5S RNA

Ribosomes (79-87) are small organelles 17-23 nm in diameter. They can exist in clusters known as polysomes or be attached to the er where they bind to pores in the er membrane. A major constituent of the er pore is translocon, the heterotrimetric Sec 61 protein complex. Sec 61 binds to the 80s ribosomes (86). Ribosomes consist of subunits, a 30s subunit (16srRNA and 21 proteins), and a 50s subunit (23s and 5s RNAs, > proteins and the catalytic site of peptidyl transferase). Ribosomes are the sites of protein synthesis. 

RNA polymerase Core enzyme RNA polymerase I rRNA RNA polymerase II mRNA snRNA RNA polymerase III tRNA, 5S RNA... 

The specific regulatory role of HI documented for the Xenopus 5S RNA gene points to the importance of AT-rich tracts in the genome as potential sites of strong and preferential HI binding. Indeed, it has been shown that histone HI is probably involved in the repression of the murine /1-interferon promoter by binding to its upstream AT-rich region [143]. 

In Xenopus, in addition to the role in 5S RNA gene regulation, somatic HI has been shown to be involved in further stages of differentiation. The restriction of myoD expression, a marker for the loss of the ability by ectodermal cells to differentiate into mesoderm, requires the presence of somatic histone HI [144]. Again, the globular domain alone and not the whole HI molecule is required to confer this effect [142]. 

Chloroplasts come in various sizes and shapes, but all contain a small number of DNA molecules ranging in size from 120-160 kb. Complete sequences are known for DNA from chloroplasts of a liverwort (121,025 bp),246 tobacco (155,844 bp),247 maize (Zea mays),248 and other plants. The 140,387 bp DNA from maize chloroplasts is a circular molecule containing the genes for 23S, 16S, 5S, and 4.5S RNA, for 30 species of tRNA, and for 70 different proteins. Among them are subunits of RNA polymerase, NADH dehydrogenase, subunits of both PSI and PSII, rubisco (large subunit), cytochromes b and/, six subunits of ATP... 

The genes for 5S ribosomal RNA and all of the tRNAs are transcribed by RNA polymerase III. In the yeast genome die 5S RNA genes are located in the spacers between the transcriptional units containing the other rRNAs. However, in animals the 5S RNA... 

Figure 29-4 Structure of 23S-28S ribosomal RNAs. (A) The three-dimensional structure of RNA from the 50S subunit of ribosomes of Halocirculci marismortui. Both the 5S RNA and the six structural domains of the 23S RNA are labeled. Also shown is the backbone structure of protein LI. From Ban et al.17 Courtesy of Thomas A. Steitz. (B) The corresponding structure of the 23S RNA from Thermus thermophilus. Courtesy of Yusupov et al.33a (C) Simplified drawing of the secondary structure of E. coli 23S RNA showing the six domains. The peptidyltransferase loop (see also Fig. 29-14) is labeled. This diagram is customarily presented in two halves, which are here connected by dashed lines. Stem-loop 1, which contains both residues 1 and 2000, is often shown in both halves but here only once. From Merryman et al.78 Similar diagrams for Haloarcula marismortui17 and for the mouse79 reveal a largely conserved structure with nearly identical active sites. (D) Cryo-electron microscopic (Cryo-EM) reconstruction of a 50S subunit of a modified E. coli ribosome. The RNA has been modified genetically to have an...

Figure 29-5 (A) Secondary structure of E. coli 5S RNA with five universal helical stems (labeled 1-5).

This small RNA is found in the central protuberance of the 50S ribosomal subunit. See Fig 29-4A. Photocrosslinking using thiouridine-containing 5S RNA suggested a close proximity of U89 (marked by arrow) with nucleotide 2477 of the 23S RNA in the loop end of helix 89 (Fig. 29-4).93 (B) Stereoscopic view of the 5S RNA as observed in ribosomes of Haloarcula marismortui. From Ban et al 7 Courtesy of Thomas A. Steitz. 

Figure 29-6 Some protein-RNA interactions within the ribosome. (A) A space-filling model of the 23S and 5S RNA with associated proteins from the ribosome of Haloarcula marismortui. The CCA ends of bound tRNA molecules in the A, P, and E sites are also included. The view is looking into the active site cleft. The proteins with e after the number are related to eukaryotic ribosomal proteins more closely than to those of E. coli.17 Courtesy of T. A. Steitz. (B) Three-dimensional structure of a 70S ribosome from Thermus thermophilus. The 30S subunit is to the right of the 50S subunit. Courtesy of Yusupov et al.33a (C) Stereoscopic view of the helix 21 to helix 23b region of the 16S RNA with associated proteins S6 (upper left), S18 (upper center, front), and S15 (lower back) from T. thermophilus. Courtesy of Agalarov et at.31 (D) Simplified in vitro assembly map of the central domain of the 30S bacterial ribosome. Courtesy of Gloria Culver. (E) Contacts of proteins with the central (platform) domain of the 16S RNA component. The sequence shown is that of Thermus thermophilus. Courtesy of Agalarov et al. (F) Three drawings showing alternative location of the four copies of protein L7/L12. The N-terminal and C-terminal...

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... 

An independent and essential structural domain of the ribosome is formed around the 5S RNA.3 111 8 13 1 136 Proteins L5, LI8, and L25, whose structure is similar to that of glutaminyl-tRNA synthetase,154 bind specifically to one loop of the 5S RNA.156a Furthermore, the L5-L18-L25-5S RNA complex binds the oligonucleotide TCC. This suggests an interaction between the 5S RNA and the TT C arm of a tRNA molecule bound to the ribosome. In addition, it has been observed that L18 + either L5 or L25 cause 5S RNA to bind to 23S RNA. 

Haloacetates. In alkaline solution lysine residues can be alkylated in the presence of iodo- or bromoacetate ions (118). Both mono- and di-carboxymethyl derivatives can be formed. Some of the characterized derivatives are listed at the end of Table VI. Number 25, t-CM-Lys-41-RNase, shows a very low activity when measured by a step 2 assay employing C > p as substrate. This same compound is active in the depolymerization of 5S RNA (119) but the evidence presented to show that it is not the result of contamination with native RNase-A can be interpreted to suggest the opposite. 

RNA polymerase I is located in the nucleolus and synthesizes a large precursor that is later processed to form rRNA. It is completely resistant to inhibition by a-amanitin. RNA polymerase II is located in the nucleoplasm and synthesizes large precursor RNAs (sometimes called heterogeneous nuclear RNA, or hnRNA) that are processed to form cytoplasmic mRNAs. It is also responsible for the synthesis of most viral RNA in virus-infected cells. PolII is very sensitive to a-amanitin, being inhibited by 50% at 0.05 /u,g/ml. RNA polymerase III is also located in the nucleoplasm and synthesizes small RNAs, such as 5S RNA and the precursors to tRNAs. This enzyme is somewhat resistant to a-amanitin, requiring about 5 /u,g/ml to reach 50% inhibition. 

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