CrcB RNA Motif
Encyclopedia
The crcB RNA motif is a conserved RNA
structure identified by bioinformatics
in a wide variety of bacteria
and archaea
. The motif exhibits the rigid or almost perfect conservation of the nucleotide identity at several positions (colored red in the diagram) across two domains
of life. Such conservation is consistent with a biochemical requirement to bind a small molecule that does not evolve (like protein
s or other RNA
s would). Given this observation, and the fact that crcB RNAs are typically located in possible 5' untranslated regions (5' UTRs) of protein-coding gene
s, it was proposed that crcB RNAs likely function as riboswitch
es.
Many genes are presumed to be regulated by crcB RNAs. The most common are mutS, which is functions within DNA repair; the crcB gene that is thought to play a role in chromosome
condensation; transporters of potassium
, sodium
or chloride
ion
s; the nifU iron-sulfur protein; and genes that encode formate hydrogen lyases. Many crcB RNAs overlap predicted rho-independent transcription terminator
stem-loop
s. Assuming that crcB RNAs are riboswitches whose conserved structure is stabilized by the interaction with their small molecule ligand, high concentrations of this ligand should destabilize the transcription terminators, and thereby lead to increased gene expression.
Only one other class of riboswitch, the TPP riboswitch, is found in organisms other than bacteria. Although several classes of RNAs are present in more than one domain of life (e.g., ribosomal
RNAs, group I introns, group II intron
s, RNase P
RNAs and HDV ribozyme
s), these RNAs are a small minority compared to classes of RNAs restricted to a single domain. Moreover, few of the highly widespread RNAs were initially discovered recently, while crcB RNAs were first published in 2010. The biological role played by crcB RNAs, although currently unknown, is apparently relevant to the physiology of both bacteria and archaea.
A predicted crcB RNA in Sulfolobus solfataricus P2 is contained within a non-coding transcript detected by transcriptome
sequencing and overlaps by 23 nucleotide
s an RNA called "sR110" that might correspond to a C/D box small nucleolar RNA. If crcB RNAs are riboswitches, the detected transcript could reflect premature termination by riboswitch-mediated repression.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure identified by bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
in a wide variety of bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
. The motif exhibits the rigid or almost perfect conservation of the nucleotide identity at several positions (colored red in the diagram) across two domains
Domain (biology)
In biological taxonomy, a domain is the highest taxonomic rank of organisms, higher than a kingdom. According to the three-domain system of Carl Woese, introduced in 1990, the Tree of Life consists of three domains: Archaea, Bacteria and Eukarya...
of life. Such conservation is consistent with a biochemical requirement to bind a small molecule that does not evolve (like protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s or other RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
s would). Given this observation, and the fact that crcB RNAs are typically located in possible 5' untranslated regions (5' UTRs) of protein-coding gene
Gene
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...
s, it was proposed that crcB RNAs likely function as riboswitch
Riboswitch
In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the...
es.
Many genes are presumed to be regulated by crcB RNAs. The most common are mutS, which is functions within DNA repair; the crcB gene that is thought to play a role in chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
condensation; transporters of potassium
Potassium
Potassium is the chemical element with the symbol K and atomic number 19. Elemental potassium is a soft silvery-white alkali metal that oxidizes rapidly in air and is very reactive with water, generating sufficient heat to ignite the hydrogen emitted in the reaction.Potassium and sodium are...
, sodium
Sodium
Sodium is a chemical element with the symbol Na and atomic number 11. It is a soft, silvery-white, highly reactive metal and is a member of the alkali metals; its only stable isotope is 23Na. It is an abundant element that exists in numerous minerals, most commonly as sodium chloride...
or chloride
Chloride
The chloride ion is formed when the element chlorine, a halogen, picks up one electron to form an anion Cl−. The salts of hydrochloric acid HCl contain chloride ions and can also be called chlorides. The chloride ion, and its salts such as sodium chloride, are very soluble in water...
ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...
s; the nifU iron-sulfur protein; and genes that encode formate hydrogen lyases. Many crcB RNAs overlap predicted rho-independent transcription terminator
Intrinsic termination
Intrinsic termination is a mechanism in prokaryotes that causes mRNA transcription to be stopped. In this mechanism, the mRNA contains a sequence that can base pair with itself to form a stem-loop structure 7-20 base pairs in length that is also rich in cytosine-guanine base pairs...
stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
s. Assuming that crcB RNAs are riboswitches whose conserved structure is stabilized by the interaction with their small molecule ligand, high concentrations of this ligand should destabilize the transcription terminators, and thereby lead to increased gene expression.
Only one other class of riboswitch, the TPP riboswitch, is found in organisms other than bacteria. Although several classes of RNAs are present in more than one domain of life (e.g., ribosomal
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....
RNAs, group I introns, group II intron
Group II intron
Group II introns are a large class of self-catalytic ribozymes as well as mobile genetic element found within the genes of all three domains of life. Ribozyme activity can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing...
s, RNase P
RNase P
Ribonuclease P is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA...
RNAs and HDV ribozyme
Hepatitis delta virus ribozyme
The hepatitis delta virus ribozyme is a non-coding RNA that is necessary for viral replication and is thought to be the only catalytic RNA known to be required for viability of a human pathogen. The ribozyme acts to process the RNA transcripts to unit lengths in a self-cleavage reaction...
s), these RNAs are a small minority compared to classes of RNAs restricted to a single domain. Moreover, few of the highly widespread RNAs were initially discovered recently, while crcB RNAs were first published in 2010. The biological role played by crcB RNAs, although currently unknown, is apparently relevant to the physiology of both bacteria and archaea.
A predicted crcB RNA in Sulfolobus solfataricus P2 is contained within a non-coding transcript detected by transcriptome
Transcriptome
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.-Scope:...
sequencing and overlaps by 23 nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s an RNA called "sR110" that might correspond to a C/D box small nucleolar RNA. If crcB RNAs are riboswitches, the detected transcript could reflect premature termination by riboswitch-mediated repression.