18S ribosomal RNA: Difference between revisions
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{{Short description|Part of the eukaryotic ribosomal RNA}} |
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'''18[[Svedberg|S]] ribosomal RNA''' (abbreviated '''18S rRNA''') is a part of the [[ribosomal RNA]]. The S in 18S represents [[Svedberg]] units. 18S rRNA is a component of the small [[eukaryotic]] ribosomal subunit ([[40S]]). 18S rRNA is the structural RNA for the small component of eukaryotic cytoplasmic [[ribosome]]s, and thus one of the basic components of all eukaryotic cells. |
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{{missing information|Rfam SSU_rRNA_eukarya|date=December 2020}} |
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'''18S ribosomal RNA''' (abbreviated '''18S rRNA''') is a part of the [[ribosomal RNA]] in [[eukaryote]]s. It is a component of the [[Eukaryotic small ribosomal subunit (40S)]] and the [[cytosol]]ic homologue of both the [[12S ribosomal RNA|12S rRNA]] in [[mitochondria]] and the [[16S ribosomal RNA|16S rRNA]] in [[plastid]]s and [[prokaryote]]s. Similar to the prokaryotic 16S rRNA, the genes of the 18S ribosomal RNA haven been widely used for [[Phylogenetics|phylogenetic studies]] and biodiversity screening of eukaryotes.<ref name="Meyer 2010">{{cite journal |vauthors=Meyer A, Todt C, Mikkelsen NT, Lieb B|title=Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity|journal=BMC Evolutionary Biology|year=2010|volume=10 |issue=1 |page=70 |article-number=70 |doi=10.1186/1471-2148-10-70|doi-access=free |pmid=20214780 |pmc=2841657 |bibcode=2010BMCEE..10...70M }}</ref> |
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It is the eukaryotic nuclear homologue of [[16S ribosomal RNA]] in [[Prokaryote]]s and [[mitochondria]]. |
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==Research history== |
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The genes coding for 18S rRNA are referred to as '''18S rDNA'''. Sequence data from these genes is widely used in molecular analysis to reconstruct the evolutionary history of organisms, especially in vertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences. |
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Along with the [[28S ribosomal RNA|28S]] and [[5.8S ribosomal RNA|5.8S rRNA]] in eukaryotes, the '''18S rRNA''' was early identified as integral structural element of [[ribosome]]s which were first characterized by their sedimentation properties and named according to measured [[Svedberg|Svedberg units]].<ref name=Graw2015Springer>{{cite book |last=Graw |first=Jochen |date=2015|edition=6th |title=Genetik |trans-title=Genetics |language=German |location=Berlin, Heidelberg |publisher= Springer-Verlag Berlin Heidelberg|isbn=978-3-662-44816-8|doi=10.1007/978-3-662-44817-5}}</ref> |
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Given its ubiquitous presence in eukaryotic life, the evolution of the 18S rRNA was soon proposed as marker for [[phylogenetics|phylogenetic studies]] to resolve the evolution of [[eukaryote]]s.<ref name="Field1988">{{cite journal |vauthors=Field KG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT, Raff EC, Pace NR, Raff RA|title=Molecular phylogeny of the animal kingdom |journal=[[Science (journal)|Science]]|year=1988|volume=239|issue=4841 |pages=748–753 |doi=10.1126/science.3277277|pmid=3277277 |bibcode=1988Sci...239..748F }}</ref> |
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== Uses in phylogeny == |
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The small subunit (SSU) 18S rRNA [[gene]] is one of the most frequently used genes in [[phylogenetic]] studies and an important marker for random target [[polymerase chain reaction]] (PCR) in environmental biodiversity screening.<ref name="Meyer 2010"/> In general, rRNA gene sequences are easy to access due to highly conserved flanking regions allowing for the use of universal [[Primer (molecular biology)|primers]].<ref name="Meyer 2010"/> Their repetitive arrangement within the genome provides excessive amounts of template DNA for PCR, even in the smallest organisms. The 18S gene is part of the ribosomal functional core and is exposed to similar selective forces in all living beings. Thus, when the first large-scale phylogenetic studies based on 18S sequences were published - first and foremost phylogeny of the animal kingdom by Field ''et al.'' (1988)<ref>Field K. G., Olsen G. J., Lane D. J., Giovannoni S. J., Ghiselin M. T., Raff E. C., Pace N. R. & Raff R. A. (1988). "Molecular phylogeny of the animal kingdom". ''[[Science (journal)|Science]]'' '''239'''(4841): 748-753. {{doi|10.1126/science.3277277}}.</ref> - the gene was celebrated as the prime candidate for reconstructing the [[metazoa]]n [[tree of life]].<ref name="Meyer 2010"/> And in fact, 18S sequences later provided evidence for the splitting of [[Ecdysozoa]] and [[Lophotrochozoa]], thus contributing to the most recent revolutionary change in our understanding of metazoan relationships.<ref name="Meyer 2010"/> |
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==Structure and function== |
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| ⚫ | During the latter part of the 2000s, and with increased numbers of taxa included into molecular phylogenies, however, two problems became apparent. First, there are prevailing sequencing impediments in representatives of certain taxa, such as the mollusk classes [[Solenogastres]] and [[Tryblidia]], selected [[bivalve]] taxa, and the enigmatic crustacean class [[Remipedia]].<ref name="Meyer 2010"/> Failure to obtain 18S sequences of single taxa is considered a common phenomenon but is rarely ever reported.<ref name="Meyer 2010"/> Secondly, in contrast to initially high hopes, 18S cannot resolve nodes at all taxonomic levels and its efficacy varies considerably among |
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The '''18S ribosomal RNA''' is the [[SSU rRNA|structural RNA of the small subunit]] in the [[eukaryote|eukaryotic]] cytoplasmic [[ribosome]]. |
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[[File:Eucaryot rdna.png|thumb|right|General organization of the eukaryotic nuclear [[ribosomal DNA|rDNA]] tandem repeats consisting of [[External transcribed spacer|ETS]], 18S rRNA, [[Internal transcribed spacer|ITS-1]], [[5.8S ribosomal RNA|5.8S rRNA]], [[Internal transcribed spacer|ITS-2]] and [[28S ribosomal RNA|28S rRNA]].]] |
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The genomic sequence of the 18S rRNA is organized in a group with the [[28S ribosomal RNA|28S]] and [[5.8S ribosomal RNA|5.8S rRNA]], separated and flanked by the [[Internal transcribed spacer|ITS-1, ITS-2]] and [[External transcribed spacer|ETS]] spacer regions.<ref name=Hillis1991>{{cite journal |vauthors=Hillis DM, Dixon MT |title=Ribosomal DNA: Molecular Evolution and Phylogenetic Inference |journal=[[The Quarterly Review of Biology]] |year=1991|volume=66 |issue=4 |pages=411–53 |doi=10.1086/417338 |pmid=1784710}}</ref> |
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These regions of [[ribosomal DNA|ribosomal DNA (rDNA)]] are present with several hundred copies in the active genome, clustered in [[Nucleolus organizer region|nucleolus organizer regions (NORs)]].<ref name=Graw2015Springer/> |
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In [[ribosome biogenesis]], these genes are transcribed together by the [[RNA polymerase I]] and are processed in the [[nucleolus]] structure of the [[Cell nucleus|nucleus]]. |
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{| class="wikitable floatright" |
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|+ 18S rRNA nucleotide length of selected species |
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|'''Species''' |
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|'''Size [nt]''' |
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|- |
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|''[[Saccharomyces cerevisiae]]'' || 1,789<ref name=Rubstov1980>{{cite journal |vauthors=Rubtsov PM, Musakhanov MM, Zakharyev VM, Krayev AS, Skryabin KG, Bayev AA |title=The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae. |journal=[[Nucleic Acids Research]]|year=1980|volume=8 |issue=23 |pages=5779–5794 |doi=10.1093/nar/8.23.5779 |pmid=7008030 |pmc=324341 }}</ref> |
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|- |
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|''[[Xenopus laevis]]''|| 1,825<ref name=Salim1981>{{cite journal |vauthors=Salim M, Maden EH|title=Nucleotide sequence of ''Xenopus laevis'' 18S ribosomal RNA inferred from gene sequence. |journal=[[Nature (journal)|Nature]]|year=1981|volume=291 |issue=5812 |pages=205–208 |doi=10.1038/291205a0 |pmid=7015146 |bibcode=1981Natur.291..205S }}</ref> |
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|- |
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|''[[Homo sapiens]]''|| 1,869<ref name=NCBI18SHomoSapiens/> |
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|- |
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|''[[Drosophila melanogaster]]''|| 1,995<ref name=Tautz1988>{{cite journal |vauthors=Tautz D, Hancock JM, Webb DA, Tautz C, Dover GA|title=Complete sequences of the rRNA genes of Drosophila melanogaster |journal=[[Molecular Biology and Evolution]] |year=1988 |volume=5 |issue=4 |pages=366–376 |doi= 10.1093/oxfordjournals.molbev.a040500 |pmid= 3136294 }}</ref> |
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|} |
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The length of the 18S rRNA varies considerably in the eukaryotic phylogenetic tree, corresponding to a range of 16S-19S in [[Svedberg|Svedberg units]],<ref name=Graw2015Springer/> with the average length commonly given as around 2000 [[nucleotide]]s.<ref name=Graw2015Springer/> The 18S rRNA of [[human]]s has a length of 1869 nucleotides.<ref name=NCBI18SHomoSapiens>Page ''Homo sapiens RNA, 18S ribosomal N5 (RNA18SN5), ribosomal RNA'' on {{cite web|url=https://www.ncbi.nlm.nih.gov/nuccore/NR_003286|title=''Homo sapiens'' 18S ribosomal RNA|date=25 March 2023 | publisher=[[National Library of Medicine]]|access-date=2024-06-29}}</ref> |
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==Uses== |
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The universal presence of the '''18S rRNA''' in [[eukaryotes]] and generally high degree of conservation in evolution allow the construction of universal [[Primer (molecular biology)|primers]] for [[DNA amplification]] by [[polymerase chain reaction]].<ref name=Hillis1991/><ref name="Meyer 2010"/> The possible applications mirror molecular methods involving [[16S ribosomal RNA|16S rRNA]] of [[prokaryotes]]. |
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=== Biodiversity screening === |
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Primers binding in highly conserved regions of the 18S rRNA are an important marker for [[biodiversity]] screening,<ref name="Meyer 2010"/> allowing the amplification of unspecified or random targets from environmental samples as well as uncharacterized [[Biological specimen|specimens]] from collections for [[DNA sequencing]]. Subsequent [[sequence alignment]] covering the less strictly conserved segments then allows the assignment of a sample to biologic [[clade (biology)|clades]]. {{Citation needed|date=July 2024|reason=general citation, also differences in resolution to genus and species level}} |
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In the case of 18S rRNA, retrieval of DNA is improved by the abundance of repeating sequences of the [[ribosomal DNA|rDNA]] within eukaryotic cells,<ref name="Meyer 2010"/> promoting the sensitivity of the analysis. |
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=== Phylogenetics === |
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Multiple properties of the genomic sequence of the 18S rRNS have established it as an important marker gene for large-scale phylogenetic analysis and the reconstruction of the [[metazoa]]n [[tree of life (biology)|tree of life]]. The integral role in formation and function of the [[ribosome]] is a key cause for its omnipresence in eukaryotic life. Meanwhile, the gene maintains a high degree of conservation under a persistent selective pressure in all living beings,<ref name="Meyer 2010"/> highlighting its potential for comparison between distantly related clades. |
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Early studies utilizing the 18S rRNA sequence constructed the first large-scale [[phylogenetic tree]]s of the [[metazoa]].<ref name=Field1988/> Evidence from further studies led to the creation of several important [[clade]]s, such as the [[Ecdysozoa]] and [[Lophotrochozoa]].<ref name="Meyer 2010"/>{{Citation needed|date=July 2024|reason=Original publications for both mentioned clades.}} |
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| ⚫ | During the latter part of the 2000s, and with increased numbers of taxa included into molecular phylogenies, however, two problems became apparent. First, there are prevailing sequencing impediments in representatives of certain taxa, such as the mollusk classes [[Solenogastres]] and [[Tryblidia]], selected [[bivalve]] taxa, and the enigmatic crustacean class [[Remipedia]].<ref name="Meyer 2010"/> Failure to obtain 18S sequences of single taxa is considered a common phenomenon but is rarely ever reported.<ref name="Meyer 2010"/> Secondly, in contrast to initially high hopes, 18S cannot resolve nodes at all taxonomic levels and its efficacy varies considerably among clades. This has been discussed as an effect of rapid ancient radiation within short periods. Multigene analyses are currently thought to give more reliable results for tracing deep branching events in Metazoa but 18S still is extensively used in phylogenetic analyses.<ref name="Meyer 2010"/> |
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== References == |
== References == |
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This article incorporates CC-By-2.0 text from the reference.<ref name="Meyer 2010" |
This article incorporates CC-By-2.0 text from the reference.<ref name="Meyer 2010"/> |
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{{reflist}} |
{{reflist}} |
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Latest revision as of 01:42, 6 August 2024
 | This article is missing information about Rfam SSU_rRNA_eukarya. (December 2020) |
18S ribosomal RNA (abbreviated 18S rRNA) is a part of the ribosomal RNA in eukaryotes. It is a component of the Eukaryotic small ribosomal subunit (40S) and the cytosolic homologue of both the 12S rRNA in mitochondria and the 16S rRNA in plastids and prokaryotes. Similar to the prokaryotic 16S rRNA, the genes of the 18S ribosomal RNA haven been widely used for phylogenetic studies and biodiversity screening of eukaryotes.[1]
Research history
[edit]Along with the 28S and 5.8S rRNA in eukaryotes, the 18S rRNA was early identified as integral structural element of ribosomes which were first characterized by their sedimentation properties and named according to measured Svedberg units.[2]
Given its ubiquitous presence in eukaryotic life, the evolution of the 18S rRNA was soon proposed as marker for phylogenetic studies to resolve the evolution of eukaryotes.[3]
Structure and function
[edit]The 18S ribosomal RNA is the structural RNA of the small subunit in the eukaryotic cytoplasmic ribosome.
The genomic sequence of the 18S rRNA is organized in a group with the 28S and 5.8S rRNA, separated and flanked by the ITS-1, ITS-2 and ETS spacer regions.[4] These regions of ribosomal DNA (rDNA) are present with several hundred copies in the active genome, clustered in nucleolus organizer regions (NORs).[2] In ribosome biogenesis, these genes are transcribed together by the RNA polymerase I and are processed in the nucleolus structure of the nucleus.
| Species | Size [nt] |
| Saccharomyces cerevisiae | 1,789[5] |
| Xenopus laevis | 1,825[6] |
| Homo sapiens | 1,869[7] |
| Drosophila melanogaster | 1,995[8] |
The length of the 18S rRNA varies considerably in the eukaryotic phylogenetic tree, corresponding to a range of 16S-19S in Svedberg units,[2] with the average length commonly given as around 2000 nucleotides.[2] The 18S rRNA of humans has a length of 1869 nucleotides.[7]
Uses
[edit]The universal presence of the 18S rRNA in eukaryotes and generally high degree of conservation in evolution allow the construction of universal primers for DNA amplification by polymerase chain reaction.[4][1] The possible applications mirror molecular methods involving 16S rRNA of prokaryotes.
Biodiversity screening
[edit]Primers binding in highly conserved regions of the 18S rRNA are an important marker for biodiversity screening,[1] allowing the amplification of unspecified or random targets from environmental samples as well as uncharacterized specimens from collections for DNA sequencing. Subsequent sequence alignment covering the less strictly conserved segments then allows the assignment of a sample to biologic clades. [citation needed]
In the case of 18S rRNA, retrieval of DNA is improved by the abundance of repeating sequences of the rDNA within eukaryotic cells,[1] promoting the sensitivity of the analysis.
Phylogenetics
[edit]Multiple properties of the genomic sequence of the 18S rRNS have established it as an important marker gene for large-scale phylogenetic analysis and the reconstruction of the metazoan tree of life. The integral role in formation and function of the ribosome is a key cause for its omnipresence in eukaryotic life. Meanwhile, the gene maintains a high degree of conservation under a persistent selective pressure in all living beings,[1] highlighting its potential for comparison between distantly related clades.
Early studies utilizing the 18S rRNA sequence constructed the first large-scale phylogenetic trees of the metazoa.[3] Evidence from further studies led to the creation of several important clades, such as the Ecdysozoa and Lophotrochozoa.[1][citation needed]
During the latter part of the 2000s, and with increased numbers of taxa included into molecular phylogenies, however, two problems became apparent. First, there are prevailing sequencing impediments in representatives of certain taxa, such as the mollusk classes Solenogastres and Tryblidia, selected bivalve taxa, and the enigmatic crustacean class Remipedia.[1] Failure to obtain 18S sequences of single taxa is considered a common phenomenon but is rarely ever reported.[1] Secondly, in contrast to initially high hopes, 18S cannot resolve nodes at all taxonomic levels and its efficacy varies considerably among clades. This has been discussed as an effect of rapid ancient radiation within short periods. Multigene analyses are currently thought to give more reliable results for tracing deep branching events in Metazoa but 18S still is extensively used in phylogenetic analyses.[1]
References
[edit]This article incorporates CC-By-2.0 text from the reference.[1]
- ^ a b c d e f g h i j Meyer A, Todt C, Mikkelsen NT, Lieb B (2010). "Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity". BMC Evolutionary Biology. 10 (1) 70: 70. Bibcode:2010BMCEE..10...70M. doi:10.1186/1471-2148-10-70. PMC 2841657. PMID 20214780.
- ^ a b c d Graw, Jochen (2015). Genetik [Genetics] (in German) (6th ed.). Berlin, Heidelberg: Springer-Verlag Berlin Heidelberg. doi:10.1007/978-3-662-44817-5. ISBN 978-3-662-44816-8.
- ^ a b Field KG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT, Raff EC, Pace NR, Raff RA (1988). "Molecular phylogeny of the animal kingdom". Science. 239 (4841): 748–753. Bibcode:1988Sci...239..748F. doi:10.1126/science.3277277. PMID 3277277.
- ^ a b Hillis DM, Dixon MT (1991). "Ribosomal DNA: Molecular Evolution and Phylogenetic Inference". The Quarterly Review of Biology. 66 (4): 411–53. doi:10.1086/417338. PMID 1784710.
- ^ Rubtsov PM, Musakhanov MM, Zakharyev VM, Krayev AS, Skryabin KG, Bayev AA (1980). "The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae". Nucleic Acids Research. 8 (23): 5779–5794. doi:10.1093/nar/8.23.5779. PMC 324341. PMID 7008030.
- ^ Salim M, Maden EH (1981). "Nucleotide sequence of Xenopus laevis 18S ribosomal RNA inferred from gene sequence". Nature. 291 (5812): 205–208. Bibcode:1981Natur.291..205S. doi:10.1038/291205a0. PMID 7015146.
- ^ a b Page Homo sapiens RNA, 18S ribosomal N5 (RNA18SN5), ribosomal RNA on "Homo sapiens 18S ribosomal RNA". National Library of Medicine. 25 March 2023. Retrieved 2024-06-29.
- ^ Tautz D, Hancock JM, Webb DA, Tautz C, Dover GA (1988). "Complete sequences of the rRNA genes of Drosophila melanogaster". Molecular Biology and Evolution. 5 (4): 366–376. doi:10.1093/oxfordjournals.molbev.a040500. PMID 3136294.