Wikipedia

28S ribosomal RNA

"28S" redirects here. For the isotope of sulfur (28S), seeSulfur-28.

28S ribosomal RNAis the structural ribosomal RNA (rRNA) for thelarge subunit (LSU)of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. It has a size of 25S in plants and 28S in mammals, hence the alias of25S–28S rRNA.[1]

Mitochondrial16Sand nuclear 28S ribosomal DNAphylogeniesof three species of mollusks belonging to the genusWaldo.

Combined with5.8S rRNAto the 5' side, it is the eukaryotic nuclear homologue of theprokaryotic 23Sandmitochondrial 16Sribosomal RNAs.[2][3][4]

Use in phylogeny

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The genes coding for 28S rRNA are referred to as 28S rDNA. The comparison of thesequencesfrom these genes are sometimes used in molecular analysis to constructphylogenetic trees,for example inprotists,[5]fungi,[6]insects,[7]arachnids,[8]tardigrades,[9]andvertebrates.[10][11]

Structure

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The 28S rRNA is typically 4000–5000 nt long.[12]

Some eukaryotes cleave 28S rRNA into two parts before assembling both into the ribosome, a phenomenon termed the "hidden break".[12]

Databases

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Severaldatabasesprovidealignmentsandannotationsof LSU rRNA sequences forcomparativepurposes:

  • RDP,[13]the Ribosomal Database Project;[14][15]
  • SILVA, a ribosomal RNA gene database project.[16]

References

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  1. ^Lodish, Harvey F.; Darnell, James E. (1995-01-01).Molecular cell biology.Scientific American Books.ISBN978-0-7167-2380-6.OCLC30783343.
  2. ^Eperon, I. C.; Anderson, S.; Nierlich, D. P. (1980-07-31). "Distinctive sequence of human mitochondrial ribosomal RNA genes".Nature.286(5772): 460–467.Bibcode:1980Natur.286..460E.doi:10.1038/286460a0.PMID6157106.S2CID4262269.
  3. ^Doris, Stephen M.; Smith, Deborah R.; Beamesderfer, Julia N.; Raphael, Benjamin J.; Nathanson, Judith A.; Gerbi, Susan A. (October 2015)."Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics".RNA.21(10): 1719–1730.doi:10.1261/rna.051144.115.PMC4574749.PMID26283689.
  4. ^Lafontaine, D. L. J.; Tollervey, D. (2001). "The function and synthesis of ribosomes".Nature Reviews Molecular Cell Biology.2(7): 514–520.doi:10.1038/35080045.hdl:1842/729.PMID11433365.S2CID2637106.
  5. ^Baroin, A.; Perasso, R.; Qu, L. H.; Brugerolle, G.; Bachellerie, J. P.; Adoutte, A. (1988-05-01)."Partial phylogeny of the unicellular eukaryotes based on rapid sequencing of a portion of 28S ribosomal RNA".Proceedings of the National Academy of Sciences.85(10): 3474–3478.Bibcode:1988PNAS...85.3474B.doi:10.1073/pnas.85.10.3474.ISSN0027-8424.PMC280234.PMID3368456.
  6. ^James, Timothy Y.; Kauff, Frank; Schoch, Conrad L.; Matheny, P. Brandon; Hofstetter, Valérie; Cox, Cymon J.; Celio, Gail; Gueidan, Cécile; Fraker, Emily (2006). "Reconstructing the early evolution of Fungi using a six-gene phylogeny".Nature.443(7113): 818–822.Bibcode:2006Natur.443..818J.doi:10.1038/nature05110.PMID17051209.S2CID4302864.
  7. ^Whiting, Michael F.; Carpenter, James C.; Wheeler, Quentin D.; Wheeler, Ward C. (1997-03-01)."The Strepsiptera Problem: Phylogeny of the Holometabolous Insect Orders Inferred from 18S and 28S Ribosomal DNA Sequences and Morphology".Systematic Biology.46(1): 1–68.doi:10.1093/sysbio/46.1.1.ISSN1063-5157.PMID11975347.
  8. ^Hedin, Marshal C.; Maddison, Wayne P. (March 2001). "A Combined Molecular Approach to Phylogeny of the Jumping Spider Subfamily Dendryphantinae (Araneae: Salticidae)".Molecular Phylogenetics and Evolution.18(3): 386–403.doi:10.1006/mpev.2000.0883.PMID11277632.
  9. ^Jørgensen, Aslak; Faurby, Søren; Hansen, Jesper G.; Møbjerg, Nadja; Kristensen, Reinhardt M. (2010-03-01). "Molecular phylogeny of Arthrotardigrada (Tardigrada)".Molecular Phylogenetics and Evolution.54(3): 1006–1015.doi:10.1016/j.ympev.2009.10.006.PMID19822216.
  10. ^Le, Hoc Lanh Vân; Lecointre, Guillaume; Perasso, Roland (1993-03-01). "A 28S rRNA-Based Phylogeny of the Gnathostomes: First Steps in the Analysis of Conflict and Congruence with Morphologically Based Cladograms".Molecular Phylogenetics and Evolution.2(1): 31–51.doi:10.1006/mpev.1993.1005.PMID8081546.
  11. ^Mallatt, Jon; Sullivan, Jack (December 1998). "28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes".Molecular Biology and Evolution.15(12): 1706–1718.doi:10.1093/oxfordjournals.molbev.a025897.PMID9866205.
  12. ^abNatsidis, Paschalis; Schiffer, Philipp H.; Salvador-Martínez, Irepan; Telford, Maximilian J. (December 2019)."Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers".Scientific Reports.9(1): 19477.Bibcode:2019NatSR...919477N.doi:10.1038/s41598-019-55573-1.PMC6925239.PMID31863008.
  13. ^"Ribosomal Database Project".RDP Release 11, Update 5.September 30, 2016. Archived fromthe originalon 2020-08-19.Retrieved2016-12-31.
  14. ^Olsen, G. J.; Overbeek, R.; Larsen, N.; Marsh, T. L.; McCaughey, M. J.; Maciukenas, M. A.; Kuan, W.-M.; Macke, T. J.; Xing, Y. (1992-05-11)."The Ribosomal Database Project".Nucleic Acids Research.20(suppl): 2199–2200.doi:10.1093/nar/20.suppl.2199.ISSN0305-1048.PMC333993.PMID1598241.
  15. ^Cole, James R.; Wang, Qiong; Fish, Jordan A.; Chai, Benli; McGarrell, Donna M.; Sun, Yanni; Brown, C. Titus; Porras-Alfaro, Andrea; Kuske, Cheryl R. (2014-01-01)."Ribosomal Database Project: data and tools for high throughput rRNA analysis".Nucleic Acids Research.42(D1): D633–D642.doi:10.1093/nar/gkt1244.ISSN0305-1048.PMC3965039.PMID24288368.
  16. ^Quast, C.; Pruesse, E.; Yilmaz, P.; Gerken, J.; Schweer, T.; Yarza, P.; Peplies, J.; Glockner, F. O. (2013-01-01)."The SILVA ribosomal RNA gene database project: improved data processing and web-based tools".Nucleic Acids Research.41(D1): D590–D596.doi:10.1093/nar/gks1219.ISSN0305-1048.PMC3531112.PMID23193283.
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