18S ribosomal RNA

Last updated

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 have 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.

General organization of the eukaryotic nuclear rDNA tandem repeats consisting of ETS, 18S rRNA, ITS-1, 5.8S rRNA, ITS-2 and 28S rRNA. Eucaryot rdna.png
General organization of the eukaryotic nuclear rDNA tandem repeats consisting of ETS, 18S rRNA, ITS-1, 5.8S rRNA, ITS-2 and 28S rRNA.

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.

18S rRNA nucleotide length of selected species
SpeciesSize [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

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

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

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]

Related Research Articles

<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.

The ribosomal DNA consists of a group of ribosomal RNA encoding genes and related regulatory elements, and is widespread in similar configuration in all domains of life. The ribosomal DNA encodes the non-coding ribosomal RNA, integral structural elements in the assembly of ribosomes, its importance making it the most abundant section of RNA found in cells of eukaryotes. Additionally, these segments includes regulatory sections, such as an promotor specific to the RNA polymerase I, as well as 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.

In molecular biology, a hybridization probe (HP) is a fragment of DNA or RNA, usually 15–10000 nucleotides long, which can be radioactively or fluorescently labeled. HPs can be used to detect the presence of nucleotide sequences in analyzed RNA or DNA that are complementary to the sequence in the probe. The labeled probe is first denatured into single stranded DNA (ssDNA) and then hybridized to the target ssDNA or RNA immobilized on a membrane or in situ.

<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.

The Kozak consensus sequence is a nucleic acid motif that functions as the protein translation initiation site in most eukaryotic mRNA transcripts. Regarded as the optimum sequence for initiating translation in eukaryotes, the sequence is an integral aspect of protein regulation and overall cellular health as well as having implications in human disease. It ensures that a protein is correctly translated from the genetic message, mediating ribosome assembly and translation initiation. A wrong start site can result in non-functional proteins. As it has become more studied, expansions of the nucleotide sequence, bases of importance, and notable exceptions have arisen. The sequence was named after the scientist who discovered it, Marilyn Kozak. Kozak discovered the sequence through a detailed analysis of DNA genomic sequences.

<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">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 coefficient in an ultracentrifuge, which is measured in Svedberg units (S).

A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation. Mostly, RBS refers to bacterial sequences, although internal ribosome entry sites (IRES) have been described in mRNAs of eukaryotic cells or viruses that infect eukaryotes. Ribosome recruitment in eukaryotes is generally mediated by the 5' cap present on eukaryotic mRNAs.

<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.

Numerous key discoveries in biology have emerged from studies of RNA, including seminal work in the fields of biochemistry, genetics, microbiology, molecular biology, molecular evolution, and structural biology. As of 2010, 30 scientists have been awarded Nobel Prizes for experimental work that includes studies of RNA. Specific discoveries of high biological significance are discussed in this article.

James A. Lake is an American evolutionary biologist and a Distinguished Professor of Molecular, Cell, and Developmental Biology and of Human Genetics at UCLA. Lake is best known for the New Animal Phylogeny and for the first three-dimensional structure of the ribosome. He has also made significant contributions to understanding genome evolution across all kingdoms of life, including discovering informational and operational genes, elucidating the complexity hypothesis for gene transfer, rooting the tree of life, and understanding the early transition from prokaryotic to eukaryotic life.

Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods.

Microbial DNA barcoding is the use of DNA metabarcoding to characterize a mixture of microorganisms. DNA metabarcoding is a method of DNA barcoding that uses universal genetic markers to identify DNA of a mixture of organisms.

References

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

  1. 1 2 3 4 5 6 7 8 9 10 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.
  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. Bibcode:1988Sci...239..748F. doi:10.1126/science.3277277. PMID   3277277.
  4. 1 2 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.
  5. ↑ 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.
  6. ↑ 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.
  7. 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.
  8. ↑ 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.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.