Biology:5S ribosomal RNA

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Short description: RNA component of the large subunit of the ribosome
5S ribosomal RNA
RF00001.jpg
Predicted secondary structure and sequence conservation of 5S ribosomal RNA
Identifiers
Symbol5S_rRNA
RfamRF00001 CL00113
Other data
RNA typeGene; rRNA
Domain(s)Eukaryota; Bacteria; Archaea
GO0005840 0003735
SO0000652
PDB structuresPDBe

The 5S ribosomal RNA (5S rRNA) is an approximately 120 nucleotide-long ribosomal RNA molecule with a mass of 40 kDa. It is a structural and functional component of the large subunit of the ribosome in all domains of life (bacteria, archaea, and eukaryotes), with the exception of mitochondrial ribosomes of fungi and animals. The designation 5S refers to the molecule's sedimentation velocity in an ultracentrifuge, which is measured in Svedberg units (S).[1]

Figure 1: A 3D representation of a 5S rRNA molecule. This structure is of the 5S rRNA from the Escherichia coli 50S ribosomal subunit and is based on a cryo-electron microscopic reconstruction.[2]

Biosynthesis

In prokaryotes, the 5S rRNA gene is typically located in the rRNA operons downstream of the small and the large subunit rRNA, and co-transcribed into a polycistronic precursor.[3] A particularity of eukaryotic nuclear genomes is the occurrence of multiple 5S rRNA gene copies (5S rDNA) clustered in tandem repeats, with copy number varying from species to species.[4][5] Eukaryotic 5S rRNA is synthesized by RNA polymerase III, whereas other eukaryotic rRNAs are cleaved from a 45S precursor transcribed by RNA polymerase I. In Xenopus oocytes, it has been shown that fingers 4–7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA.[6][7] Binding between 5S rRNA and TFIIIA serves to both repress further transcription of the 5S RNA gene and stabilize the 5S RNA transcript until it is required for ribosome assembly.[8]

Structure

The secondary structure of 5S rRNA consists of five helices (denoted I-V in roman numerals), four loops (B-E), and one hinge (A), which form together a Y-like structure. Loops C and D are terminal hairpins and loops B and E are internal.[4] According to phylogenetic studies, helices I and III are likely ancestral.[9] Helix III includes two highly conserved adenosines.[10] Helix V, with its hairpin structure, is thought to interact with TFIIIA.[4]

Location within the ribosome

Figure 2: Atomic 3D structure of the 50S subunit from Haloarcula marismortui, PDB 1FFK. Proteins are shown in blue, 23S rRNA in orange and 5S rRNA in yellow.[11] 5S rRNA together with the ribosomal proteins L5 and L18 and the domain V of 23S rRNA constitute the bulk of the central protuberance (CP).

Using a variety of molecular techniques, including immuno-electron microscopy, cryo-electron microscopy, intermolecular chemical cross-linking, and X-ray crystallography, the location of the 5S rRNA within the large ribosomal subunit has been determined to great precision. In bacteria and archaea, the large ribosomal subunit (LSU) itself is composed of two RNA moieties, the 5S rRNA and another larger RNA known as 23S rRNA, along with numerous associated proteins.[3][12]

In eukaryotes, the LSU contains 5S, 5.8S, and 28S rRNAs and even more proteins.[13][14] The structure of LSU in 3-dimensions shows one relatively smooth surface and the opposite surface having three projections, notably the L1 protuberance, the central protuberance (CP), and the L7/L12 stalk. The L1 protuberance and L7/L12 stalk are arranged laterally surrounding CP. The 5S rRNA is located in the CP and participates in formation and structure of this projection. The other major constituents of the central protuberance include the 23S rRNA (or alternatively 28S in eukaryotes) and several proteins including L5, L18, L25, and L27.[15]

Ribosomal functions

The exact function of 5S rRNA is not yet clear. In Escherichia coli, 5S rRNA gene deletions reduce the protein synthesis rate and have a more profound detrimental effect on cell fitness than deletions of a comparable number of copies of other (16S and 23S) rRNA genes.[16] Crystallographic studies indicate that 5S rRNA-binding proteins and other proteins of the central protuberance of the LSU plays a role in binding tRNAs.[15] Also, the topographical and physical proximity between 5S rRNA and 23S rRNA, which forms the peptidyl transferase and GTPase-associating center, suggests that 5S rRNA acts as a mediator between the two functional centers of the ribosome by forming, together with 5S rRNA-binding proteins and other components of the central protuberance, intersubunit bridges and tRNA-binding sites.[15]

Roles in ribosomal assembly

In eukaryotes, the cytosolic ribosome is assembled from four rRNAs and over 80 proteins.[14][17] Once transcribed, the 3' ends of 5S rRNA can only be trimmed to mature length by functional homologues of RNase T, for example Rex1p in Saccharomyces cerevisiae.[18] The 60S and 40S ribosomal subunits are exported from the nucleus to the cytoplasm where they join to form the mature and translation-competent 80S ribosome. When exactly 5S rRNA is integrated into the ribosome remains controversial,[4] but it is generally accepted that 5S rRNA is incorporated into the 90S particle, which is a precursor to 60S particle, as part of a small ribosome-independent RNP complex formed by 5S rRNA and ribosomal protein L5.[17]

Interactions with proteins

Several important proteins which interact with 5S rRNA are listed below.

La protein

Interaction of 5S rRNA with the La protein prevents the RNA from degradation by exonucleases in the cell.[19] La protein is found in the nucleus in all eukaryotic organisms and associates with several types of RNAs transcribed by RNA pol III. La protein interacts with these RNAs (including the 5S rRNA) through their 3' oligo-uridine tract, aiding stability and folding of the RNA.[4][20]

L5 protein

In eukaryotic cells, ribosomal protein L5 associates and stabilizes the 5S rRNA forming a pre-ribosomal ribonucleoprotein particle (RNP) that is found in both cytosol and the nucleus. L5 deficiency prevents transport of 5S rRNA to the nucleus and results in decreased ribosomal assembly.[4]

Other ribosomal proteins

In prokaryotes the 5S rRNA binds to the L5, L18 and L25 ribosomal proteins, whereas in eukaryotes 5S rRNA is only known to bind the L5 ribosomal protein.[21] In T. brucei, the causative agent of sleeping sickness, 5S rRNA interacts with two closely related RNA-binding proteins, P34 and P37, whose loss results in a lower global level of 5S rRNA.[4]

Presence in organelle ribosomes

Permuted mitochondrial genome encoded 5S rRNA
Identifiers
SymbolmtPerm-5S
RfamRF02547 CL00113
Other data
RNA typeGene; rRNA
Domain(s)Eukaryota;
GO0005840 0003735
SO0000652
PDB structuresPDBe

File:Consensus secondary structure models of 5S rRNAs.tiff

Translation machineries of mitochondria and plastids (organelles of endosymbiotic bacterial origin), and their bacterial relatives share many features but also display marked differences. Organelle genomes encode SSU and LSU rRNAs without exception, yet the distribution of 5S rRNA genes (rrn5) is most uneven. Rrn5 is easily identified and common in genomes of most plastids. In contrast, mitochondrial rrn5 initially appeared to be restricted to plants and a small number of protists.[22][23] Additional, more divergent organellar 5S rRNAs were only identified with specialized covariance models that incorporate information on the pronounced sequence composition bias and structural variation.[24] This analysis pinpointed additional 5S rRNA genes not only in mitochondrial genomes of most protist lineages, but also in genomes of certain apicoplasts (non-photosynthetic plastids of pathogenic protozoa such as Toxoplasma gondii and Eimeria tenella).

File:5S-rRNA-topologies.tiff

Mitochondrial 5S rRNAs of most stramenopiles comprise the largest diversity of secondary structures.[24] The permuted mitochondrial 5S rRNAs in brown algae represent the most unconventional case, where the closing helix I, which otherwise brings together the molecule's 5′ and 3′ ends, is replaced by a (closed) hairpin resulting in an open three-way junction.

Current evidence indicates that mitochondrial DNA of only a few groups, notably animals, fungi, alveolates and euglenozoans lacks the gene.[24] The central protuberance, otherwise occupied by 5S rRNA and its associated proteins (see Figure 2), was remodeled in various ways. In the fungal mitochondrial ribosomes, 5S rRNA is replaced by LSU rRNA expansion sequences.[25] In kinetoplastids (euglenozoans), the central protuberance is made entirely of evolutionarily novel mitochondrial ribosomal proteins.[26] Lastly, animal mitochondrial ribosomes have coopted a specific mitochondrial tRNA (Val in vertebrates) to substitute the missing 5S rRNA.[27][28]

See also

References

  1. ↑ "5S Ribosomal RNA Database". Nucleic Acids Research 30 (1): 176–178. January 2002. doi:10.1093/nar/30.1.176. PMID 11752286. 
  2. ↑ "The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution". Journal of Molecular Biology 298 (1): 35–59. April 2000. doi:10.1006/jmbi.2000.3635. PMID 10756104. 
  3. ↑ 3.0 3.1 "Ribosome biogenesis and the translation process in Escherichia coli". Microbiology and Molecular Biology Reviews 71 (3): 477–494. September 2007. doi:10.1128/MMBR.00013-07. PMID 17804668. 
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 "Eukaryotic 5S rRNA biogenesis". Wiley Interdisciplinary Reviews. RNA 2 (4): 523–533. 2011. doi:10.1002/wrna.74. PMID 21957041. 
  5. ↑ "Transcription of the 5S rRNA heterochromatic genes is epigenetically controlled in Arabidopsis thaliana and Xenopus laevis". Heredity 99 (1): 5–13. July 2007. doi:10.1038/sj.hdy.6800964. PMID 17487217. 
  6. ↑ "Interaction of the RNA binding fingers of Xenopus transcription factor IIIA with specific regions of 5 S ribosomal RNA". Journal of Molecular Biology 248 (1): 44–57. April 1995. doi:10.1006/jmbi.1995.0201. PMID 7731045. 
  7. ↑ "The role of the central zinc fingers of transcription factor IIIA in binding to 5 S RNA". Journal of Molecular Biology 301 (1): 47–60. August 2000. doi:10.1006/jmbi.2000.3946. PMID 10926492. 
  8. ↑ "A specific transcription factor that can bind either the 5S RNA gene or 5S RNA". Proceedings of the National Academy of Sciences of the United States of America 77 (7): 4170–4174. July 1980. doi:10.1073/pnas.77.7.4170. PMID 7001457. Bibcode: 1980PNAS...77.4170P. 
  9. ↑ "The evolutionary history of the structure of 5S ribosomal RNA". Journal of Molecular Evolution 69 (5): 430–443. November 2009. doi:10.1007/s00239-009-9264-z. PMID 19639237. Bibcode: 2009JMolE..69..430S. 
  10. ↑ "A role for aromatic amino acids in the binding of Xenopus ribosomal protein L5 to 5S rRNA". Biochemistry 40 (42): 12645–12653. October 2001. doi:10.1021/bi011439m. PMID 11601989. 
  11. ↑ "The complete atomic structure of the large ribosomal subunit at 2.4 A resolution". Science 289 (5481): 905–920. August 2000. doi:10.1126/science.289.5481.905. PMID 10937989. Bibcode: 2000Sci...289..905B. 
  12. ↑ "Cryo-electron microscopy visualization of a large insertion in the 5S ribosomal RNA of the extremely halophilic archaeon Halococcus morrhuae". FEBS Open Bio 10 (10): 1938–1946. October 2020. doi:10.1002/2211-5463.12962. PMID 32865340. 
  13. ↑ "Cotranscriptional events in eukaryotic ribosome synthesis". Wiley Interdisciplinary Reviews. RNA 6 (1): 129–139. 2015. doi:10.1002/wrna.1263. PMID 25176256. 
  14. ↑ 14.0 14.1 "High-resolution structure of the eukaryotic 80S ribosome". Annual Review of Biochemistry 83: 467–486. February 2014. doi:10.1146/annurev-biochem-060713-035445. PMID 24580643. 
  15. ↑ 15.0 15.1 15.2 "5S rRNA and ribosome". Biochemistry. Biokhimiia 76 (13): 1450–1464. December 2011. doi:10.1134/S0006297911130062. PMID 22339598. 
  16. ↑ "5S rRNA gene deletions cause an unexpectedly high fitness loss in Escherichia coli". Nucleic Acids Research 27 (2): 637–642. January 1999. doi:10.1093/nar/27.2.637. PMID 9862991. 
  17. ↑ 17.0 17.1 "The post-transcriptional steps of eukaryotic ribosome biogenesis". Cellular and Molecular Life Sciences 65 (15): 2334–2359. August 2008. doi:10.1007/s00018-008-8027-0. PMID 18408888. 
  18. ↑ "Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast". The EMBO Journal 19 (6): 1357–1365. March 2000. doi:10.1093/emboj/19.6.1357. PMID 10716935. 
  19. ↑ "The La protein". Annual Review of Biochemistry 71: 375–403. 2002. doi:10.1146/annurev.biochem.71.090501.150003. PMID 12045101. 
  20. ↑ "La protein and its associated small nuclear and nucleolar precursor RNAs". Gene Expression 10 (1–2): 41–57. 2002. PMID 11868987. 
  21. ↑ "The ribosome at atomic resolution". Biochemistry 40 (11): 3243–3250. March 2001. doi:10.1021/bi0029402. PMID 11258942. 
  22. ↑ "Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA". RNA 9 (3): 287–292. March 2003. doi:10.1261/rna.2170803. PMID 12592002. 
  23. ↑ "Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa". Eukaryotic Cell 9 (5): 762–773. May 2010. doi:10.1128/EC.00013-10. PMID 20304999. 
  24. ↑ 24.0 24.1 24.2 "Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules". Nucleic Acids Research 42 (22): 13764–13777. December 2014. doi:10.1093/nar/gku1266. PMID 25429974. 
  25. ↑ "Structure of the yeast mitochondrial large ribosomal subunit". Science 343 (6178): 1485–1489. March 2014. doi:10.1126/science.1249410. PMID 24675956. Bibcode: 2014Sci...343.1485A. 
  26. ↑ "Structure of a mitochondrial ribosome with minimal RNA". Proceedings of the National Academy of Sciences of the United States of America 106 (24): 9637–9642. June 2009. doi:10.1073/pnas.0901631106. PMID 19497863. Bibcode: 2009PNAS..106.9637S. 
  27. ↑ "Structure of the large ribosomal subunit from human mitochondria". Science 346 (6210): 718–722. November 2014. doi:10.1126/science.1258026. PMID 25278503. Bibcode: 2014Sci...346..718B. 
  28. ↑ "The complete structure of the large subunit of the mammalian mitochondrial ribosome". Nature 515 (7526): 283–286. November 2014. doi:10.1038/nature13895. PMID 25271403. Bibcode: 2014Natur.515..283G. 

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