Preribosomal RNA

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Preribosomal RNA (pre-rRNA) is the precursor to mature ribosomal RNA (rRNA), which is a component of ribosomes. Pre-rRNA is first transcribed from ribosomal DNA (rDNA), then cleaved and processed into mature rRNA.

Contents

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.

Related Research Articles

Nucleolus Largest structure in the nucleus of eukaryotic cells

The nucleolus is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis. Nucleoli also participate in the formation of signal recognition particles and play a role in the cell's response to stress. Nucleoli are made of proteins, DNA and RNA and form around specific chromosomal regions called nucleolar organizing regions. Malfunction of nucleoli can be the cause of several human conditions called "nucleolopathies" and the nucleolus is being investigated as a target for cancer chemotherapy.

Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed by either RNA polymerase II or RNA polymerase III. Their primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus. They have also been shown to aid in the regulation of transcription factors or RNA polymerase II, and maintaining the telomeres.

In molecular biology, Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs, which are associated with methylation, and the H/ACA box snoRNAs, which are associated with pseudouridylation. SnoRNAs are commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes.

Ribonuclease III

Ribonuclease III (BRENDA 3.1.26.3) is a type of ribonuclease that recognizes dsRNA and cleaves it at specific targeted locations to transform them into mature RNAs. These enzymes are a group of endoribonucleases that are characterized by their ribonuclease domain, which is labelled the RNase III domain. They are ubiquitous compounds in the cell and play a major role in pathways such as RNA precursor synthesis, RNA Silencing, and the pnp autoregulatory mechanism.

Ribosome biogenesis Cellular process

Ribosome biogenesis is the process of making ribosomes. In prokaryotes, this process takes place in the cytoplasm with the transcription of many ribosome gene operons. In eukaryotes, it takes place both in the cytoplasm and in the nucleolus. It involves the coordinated function of over 200 proteins in the synthesis and processing of the three prokaryotic or four eukaryotic rRNAs, as well as assembly of those rRNAs with the ribosomal proteins. Most of the ribosomal proteins fall into various energy-consuming enzyme families including ATP-dependent RNA helicases, AAA-ATPases, GTPases, and kinases. About 60% of a cell's energy is spent on ribosome production and maintenance.

Shq1

Shq1p is a protein involved in the rRNA processing pathway. It was discovered by Pok Yang in the Chanfreau laboratory at UCLA. Depletion of Shq1p has led to decreased level of various H/ACA box snoRNAs and certain pre-rRNA intermediates.

Small nucleolar RNA U3

In molecular biology, U3 snoRNA is a non-coding RNA found predominantly in the nucleolus. U3 has C/D box motifs that technically make it a member of the box C/D class of snoRNAs; however, unlike other C/D box snoRNAs, it has not been shown to direct 2'-O-methylation of other RNAs. Rather, U3 is thought to guide site-specific cleavage of ribosomal RNA (rRNA) during pre-rRNA processing.

Small nucleolar RNA SNORD14

In molecular biology, U14 small nucleolar RNA is a non-coding RNA required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. In human there are two closely related copies called SNORD14A and SNORD14B that are expressed from the intron of their host gene ribosomal protein Rps13.

Small nucleolar RNA SNORA74

In molecular biology, Small nucleolar RNA SNORA74 (U19) belongs to the H/ACA class of snoRNAs. snoRNAs bind a number of proteins to form snoRNP complexes. This class is thought to guide the sites of modification of uridines to pseudouridines by forming direct base pairing interactions with substrate RNAs. Targets may include ribosomal and spliceosomal RNAs but the exact functions of many snoRNAs, including U19, are not confirmed. Co-precipitation of U19 snoRNA with RNase MRP RNA suggests that U19 may be involved in pre-rRNA processing.

Small nucleolar RNA SNORA75 RNA type

In molecular biology, U23 belongs to the H/ACA class of snoRNAs. snoRNAs bind a number of proteins to form snoRNP complexes. This class are thought to guide the sites of modification of uridines to pseudouridines by forming direct base pairing interactions with substrate RNAs. Targets include ribosomal and spliceosomal RNAs as well as the Trypanosoma spliced leader RNA as possibly other, still unknown cellular RNAs. U23 can direct the pseudouridylation of U97 in human 18S rRNA. U23 is encoded within intron 12 of the nucleolin gene in human, mouse, rat chicken, and Xenopus laevis.

Small nucleolar RNA SNORD15

In molecular biology, SNORD15 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

Small nucleolar RNA SNORD16

In molecular biology, snoRNA U16 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

Small nucleolar RNA SNORD18

In molecular biology, SNORD18 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

Small nucleolar RNA SNORD27

In molecular biology, Small nucleolar RNA SNORD27 is a member of the C/D class of snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs. U27 is encoded within the U22 snoRNA host gene (UHG) in mammals and is thought to act as a 2'-O-ribose methylation guide for ribosomal RNA. This family also contains several related snoRNAs from yeast and plants.

Small nucleolar RNA SNORD62

In molecular biology, snoRNA U62 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

Small nucleolar RNA SNORD63

In molecular biology, snoRNA U63 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

Small nucleolar RNA SNORD73

In molecular biology, snoRNA U73 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

U8 small nucleolar RNA

In molecular biology, U8 small nucleolar RNA is the RNA component of a small RNA:protein complex which is required for biogenesis of mature large subunit ribosomal RNAs, 5.8S and 28S rRNAs.

Fibrillarin Protein-coding gene in the species Homo sapiens

rRNA 2'-O-methyltransferase fibrillarin is an enzyme that in humans is encoded by the FBL gene.

Endoribonuclease XendoU

In molecular biology, Endoribonuclease XendoU refers to a protein domain. This particular entry represents endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. This protein domain belongs to a family of evolutionarily related proteins. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.

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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