28S ribosomal RNA explained

28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large 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 of 25S - 28S rRNA.[1]

Combined with 5.8S rRNA to the 5' side, it is the eukaryotic nuclear homologue of the prokaryotic 23S and mitochondrial 16S ribosomal RNAs.[2] [3] [4]

Use in phylogeny

The genes coding for 28S rRNA are referred to as 28S rDNA. The comparison of the sequences from these genes are sometimes used in molecular analysis to construct phylogenetic trees, for example in protists,[5] fungi,[6] insects,[7] arachnids,[8] tardigrades,[9] and vertebrates.[10] [11]

Structure

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

Several databases provide alignments and annotations of LSU rRNA sequences for comparative purposes:

Notes and References

  1. Book: Molecular cell biology. Lodish. Harvey F.. Darnell. James E.. 1995-01-01. Scientific American Books. 978-0-7167-2380-6. 30783343. registration.
  2. Eperon. I. C.. Anderson. S.. Nierlich. D. P.. 1980-07-31. Distinctive sequence of human mitochondrial ribosomal RNA genes. Nature. en. 286. 5772. 460–467. 10.1038/286460a0. 6157106. 1980Natur.286..460E. 4262269.
  3. Doris . Stephen M. . Smith . Deborah R. . Beamesderfer . Julia N. . Raphael . Benjamin J. . Nathanson . Judith A. . Gerbi . Susan A. . Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics . RNA . October 2015 . 21 . 10 . 1719–1730 . 10.1261/rna.051144.115. 26283689 . 4574749 . free .
  4. 10.1038/35080045. 11433365. The function and synthesis of ribosomes. Nature Reviews Molecular Cell Biology. 2. 7. 514–520. 2001. Lafontaine . D. L. J. . Tollervey . D. . 1842/729. 2637106. free.
  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. en. 85. 10. 3474–3478. 0027-8424. 280234. 3368456. 10.1073/pnas.85.10.3474. 1988PNAS...85.3474B. free.
  6. James. Timothy Y.. Kauff. Frank. Schoch. Conrad L.. Matheny. P. Brandon. Hofstetter. Valérie. Cox. Cymon J.. Celio. Gail. Gueidan. Cécile. Fraker. Emily. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature. 443. 7113. 818–822. 10.1038/nature05110. 17051209. 2006. 2006Natur.443..818J. 4302864.
  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. en. 46. 1. 1–68. 10.1093/sysbio/46.1.1. 1063-5157. 11975347. free.
  8. Hedin . Marshal C. . Maddison . Wayne P. . A Combined Molecular Approach to Phylogeny of the Jumping Spider Subfamily Dendryphantinae (Araneae: Salticidae) . Molecular Phylogenetics and Evolution . March 2001 . 18 . 3 . 386–403 . 10.1006/mpev.2000.0883. 11277632 .
  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. 10.1016/j.ympev.2009.10.006. 19822216.
  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. 10.1006/mpev.1993.1005. 8081546.
  11. Mallatt. Jon. Sullivan, Jack . 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. Molecular Biology and Evolution. December 1998. 15. 12. 1706–1718. 9866205. 10.1093/oxfordjournals.molbev.a025897.
  12. Natsidis . Paschalis . Schiffer . Philipp H. . Salvador-Martínez . Irepan . Telford . Maximilian J. . Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers . Scientific Reports . December 2019 . 9 . 1 . 19477 . 10.1038/s41598-019-55573-1 . 31863008 . 6925239 . 2019NatSR...919477N . free.
  13. Web site: Ribosomal Database Project. September 30, 2016. RDP Release 11, Update 5. 2016-12-31. 2020-08-19. https://web.archive.org/web/20200819061707/http://rdp.cme.msu.edu/. dead.
  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. 10.1093/nar/20.suppl.2199. 1598241. 0305-1048. 333993.
  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. 10.1093/nar/gkt1244. 0305-1048. 3965039. 24288368.
  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. 10.1093/nar/gks1219. 0305-1048. 3531112. 23193283.

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "28S ribosomal RNA".

Except where otherwise indicated, Everything.Explained.Today is © Copyright 2009-2024, A B Cryer, All Rights Reserved. Cookie policy.