18S ribosomal RNA

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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]

Contents

Research history

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

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, of which several hundred copies form the 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.

18S rRNA nucleotide length of selected species
SpeciesSize [nt]
Saccharomyces cerevisiae 1,789 [4]
Xenopus laevis 1,825 [5]
Homo sapiens 1,869 [6]
Drosophila melanogaster 1,995 [7]

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. [6]

Uses

Phylogenetics

The genes coding for 18S rRNA are referred to as 18S rRNA genes. 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.

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. [1] In general, rRNA gene sequences are easy to access due to highly conserved flanking regions allowing for the use of universal primers. [1] 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 (e.g. by Field et al., 1988), [3] the gene was celebrated as the prime candidate for reconstructing the metazoan tree of life. [1] 18S sequences later provided evidence for the splitting of Ecdysozoa and Lophotrochozoa clades (monophyletic group of organisms composed of a common ancestor and all its lineal descendants), thus contributing to a revolutionary change in our understanding of metazoan relationships. [1]

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]

Related Research Articles

<span class="mw-page-title-main">Nucleolus</span> Largest structure in the nucleus of eukaryotic cells

The nucleolus is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis, which is the synthesis of ribosomes. The nucleolus also participates in the formation of signal recognition particles and plays a role in the cell's response to stress. Nucleoli are made of proteins, DNA and RNA, and form around specific chromosomal regions called nucleolar organizing regions. Malfunction of nucleoli can be the cause of several human conditions called "nucleolopathies" and the nucleolus is being investigated as a target for cancer chemotherapy.

<span class="mw-page-title-main">Ribosome</span> Synthesizes proteins in cells

Ribosomes are macromolecular machines, found within all cells, that perform biological protein synthesis. Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA molecules and many ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.

<span class="mw-page-title-main">RNA polymerase</span> Enzyme that synthesizes RNA from DNA

In molecular biology, RNA polymerase, or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template.

<span class="mw-page-title-main">Ribosomal DNA</span>

Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA. These sequences regulate transcription initiation and amplification, and contain both transcribed and non-transcribed spacer segments.

Internal transcribed spacer (ITS) is the spacer DNA situated between the small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript.

The Shine–Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon. Once recruited, tRNA may add amino acids in sequence as dictated by the codons, moving downstream from the translational start site.

<span class="mw-page-title-main">Ribosomal RNA</span> RNA component of the ribosome, essential for protein synthesis in all living organisms

Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins, though this ratio differs between prokaryotes and eukaryotes.

RNA polymerase 1 is, in higher eukaryotes, the polymerase that only transcribes ribosomal RNA, a type of RNA that accounts for over 50% of the total RNA synthesized in a cell.

<span class="mw-page-title-main">Ribosome biogenesis</span> Cellular process

Ribosome biogenesis is the process of making ribosomes. In prokaryotes, this process takes place in the cytoplasm with the transcription of many ribosome gene operons. In eukaryotes, it takes place both in the cytoplasm and in the nucleolus. It involves the coordinated function of over 200 proteins in the synthesis and processing of the three prokaryotic or four eukaryotic rRNAs, as well as assembly of those rRNAs with the ribosomal proteins. Most of the ribosomal proteins fall into various energy-consuming enzyme families including ATP-dependent RNA helicases, AAA-ATPases, GTPases, and kinases. About 60% of a cell's energy is spent on ribosome production and maintenance.

<span class="mw-page-title-main">Ribosomal protein</span> Proteins found in ribosomes

A ribosomal protein is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. E. coli, other bacteria and Archaea have a 30S small subunit and a 50S large subunit, whereas humans and yeasts have a 40S small subunit and a 60S large subunit. Equivalent subunits are frequently numbered differently between bacteria, Archaea, yeasts and humans.

<span class="mw-page-title-main">5.8S ribosomal RNA</span> RNA component of the large subunit of the eukaryotic ribosome

In molecular biology, the 5.8S ribosomal RNA is a non-coding RNA component of the large subunit of the eukaryotic ribosome and so plays an important role in protein translation. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Its function is thought to be in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5.8S rRNA can be used as a reference gene for miRNA detection. The 5.8S ribosomal RNA is used to better understand other rRNA processes and pathways in the cell.

<span class="mw-page-title-main">5S ribosomal RNA</span> RNA component of the large subunit of the ribosome

The 5S ribosomal RNA is an approximately 120 nucleotide-long ribosomal RNA molecule with a mass of 40 kDa. It is a structural and functional component of the large subunit of the ribosome in all domains of life, with the exception of mitochondrial ribosomes of fungi and animals. The designation 5S refers to the molecule's sedimentation velocity in an ultracentrifuge, which is measured in Svedberg units (S).

<span class="mw-page-title-main">Small nucleolar RNA SNORA40</span> Member of the H/ACA class of small nucleolar RNA

In molecular biology, the small nucleolar RNA ACA40 belongs to the H/ACA family of snoRNAs and guides the pseudouridylation of 28S rRNA subunit at position U4565. snoRNA ACA40 was discovered using large-scale cloning by Kiss et al. (2004) from a HeLa cell extract immunoprecipitated with an anti-GAR1 antibody. It is predicted to guide the pseudouridylation of residues 28S rRNA U4546 and 18S rRNA 1174. The pseudouridylation of these residues was reported by Ofengand and Bakin (1997) and Maden (1990). ACA1, ACA8, ACA18, ACA25, ACA32 and ACA40 and the C/D box snoRNAs mgh28S-2409 and mgh28S-2411 share the same host gene (MGC5306).

The RNA integrity number (RIN) is an algorithm for assigning integrity values to RNA measurements.

Ribosomal particles are denoted according to their sedimentation coefficients in Svedberg units. The 60S subunit is the large subunit of eukaryotic 80S ribosomes, with the other major component being the eukaryotic small ribosomal subunit (40S). It is structurally and functionally related to the 50S subunit of 70S prokaryotic ribosomes. However, the 60S subunit is much larger than the prokaryotic 50S subunit and contains many additional protein segments, as well as ribosomal RNA expansion segments.

<span class="mw-page-title-main">16S ribosomal RNA</span> RNA component

16S ribosomal RNA is the RNA component of the 30S subunit of a prokaryotic ribosome. It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.

<span class="mw-page-title-main">28S ribosomal RNA</span> RNA component of the large subunit of the eukaryotic ribosome

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.

The eukaryotic small ribosomal subunit (40S) is the smaller subunit of the eukaryotic 80S ribosomes, with the other major component being the large ribosomal subunit (60S). The "40S" and "60S" names originate from the convention that ribosomal particles are denoted according to their sedimentation coefficients in Svedberg units. It is structurally and functionally related to the 30S subunit of 70S prokaryotic ribosomes. However, the 40S subunit is much larger than the prokaryotic 30S subunit and contains many additional protein segments, as well as rRNA expansion segments.

<span class="mw-page-title-main">Eukaryotic ribosome</span> Large and complex molecular machine

Ribosomes are a large and complex molecular machine that catalyzes the synthesis of proteins, referred to as translation. The ribosome selects aminoacylated transfer RNAs (tRNAs) based on the sequence of a protein-encoding messenger RNA (mRNA) and covalently links the amino acids into a polypeptide chain. Ribosomes from all organisms share a highly conserved catalytic center. However, the ribosomes of eukaryotes are much larger than prokaryotic ribosomes and subject to more complex regulation and biogenesis pathways. Eukaryotic ribosomes are also known as 80S ribosomes, referring to their sedimentation coefficients in Svedberg units, because they sediment faster than the prokaryotic (70S) ribosomes. Eukaryotic ribosomes have two unequal subunits, designated small subunit (40S) and large subunit (60S) according to their sedimentation coefficients. Both subunits contain dozens of ribosomal proteins arranged on a scaffold composed of ribosomal RNA (rRNA). The small subunit monitors the complementarity between tRNA anticodon and mRNA, while the large subunit catalyzes peptide bond formation.

Ribosomopathies are diseases caused by abnormalities in the structure or function of ribosomal component proteins or rRNA genes, or other genes whose products are involved in ribosome biogenesis.

References

This article incorporates CC-By-2.0 text from the reference. [1]

  1. 1 2 3 4 5 6 7 8 9 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 70: 70. doi: 10.1186/1471-2148-10-70 . PMC   2841657 . PMID   20214780.
  2. 1 2 3 4 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.
  3. 1 2 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. doi:10.1126/science.3277277.
  4. ↑ 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. PMID   7008030.
  5. ↑ Salim M, Maden EH (1981). "Nucleotide sequence of Xenopus laevis 18S ribosomal RNA inferred from gene sequence". Nature . 291: 205–208. doi:10.1038/291205a0. PMID   7015146.
  6. 1 2 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.
  7. ↑ 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: 366–376. doi:10.1093/oxfordjournals.molbev.a040500. PMID   3136294.
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