28S ribosomal RNA

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:

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

References

^ Lodish, Harvey F.; Darnell, James E. (1995-01-01). Molecular cell biology. Scientific American Books. ISBN 978-0-7167-2380-6. OCLC 30783343.
^ 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. PMID 6157106. S2CID 4262269.
^ 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. PMC 4574749. PMID 26283689.
^ 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. PMID 11433365. S2CID 2637106.
^ 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. ISSN 0027-8424. PMC 280234. PMID 3368456.
^ 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. PMID 17051209. S2CID 4302864.
^ 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. ISSN 1063-5157. PMID 11975347.
^ 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. PMID 11277632.
^ 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. PMID 19822216.
^ 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. PMID 8081546.
^ 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. PMID 9866205.
^ ^a ^b Natsidis, 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. PMC 6925239. PMID 31863008.
^ "Ribosomal Database Project". RDP Release 11, Update 5. September 30, 2016. Archived from the original on 2020-08-19. Retrieved 2016-12-31.
^ 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. ISSN 0305-1048. PMC 333993. PMID 1598241.
^ 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. ISSN 0305-1048. PMC 3965039. PMID 24288368.
^ 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. ISSN 0305-1048. PMC 3531112. PMID 23193283.

[1] Lodish, Harvey F.; Darnell, James E. (1995-01-01). Molecular cell biology. Scientific American Books. ISBN 978-0-7167-2380-6. OCLC 30783343.

[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. PMID 6157106. S2CID 4262269.

[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. PMC 4574749. PMID 26283689.

[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. PMID 11433365. S2CID 2637106.

[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. ISSN 0027-8424. PMC 280234. PMID 3368456.

[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. PMID 17051209. S2CID 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. 46 (1): 1–68. doi:10.1093/sysbio/46.1.1. ISSN 1063-5157. PMID 11975347.

[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. PMID 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. doi:10.1016/j.ympev.2009.10.006. PMID 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. doi:10.1006/mpev.1993.1005. PMID 8081546.

[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. PMID 9866205.

[hb-12] Natsidis, 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. PMC 6925239. PMID 31863008.

[13] "Ribosomal Database Project". RDP Release 11, Update 5. September 30, 2016. Archived from the original on 2020-08-19. Retrieved 2016-12-31.

[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. ISSN 0305-1048. PMC 333993. PMID 1598241.

[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. ISSN 0305-1048. PMC 3965039. PMID 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. doi:10.1093/nar/gks1219. ISSN 0305-1048. PMC 3531112. PMID 23193283.

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