5S ribosomal RNA

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5S ribosomal RNA
Predicted secondary structure and sequence conservation of 5S ribosomal RNA
Symbol 5S_rRNA
Rfam RF00001
Other data
RNA type Gene; rRNA
Domain(s) Eukaryota; Bacteria; Archaea
GO 0005840 0003735
SO 0000652

The 5S ribosomal RNA (5S rRNA) is a small ribosomal RNA molecule. It makes an important contribution to both the structure and function of the large ribosomal subunit, which in turn, is a major component of the fully functional ribosome. 5S rRNA has been found to be present in the cytosolic ribosomes from all domains of life (bacteria, archaea, and eukaryotes), but is not found in the mitochondrial ribosomes of fungi and animals. The naming of the 5S rRNA follows the standard convention for ribosomal RNA molecules, where the Svedberg unit (S) is used as a measure of the molecule’s sedimentation velocity in an ultracentrifuge.[1]


The 5S rRNA is a relatively small RNA of 120 nucleotides in length and a mass of approximately 40kDa. The secondary structure has been determined and is known to consist of five helices, four loops, and one hinge[2] which forms a Y structure. In the eukaryotic genome the 5S rDNA genes cluster in tandem repeats.[3] The number of these genes is variable from species to species.[4]

The five helices are identified as I-V and the four loops plus one hinge, are identified as A-E. Two of the four loops (C and D) are hairpin loops, and loop B and E are internal loops. Loop A forms the hinge structure.[4]

Helix III has two adenosines that are highly conserved.[5] Phylogenetic studies show that helices I and III are likely ancestral in their structure.[6] Helix V can form a hairpin structure that is thought to interact with TFIIIA.[4]

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.[7]
A 3D representation of the ribosome.[8]


Eukaryotic 5S rRNA is synthesized by RNA polymerase III, whereas most other eukaroytic 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.[9][10] 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.[11]

Mapping of 5S rRNA within the ribosome[edit]

Using a variety of molecular techniques, including immuno-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. The large ribosomal subunit, itself is composed of two RNA components, the 5S rRNA and another larger RNA known as 23S rRNA, along with multiple associated proteins. The structure of the large ribosomal subunit in 3-dimensions shows one surface that is relatively smooth and the opposite surface with three projections. These projections are known as the L1 protuberance, the central protuberance, and the L7/L12 stalk. The L1 protuberance and L7/L12 stalk are arranged laterally and surround the central protuberance. When apart of the large ribosomal subunit, the 5S rRNA is located in the central protuberance. In fact, its presence is integral to the formation and structure of the central protuberance. The other major components of the central protuberance include the 23S rRNA and several proteins including L5, L18, L25, and L27.[12]


The exact function of 5S rRNA is not clear yet. But in Escherichia coli cells, a deficiency of 5S rRNA has a detrimental effect on cell fitness with greater magnitude than the effects of deleting other rRNA genes such as 16S and 23S.[13] Escherichia coli cells that have lost 5S rDNA, 5S rRNA, or 5S rRNA-binding proteins have reduced ability to synthesize protein.[13] In addition, crystallographic studies on ribosomes and their functional complexes show that 5S rRNA-binding proteins and other proteins of the central protuberance of the large ribosomal subparticle could play a role in the binding of tRNA with the ribosome.[12] Also, the topographical and physical proximity between 5S rRNA and 23S rRNA which form two functional centers of the ribosome, peptidyl transferase and GTPase-associating ones, has yielded a hypothesis that 5S rRNA could act as a mediator that coordinates functional centers of the ribosome.[12] Crystallographic studies on ribosomes confirmed the topography and intermolecular contacts among 5S rRNA and proteins. The components of the central protuberance of the large ribosomal subparticles may play a role in forming intersubunit bridges and tRNA-binding sites.[12]

5S rRNA in ribosomal assembly[edit]

In eukaryotic organisms, biogenesis of the ribosome is a complex process that requires the assembly of four rRNAs and over 80 proteins.[14] While the biogenesis of the other RNA components of the 60S and 40S ribosomal subunits starts out in the nucleolus with transcription by RNA polymerase I, the 5S rRNA is unique in that it is transcribed by RNA polymerase III from independent genes located in a different chromosomal locus.[15] Rex1p, Rex2p, and Rex3p are exonucleases that process the 3’ ends of 5S rRNA. Once the RNA components are transcribed the final assembly of the ribosome occurs in the cytoplasm. The ribosomal RNA is first exported from the nucleus to the cytoplasm. It is here that the 60S and 40S subunits join to form the mature 80S ribosome,[15] and the process of translation can begin.

The studies present conflicting findings with regard to the stage at which 5S rRNA is integrated into the ribosome; a recent study suggests that 5S rRNAs are associated in the very early 90S step in the ribosomal assembly, but the earlier work suggested that association occurred much later.[15] The recent data obtained with yeast suggest that 5S rRNA is incorporated into 90S particles as part of a small RNP complex, and particularly, in both yeast and mammalian cells, 5S rRNA is found associated with (a homolog of) ribosomal protein L5 (RPL5) in a ribosome-independent small RNP; it seems at least established that it forms pre-ribosomal particles as a 5S rRNA-RPL5 complex.[16]

Protein interactions[edit]

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

La protein[edit]

Interaction of 5S rRNA with the La protein is necessary to prevent the RNA from being degraded by exonucleases in the cell.[17] La protein is found in all eukaryotic organisms and is localized to the nucleus, where it 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]

L5 protein[edit]

Ribosomal protein L5 also associates and stabilizes the 5S rRNA. 5S rRNA is unique among ribosomal RNAs in that it can be found outside of the ribosome as part of a ribonucleoprotein particle (RNP). L5 forms a complex with 5S rRNA that is transported to the nucleus for assembly into the ribosome. L5 is therefore, found both in the nucleus and the cytoplasm of eukaryotic cells. Deficiency in normal L5 prevents transport of 5S rRNA to the nucleus and results in decreased ribosomal assembly.[4][18]

Other ribosomal proteins[edit]

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.[19] Also, in T. brucei, the causative agent of African typanosomiasis, 5S rRNA interacts with two closely related RNA-binding proteins, P34 and P37, whose loss results in a lowered level of 5S rRNA.[4]

See also[edit]


  1. ^ Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J (January 2002). "5S Ribosomal RNA Database". Nucleic Acids Res. 30 (1): 176–8. doi:10.1093/nar/30.1.176. PMC 99124. PMID 11752286. 
  2. ^ Lee, BM; Xu, J; Clarkson, BK; Martinez-Yamout, MA; Dyson, HJ; Case, DA; Gottesfeld, JM; Wright, PE (Mar 17, 2006). "Induced fit and "lock and key" recognition of 5S RNA by zinc fingers of transcription factor IIIA.". Journal of Molecular Biology 357 (1): 275–91. doi:10.1016/j.jmb.2005.12.010. PMID 16405997. 
  3. ^ Douet, J; Tourmente, S (Jul 2007). "Transcription of the 5S rRNA heterochromatic genes is epigenetically controlled in Arabidopsis thaliana and Xenopus laevis.". Heredity 99 (1): 5–13. doi:10.1038/sj.hdy.6800964. PMID 17487217. 
  4. ^ a b c d e f Ciganda, Martin; Williams, Noreen (undefined NaN). "Eukaryotic 5S rRNA biogenesis". Wiley Interdisciplinary Reviews: RNA 2 (4): 523–533. doi:10.1002/wrna.74.  Check date values in: |date= (help)
  5. ^ DiNitto, JP; Huber, PW (Oct 23, 2001). "A role for aromatic amino acids in the binding of Xenopus ribosomal protein L5 to 5S rRNA.". Biochemistry 40 (42): 12645–53. doi:10.1021/bi011439m. PMID 11601989. 
  6. ^ Sun, FJ; Caetano-Anollés, G (Nov 2009). "The evolutionary history of the structure of 5S ribosomal RNA.". Journal of molecular evolution 69 (5): 430–43. doi:10.1007/s00239-009-9264-z. PMID 19639237. 
  7. ^ Mueller F, Sommer I, Baranov P, Matadeen R, Stoldt M, Wöhnert J, Görlach M, van Heel M, Brimacombe R (2000). "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.". J Mol Biol 298 (1): 35–59. doi:10.1006/jmbi.2000.3635. PMID 10756104. 
  8. ^ Mitra K, Schaffitzel C, Fabiola F, Chapman MS, Ban N, Frank J (2006). "Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.". Mol Cell 22 (4): 533–43. doi:10.1016/j.molcel.2006.05.003. PMID 16713583. 
  9. ^ McBryant, SJ; Veldhoen, N; Gedulin, B; Leresche, A; Foster, MP; Wright, PE; Romaniuk, PJ; Gottesfeld, JM (1995). "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. doi:10.1006/jmbi.1995.0201. PMID 7731045. 
  10. ^ Searles, MA; Lu D; Klug A (2000). "The role of the central zinc fingers of transcription factor IIIA in binding to 5 S RNA". J Mol Biol 301 (1): 47–60. doi:10.1006/jmbi.2000.3946. PMID 10926492. 
  11. ^ Pelham, HRB; Brown DD (1980). "A specific transcription factor that can bind either the 5S RNA gene or 5S RNA". Proc. Natl. Acad. Sci. USA 77 (7): 4170–4174. doi:10.1073/pnas.77.7.4170. PMC 349792. PMID 7001457. 
  12. ^ a b c d Gongadze, G. M. (7 January 2012). "5S rRNA and ribosome". Biochemistry (Moscow) 76 (13): 1450–1464. doi:10.1134/S0006297911130062. 
  13. ^ a b Ammons, D; Rampersad, J; Fox, GE (Jan 15, 1999). "5S rRNA gene deletions cause an unexpectedly high fitness loss in Escherichia coli.". Nucleic Acids Research 27 (2): 637–42. doi:10.1093/nar/27.2.637. PMC 148226. PMID 9862991. 
  14. ^ Henras, AK; Soudet, J; Gérus, M; Lebaron, S; Caizergues-Ferrer, M; Mougin, A; Henry, Y (Aug 2008). "The post-transcriptional steps of eukaryotic ribosome biogenesis.". Cellular and molecular life sciences : CMLS 65 (15): 2334–59. doi:10.1007/s00018-008-8027-0. PMID 18408888. 
  15. ^ a b c Ciganda, Martin; Williams, Noreen (July 2011). "Eukaryotic 5S rRNA biogenesis". Wiley Interdisciplinary Reviews: RNA 2 (4): 526. doi:10.1002/wrna.74. 
  16. ^ Henras, A. K.; Soudet, J.; Gérus, M.; Lebaron, S.; Caizergues-Ferrer, M.; Mougin, A.; Henry, Y. (14 April 2008). "The post-transcriptional steps of eukaryotic ribosome biogenesis". Cellular and Molecular Life Sciences 65 (15): 2334–2359. doi:10.1007/s00018-008-8027-0. PMID 18408888. 
  17. ^ Wolin, SL; Cedervall, T (2002). "The La protein.". Annual review of biochemistry 71: 375–403. doi:10.1146/annurev.biochem.71.090501.150003. PMID 12045101. 
  18. ^ Maraia, RJ; Intine, RV (2002). "La protein and its associated small nuclear and nucleolar precursor RNAs.". Gene expression 10 (1-2): 41–57. PMID 11868987. 
  19. ^ Moore PB (March 2001). "The ribosome at atomic resolution". Biochemistry 40 (11): 3243–50. doi:10.1021/bi0029402. PMID 11258942. 

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