Pre-rRNA precursor

These are designated, according to their sedimentation constants, as 5S, 16S, and 23S and contain about 120, 1700, and 3300 nucleotides, respectively. All three pieces appear in cells as parts of larger pre-rRNA precursor molecules with extra nucleotide sequences at both the 3 and 5 ends.207 208... 

RNA polymerase I (Pol I) is responsible for the synthesis of only one type of RNA, a transcript called pre-ribosomal RNA (or pre-rRNA), which contains the precursor for the 18S, 5.8S, and 28S rRNAs (see Fig. 26-22). Pol I promoters vary greatly in sequence from one species to another. The principal function of RNA polymerase II (Pol II) is synthesis of mRNAs and some specialized RNAs. This enzyme can recognize thousands of promoters that vary greatly in sequence. Many Pol II promoters have a few sequence features in common, including a TATA box (eukaryotic consensus sequence TATAAA) near base pair —30 and an Inr sequence (initiator) near the RNA start site at +1 (Fig. 26-8). 

Posttranscriptional processing is not limited to mRNA. Ribosomal RNAs of both prokaryotic and eukaryotic cells are made from longer precursors called preribosomal RNAs, or pre-rRNAs, synthesized by Pol I. In bacteria, 16S, 23S, and 5S rRNAs (and some tRNAs, although most tRNAs are encoded elsewhere) arise from a single 30S RNA precursor of about 6,500 nucleotides. RNA at both ends of the 30S precursor and segments between the rRNAs are removed during processing (Fig. 26-21). 

FIGURE 26-22 Processing of pre-rRNA transcripts in vertebrates. In step (T), the 45S precursor is methylated at more than 100 of its 14,000 nucleotides, mostly on the 2 -OH groups of ribose units retained in the final products. (5) A series of enzymatic cleavages produces the 18S, 5.8S, and 28S rRNAs. The cleavage reactions require RNAs found in the nucleolus, called small nucleolar RNAs (snoRNAs), within protein complexes reminiscent of spliceosomes. The 5S rRNA is produced separately. 

Self-splicing KNA. The precursor to the 26S rRNA of Tetrahymena contains a 413-nucleotide intron, which was shown by Cedi and coworkers to be selfsplicing, i.e., not to require a protein catalyst for maturation.581 582 This pre-rRNA is a ribozyme with true catalytic properties (Chapter 12). It folds into a complex three-dimensional structure which provides a binding site for free guanosine whose 3-OH attacks the phosphorus at the 5 end of the intron as shown in Fig. 28-18A, step a. The reaction is a simple displacement on phosphorus, a transesterification similar to that in the first step of pancreatic ribonuclease action (Eq. 12-25). The resulting free 3-OH then attacks the phosphorus atom at the other end of the intron (step b) to accomplish the splicing and to release the intron as a linear polynucleotide. The excised intron undergoes... 

Nuclear rRNA precursors and cytoplasmic rRNA formed by RNA polymerase I account for some 70+% of mammalian cell RNA and 35-40% of total RNA synthesis. The products of RNA polymerase II, hnRNA and mRNA, comprise some 10% of the total RNA and 55-60% of total synthesis. The hnRNA and mRNA transcripts are unstable and have half-lives in higher eukaryotes of about 24 h, compared with an average half-life in bacteria of 90 s. Pre-tRNAs, synthesized along with 5 S rRNA by RNA polymerase III, are relatively stable, with an average half-life of 4-6 days. 

The cleavage of the precursor into three separate rRNAs is actually the final step in its processing. First, the nucleotides of the pre-rRNA sequences destined for the ribosome undergo extensive modification, on both ribose and base components, directed by many small nucleola.r ribonucleo-proteins (snoRNPs), each of which consists of one snoRNA and several proteins. The pre-rRNA is assembled with ribosomal proteins, as guided by... 

Transcription of rRNA and its assembly into precursor-ribosomes can be visualized by electron microscopy. The structures resemble Christmas trees the trunk is the rDNA and each branch is a pre-rRNA transcript. Transcription starts at the top of the tree, where the shortest transcripts can be seen, and progresses down the rDNA to the end of the gene. The terminal knobs visible at the end of some pre-rRNA transcripts likely correspond to the SSU processome. a large ribonucleoprotein required for processing the pre-rRNA. 

A large precursor pre-rRNA (45S in humans) synthesized by RNA polymerase I undergoes cleavage, exonucle-... 

EXAMPLE 7.17 Ribosomal RNA in eukaryotes is actually four separate RNA species 28S RNA, 18S RNA, 5.8S RNA, and 5S RNA. (The S notation is related to how fast a molecule sediments in an analytical ultracentrifuge cell.) The larger the number, the faster the sedimentation rate. A globular protein of 100 kDa has an S value of 6S, but note that the relationship between size and S value is a sublinear one see Chap. 4. The 28S, 18S, and 5.8S rRNAs are transcribed as long precursor pre-rRNAs of size 45S. 

Prokaryotic and eukaryotic RNA transcriptions show strong parallels though there are several important differences. A major distinction between prokaryotes and eukaryotes is the move from one prokaryotic enzyme that can faithfully transcribe DNA into RNA to three eukaryotic RNA polymerases. The eukaryotic RNA transcripts are precursors (e.g. pre-mRNA, pre-rRNA and pre-tRNA), which undergo processing to form respective mature RNAs. Furthermore, eukaryotic mRNAs are polyadenylated. A database for mammalian mRNA polyadenylation is available at PolyA DB (http // polya.umdnj.edu/polyadb). The eukaryotic transcription is tightly regulated and various proteins/factors known as transcription factors (TF) are involved in the eukaryotic transcription. The classification of transcription factors can be found at TRANFAC (http //transfac.gbf.de/TRANFAC/cl/cl.html). 

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. 

Transfer RNAs are transcribed as a cluster in a precursor form. The pre-tRNA usually contains rRNAs as well. All (eukaryotic and prokaryotic) pre-tRNA transcripts are processed to mature 5 termini by RNase P. [Note Mito-... 

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