SAM-V riboswitch is the fifth known

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 production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly in ...

to bind

S-adenosyl methionine ''S''-Adenosyl methionine (SAM), also known under the commercial names of SAMe, SAM-e, or AdoMet, is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation. Although these anabolic reactions occur throug ...

(SAM). It was first discovered in the

marine bacterium Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellula ...

Candidatus Pelagibacter ubique "''Candidatus'' Pelagibacter", with the single species "''Ca.'' P. communis", was isolated in 2002 and given a specific name, although it has not yet been described as required by the bacteriological code. It is an abundant member of the SAR11 ...

'' and can also be found in marine metagenomes. SAM-V features a similar

consensus sequence In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It serves as a simplified r ...

and

secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...

as the binding site of

SAM-II riboswitch The SAM-II riboswitch is a RNA element found predominantly in Alphaproteobacteria that binds S-adenosyl methionine (SAM). Its structure and sequence appear to be unrelated to the SAM riboswitch found in Gram-positive bacteria. This SAM riboswit ...

, but

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

scans cluster the two

aptamer Aptamers are short sequences of artificial DNA, RNA, XNA, or peptide that bind a specific target molecule, or family of target molecules. They exhibit a range of affinities ( KD in the pM to μM range), with little or no off-target binding ...

s independently. These similar binding pockets suggest that the two riboswitches have undergone

convergent evolution Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last com ...

. SAM-binding was confirmed using

equilibrium dialysis In chemistry, dialysis is the process of separating molecules in Solution (chemistry), solution by the difference in their rates of diffusion through a semipermeable membrane, such as dialysis tubing. Dialysis is a common laboratory technique th ...

. The riboswitch has been characterised as a 'tandem riboswitch' - it is able to regulate both

translation Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...

and

transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...

. When SAM is present in high concentration, SAM-II will bind its

ligand In coordination chemistry, a ligand is an ion or molecule ( functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's ele ...

and form a

terminator Terminator may refer to: Science and technology Genetics * Terminator (genetics), the end of a gene for transcription * Terminator technology, proposed methods for restricting the use of genetically modified plants by causing second generation s ...

stem to halt transcription. If SAM exists in lower concentrations, SAM-V will be transcribed and, if SAM concentration should then increase, it can bind SAM and occlude the Shine-Dalgarno sequence of the downstream

open reading frame In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a Prokaryote, prokaryotic DNA sequence, where only one of the #Six-fra ...

. This regulation controls parts of the

sulfur metabolism Sulfur is metabolized by all organisms, from bacteria and archaea to plants and animals. Sulfur is reduced or oxidized by organisms in a variety of forms. The element is present in proteins, sulfate esters of polysaccharides, steroids, pheno ...

marine bacteria Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellula ...

. The crystal structure of the riboswitch has been solved (PDB 6FZ0). It contains a

pseudoknot __NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow ...

References

External links

* {{Rfam, id=RF01826, name=SAM-V riboswitch Riboswitch Cis-regulatory RNA elements

See also

References

Further reading

External links