contain more protein subunits than do those of bacteria 30 for the small subunit and 49 for the large subunit.63 However, the number of essential proteins may be the same. Both eukaryotic ribosomal proteins and rRNA molecules are larger than those of... 

S and 5S RNAs. Reconstitution of the large ribosomal subunit reveals that proteins L3 and L24 act as assembly initiators.115118 LI, L9, L20, and several other proteins (Table 29-2) also bind directly and independently to the 23S RNA. Assembly maps similar to that in Fig. 19-6A have been prepared for the 50S subunit.117... 

The RNA genomes of single-stranded RNA bacterial viruses, such as Q/3, MS2, R17, and f2, are themselves mRNAs. Bacteriophage Q/3 codes for a polypeptide that combines with three host proteins to form an RNA-depen-dent RNA polymerase (replicase). The three host proteins are ribosomal protein SI and two elongation factors for protein synthesis EF-Tu and EF-Ts (see table 28.5). The Q/3 replicase functions exclusively with the Q/3 RNA plus strand template. It first makes a complementary RNA transcript (minus strand) and ultimately uses the minus strand as... 

Incubations of crude pH 5 Supernatant with several C14-aminoacyl sRNA preparations, differing only in the nature of the C14-amino acid, showed that all amino acids tested were incorporated into ribosomal protein. With combined transferases I and n, the results presented in Table VII indicated that all of the amino acids tested were also incorporated in the presence of these purified fractions (8). When either of the transferases was omitted from these incubations, little amino acid transfer was observed with any of the C14-aminoacyl sRNA preparations. Variations in total amounts of C14 incorporated, as shown here, are probably due to variations in the specific radioactivity of the various sRNA-bound amino acids used. These purified transferase preparations did not catalyze the incorporation of free amino acids into sRNA or ribosomes. 

Apart from that, presence of eucarya-like bulges and protuberances on archaeal ribosomes clearly correlates with the relative abundance of the protein moiety inferred from buoyancy data, from SDS gel-electrophoretic comparisons and from sequencing of ribosomal protein genes. Reference to Table 4 shows that within the archaea all of the eucaryal attributes are in fact present in the protein-rich ribosomes of Methanococcales and sulfur-dependent thermophiles (eocytes) but are absent, or nearly so, in the protein-poor particles of the remaining methanogens, the halophiles and most bacteria. 

Fig. 3. Comparison of the amino-acid sequence of ribosomal protein L2 from eucarya (Ddi [112] and Spo [113]), archaea (Mva[109] and Hma[l 14]) and bacteria (Eco[115] and Bst[116]). See Table 2 for abbreviations. An asterisk, indicates amino acids conserved in all L2 proteins while a dot indicates...

RNA binding proteins are structurally very diverse. Most of the ribosomal proteins are devoid of recognizable RNA binding motifs, whereas, the evolution of proteins involved with RNA processing, such as hnRNA, mRNA and snRNA binding proteins, has resulted in several fairly conserved RNA binding motifs (Table 1.1). 

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