The 5S ribosomal RNA (5S rRNA) is an approximately 120 nucleotide-long
ribosomal RNA
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 ribosom ...
molecule with a mass of 40
kDa
The dalton or unified atomic mass unit (symbols: Da or u) is a non-SI unit of mass widely used in physics and chemistry. It is defined as of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state and at re ...
. It is a structural and functional component of the large subunit of the
ribosome in all domains of life (
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
,
archaea, and
eukaryotes), with the exception of mitochondrial ribosomes of
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
and
animal
Animals are multicellular, eukaryotic organisms in the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, are Motilit ...
s. The designation 5S refers to the molecule's
sedimentation
Sedimentation is the deposition of sediments. It takes place when particles in suspension settle out of the fluid in which they are entrained and come to rest against a barrier. This is due to their motion through the fluid in response to the ...
velocity in an ultracentrifuge, which is measured in
Svedberg units (S).
Biosynthesis
In prokaryotes, the 5S rRNA gene is typically located in the rRNA
operons
In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splic ...
downstream of the small and the large
subunit rRNA, and co-transcribed into a
polycistronic
A cistron is an alternative term for "gene". The word cistron is used to emphasize that genes exhibit a specific behavior in a cis-trans test; distinct positions (or loci) within a genome are cistronic.
History
The words ''cistron'' and ''gene ...
precursor.
A particularity of eukaryotic nuclear genomes is the occurrence of multiple 5S rRNA gene copies (5S rDNA) clustered in tandem repeats, with copy number varying from species to species.
Eukaryotic 5S rRNA is synthesized by
RNA polymerase III
In eukaryote cells, RNA polymerase III (also called Pol III) is a protein that transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs.
The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose e ...
, whereas other eukaryotic rRNAs are cleaved from a 45S precursor transcribed by
RNA polymerase I. In ''
Xenopus
''Xenopus'' () (Gk., ξενος, ''xenos''=strange, πους, ''pous''=foot, commonly known as the clawed frog) is a genus of highly aquatic frogs native to sub-Saharan Africa. Twenty species are currently described within it. The two best-know ...
''
oocyte
An oocyte (, ), oöcyte, or ovocyte is a female gametocyte or germ cell involved in reproduction. In other words, it is an immature ovum, or egg cell. An oocyte is produced in a female fetus in the ovary during female gametogenesis. The femal ...
s, it has been shown that fingers 4–7 of the nine-
zinc finger
A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold. It was originally coined to describe the finger-like appearance of a hypothesized struct ...
transcription factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The f ...
TFIIIA can bind to the central region of 5S RNA.
Binding between 5S rRNA and TFIIIA serves to both repress further
transcription of the 5S RNA
gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
and stabilize the 5S RNA transcript until it is required for ribosome assembly.
Structure
The
secondary structure of 5S rRNA consists of five helices (denoted I-V in
roman numerals), four loops (B-E), and one hinge (A), which form together a Y-like structure. Loops C and D are terminal hairpins and loops B and E are internal.
According to phylogenetic studies, helices I and III are likely ancestral. Helix III includes two highly conserved adenosines. Helix V, with its hairpin structure, is thought to interact with TFIIIA.
Location within the ribosome
Using a variety of molecular techniques, including
immuno-electron microscopy,
cryo-electron microscopy
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample s ...
, intermolecular
chemical cross-linking, and
X-ray crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
, the location of the 5S rRNA within the large ribosomal subunit has been determined to great precision. In
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
and
archaea, the large ribosomal subunit (LSU) itself is composed of two RNA moieties, the 5S rRNA and another larger RNA known as
23S rRNA, along with numerous associated proteins.
In eukaryotes, the LSU contains 5S,
5.8S, and
28S rRNA
Crazy Eights is a shedding-type card game for two to seven players and the best known American member of the Eights Group which also includes Pig and Spoons. The object of the game is to be the first player to discard all of their cards. The ga ...
s and even more proteins.
The structure of LSU in 3-dimensions shows one relatively smooth surface and the opposite surface having three projections, notably the L1 protuberance, the central protuberance (CP), and the L7/L12 stalk. The L1 protuberance and L7/L12 stalk are arranged laterally surrounding CP. The 5S rRNA is located in the CP and participates in formation and structure of this projection. The other major constituents of the central protuberance include the 23S rRNA (or alternatively 28S in eukaryotes) and several proteins including L5, L18, L25, and L27.
Ribosomal functions
The exact function of 5S rRNA is not yet clear. In ''
Escherichia coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...
'', 5S rRNA gene deletions reduce the protein synthesis rate and have a more profound detrimental effect on cell fitness than deletions of a comparable number of copies of other (
16S and
23S) rRNA genes.
Crystallographic studies indicate that 5S rRNA-binding proteins and other proteins of the central protuberance of the LSU plays a role in binding tRNAs.
Also, the topographical and physical proximity between 5S rRNA and 23S rRNA, which forms the peptidyl transferase and GTPase-associating center, suggests that 5S rRNA acts as a mediator between the two functional centers of the ribosome by forming, together with 5S rRNA-binding proteins and other components of the central protuberance, intersubunit bridges and tRNA-binding sites.
Roles in ribosomal assembly
In eukaryotes, the cytosolic ribosome is assembled from four rRNAs and over 80 proteins.
Once transcribed, the 3' ends of 5S rRNA are processed by the exonucleases Rex1p, Rex2p, and Rex3p.
The
60S and
40S ribosomal subunits are exported from the nucleus to the cytoplasm where they join to form the mature and
translation
Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
-competent 80S ribosome. When exactly 5S rRNA is integrated into the ribosome remains controversial,
but it is generally accepted that 5S rRNA is incorporated into the 90S particle, which is a precursor to 60S particle, as part of a small ribosome-independent RNP complex formed by 5S rRNA and ribosomal protein L5.
Interactions with proteins
Several important proteins which interact with 5S rRNA are listed below.
La protein
Interaction of 5S rRNA with the
La protein prevents the RNA from degradation by exonucleases in the cell.
La protein is found in the nucleus in all eukaryotic organisms and associates with several types of RNAs transcribed by RNA pol III. La protein interacts with these RNAs (including the 5S rRNA) through their 3' oligo-uridine tract, aiding stability and folding of the RNA.
L5 protein
In eukaryotic cells, ribosomal protein L5 associates and stabilizes the 5S rRNA forming a pre-ribosomal
ribonucleoprotein particle
A ribonucleoprotein particle or RNP is vessicle complex formed between RNA and RNA-binding proteins (RBPs). The term RNP foci can also be used to denote intracellular compartments involved in processing of RNA transcripts.
RNA/RBP complexes
R ...
(RNP) that is found in both cytosol and the nucleus. L5 deficiency prevents transport of 5S rRNA to the nucleus and results in decreased ribosomal assembly.
Other ribosomal proteins
In prokaryotes the 5S rRNA binds to the L5, L18 and L25 ribosomal proteins, whereas in eukaryotes 5S rRNA is only known to bind the
L5 ribosomal protein.
In ''T. brucei'', the causative agent of
sleeping sickness
African trypanosomiasis, also known as African sleeping sickness or simply sleeping sickness, is an insect-borne parasitic infection of humans and other animals. It is caused by the species ''Trypanosoma brucei''. Humans are infected by two typ ...
, 5S rRNA interacts with two closely related RNA-binding proteins, P34 and P37, whose loss results in a lower global level of 5S rRNA.
Presence in organelle ribosomes
Translation machineries of
mitochondria and
plastids (organelles of endosymbiotic bacterial origin), and their bacterial relatives share many features but also display marked differences. Organelle genomes encode SSU and LSU rRNAs without exception, yet the distribution of 5S rRNA genes (''rrn5'') is most uneven. ''Rrn5'' is easily identified and common in genomes of most plastids. In contrast, mitochondrial ''rrn5'' initially appeared to be restricted to plants and a small number of protists. Additional, more divergent organellar 5S rRNAs were only identified with specialized covariance models that incorporate information on the pronounced sequence composition bias and structural variation.
This analysis pinpointed additional 5S rRNA genes not only in mitochondrial genomes of most
protist
A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the exc ...
lineages, but also in genomes of certain
apicoplasts (non-photosynthetic plastids of pathogenic protozoa such as ''
Toxoplasma gondii'' and ''
Eimeria tenella
''Eimeria tenella'' is a species of ''Eimeria'' that causes hemorrhagic cecum, cecal coccidiosis in young poultry. It is found worldwide.
Description
This species has a Monoxenous development, monoxenous life cycle with the only definitive hos ...
'').
Mitochondrial 5S rRNAs of most
stramenopiles
Stramenopile is a clade of organisms distinguished by the presence of stiff tripartite external hairs. In most species, the hairs are attached to flagella, in some they are attached to other areas of the cellular surface, and in some they have be ...
comprise the largest diversity of secondary structures.
The permuted mitochondrial 5S rRNAs in
brown algae
Brown algae (singular: alga), comprising the class Phaeophyceae, are a large group of multicellular algae, including many seaweeds located in colder waters within the Northern Hemisphere. Brown algae are the major seaweeds of the temperate and p ...
represent the most unconventional case, where the closing helix I, which otherwise brings together the molecule's 5′ and 3′ ends, is replaced by a (closed) hairpin resulting in an open three-way junction.
Current evidence indicates that
mitochondrial DNA of only a few groups, notably
animal
Animals are multicellular, eukaryotic organisms in the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, are Motilit ...
s,
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
,
alveolates and
euglenozoans lacks the gene.
The
central protuberance, otherwise occupied by 5S rRNA and its associated proteins (see Figure 2), was remodeled in various ways. In the fungal mitochondrial ribosomes, 5S rRNA is replaced by LSU rRNA expansion sequences. In
kinetoplastids (euglenozoans), the central protuberance is made entirely of evolutionarily novel mitochondrial ribosomal proteins. Lastly, animal mitochondrial ribosomes have coopted a specific mitochondrial tRNA (Val in vertebrates) to substitute the missing 5S rRNA.
See also
*
50S
*
Ribosome
*
Translation (biology)
In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire proces ...
References
External links
*
5SData
*
*
''Halococcus morrhuae'' (archaebacterium) 5S rRNA
{{Ribosome subunits
Ribosomal RNA