28SリボソームRNA

28SリボソームRNA（英: 28S ribosomal RNA）は、真核生物の細胞質のリボソームの大サブユニット（LSU）に含まれるリボソームRNA（rRNA）であり、全ての真核細胞の基本的構成要素の1つである。サイズは哺乳類では28S、植物では25Sであるため、25S/28S rRNAとも呼ばれる。

5.8S rRNAとあわせて、原核生物の23S rRNAやミトコンドリアの16S rRNA（英語版）のホモログとなる^[1]^[2]^[3]。

系統学における利用

28S rRNAをコードする遺伝子は28S rDNAと呼ばれる。系統樹の作製のためにこれらの遺伝子の配列比較が用いられることがあり、原生生物^[4]、菌類^[5]、昆虫^[6]、クモ綱^[7]、緩歩動物^[8]、脊椎動物^[9]^[10]での系統樹作成での利用例がある。

構造

28S rRNAの長さは、一般的には4000から5000ヌクレオチドである^[11]。一部の真核生物ではリボソームへと組み立てられる前に2つの部分へ切断され、この現象は"hidden break"と呼ばれている^[11]。

データベース

比較生物学用途のために、LSU rRNAのアラインメントとアノテーションを行ったデータベースがいくつか存在する。

RDP（the Ribosomal Database Project）^[12]^[13]^[14]
SILVA^[15]

出典

^ Eperon, I. C.; Anderson, S.; Nierlich, D. P. (1980-07-31). “Distinctive sequence of human mitochondrial ribosomal RNA genes” (英語). Nature 286 (5772): 460–467. Bibcode: 1980Natur.286..460E. doi:10.1038/286460a0. PMID 6157106.
^ 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.
^ 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” (英語). 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 et al. (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.
^ 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” (英語). 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.
^ 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). 2020年8月19日時点のオリジナルよりアーカイブ。2016年12月31日閲覧。
^ Olsen, G. J.; Overbeek, R.; Larsen, N.; Marsh, T. L.; McCaughey, M. J.; Maciukenas, M. A.; Kuan, W.-M.; Macke, T. J. et al. (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 et al. (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.

[:0-1] Eperon, I. C.; Anderson, S.; Nierlich, D. P. (1980-07-31). “Distinctive sequence of human mitochondrial ribosomal RNA genes” (英語). Nature 286 (5772): 460–467. Bibcode: 1980Natur.286..460E. doi:10.1038/286460a0. PMID 6157106.

[:1-2] 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.

[:2-3] 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.

[:3-4] 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” (英語). 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.

[:4-5] James, Timothy Y.; Kauff, Frank; Schoch, Conrad L.; Matheny, P. Brandon; Hofstetter, Valérie; Cox, Cymon J.; Celio, Gail; Gueidan, Cécile et al. (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.

[:5-6] 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” (英語). Systematic Biology 46 (1): 1–68. doi:10.1093/sysbio/46.1.1. ISSN 1063-5157. PMID 11975347.

[:6-7] 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.

[:7-8] 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.

[:8-9] 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.

[:9-10] 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-11] 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.

[12] “Ribosomal Database Project”. RDP Release 11, Update 5 (September 30, 2016). 2020年8月19日時点のオリジナルよりアーカイブ。2016年12月31日閲覧。

[13] Olsen, G. J.; Overbeek, R.; Larsen, N.; Marsh, T. L.; McCaughey, M. J.; Maciukenas, M. A.; Kuan, W.-M.; Macke, T. J. et al. (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.

[14] Cole, James R.; Wang, Qiong; Fish, Jordan A.; Chai, Benli; McGarrell, Donna M.; Sun, Yanni; Brown, C. Titus; Porras-Alfaro, Andrea et al. (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.

[15] 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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