18S ribosomal RNA
Encyclopedia
18S
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.
It is the eukaryotic nuclear homologue of 16S ribosomal RNA
in Prokaryote
s and mitochondria.
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 invertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences.
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. In general, rRNA gene sequences are easy to access due to highly conserved flanking regions allowing for the use of universal primer
s. Their repetitive arrangement within the genome provides excessive amounts of template DNA for PCR, even in 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) - the gene was celebrated as the prime candidate for reconstructing the metazoan tree of life
. 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.
During recent years 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
. Failure to obtain 18S sequences of single taxa is considered a common phenomenon but is rarely ever reported. Secondly, in contrast to initially high hopes, 18S cannot resolve nodes at all taxonomic levels and its efficacy varies considerably among clade
s. 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.
Svedberg
A svedberg is a non-SI physical unit used for sedimentation coefficients. It characterizes the behaviour of a particle type in sedimentation processes, notably centrifugation. The svedberg is technically a measure of time, and is defined as exactly 10-13 seconds A svedberg (symbol S, sometimes...
ribosomal RNA (abbreviated 18S rRNA) is a part of the ribosomal RNA
Ribosomal RNA
Ribosomal ribonucleic acid is the RNA component of the ribosome, the enzyme that is the site of protein synthesis in all living cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity...
. The S in 18S represents Svedberg
Svedberg
A svedberg is a non-SI physical unit used for sedimentation coefficients. It characterizes the behaviour of a particle type in sedimentation processes, notably centrifugation. The svedberg is technically a measure of time, and is defined as exactly 10-13 seconds A svedberg (symbol S, sometimes...
units. 18S rRNA is a component of the small eukaryotic ribosomal subunit (40S
40S
40S is the small subunit of eukaryotic ribosomes.It interacts with the internal ribosome entry site of the hepatitis C virus.The following is a list of proteins contained in the 40S ribosome:...
). 18S rRNA is the structural RNA for the small component of eukaryotic cytoplasmic ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
s, and thus one of the basic components of all eukaryotic cells.
It is the eukaryotic nuclear homologue of 16S ribosomal RNA
16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
in Prokaryote
Prokaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...
s and mitochondria.
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 invertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences.
Uses in phylogeny
The small subunit (SSU) 18S rRNA geneGene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
is one of the most frequently used genes in phylogenetic studies and an important marker for random target polymerase chain reaction
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
(PCR) in environmental biodiversity screening. In general, rRNA gene sequences are easy to access due to highly conserved flanking regions allowing for the use of universal primer
Primer
Primer may refer to:*Primer , a 1995 music album by the musical group Rockapella*Primer *Primer , a 2004 feature film written and directed by Shane Carruth...
s. Their repetitive arrangement within the genome provides excessive amounts of template DNA for PCR, even in 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) - the gene was celebrated as the prime candidate for reconstructing the metazoan tree of life
Tree of life
The concept of a tree of life, a many-branched tree illustrating the idea that all life on earth is related, has been used in science , religion, philosophy, mythology, and other areas...
. And in fact, 18S sequences later provided evidence for the splitting of Ecdysozoa
Ecdysozoa
Ecdysozoa is a group of protostome animals, including Arthropoda , Nematoda, and several smaller phyla. They were first defined by Aguinaldo et al. in 1997, based mainly on trees constructed using 18S ribosomal RNA genes...
and Lophotrochozoa
Lophotrochozoa
The Lophotrochozoa are a major grouping of protostome animals. The taxon was discovered based on molecular data. Molecular evidence such as a result of studies of the evolution of small-subunit ribosomal RNA supports the monophyly of the phyla listed in the infobox shown at right.-Terminology:The...
, thus contributing to the most recent revolutionary change in our understanding of metazoan relationships.
During recent years 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
Remipedia
Remipedia is a class of blind crustaceans found in coastal aquifers which contain saline groundwater, with populations identified in almost every ocean basin so far explored, including in Australia, the Caribbean Sea, the Atlantic Ocean...
. Failure to obtain 18S sequences of single taxa is considered a common phenomenon but is rarely ever reported. Secondly, in contrast to initially high hopes, 18S cannot resolve nodes at all taxonomic levels and its efficacy varies considerably among clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
s. 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.