Transcription of rRNA
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Transcription of rRNA
rRNA (Ribosomal RNA) is the central component of the Ribosome, the protein manufacturing machinery of all living cells. The rRNA is synthesized in the nucleolus. These machines then self-assemble into the two complex folded structures (the large 60S and the small 40S subunits) in the presence of 70 - 80 rProteins (Ribosomal Proteins). The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids (at center of small ribosomal subunit) and to interact with the tRNAs during translation by providing peptidyl transferase activity (large subunit). Accuracy of translation is provided by both subunits. In Bacteria, Archaea, Mitochondria, and Chloroplasts a small ribosomal subunit contains the 16S rRNA, where the S in 16S represents Svedberg units; the large ribosomal subunit contains two rRNA species (the 5S and 23S rRNAs). Bacterial 16S, 23S, and 5S rRNA genes are typically organized as a co-transcribed operon. Eukaryotes generally have many copies of the rRNA genes organized in tandem repeats; in humans approximately 300-400 rDNA repeats are present in five clusters (on chromosomes 13, 14, 15, 21 and 22). The 18S rRNA in most eukaryotes is in the small ribosomal subunit i.e 40S, and the large subunit i.e 60S, contains three rRNAs (the 5S, 5.8S and 28S rRNAs) (Ref.1 & 2).

rRNAs are generally transcribed by RNA Pol-I (RNA Polymerase-I) except 5S rRNA, which is transcribed by RNA Pol-III (RNA Polymerase-III)). Many transcription units for rRNAs are arranged in tandem arrays. They are localized in a structure called NOR (Nucleolar Organizer Region). There nucleolus forms, where most of the ribosome biogenesis takes place: Transcription of rRNA genes, processing of the transcripts to mature rRNAs and assembly with proteins to form both ribosome subunits. The promoter for rRNA synthesis consists of atleast 2 elements, a GC rich UCE (Upstream Control Element) and a Core Region at the transcription start site. Both elements are recognized by the UBF  (Upstream Binding Factor), which causes sharp bends to the DNA. TFIB (Transcription Factor-IB) binds to the Core region leading to the Pre-Initiation Complex. In Humans, TFIB includes SL1 (Selectivity Factor-1), consisting of TBP  (TATA-Binding Protein) and 3 TAF1  (TBP-Associated Factors) with molecular weights of 110, 63, and 48 kDa. Once both factors are bound, RNA Pol-I and TFIC (Transcription Factor-IC) binds to the core promoter forming the Initiation Complex (Ref.3 & 4).

The second step in the process of Transcription is Elongation.  This step involves the actual transcription of the majority of the gene into a corresponding RNA sequence, highly moderated by several methods. Elongation proceeds upon binding of DNA TopI (Topoisomerase-I) to the Initiation Complex. Eukaryotic transcription units for ribosomal genes carry short DNA sequences at their 3’ ends which contain a SalI site (Sal-Box) and cause termination of transcription. TTF1;(Transcription Termination Factor, RNA Polymerase-I) protein binds to this region as a monomer and causes DNA bending. Terminator sites for RNA Pol-I function only in one orientation. Termination is the final step in rRNA transcription i.e; it causes the cessation of RNA transcription and the disassembly of the RNA Pol-I complex. After termination, the 80S RNP (Ribonucleoprotein) precursor is formed, which contains a 5’ leader sequence and an 18, 5.8 and 28S rRNAs separated by spacer RNAs. It is processed by cleavage of the 5’ leader, splicing and nucleolytic degradation of the spacer RNA. As in mRNA, splicing is directed by snRNPs (small nuclear Ribonucleoproteins). This leads to 20S (containing 18SrRNA) and 32S intermediates (containing 5.8 and 28S rRNAs) which are further processed to yield mature 28, 18 and 5.8S rRNAs. Post transcriptional modification of the nucleotides results in methylation of about 100 nucleotides per ribosome at the 2’OH of ribose and isomerization of more than 100 uridine residues per ribosome to pseudo-uridine. The rRNAs are complexed with ribosomal proteins in a self-organizing mode, forming both the large and small ribosomal subunits which are then separately transported to the cytoplasm, to take part in protein synthesis (Ref.5, 6 & 7).

Unlike all other rRNAs, 5S rRNA is transcribed by RNA Pol-III. 5S rRNA is a short (120nt) molecule, which is highly conserved in sequence and structure (5 stem loops). It is transcribed from a group of tandemly arranged genes outside of the nucleolus. The procedure is similar to tRNA transcription, starting with binding of TFIIIA (Transcription Factor for polymerase IIIA) to the intragenic (lying within the transcribed DNA sequence) 5S rRNA control sequence, the C Block (also termed box C). TFIIIA Binding is then followed by TFIIIB (Transcription Factor for polymerase IIIB)  and TFIIIC (Transcription Factor for polymerase IIIC) binding. TFIIIA Serves as a platform that replaces the A and B Blocks for positioning TFIIIC in an orientation with respect to the start site of transcription that is equivalent to that for tRNA genes. Once TFIIIC is bound to the TFIIIA-DNA complex, the assembly of TFIIIB proceeds. TFIIIC causes correct positioning of TFIIIB (Pre-Initiation Complex), which then recruits RNA Pol-III. This DNA/TFIIIB (General Transcription Factor-IIIB) / RNA Pol-III initiation Complex is very stable and may pass through many rounds of tRNA transcription. TFIIIB is made up of three subunits. One is TBP  (TATA-Binding Protein), which is a subunit of a general initiation factor for all three nuclear RNA Polymerases. The second, called BRF (TFIIB-Related Factor) is similar in sequence to TFIIB, and performs a similar function in initiation by RNA Polymerase-III as TFIIB  does for RNA Polymerase-II. The third subunit of TFIIIB is a 90-kDa polypeptide called B". Once TFIIIB has bound, then RNA Pol-III can bind and initiate transcription in the presence of ribonucleoside triphosphates (Ref.8, 9 & 10). Transcription and elongation start immediately after assembly of the Initiation Complex. RNA Pol-III moves along the DNA and matches the DNA nucleotides with a complementary RNA nucleotide to create a new RNA molecule that is patterned after the DNA. The copying of the DNA continues until the RNA Pol-III reaches a termination signal, which is a specific set of nucleotides that mark the end of the gene to be copied and also signals the disconnecting of the DNA with the newly minted RNA. The primary transcript formed after elongation and termination, undergoes only minor processing, e.g removal of 10-50 nucleotides from the 3’end. Surplus 5S RNA is degraded in the nucleus. Ribosomal RNA characteristics are important in medicine and in evolution. rRNA is the target of several clinically relevant antibiotics: Chloramphenicol, Erythromycin, Kasugamycin, Micrococcin, Paromomycin, Ricin, Sarcin, Spectinomycin, Streptomycin, and Thiostrepton.  rRNA is the most conserved (least variable) gene in all cells. For this reason, genes that encode the rRNA (rDNA) are sequenced to identify an organisms taxonomic group, calculate related groups, and estimate rates of species divergence (Ref.1, 2 & 11).