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Ribosomal ribonucleic acid (rRNA) is a type of
non-coding RNA A non-coding RNA (ncRNA) is an RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consisting of very large molecule File:Pentacene on Ni(111) STM.jpg, A s ...
which is the primary component of
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
s, essential to all cells. rRNA is a
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonst ...

ribozyme
which carries out
protein synthesis Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside Cell (biology), cells, homeostasis, balancing the loss of cellular proteins (via Proteolysis, degradation or Protein targeting, export) through the producti ...

protein synthesis
in ribosomes. Ribosomal RNA is transcribed from
ribosomal DNA Ribosomal DNA (rDNA) is a sequence that codes for . These sequences regulate initiation and amplification, and contain both transcribed and non-transcribed segments. In the there are 5 chromosomes with nucleolus organizer regions: the chrom ...
(rDNA) and then bound to
ribosomal protein A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with Ribosomal RNA, rRNA, make up the Ribosome, ribosomal subunits involved in the cellular process of translation (genetics), translation. ''E. coli'', other b ...
s to form
small Small may refer to: Science and technology * SMALL Small may refer to: Science and technology * SMALL, an ALGOL-like programming language * Small (anatomy), the lumbar region of the back * Small (journal), ''Small'' (journal), a nano-science pub ...
and
large Large means of great size. Large may also refer to: Mathematics * Arbitrarily large, a phrase in mathematics * Large cardinal, a property of certain transfinite numbers * Large category, a category with a proper class of objects and morphisms (or ...
ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces
transfer RNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor composed of , typically 76 to 90 in length (in eukaryotes), that serves as the physical link between the and the sequence of proteins. Transfer RN ...
(tRNA) and
messenger RNA In molecular biology Molecular biology is the branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, molecular synthesis, modification, m ...
(mRNA) to process and
translate 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 ...

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 by mass.


Structure

Although the
primary structure Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon ...

primary structure
of rRNA sequences can vary across organisms,
base-pairing A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both D ...
within these sequences commonly forms
stem-loop An example of an RNA stem-loop Stem-loop intramolecular base pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids Nucleic acids are biopolymer Biopolymers are natural polymers produced by the cells of Organism, living ...

stem-loop
configurations. The length and position of these rRNA stem-loops allow them to create three-dimensional rRNA structures that are similar across
species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individu ...

species
. Because of these configurations, rRNA can form tight and specific interactions with ribosomal proteins to form ribosomal subunits. These ribosomal proteins contain basic residues (as opposed to acidic residues) and aromatic residues (i.e.
phenylalanine Phenylalanine (symbol Phe or F) is an essential α-amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen ...

phenylalanine
,
tyrosine -Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemi ...

tyrosine
and
tryptophan Tryptophan (symbol Trp or W) is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a non-polar Aromatic hydrocarbon, aromatic amino ...

tryptophan
) allowing them to form chemical interactions with their associated RNA regions, such as stacking interactions. Ribosomal proteins can also cross-link to the sugar-phosphate backbone of rRNA with binding sites that consist of basic residues (i.e. lysine and arginine). All ribosomal proteins (including the specific sequences that bind to rRNA) have been identified. These interactions along with the association of the small and large ribosomal subunits result in a functioning ribosome capable of synthesizing
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s. Ribosomal RNA organizes into two ribosomal subunits: the large ribosomal subunit (
LSU Louisiana State University (officially Louisiana State University and Agricultural and Mechanical College, commonly referred to as LSU) is a public In public relations and communication science, publics are groups of individual people, and ...
) and small ribosomal subunit ( SSU). Between these subunits, the rRNA types used to form the subunit differ. In the ribosomes of prokaryotes such as
bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of biological cell The cell (from Latin ''cella'', meaning "small room") is the basic structural, functional, and biological unit of all known organisms. Cells are the sm ...

bacteria
, the SSU contains a single small rRNA molecule (~1500 nucleotides) while the LSU contains one single small rRNA and a single large rRNA molecule (~3000 nucleotides). These are combined with ~50 ribosomal
proteins Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a Nobe ...
to form ribosomal subunits. There are three types of rRNA found in prokaryotic ribosomes: 23S and 5S rRNA in the LSU and 16S rRNA in the SSU. In the ribosomes of eukaryotes such as
human Humans (''Homo sapiens'') are the most abundant and widespread species In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes ...

human
s, the SSU contains a single small rRNA (~1800 nucleotides) while the LSU contains two small rRNAs and one molecule of large rRNA (~5000 nucleotides). Eukaryotic rRNA has over 70 ribosomal
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s which interact to form larger and more polymorphic ribosomal units in comparison to prokaryotes. There are four types of rRNA in eukaryotes: 3 species in the LSU and 1 in the SSU.
Yeast Yeasts are eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classifie ...

Yeast
has been the traditional model for observation of
eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryotic
rRNA behavior and processes, leading to a deficit in diversification of research. It has only been within the last decade that technical advances (specifically in the field of
Cryo-EM Cryo-TEM image of GroEL suspended in amorphous ice">GroEL.html" ;"title="Cryo-TEM image of GroEL">Cryo-TEM image of GroEL suspended in amorphous ice at × magnification Cryogenic electron microscopy (cryo-EM) is an electron microscopy An el ...
) have allowed for preliminary investigation into ribosomal behavior in other
eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryote
s. In
yeast Yeasts are eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classifie ...

yeast
, the LSU contains the 5S, 5.8S and 28S rRNAs. The combined 5.8S and 28S are roughly equivalent in size and function to the prokaryotic 23S rRNA subtype, minus expansion segments (ESs) that are localized to the surface of the
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
which were thought to occur only in
eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryote
s. However recently, the
Asgard Asgard (Old Norse Old Norse, Old Nordic, or Old Scandinavian is a stage of development of North Germanic languages, North Germanic dialects before their final divergence into separate Nordic languages. Old Norse was spoken by inhabitants ...
phyla, namely,
Lokiarchaeota Lokiarchaeota is a proposed phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical category of number. The ...
and
Heimdallarchaeota Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea Archaea ( ; singular archaeon ) constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Ar ...
, considered the closest archaeal relatives to
Eukarya Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...
, were reported to possess two supersized ESs in their 23S rRNAs. Likewise, the 5S rRNA contains a 108‐nucleotide insertion in the ribosomes of the halophilic archaeon ''Halococcus morrhuae''. A eukaryotic SSU contains the 18S rRNA subunit, which also contains ESs. SSU ESs are generally smaller than LSU ESs. SSU and LSU rRNA sequences are widely used for study of
evolutionary relationships
evolutionary relationships
among organisms, since they are of ancient origin, are found in all known forms of life and are resistant to
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
. rRNA sequences are conserved (unchanged) over time due to their crucial role in the function of the ribosome.
Phylogenic In biology, phylogenetics (from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον () "tribe, clan, race", and wikt:γενετικός, γενετικός () "origin, source, birth") is a part of systematics that addresse ...

Phylogenic
information derived from the 16s rRNA is currently used as the main method of delineation between similar prokaryotic species by calculating
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, c ...

nucleotide
similarity. The canonical tree of life is the lineage of the translation system. LSU rRNA subtypes have been called
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonst ...

ribozyme
s because ribosomal proteins cannot bind to the catalytic site of the
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
in this area (specifically the
peptidyl transferase The peptidyl transferase is an aminoacyltransferase () as well as the primary enzymatic Enzymes () are protein Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residue (biochem ...
center, or PTC). The SSU rRNA subtypes decode mRNA in its decoding center (DC). Ribosomal proteins cannot enter the DC. The structure of rRNA is able to drastically change to affect tRNA binding to the ribosome during translation of other mRNAs. In 16s rRNA, this is thought to occur when certain nucleotides in the rRNA appear to alternate base pairing between one nucleotide or another, forming a "switch" that alters the rRNA's conformation. This process is able to affect the structure of the LSU and SSU, suggesting that this conformational switch in the rRNA structure affects the entire ribosome in its ability to match a codon with its anticodon in tRNA selection as well as decode mRNA.


Assembly

Ribosomal RNA's integration and assembly into
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
s begins with their folding, modification, processing and assembly with
ribosomal protein A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with Ribosomal RNA, rRNA, make up the Ribosome, ribosomal subunits involved in the cellular process of translation (genetics), translation. ''E. coli'', other b ...
s to form the two ribosomal subunits, the LSU and the SSU. In
Prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s, rRNA incorporation occurs in the cytoplasm due to the lack of membrane-bound organelles. In
Eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

Eukaryote
s, however, this process primarily takes place in the
nucleolus The nucleolus (, plural: nucleoli ) is the largest structure in the nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucl ...

nucleolus
and is initiated by the synthesis of pre-RNA. This requires the presence of all three RNA polymerases. In fact, the transcription of pre-RNA by RNA polymerase I accounts for about 60% of cell's total cellular RNA transcription. This is followed by the folding of the pre-RNA so that it can be assembled with ribosomal proteins. This folding is catalyzed by endo- and
exonuclease Exonucleases are enzymes Enzymes () are protein Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions wi ...
s, RNA
helicase Structure of ''Escherichia coli, E. coli'' helicase RuvA Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genes. They are motor proteins that move Directionality (molecular biolo ...

helicase
s,
GTPase GTPases are a large family of hydrolase Hydrolase is a class of enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substr ...
s and
ATPase ATPases (, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, SV40 T-antigen, adenosine 5'-triphosphatase, ATP hydrolase, complex V (mitochondrial electron transport), (Ca2+ + Mg2+)-ATPase, HCO3−-ATPase, adenosine triphosphatase) a ...
s. The rRNA subsequently undergoes endo- and exonucleolytic processing to remove external and
internal transcribed spacer Internal transcribed spacer (ITS) is the spacer DNA situated between the small-subunit ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosome Ribosomes () are macromolecular m ...
s. The pre-RNA then undergoes modifications such as
methylation In the chemical sciences, methylation denotes the addition of a methyl group A methyl group is an alkyl derived from methane, containing one carbon atom chemical bond, bonded to three hydrogen atoms — CH3. In chemical formula, fo ...

methylation
or pseudouridinylation before ribosome assembly factors and ribosomal proteins assemble with the pre-RNA to form pre-ribosomal particles. Upon going under more maturation steps and subsequent exit from the nucleolus into the cytoplasm, these particles combine to form the ribosomes. The basic and
aromatic forms of benzene (top) combine to produce an average structure (bottom) In chemistry, aromaticity is a property of cyclic compound, cyclic (ring (chemistry), ring-shaped), plane (geometry), planar (flat) structures with pi bonds in Resonance (che ...
residues found within the primary structure of rRNA allow for favorable
stacking Stacking may refer to: Arts and media * Stacking (video game), ''Stacking'' (video game), a 2011 game from Double Fine * ''Stacking'', a 1987 TV movie directed and produced by Martin Rosen (director), Martin Rosen * Stacking, a technique in Broad ...
interactions and attraction to ribosomal proteins, creating a cross-linking effect between the backbone of rRNA and other components of the ribosomal unit. More detail on the initiation and beginning portion of these processes can be found in the "Biosynthesis" section.


Function

Universally conserved secondary structural elements in rRNA among different species show that these sequences are some of the oldest discovered. They serve critical roles in forming the catalytic sites of translation of mRNA. During translation of mRNA, rRNA functions to bind both mRNA and tRNA to facilitate the process of translating mRNA's codon sequence into amino acids. rRNA initiates the catalysis of protein synthesis when tRNA is sandwiched between the SSU and LSU. In the SSU, the mRNA interacts with the anticodons of the tRNA. In the LSU, the amino acid acceptor stem of the tRNA interacts with the LSU rRNA. The ribosome catalyzes ester-amide exchange, transferring the C-terminus of a nascent peptide from a tRNA to the amine of an amino acid. These processes are able occur due to sites within the ribosome in which these molecules can bind, formed by the rRNA stem-loops. A ribosome has three of these binding sites called the A, P and E sites: * In general, the A (aminoacyl) site contains an aminoacyl-tRNA (a
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five ca ...
esterified to an amino acid on the 3' end). * The P (peptidyl) site contains a
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five ca ...
esterified An ester is a chemical compound A chemical compound is a chemical substance composed of many identical molecules (or molecular entity, molecular entities) composed of atoms from more than one chemical element, element held together by chemical ...
to the nascent peptide. The free amino (NH2) group of the A site
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five ca ...
attacks the ester linkage of P site tRNA, causing transfer of the nascent peptide to the amino acid in the A site. This reaction is takes place in the peptidyl transferase center * The E (exit) site contains a
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five ca ...
that has been discharged, with a free 3' end (with no amino acid or nascent peptide). A single
mRNA upright=1.2, The "life cycle" of an mRNA in a eukaryotic cell. transcribed in the cell nucleus">nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central r ...
can be translated simultaneously by multiple ribosomes. This is called a
polysome A polyribosome (or polysome or ergosome) is a group of ribosomes bound to an mRNA molecule like “beads” on a “thread”. It consists of a complex of an mRNA molecule and two or more ribosome Ribosomes ( ), also called Palade granules, are ...
. In
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s, much work has been done to further identify the importance of rRNA in translation of
mRNA upright=1.2, The "life cycle" of an mRNA in a eukaryotic cell. transcribed in the cell nucleus">nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central r ...
. For example, it has been found that the A site consists primarily of 16S rRNA. Apart from various protein elements that interact with
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five ca ...
at this site, it is hypothesized that if these proteins were removed without altering ribosomal structure, the site would continue to function normally. In the P site, through the observation of
crystal structure In crystallography Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids (see crystal structure). The word "crystallography" is derived from the Greek words ''crystallon'' "cold drop, frozen ...

crystal structure
s it has been shown the 3' end of 16s rRNA can fold into the site as if a molecule of
mRNA upright=1.2, The "life cycle" of an mRNA in a eukaryotic cell. transcribed in the cell nucleus">nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central r ...
. This results in intermolecular interactions that stabilize the subunits. Similarly, like the A site, the P site primarily contains rRNA with few
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s. The
peptidyl transferase The peptidyl transferase is an aminoacyltransferase () as well as the primary enzymatic Enzymes () are protein Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residue (biochem ...
center, for example, is formed by
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, c ...

nucleotide
s from the 23S rRNA subunit. In fact, studies have shown that the
peptidyl transferase The peptidyl transferase is an aminoacyltransferase () as well as the primary enzymatic Enzymes () are protein Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residue (biochem ...
center contains no proteins, and is entirely initiated by the presence of rRNA. Unlike the A and P sites, the E site contains more
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s. Because
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s are not essential for the functioning of the A and P sites, the E site molecular composition shows that it is perhaps evolved later. In primitive
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
s, it is likely that
tRNAs A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the Messenger RNA, mRNA ...
exited from the P site. Additionally, it has been shown that E-site
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five ca ...
bind with both the 16S and 23S rRNA subunits.


Subunits and associated ribosomal RNA

Both
prokaryotic A prokaryote is a typically unicellular organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biology, properties of life. It is a syn ...
and
eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryotic
ribosomes can be broken down into two subunits, one large and one small. The exemplary species used in the table below for their respective rRNAs are the bacterium ''
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 Gram-negative bacteria are bacteria that do not retain the crystal violet st ...

Escherichia coli
'' (
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
) and human (
eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryote
). Note that "nt" represents the length of the rRNA type in nucleotides and the "S" (such as in "16S) represents
Svedberg A Svedberg unit (symbol S, sometimes Sv) is a non- SI metric unit for sedimentation coefficientThe sedimentation coefficient ''(s)'' of a particle characterizes its sedimentation during centrifugation. It is defined as the ratio of a particle's s ...
units. S units of the subunits (or the rRNAs) cannot simply be added because they represent measures of sedimentation rate rather than of mass. The sedimentation rate of each subunit is affected by its shape, as well as by its mass. The nt units can be added as these represent the integer number of units in the linear rRNA polymers (for example, the total length of the human rRNA = 7216 nt).
Gene cluster A gene family is a set of homologous genes within one organism. A gene cluster is a group of two or more gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mend ...
s coding for rRNA are commonly called "
ribosomal DNA Ribosomal DNA (rDNA) is a sequence that codes for . These sequences regulate initiation and amplification, and contain both transcribed and non-transcribed segments. In the there are 5 chromosomes with nucleolus organizer regions: the chrom ...
" or rDNA (note that the term seems to imply that ribosomes contain DNA, which is not the case).


In prokaryotes

In
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s a small 30S ribosomal subunit contains the 16S ribosomal RNA. The large 50S ribosomal subunit contains two rRNA species (the 5S and 23S ribosomal RNAs). Therefore it can be deduced that in both
bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of biological cell The cell (from Latin ''cella'', meaning "small room") is the basic structural, functional, and biological unit of all known organisms. Cells are the sm ...

bacteria
and
archaea Archaea ( ; singular archaeon ) constitute a domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a pa ...

archaea
there is one rRNA gene that codes for all three rRNA types :16S, 23S and 5S. Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed
operon In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions ...

operon
. As shown by the image in this section, there is an
internal transcribed spacer Internal transcribed spacer (ITS) is the spacer DNA situated between the small-subunit ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosome Ribosomes () are macromolecular m ...
between 16S and 23S rRNA
gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meaning ''generation'' or ''birth'' ) is a basic unit of her ...

gene
s. There may be one or more copies of the
operon In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions ...

operon
dispersed in the
genome In the fields of molecular biology and genetics, a genome is all genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The genome includes both the genes (the coding regions) and the noncodin ...

genome
(for example, ''
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 Gram-negative bacteria are bacteria that do not retain the crystal violet st ...

Escherichia coli
'' has seven). Typically in bacteria there are between one and fifteen copies.
Archaea Archaea ( ; singular archaeon ) constitute a domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a pa ...

Archaea
contains either a single rRNA gene
operon In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions ...

operon
or up to four copies of the same
operon In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions ...

operon
. The 3' end of the 16S ribosomal RNA (in a ribosome) recognizes a sequence on the 5' end of
mRNA upright=1.2, The "life cycle" of an mRNA in a eukaryotic cell. transcribed in the cell nucleus">nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central r ...
called the .


In eukaryotes

In contrast,
eukaryotes Eukaryotes () are organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biology, properties of life. It is a synonym for "Outline ...
generally have many copies of the rRNA genes organized in
tandem repeats Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form tandem repeats within their amino acid primary structure, such as armadil ...
. In humans, approximately 300–400 repeats are present in five clusters, located on
chromosomes A chromosome is a long DNA molecule with part or all of the genome, genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by Chaperone (protein), chaperone proteins, bind to and D ...
13 (
RNR1 RNA, ribosomal 1, also known as RNR1, is a human gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meanin ...
), 14 (
RNR2RNA, ribosomal 2, also known as RNR2, is a human gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meaning ...
), 15 (
RNR3 RNA, ribosomal 3, also known as RNR3, is a human gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meanin ...
), 21 (
RNR4 RNA, ribosomal 4, also known as RNR4, is a human gene. References Further reading

* Nucleolus organizer regions are chromosomal regions crucial for the formation of the nucleolus, located on the short arms of the acrocentric chromosomes 13, ...
) and 22 (
RNR5 RNA, ribosomal 5, also known as RNR5, is a human gene. Genes for ribosomal RNA are clustered on the short arms of chromosomes Chromosome 13 (human), 13, Chromosome 14 (human), 14, Chromosome 15 (human), 15, Chromosome 20 (human), 20, Chromosome 21 ( ...
). Diploid humans have 10 clusters of genomic rDNA which in total make up less than 0.5% of the
human genome The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual Mitochondrial DNA, mitochondria. These are usually treated se ...

human genome
. It was previously accepted that repeat rDNA sequences were identical and served as redundancies or failsafes to account for natural replication errors and
point mutation 350px, Schematic of a single-stranded RNA molecule illustrating a series of three-base codons. Each three-nucleotide codon corresponds to an amino acid">nucleotide.html" ;"title="codons. Each three-nucleotide">codons. Each three-nucleotide codon ...

point mutation
s. However, sequence variation in rDNA (and subsequently rRNA) in humans across multiple
chromosome A chromosome is a long DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A mole ...

chromosome
s has been observed, both within and between human individuals. Many of these variations are
palindromic sequence A palindromic sequence is a nucleic acid sequence in a double-stranded DNA or RNA molecule wherein reading in a certain direction (e.g. 5' to 3') on one strand matches the sequence reading in the opposite direction (e.g. 5' to 3') on the complem ...
s and potential errors due to replication. Certain variants are also expressed in a tissue-specific manner in mice. Mammalian cells have 2 mitochondrial ( 12S and 16S) rRNA molecules and 4 types of cytoplasmic rRNA (the 28S, 5.8S, 18S, and 5S subunits). The 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by 2 internally transcribed spacers. The first spacer corresponds to the one found in bacteria and
archaea Archaea ( ; singular archaeon ) constitute a domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a pa ...

archaea
, and the other spacer is an insertion into what was the 23S rRNA in prokaryotes. The 45S rDNA is organized into 5 clusters (each has 30–40 repeats) on chromosomes 13, 14, 15, 21, and 22. These are transcribed by
RNA polymerase I RNA polymerase 1 (also known as Pol I) is, in higher eukaryotes Eukaryotes () are organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the ...
. The DNA for the 5S subunit occurs in tandem arrays (~200–300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is transcribed by
RNA polymerase III In eukaryote cells, RNA polymerase III (also called Pol III) 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 expression is requi ...
. The 18S rRNA in most
eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryote
s is in the small ribosomal subunit, and the large subunit contains three rRNA species (the 5S, 5.8S and
28S 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 ...
in mammals, 25S in plants, rRNAs). The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by
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 Diffraction, diffract into many specific directions. By measurin ...

X-ray crystallography
. The secondary structure of SSU rRNA contains 4 distinct domains—the 5', central, 3' major and 3' minor domains. A model of the
secondary structure Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an elect ...
for the 5' domain (500-800
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, c ...

nucleotide
s) is shown.


Biosynthesis


In eukaryotes

As the building-blocks for the
organelle In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, ...
, production of rRNA is ultimately the
rate-limiting step In chemical kinetics Chemical kinetics, also known as reaction kinetics, is the branch of physical chemistry Physical chemistry is the study of macroscopic The macroscopic scale is the length scale on which objects or phenomena are large enoug ...
in the synthesis of a
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
. In the
nucleolus The nucleolus (, plural: nucleoli ) is the largest structure in the nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucl ...

nucleolus
, rRNA is synthesized by
RNA polymerase I RNA polymerase 1 (also known as Pol I) is, in higher eukaryotes Eukaryotes () are organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the ...
using the specialty genes ( rDNA) that encode for it, which are found repeatedly throughout the
genome In the fields of molecular biology and genetics, a genome is all genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The genome includes both the genes (the coding regions) and the noncodin ...

genome
. The genes coding for 18S, 28S and 5.8S rRNA are located in the
nucleolus organizer region] Nucleolus organizer regions (NORs) are chromosome, chromosomal regions crucial for the formation of the nucleolus The nucleolus (, plural: nucleoli ) is the largest structure in the nucleus of eukaryotic cells. It is best known as the site ...
and are transcribed into large precursor rRNA (pre-rRNA) molecules by
RNA polymerase I RNA polymerase 1 (also known as Pol I) is, in higher eukaryotes Eukaryotes () are organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the ...
. These pre-rRNA molecules are separated by external and internal spacer sequences and then Methylation, methylated, which is key for later assembly and Protein folding, folding. After separation and release as individual molecules, assembly proteins bind to each naked rRNA strand and fold it into its functional form using cooperative assembly and progressive addition of more folding proteins as needed. The exact details of how the folding proteins bind to the rRNA and how correct folding is achieved remains unknown. The rRNA complexes are then further processed by reactions involving exo- and endo-nucleolytic cleavages guided by Small nucleolar RNA, snoRNA (small nucleolar RNAs) in complex with proteins. As these complexes are compacted together to form a cohesive unit, interactions between rRNA and surrounding ribosomal
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s are constantly remodeled throughout assembly in order to provide stability and protect binding sites. This process is referred to as the "maturation" phase of the rRNA lifecycle. The modifications that occur during maturation of rRNA have been found to contribute directly to control of gene expression by providing physical regulation of translational access of tRNA and
mRNA upright=1.2, The "life cycle" of an mRNA in a eukaryotic cell. transcribed in the cell nucleus">nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central r ...
. Some studies have found that extensive
methylation In the chemical sciences, methylation denotes the addition of a methyl group A methyl group is an alkyl derived from methane, containing one carbon atom chemical bond, bonded to three hydrogen atoms — CH3. In chemical formula, fo ...

methylation
of various rRNA types is also necessary during this time to maintain
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
stability. The genes for 5S rRNA are located inside the
nucleolus The nucleolus (, plural: nucleoli ) is the largest structure in the nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucl ...

nucleolus
and are transcribed into pre-5S rRNA by
RNA polymerase III In eukaryote cells, RNA polymerase III (also called Pol III) 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 expression is requi ...
. The pre-5S rRNA enters the
nucleolus The nucleolus (, plural: nucleoli ) is the largest structure in the nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucl ...

nucleolus
for processing and assembly with 28S and 5.8S rRNA to form the LSU. 18S rRNA forms the SSUs by combining with numerous
ribosomal protein A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with Ribosomal RNA, rRNA, make up the Ribosome, ribosomal subunits involved in the cellular process of translation (genetics), translation. ''E. coli'', other b ...
s. Once both subunits are assembled, they are individually exported into the cytoplasm to form the 80S unit and begin initiation of translation of
mRNA upright=1.2, The "life cycle" of an mRNA in a eukaryotic cell. transcribed in the cell nucleus">nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central r ...
. Ribosomal RNA is Non-coding RNA, non-coding and is never translated into
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s of any kind: rRNA is only Transcription (biology), transcribed from rDNA and then matured for use as a structural building block for ribosomes. Transcribed rRNA is bound to
ribosomal protein A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with Ribosomal RNA, rRNA, make up the Ribosome, ribosomal subunits involved in the cellular process of translation (genetics), translation. ''E. coli'', other b ...
s to form the subunits of
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
s and acts as the physical structure that pushes
mRNA upright=1.2, The "life cycle" of an mRNA in a eukaryotic cell. transcribed in the cell nucleus">nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central r ...
and
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five ca ...
through the
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
to process and translate them.


Eukaryotic regulation

Synthesis of rRNA is Downregulation and upregulation, up-regulated and down-regulated to maintain homeostasis by a variety of processes and interactions: * The kinase AKT indirectly promotes synthesis of rRNA as RNA polymerase I is AKT-dependent. * Certain angiogenic ribonucleases, such as angiogenin (ANG), can translocate and accumulate in the
nucleolus The nucleolus (, plural: nucleoli ) is the largest structure in the nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucl ...

nucleolus
. When the concentration of ANG becomes too high, some studies have found that ANG can bind to the Promoter (genetics), promoter region of rDNA and unnecessarily increase rRNA transcription. This can be damaging to the nucleolus and can even lead to unchecked transcription and cancer. * During times of cellular glucose restriction, AMP-activated protein kinase (AMPK) discourages Metabolism, metabolic processes that consume energy but are non-essential. As a result, it is capable of phosphorylating
RNA polymerase I RNA polymerase 1 (also known as Pol I) is, in higher eukaryotes Eukaryotes () are organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the ...
(at the Ser-635 site) in order to down-regulate rRNA synthesis by disrupting transcription initiation. * Impairment or removal of more than one pseudouridine or 29-O-methylation regions from the ribosome decoding center significantly reduces rate of rRNA Transcription (biology), transcription by reducing the rate of incorporation of new amino acids. * Formation of heterochromatin is essential to silencing rRNA transcription, without which ribosomal RNA is synthesized unchecked and greatly decreases the lifespan of the organism.


In prokaryotes

Similar to
eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryote
s, the production of rRNA is the Rate-determining step, rate-limiting step in the
prokaryotic A prokaryote is a typically unicellular organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biology, properties of life. It is a syn ...
synthesis of a
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
. In ''E. coli,'' it has been found that rRNA is Transcription (biology), transcribed from the two promoters P1 and P2 found within seven different ''rrn''
operon In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions ...

operon
s. The P1 Promoter (genetics), promoter is specifically responsible for regulating rRNA synthesis during moderate to high bacterial growth rates. Because the transcriptional activity of this Promoter (genetics), promoter is directly proportional to the growth rate, it is primarily responsible for rRNA Regulation of gene expression, regulation. An increased rRNA concentration serves as a negative feedback mechanism to ribosome synthesis. High NTP concentration has been found to be required for efficient Transcription (biology), transcription of the ''rrn'' P1 promoters. They are thought to form stabilizing complexes with RNA polymerase and the Promoter (genetics), promoters. In
bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of biological cell The cell (from Latin ''cella'', meaning "small room") is the basic structural, functional, and biological unit of all known organisms. Cells are the sm ...

bacteria
specifically, this association of high NTP concentration with increased rRNA synthesis provides a molecular explanation as to why ribosomal and thus protein synthesis is dependent on growth-rate. A low growth-rate yields lower rRNA / ribosomal synthesis rates while a higher growth rate yields a higher rRNA / ribosomal synthesis rate. This allows a cell to save energy or increase its metabolic activity dependent on its needs and available resources. In Prokaryote, prokaryotic cells, each rRNA gene or
operon In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions ...

operon
is transcribed into a single RNA precursor that includes 16S, 23S, 5S rRNA and tRNA sequences along with transcribed spacers. The RNA processing then begins before the Transcription (biology), transcription is complete. During processing reactions, the rRNAs and
tRNAs A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the Messenger RNA, mRNA ...
are released as separate molecules.


Prokaryotic regulation

Because of the vital role rRNA plays in the cell physiology of
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s, there is much overlap in rRNA Regulation of gene expression, regulation mechanisms. At the transcriptional level, there are both positive and negative effectors of rRNA transcription that facilitate a cell's maintenance of homeostasis: * An UP element upstream of the ''rrn'' P1 promoter can bind a subunit of RNA polymerase, thus promoting Transcription (biology), transcription of rRNA. * Transcription (biology), Transcription factors such as FIS bind upstream of the Promoter (genetics), promoter and interact with RNA polymerase which facilitates Transcription (biology), transcription. * Anti-termination factors bind downstream of the ''rrn'' P2 Promoter (genetics), promoter, preventing premature transcription termination. * Due to the stringent response, when the availability of amino acids is low, ppGpp (a negative effector) can inhibit Transcription (biology), transcription from both the P1 and P2 Promoter (genetics), promoters.


Degradation

Ribosomal RNA is quite stable in comparison to other common types of RNA and persists for longer periods of time in a healthy cellular environment. Once assembled into functional units, ribosomal RNA within ribosomes are stable in the stationary phase of the cell life cycle for many hours. Degradation can be triggered via "stalling" of a ribosome, a state that occurs when the ribosome recognizes faulty mRNA or encounters other processing difficulties that causes translation by the ribosome to cease. Once a ribosome stalls, a specialized pathway on the ribosome is initiated to target the entire complex for disassembly.


In eukaryotes

As with any
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
or RNA, rRNA production is prone to errors resulting in the production of non-functional rRNA. To correct this, the cell allows for degradation of rRNA through the non-functional rRNA decay (NRD) pathway. Much of the research in this topic was conducted on eukaryotic cells, specifically ''Saccharomyces cerevisiae'' yeast. Currently, only a basic understanding of how Cell (biology), cells are able to target functionally defective
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
s for ubiquination and degradation in eukaryotes is available. * The NRD pathway for the 40S subunit may be independent or separate from the NRD pathway for the 60S subunit. It has been observed that certain
gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meaning ''generation'' or ''birth'' ) is a basic unit of her ...

gene
s were able to affect degradation of certain pre-RNAs, but not others. * Numerous
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s are involved in the NRD pathway, such as Mms1p and Rtt101p, which are believed to complex together to target
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
s for degradation. Mms1p and Rtt101p are found to bind together and Rtt101p is believed to recruit a ubiquitin E3 ligase complex, allowing for the non-functional
ribosome Ribosomes ( ), also called Palade granules, are , found within all , that perform (mRNA translation). Ribosomes link together in the order specified by the s of (mRNA) molecules to form chains. Ribosomes consist of two major components: the ...

ribosome
s to be ubiquinated before being degraded. ** Prokaryotes lack a Homology (biology), homolog for Mms1, so it is unclear how
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s are able to degrade non-functional rRNAs. * The growth rate of Eukaryotic Cells, eukaryotic cells did not seem to be significantly affected by the accumulation of non-functional rRNAs.


In prokaryotes

Although there is far less research available on ribosomal RNA degradation in
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s in comparison to
eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryote
s, there has still been interest on whether
bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of biological cell The cell (from Latin ''cella'', meaning "small room") is the basic structural, functional, and biological unit of all known organisms. Cells are the sm ...

bacteria
follow a similar degradation scheme in comparison to the NRD in eukaryotes. Much of the research done for
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s has been conducted on ''
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 Gram-negative bacteria are bacteria that do not retain the crystal violet st ...

Escherichia coli
''. Many differences were found between eukaryotic and prokaryotic rRNA degradation, leading researchers to believe that the two degrade using different pathways. * Certain mutations in rRNA that were able to trigger rRNA degradation in
eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryote
s were unable to do so in
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s. * Point mutations in a 23S rRNA would cause both 23S and 16S rRNAs to be degraded, in comparison to
eukaryote Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...

eukaryote
s, in which mutations in one subunit would only cause that subunit to be degraded. * Researchers found that removal of a whole helix structure (H69) from the 23S rRNA did not trigger its degradation. This led them to believe that H69 was critical for endonucleases to recognize and degrade the mutated rRNA.


Sequence conservation and stability

Due to the prevalent and unwavering nature of rRNA across all organisms, the study of its resistance to gene transfer, mutation, and alteration without destruction of the organism has become a popular field of interest. Ribosomal RNA genes have been found to be tolerant to modification and incursion. When rRNA sequencing ''is'' altered, cells have been found to become compromised and quickly cease normal function. These key traits of rRNA have become especially important for gene database projects (comprehensive online resources such as SILVA or SINA) where alignment of ribosomal RNA sequences from across the different biologic domains greatly eases "Taxonomy (biology), taxonomic assignment, Phylogenetics, phylogenetic analysis and the investigation of microbial diversity." Examples of resilience: * Addition of large, nonsensical RNA fragments into many parts of the 16S rRNA unit does not observably alter the function of the Ribosome, ribosomal unit as a whole. * Non-coding RNARD7 has the capability to alter processing of rRNA to make the molecules resistant to degradation by carboxylic acid. This is a crucial mechanism in maintaining rRNA concentrations during active growth when acid build-up (due to the substrate phosphorylation required to produce Adenosine triphosphate, ATP) can become toxic to intracellular functions. * Insertion of hammerhead ribozymes that are capable of cis-cleavages along 16S rRNA greatly inhibit function and diminish stability. * While most cellular functions degrade heavily after only short period of exposure to Hypoxic tissue, hypoxic environments, rRNA remains un-degraded and resolved after six days of prolonged hypoxia. Only after such an extended period of time do rRNA intermediates (indicative of degradation finally occurring) begin to present themselves.


Significance

Ribosomal RNA characteristics are important in evolution, thus taxonomy and medicine. * rRNA is one of only a few gene products present in all Cell (biology), cells. For this reason, genes that encode the rRNA ( rDNA) are sequenced to identify an organism's Taxonomy (biology), taxonomic group, calculate related groups, and estimate rates of Genetic divergence, species divergence. As a result, many thousands of rRNA sequences are known and stored in specialized databases such as RDP-II and SILVA. * Alterations to rRNA are what allow certain disease-causing
bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of biological cell The cell (from Latin ''cella'', meaning "small room") is the basic structural, functional, and biological unit of all known organisms. Cells are the sm ...

bacteria
, such as ''Mycobacterium tuberculosis'' (the bacterium that causes tuberculosis) to develop extreme drug resistance. Due to similar issues, this has become a prevalent problem in veterinary medicine where the main method for handling bacterial infection in pets is administration of drugs that attack the Peptidyl transferase, peptidyl-transferase centre (PTC) of the Bacterial ribosomes, bacterial ribosome. Mutations in 23S rRNA have created perfect resistance to these drugs as they operate together in an unknown fashion to bypass the PTC enitrely. * rRNA is the target of numerous clinically relevant antibiotics: chloramphenicol, erythromycin, kasugamycin, Thiopeptide, micrococcin, paromomycin, ricin, alpha-sarcin, spectinomycin, streptomycin, and thiostrepton. * rRNA have been shown to be the origin of species-specific microRNAs, like Mir-663 microRNA precursor family, miR-663 in humans and MicroRNA#miRNA-712, miR-712 in mice. These particular MicroRNA, miRNAs originate from the
internal transcribed spacer Internal transcribed spacer (ITS) is the spacer DNA situated between the small-subunit ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosome Ribosomes () are macromolecular m ...
s of the rRNA.


Human genes

* 45S:
RNR1 RNA, ribosomal 1, also known as RNR1, is a human gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meanin ...
,
RNR2RNA, ribosomal 2, also known as RNR2, is a human gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meaning ...
RNR3 RNA, ribosomal 3, also known as RNR3, is a human gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meanin ...
,
RNR4 RNA, ribosomal 4, also known as RNR4, is a human gene. References Further reading

* Nucleolus organizer regions are chromosomal regions crucial for the formation of the nucleolus, located on the short arms of the acrocentric chromosomes 13, ...
,
RNR5 RNA, ribosomal 5, also known as RNR5, is a human gene. Genes for ribosomal RNA are clustered on the short arms of chromosomes Chromosome 13 (human), 13, Chromosome 14 (human), 14, Chromosome 15 (human), 15, Chromosome 20 (human), 20, Chromosome 21 ( ...
; (unclustered) RNA18SN1, RNA18SN2, RNA18SN3, RNA18SN4, RNA18SN5, RNA28SN1, RNA28SN2, RNA28SN3, RNA28SN4, RNA28SN5, RNA45SN1, RNA45SN2, RNA45SN3, RNA45SN4, RNA45SN5, RNA5-8SN1, RNA5-8SN2, RNA5-8SN3, RNA5-8SN4, RNA5-8SN5 * 5S: RNA5S1, RNA5S2, RNA5S3, RNA5S4, RNA5S5, RNA5S6, RNA5S7, RNA5S8, RNA5S9, RNA5S10, RNA5S11, RNA5S12, RNA5S13, RNA5S14, RNA5S15, RNA5S16, RNA5S17 * Mt: MT-RNR1, MT-TV (mitochondrial), MT-TV (co-opted), MT-RNR2


See also

* Ribotyping * Diazaborine B, a maturation inhibitor of rRNAs for the large ribosomal subunit


References


External links


16S rRNA, BioMineWiki

Ribosomal Database Project II
*
SILVA rRNA Database Project
(also includes Eukaryotes (18S) and LSU (23S/28S))


''Halococcus morrhuae'' (archaebacterium) 5S rRNA
{{Ribosome subunits Ribosomal RNA, Protein biosynthesis RNA Non-coding RNA Ribozymes