The glutamine riboswitch (formerly ''glnA'' RNA motif) is a conserved

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

structure that was predicted by

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

. It is present in a variety of lineages of

cyanobacteria Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...

, as well as some

phage A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria. The term is derived . Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures tha ...

s that infect cyanobacteria. It is also found in

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

extracted from uncultivated

bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

living in the

ocean The ocean is the body of salt water that covers approximately 70.8% of Earth. The ocean is conventionally divided into large bodies of water, which are also referred to as ''oceans'' (the Pacific, Atlantic, Indian Ocean, Indian, Southern Ocean ...

that are presumably species of cyanobacteria. ''glnA'' RNAs are found in the presumed

5' untranslated region The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly upstream from the initiation codon. This region is important for the regulation of ...

s of

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

s encoding multiple classes of

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

that are involved in

nitrogen metabolism The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biologi ...

. The most prominent of these protein classes are

ammonium Ammonium is a modified form of ammonia that has an extra hydrogen atom. It is a positively charged (cationic) polyatomic ion, molecular ion with the chemical formula or . It is formed by the protonation, addition of a proton (a hydrogen nucleu ...

transporters, the enzymes

glutamine synthetase Glutamine synthetase (GS) () is an enzyme that catalyzes the condensation of glutamate and ammonia to form glutamine: Glutamate + ATP + NH3 → Glutamine + ADP + phosphate Glutamine synthetase uses ammonia produced by nitrate reduction ...

and

glutamate synthase Glutamate synthase (also known as Glutamine oxoglutarate aminotransferase) is an enzyme and frequently abbreviated as GOGAT. This enzyme manufactures glutamate from glutamine and α-ketoglutarate, and thus along with glutamine synthetase (abbreviat ...

and P_II protein, which itself regulates nitrogen metabolism. Further supporting a possible role as a

cis-regulatory element ''Cis''-regulatory elements (CREs) or ''cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morpho ...

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 is a chemical element; it has Symbol (chemistry), symbol N and atomic number 7. Nitrogen is a Nonmetal (chemistry), nonmetal and the lightest member of pnictogen, group 15 of the periodic table, often called the Pnictogen, pnictogens. ...

. It was demonstrated that ''glnA'' RNAs correspond to

glutamine Glutamine (symbol Gln or Q) is an α-amino acid that is used in the biosynthesis of proteins. Its side chain is similar to that of glutamic acid, except the carboxylic acid group is replaced by an amide. It is classified as a charge-neutral ...

-binding

riboswitch In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in Translation (biology), production of the proteins encoded by the mRNA. Thus, an mRNA that contains a ribo ...

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 riboswitches and

TPP riboswitch The TPP riboswitch, also known as the THI element and Thi-box riboswitch, is a highly conserved RNA secondary structure. It serves as a riboswitch that binds thiamine pyrophosphate (TPP) directly and modulates gene expression through a variety o ...

es 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 Digital usually refers to something using discrete digits, often binary digits. Businesses *Digital bank, a form of financial institution *Digital Equipment Corporation (DEC) or Digital, a computer company *Digital Research (DR or DRI), a software ...

function. However, such

cooperative binding Cooperative binding occurs in molecular binding systems containing more than one type, or species, of molecule and in which one of the partners is not mono-valent and can bind more than one molecule of the other species. In general, molecular bindi ...

was not observed. The first ''in vivo'' evidence that the RNAs function as glutamine riboswitches revealed that these riboswitches control expression of the

inhibiting protein IF17 in ''Synechocystis'' sp. PCC 6803 thus representing a pivotal control element for GS activity in

Cyanobacteria Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...

. 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.

References

External links

* {{Rfam, id=RF01739, name=glnA RNA Cis-regulatory RNA elements Riboswitch

See also

References

External links