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Ribosomal RNA

Three-dimensional views of the ribosome, showing rRNA in dark blue (small subunit) and dark red (large subunit). Lighter colors represent ribosomal proteins.

Ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome, which is essential for protein synthesis in all living organisms. rRNA is the predominant RNA in most cells, composing around 80% of cellular RNA. Ribosomes are approximately 60% rRNA and 40% protein by weight. A ribosome contains two subunits, the large ribosomal subunit (LSU) and small ribosomal subunit (SSU).

Prokaryotic ribosomes contain three rRNAs, which are the 23S and 5S rRNAs in the LSU and the 16S rRNA in the SSU. The prokaryotic ribosome contains around 50 ribosomal proteins.

Eukaryotic ribosomes and rRNAs are larger and more polymorphic than those of prokaryotes. In yeast, the LSU contains the 5S, 5.8S and 28S rRNAs. The combined 5.8S and 28S are roughly equivalent to the prokaryotic 23S rRNA, except for expansion segments (ESs) that are localized to the surface of the ribosome. The SSU contains the 18S rRNA, which also contains ESs. SSU ESs are generally smaller than LSU ESs.

The LSU rRNA has been called a ribozyme, because ribosomal protein does not penetrate into the catalytic site of the ribosome (the peptidyl transferase center, PTC). However, rRNA has not been shown to be catalytic in the absence of proteins. The SSU rRNA decodes the mRNA in the decoding center (DC). Ribosomal proteins do not penetrate into the DC.

SSU and LSU rRNA sequences are widely used for working out evolutionary relationships among organisms, since they are of ancient origin, are found in all known forms of life, and are resistant to horizontal gene transfer. The canonical tree of life is the lineage of the translation system.

Structure

During translation, tRNA is sandwiched between the small and large ribosomal subunits. In the SSU, the mRNA interacts with the anticodons of the tRNA. In the LSU, the amino acid acceptor stem of the tRNA interacts with the LSU rRNA. The ribosome catalyzes ester-amide exchange, transferring the C-terminus of a nascent peptide from a tRNA to the amino group of an amino acid.

A ribosome has three tRNA binding sites called the A, P, and E sites.

  • The A site contains an aminoacyl-tRNA (a tRNA esterified to an amino acid on the 3' end).
  • The P site contains a tRNA esterified to the nascent peptide. The free amino (NH2) group of the A site tRNA attacks the ester linkage of P site tRNA, causing transfer of the nascent peptide to the amino acid in the A site. This reaction is takes place in the peptidyl transferase center.
  • The E site contains a tRNA that has been discharged, with a free 3' end (with no amino acid or nascent peptide).

A single mRNA can be translated simultaneously by multiple ribosomes.

Subunits and ribosomal RNA genes

Both prokaryotic and eukaryotic ribosomes can be broken down into two subunits (the S in 16S represents Svedberg units), nt= length in nucleotides of the respective rRNAs, for exemplary species Escherichia coli (prokaryote) and human (eukaryote):

Type Size Large subunit (LSU rRNA) Small subunit (SSU rRNA)
prokaryotic 70S 50S (5S : 120 nt, 23S : 2906 nt) 30S (16S : 1542 nt)
eukaryotic 80S 60S (5S : 121 nt,[1] 5.8S : 156 nt,[2] 28S : 5070 nt[3]) 40S (18S : 1869 nt[4])

Note that the S units of the subunits (or the rRNAs) cannot simply be added because they represent measures of sedimentation rate rather than of mass. The sedimentation rate of each subunit is affected by its shape, as well as by its mass. The nt units can be added as these represent the integer number of units in the linear rRNA polymers (for example, the total length of the human rRNA = 7216 nt).

In prokaryotes

In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA. The large 50S ribosomal subunit contains two rRNA species (the 5S and 23S ribosomal RNAs).

Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed operon. There is an internal transcribed spacer between 16S and 23S rRNA genes.[5] There may be one or more copies of the operon dispersed in the genome (for example, Escherichia coli has seven).

Archaea contains either a single rDNA operon or multiple copies of the operon.

The 3' end of the 16S ribosomal RNA (in a ribosome) recognizes a sequence on the 5' end of mRNA called the Shine-Dalgarno sequence.

In eukaryotes

Small subunit ribosomal RNA, 5' domain taken from the Rfam database. This example is RF00177

In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats. In humans, approximately 300–400 repeats are present in five clusters, located on chromosomes 13 (RNR1), 14 (RNR2), 15 (RNR3), 21 (RNR4) and 22 (RNR5). Sequence variation in rRNA has been observed both within and between human individuals and certain variants are expressed in a tissue-specific manner in mice.[6] Because of their special structure and transcription behaviour, rRNA gene clusters are commonly called "ribosomal DNA" (note that the term seems to imply that ribosomes contain DNA, which is not the case).

The 18S rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the 5S, 5.8S and 28S in mammals, 25S in plants, rRNAs).

Mammalian cells have 2 mitochondrial (12S and 16S) rRNA molecules and 4 types of cytoplasmic rRNA (the 28S, 5.8S, 18S, and 5S subunits). The 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by 2 internally transcribed spacers. One of them corresponds to the one found in bacteria and archaea, and the other is an insertion into what was the 23S rRNA in prokaryotes.[5] The 45S rDNA is organized into 5 clusters (each has 30–40 repeats) on chromosomes 13, 14, 15, 21, and 22. These are transcribed by RNA polymerase I. 5S occurs in tandem arrays (~200–300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is transcribed by RNA polymerase III.

The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography.[7] The secondary structure of SSU rRNA contains 4 distinct domains—the 5', central, 3' major and 3' minor domains. A model of the secondary structure for the 5' domain (500-800 nucleotides) is shown.

Transcription

In prokaryotes

In prokaryotic cells, each rRNA gene or operon is transcribed into a single RNA precursor that includes 16S, 23S, 5S rRNA and tRNA sequences along with transcribed spacers. The RNA processing then begins before the transcription is complete. During processing reactions, the rRNAs and tRNAs are released as separate molecules.[8]

In eukaryotes

The genes coding for 18S, 28S and 5.8S rRNA, located in the nucleolus organizer region, are transcribed into a large pre-rRNA molecule by RNA polymerase I.[9][10] Each large pre-rRNA contains 18S, 28S and 5.8S sequences which are separated by external and internal transcribed spacer sequences. During processing reactions, the 18S, 28S and 5.8S rRNA are released as individual molecules. Processing reactions involve exo- and endo-nucleolytic cleavages guided by snoRNA (small nucleolar RNAs) in complex with proteins. The genes for 5S rRNA are located inside the nucleolus and are transcribed into pre-5S rRNA by RNA polymerase III.[11] The pre-5S rRNA enters the nucleolus for processing and assembly with 28S and 5.8S rRNA to form the large subunit. 18S rRNA forms the small ribosomal subunits by combining with ribosomal proteins.[12][8]

Translation

Translation is the net effect of proteins being synthesized by ribosomes, from a copy (mRNA) of the DNA template in the nucleus. One of the components of the ribosome (16S rRNA) base pairs complementary to a Shine–Dalgarno sequence upstream of the start codon in mRNA.

Importance

Ribosomal RNA characteristics are important in evolution, thus taxonomy, and medicine.

Genes coding for ribosomal proteins

These denote genes encoding for the proteins of the ribosome and are transcribed as mRNA, not rRNA.

See also

References

  1. ^ "Homo sapiens 5S ribosomal RNA".
  2. ^ "Homo sapiens 5.8S ribosomal RNA".
  3. ^ "Homo sapiens 28S ribosomal RNA".
  4. ^ "Homo sapiens 18S ribosomal RNA".
  5. ^ a b Lafontaine DL, Tollervey D (July 2001). "The function and synthesis of ribosomes". Nature Reviews. Molecular Cell Biology. 2 (7): 514–20. doi:10.1038/35080045. PMID 11433365.
  6. ^ Parks MM, Kurylo CM, Dass RA, Bojmar L, Lyden D, Vincent CT, Blanchard SC (February 2018). "Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression". Science Advances. 4 (2): eaao0665. doi:10.1126/sciadv.aao0665. PMC 5829973. PMID 29503865.
  7. ^ Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF (May 2001). "Crystal structure of the ribosome at 5.5 A resolution". Science. 292 (5518): 883–96. doi:10.1126/science.1060089. PMID 11283358.
  8. ^ a b Wolfe, Stephen (1993). Molecular and Cellular Biology. ISBN 978-0534124083.
  9. ^ Fernández-Tornero, Carlos; Moreno-Morcillo, María; Rashid, Umar J.; Taylor, Nicholas M. I.; Ruiz, Federico M.; Gruene, Tim; Legrand, Pierre; Steuerwald, Ulrich; Müller, Christoph W. (October 2013). "Crystal structure of the 14-subunit RNA polymerase I". Nature. 502 (7473): 644–649. doi:10.1038/nature12636. ISSN 0028-0836.
  10. ^ Engel, Christoph; Sainsbury, Sarah; Cheung, Alan C.; Kostrewa, Dirk; Cramer, Patrick (October 2013). "RNA polymerase I structure and transcription regulation". Nature. 502 (7473): 650–655. doi:10.1038/nature12712. ISSN 0028-0836.
  11. ^ Thompson M, Haeusler RA, Good PD, Engelke DR (November 2003). "Nucleolar clustering of dispersed tRNA genes". Science. 302 (5649): 1399–401. doi:10.1126/science.1089814. PMC 3783965. PMID 14631041.
  12. ^ "rRNA synthesis and processing".
  13. ^ Smit S, Widmann J, Knight R (2007). "Evolutionary rates vary among rRNA structural elements". Nucleic Acids Research. 35 (10): 3339–54. doi:10.1093/nar/gkm101. PMC 1904297. PMID 17468501.
  14. ^ Meyer A, Todt C, Mikkelsen NT, Lieb B (March 2010). "Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity". BMC Evolutionary Biology. 10 (1): 70. doi:10.1186/1471-2148-10-70. PMC 2841657. PMID 20214780.
  15. ^ Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (January 2003). "The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy". Nucleic Acids Research. 31 (1): 442–3. doi:10.1093/nar/gkg039. PMC 165486. PMID 12520046.
  16. ^ Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO (2007). "SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB". Nucleic Acids Research. 35 (21): 7188–96. doi:10.1093/nar/gkm864. PMC 2175337. PMID 17947321.
  17. ^ The atypical mechanosensitive microRNA-712 derived from pre-ribosomal RNA induces endothelial inflammation and atherosclerosis Nature Communications, 2013 doi:10.1038/ncomms4000

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