Preribosomal RNA

Preribosomal RNA (pre-rRNA) represents a small class of RNA that is copied from DNA representing the genome sequence. However the pre-rRNA cannot be used for protein production until splicing of the introns occurs, forming a new bond between the exons and resulting in mature ribosomal RNA (rRNA).

Overview

During or immediately following transcription of pre-rRNA from rDNA in the nucleolus, the ribosomal RNA precursor (pre-rRNA) is modified and associates with a few ribosomal proteins.[1] Small nucleolar RNAs (snoRNA) dictate the modifications, by base-pairing with target sites in eukaryotic pre-rRNA and may also play a role in pre-rRNA folding. Pre-rRNA contains external transcribed spacers (5'-ETS, 3'-ETS) at both ends as well as internal transcribed spacers (ITS1, ITS2). Cleavages at sites A’ and T1 remove the 5’-ETS and 3’-ETS, respectively. Cleavages at sites A0, 1 and 2 give rise to 18S rRNA. Site 3 cleavage can take place before or after cleavage at sites A0, 1, and 2 and may be responsible for the linkage between 18S and 28S rRNA processing pathways. The last steps of rRNA processing require cleavages at 3, 4’, 4 and 5 in order to generate mature 5.8S and 28S rRNA.

Modifications

Research suggests that either simultaneous to or immediately following synthesis of pre-rRNA, internal modifications are made at regions in the rRNA components, 18S, 5.8S, and 28S, which vary depending on cell type. Xenopus pre-rRNA modifications include ten base methylations, 105 2’-O-methylations of ribose and around 100 pseudouridines while yeast rRNA has merely half of these modifications.[2] Small nucleolar RNA base-pairs with the pre-rRNA and determines the site of modifications. Individual snoRNA families perform different modifications. Box C/D snoRNA guides the formation of 2’-O-Me, while Box H/ACA snoRNA guide the pseudouridines formation. There is thought that the base-pairing of snoRNA to pre-rRNA acts as a chaperone in the folding of mature rRNA.

Ribosomal proteins

Pre-rRNA comprise three main sizes; 37S (yeast), 40S (Xenopus) and 45S (mammals). In a series of steps, nearly 80 ribosomal proteins assemble with the pre-rRNA. During transcription of pre-rRNA, early ribosomal binding proteins associate.[3] It is thought that this 30S RNP containing 45S pre-rRNA is the precursor for 80S RNP, which in turn, is the precursor to 55S RNP. 55S RNP makes up ~75% of the nucleolar population of pre-ribosomes.[4]

Ribosomal RNA processing

To form mature rRNA 18S, 5.8S, and 28S, pre-rRNA 40S (Xenopus) and 45S (mammals) must go through a series of cleavages to remove the external and internal spacers (ETS/ITS). This can be done in one of two pathways. Pathway 1 begins by cleavage at site 3, which separates the 5.8S and 28S rRNA coding regions in 32S pre-RNA from the 18S rRNA coding region in 20S pre-rRNA. Pathway 2 cleaves at sites A0, 1, and 2 initially, before cleaving at site 3.[5]

U3 snoRNA

U3 snoRNA, the most abundant snoRNA required for rRNA processing, influences the pathway chosen.[6] It associates with pre-rRNA through protein-protein interactions as well as base-pairing. To allow the U3 to function properly, base-pairing between the 3’ hinge region of U3 and complementary sequences in the 5’-ETS is required. However, pairing between the 5’-hinge of U3 and 5’-ETS may occur but is not necessary for function.[7] Nucleolin, an abundant phosphoprotein, binds to the pre-rRNA immediately after transcription and facilitates the base-pairing between the U3 snoRNA hinges and the ETS.[8]

Site A’ and T1 cleavage

The area where 5’-ETS is cross-linked to U3 is known as site A’, and is sometimes cleaved in a primary processing event in mammalian pre-rRNA. The cleavage of this site is dependent on U3, U14, E1 and E3 snoRNAs, and although this cleavage is not a prerequisite for the processing of pre-rRNA, the docking of snoRNP is crucial for 18S rRNA production. Shortly after the A’ cleavage, the 3’-ETS is cleaved at site T1 by U8 snoRNA.

Site A0, 1, and 2 cleavage

Subsequent cleaving at sites A0, 1, and 2 requires U3 snoRNA, U14 snoRNA snR30 and snR10 in yeast as well as U22 snoRNA in Xenopus. The cleavage of these sites is coordinated to result in a mature 18S rRNA. A0 cleavage requires Box A of U3 snoRNA.[9] If Box A of U3 is mutated, A0 cleavage is inhibited and while 20S pre-rRNA accumulates it is not processed into 19S rRNA and cleavage at sites and 2 are also inhibited, which suggests that cleavage at A0 precedes that of sites 1 and 2. The mechanism for the cleavage of site 1 is not yet known however the position of U3 Box A near site 1 helps to prove that Box A is once again needed for site A1 cleavage.[10] However site 2 requires the 3’-end of BoxA’ and U3 snoRNA for cleavage. Once site 2 is cleaved, 18S rRNA is liberated from the pre-rRNA.

Site 3 cleavage

Whereas U3 snoRNA is required for 18S rRNA formation, U8 snoRNA is required for 5.8S and 28S rRNA formation.[11] The cleavage occurs at site 3, which is near the end of ITS1 and subsequently forms 32S pre-rRNA, a long-lived intermediate. Cleavage at site 4’, within ITS2, produces a precursor of 5.8S RNA that is longer at its 3’-end. To trim the 3’-end, cleavage must occur at sites 4 and 5. It is hypothesized that site 3 may serve as a link between 18S and 28S rRNA processing pathways in higher organisms.[12]

Different types

Pre-rRNA in all of biological kingdoms show similarities and differences. Eubacteria contain 16S and 23S rRNA that reside at the top of long base-paired stems that serve as the site for processing of RNase III cleavage.[13] These two stems are also found in pre-rRNA from archaebacteria, however they do not exist in Xenopus pre-rRNA. It is thought that while base-pairing occurs in all types of pre-rRNA, they occur in cis in eubacterial pre-rRNA, whereas in eukaryotes it occurs in trans between snoRNAs and the termini of the rRNA coding regions in pre-rRNA. It is not fully clear why all three kingdoms possess pre-rRNA, rather than directly transcribing mature forms of rRNA, but it is believed that the transcribed spaces in the pre-rRNA may have some type of role in the proper folding of rRNA.

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References
  1. Marmier-Gourrier N, Cle´ry A, Schlotter F, Branlant C. A second base pair interaction between U3 small nucleolar RNA and the 5’-ETS region is required for early cleavage of the yeast pre-ribosomal RNA. Nucleic Acids Research. 2011; 39.
  2. Gerbi SA, Borovjagin AV. Pre-Ribosomal RNA Processing in Multicellular Organisms. In: Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-.
  3. Chooi WY, Leiby KR. An electron microscopic method for localization of ribosomal proteins during transcription of ribosomal DNA: A method for studying protein assembly. Proc Natl Acad Sci. 1981;78:4823–4827
  4. Hadjiolov AA. The Nucleolus and Ribosome Biogenesis. Vienna: Springer-Verlag KG. 1985 .
  5. Gerbi SA, Borovjagin AV. Pre-Ribosomal RNA Processing in Multicellular Organisms. In: Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-.
  6. Borovjagin AV, Gerbi SA. U3 small nucleolar RNA is essential for cleavage at sites 1, 2, and 3 in pRNA and determines which rRNA processing pathway is taken in Xenopus oocytes. J Mol Biol. 1999;286:1347–1363
  7. Borovjagin AV, Gerbi SA. Xenopus U3 snoRNA docks on pre-rRNA through a novel base-pairing interaction. submitted. 2003
  8. Herrera A, Olson MOJ. Association of protein C23 with rapidly labeled nucleolar RNA. Biochemistry. 1986;25:6258–6264.
  9. Savino R, Hitti Y, Gerbi SA. Genes for Xenopus laevis U3 small nuclear RNA. Nucleic Acids Res. 1992;20:5435–5442.
  10. Marmier-Gourrier N, Cle´ry A, Schlotter F, Branlant C. A second base pair interaction between U3 small nucleolar RNA and the 5’-ETS region is required for early cleavage of the yeast pre-ribosomal RNA. Nucleic Acids Research. 2011; 39.
  11. Marmier-Gourrier N, Cle´ry A, Schlotter F, Branlant C. A second base pair interaction between U3 small nucleolar RNA and the 5’-ETS region is required for early cleavage of the yeast pre-ribosomal RNA. Nucleic Acids Research. 2011; 39.
  12. Gerbi SA, Borovjagin AV. Pre-Ribosomal RNA Processing in Multicellular Organisms. In: Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-.
  13. Gerbi SA, Borovjagin AV. Pre-Ribosomal RNA Processing in Multicellular Organisms. In: Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-.
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