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The SMKbox riboswitch (also known as SAM-III) is an RNA element that regulates gene expression in bacteria. The SMK box
The SMKbox riboswitch (also known as SAM-III) is an RNA element that regulates gene expression in bacteria. The SMK box 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 ...
is found in the 5' UTR
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 o ...
of the MetK gene in lactic acid bacteria
Lactobacillales are an order of gram-positive, low-GC, acid-tolerant, generally nonsporulating, nonrespiring, either rod-shaped ( bacilli) or spherical ( cocci) bacteria that share common metabolic and physiological characteristics. These bact ...
. The structure of this element changes upon binding to S-adenosyl methionine (SAM) to a conformation that blocks the shine-dalgarno sequence and blocks translation of the gene.
There are other known SAM-binding riboswitches such as SAM-I and SAM-II, but these appear to share no similarity in sequence or structure to SAM-III.
Structure
The crystal structure of the riboswitch from ''E. faecalis'' was solved byX-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 diffract into many specific directions. By measuring the angle ...
. The structure showed that the most conserved nucleotides involved in SAM
Sam, SAM or variants may refer to:
Places
* Sam, Benin
* Sam, Boulkiemdé, Burkina Faso
* Sam, Bourzanga, Burkina Faso
* Sam, Kongoussi, Burkina Faso
* Sam, Iran
* Sam, Teton County, Idaho, United States, a populated place
People and fictional c ...
binding were organised around a junction between three helices. In some species there are large insertions of up to 210 nucleotides within this structure.
See also
*SAH riboswitch
SAH riboswitches are a kind of riboswitch that bind S-adenosylhomocysteine (SAH). When the coenzyme S-adenosylmethionine (SAM) is used in a methylation reaction, SAH is produced. SAH riboswitches typically up-regulate genes involved in recycli ...
* SAM-I riboswitch
* 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 ...
* SAM-IV riboswitch
SAM-IV riboswitches are a kind of riboswitch that specifically binds S-adenosylmethionine (SAM), a cofactor used in many methylation reactions. Originally identified by bioinformatics, SAM-IV riboswitches are largely confined to the Actinomyceta ...
* SAM-V riboswitch
SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine (SAM). It was first discovered in the marine bacterium ''Candidatus Pelagibacter ubique'' and can also be found in marine metagenomes. SAM-V features a similar consensus ...
* SAM-VI riboswitch
* SAM-Chlorobi RNA motif
The SAM-Chlorobi RNA motif is a conserved RNA structure that was identified by bioinformatics. The RNAs are found only in bacteria classified as within the phylum Chlorobiota. These RNAs are always in the 5' untranslated regions of operons tha ...
* SAM–SAH riboswitch
References
External links
* Cis-regulatory RNA elements Riboswitch {{molecular-cell-biology-stub