GlnA RNA motif
Encyclopedia
The glnA RNA motif is a conserved RNA
structure that was predicted by bioinformatics
. It is present in a variety of lineages of cyanobacteria, as well as some phages that infect cyanobacteria. It is also found in DNA
extracted from uncultivated bacteria
living in the ocean
that are presumably species of cyanobacteria.
glnA RNAs are found in the presumed 5' untranslated regions of gene
s encoding multiple classes of protein
that are involved in nitrogen metabolism. The most prominent of these protein classes are ammonium
transporters, the enzymes glutamine synthetase
and glutamate synthase
and PII protein, which itself regulates nitrogen metabolism. Further supporting a possible role as a cis-regulatory element
in control of nitrogen metabolism, the Prochlorococcus marinus gene designed as PMT1479 was more repressed than another other gene in this organism when it was growth without a sufficient supply of nitrogen
.
It was demonstrated that glnA RNAs correspond to glutamine
-binding riboswitch
es, i.e., they sense glutamine concentrations in order to measure overall nitrogen availability, and regulate the downstream genes appropriately. The original proposal of a riboswitch function was based on the above evidence that glnA RNAs are cis-regulatory, as well as the moderate structural complexity in the three-stem junction of the glnA RNA motif that is comparable to the structures of other known riboswitches. Some glnA RNAs are located adjacent to other glnA RNAs. These "tandem arrangements" are also exhibited by glycine riboswitch
es and TPP riboswitches where they allow the cell to turn genes off or on within a smaller change of concentration of the riboswitch ligand. In other words, the response curve
of the riboswitch better resembles a digital
function. However, such cooperative binding was not observed.
A possible structural resemblance was observed between the glnA RNA motif and the Downstream-peptide motif
. The most apparent similarity is between the stems labeled "P1" in each motif, but other similarities were observed. It was proposed that both motifs represent riboswitches involved in nitrogen metabolism. The fact that RNAs from both motifs selectively bind glutamine supports this hypothesis, but detailed structural data is not yet available. The glnA motif has an E-loop structure (also called a bulged-G module) within it.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure that was predicted 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...
. It is present in a variety of lineages of cyanobacteria, as well as some phages that infect cyanobacteria. It is also found in DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
extracted from uncultivated 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...
living in the ocean
Ocean
An ocean is a major body of saline water, and a principal component of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas.More than half of this area is over 3,000...
that are presumably species of cyanobacteria.
glnA RNAs are found in the presumed 5' untranslated regions of 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 encoding multiple classes of 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...
that are involved in nitrogen metabolism. The most prominent of these protein classes are ammonium
Ammonium
The ammonium cation is a positively charged polyatomic cation with the chemical formula NH. It is formed by the protonation of ammonia...
transporters, the enzymes glutamine synthetase
Glutamine synthetase
Glutamine synthetase is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine:Glutamate + ATP + NH3 → Glutamine + ADP + phosphate...
and glutamate synthase
Glutamate synthase (NADPH)
In enzymology, a glutamate synthase is an enzyme that catalyzes the chemical reactionThus, the four substrates of this enzyme are L-glutamine, 2-oxoglutarate , NADPH, and H+, whereas the two products are L-glutamate and NADP+....
and PII protein, which itself regulates nitrogen metabolism. Further supporting a possible role as a cis-regulatory element
Cis-regulatory element
A cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA . This term is constructed from the Latin word cis, which means "on the same side as". These cis-regulatory elements are often binding sites for one or...
in control of nitrogen metabolism, the Prochlorococcus marinus gene designed as PMT1479 was more repressed than another other gene in this organism when it was growth without a sufficient supply of nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
.
It was demonstrated that glnA RNAs correspond to glutamine
Glutamine
Glutamine is one of the 20 amino acids encoded by the standard genetic code. It is not recognized as an essential amino acid but may become conditionally essential in certain situations, including intensive athletic training or certain gastrointestinal disorders...
-binding 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, i.e., they sense glutamine concentrations in order to measure overall nitrogen availability, and regulate the downstream genes appropriately. The original proposal of a riboswitch function was based on the above evidence that glnA RNAs are cis-regulatory, as well as the moderate structural complexity in the three-stem junction of the glnA RNA motif that is comparable to the structures of other known riboswitches. Some glnA RNAs are located adjacent to other glnA RNAs. These "tandem arrangements" are also exhibited by glycine riboswitch
Glycine riboswitch
The bacterial glycine riboswitch is an RNA element that can bind the amino acid glycine. Glycine riboswitches usually consist of two metabolite-binding aptamers domains with similar structures in tandem. The aptamers cooperatively bind glycine to regulate the expression of downstream genes...
es and TPP riboswitches where they allow the cell to turn genes off or on within a smaller change of concentration of the riboswitch ligand. In other words, the response curve
Dose-response relationship
The dose-response relationship, or exposure-response relationship, describes the change in effect on an organism caused by differing levels of exposure to a stressor after a certain exposure time...
of the riboswitch better resembles a digital
Digital
A digital system is a data technology that uses discrete values. By contrast, non-digital systems use a continuous range of values to represent information...
function. However, such cooperative binding was not observed.
A possible structural resemblance was observed between the glnA RNA motif and the Downstream-peptide motif
Downstream-peptide motif
The Downstream-peptide motif refers to a conserved RNA structure identified by bioinformatics in the cyanobacterial genera Synechococcus and Prochlorococcus and one phage that infects such bacteria...
. The most apparent similarity is between the stems labeled "P1" in each motif, but other similarities were observed. It was proposed that both motifs represent riboswitches involved in nitrogen metabolism. The fact that RNAs from both motifs selectively bind glutamine supports this hypothesis, but detailed structural data is not yet available. The glnA motif has an E-loop structure (also called a bulged-G module) within it.