SMK box riboswitch
Encyclopedia
The SMKbox riboswitch (also known as SAM-III) is a RNA element
that regulates gene expression in bacteria. The SMK box riboswitch
is found in the 5' UTR of the MetK gene in lactic acid bacteria
. 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.
. The structure showed that the most conserved nucleotides involved in SAM
binding were organised around a junction between three helices. In some species there are large insertions of up to 210 nucleotides within this structure.
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...
that regulates gene expression in bacteria. The SMK box 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...
is found in the 5' UTR of the MetK gene in lactic acid bacteria
Lactic acid bacteria
The lactic acid bacteria comprise a clade of Gram-positive, low-GC, acid-tolerant, generally non-sporulating, non-respiring rod or cocci that are associated by their common metabolic and physiological characteristics. These bacteria, usually found in decomposing plants and lactic products, produce...
. The structure of this element changes upon binding to S-adenosyl methionine (SAM) to a conformation that blocks the shine-dalgarno sequence
Shine-Dalgarno sequence
The Shine-Dalgarno sequence , proposed by Australian scientists John Shine and Lynn Dalgarno , is a ribosomal binding site in the mRNA, generally located 8 basepairs upstream of the start codon AUG. The Shine-Dalgarno sequence exists only in prokaryotes. The six-base consensus sequence is AGGAGG;...
and blocks translation of the gene.
There are other known SAM-binding riboswitches such as SAM-I
SAM riboswitch (S box leader)
The SAM riboswitch is found upstream of a number of genes which code for proteins involved in methionine or cysteine biosynthesis in Gram-positive bacteria. Two SAM riboswitches in Bacillus subtilis that were experimentally studied act at the level of transcription termination control...
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 by X-ray crystallographyX-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
. The structure showed that the most conserved nucleotides involved in SAM
S-Adenosyl methionine
S-Adenosyl methionine is a common cosubstrate involved in methyl group transfers. SAM was first discovered in Italy by G. L. Cantoni in 1952. It is made from adenosine triphosphate and methionine by methionine adenosyltransferase . Transmethylation, transsulfuration, and aminopropylation are the...
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 riboswitchSAH riboswitchSAH riboswitches are a kind of riboswitch that bind S-adenosylhomocysteine . When the coenzyme S-adenosylmethionine is used in a methylation reaction, SAH is produced. SAH riboswitches typically up-regulate genes involved in recycling SAH to create more SAM...
- SAM-I riboswitchSAM riboswitch (S box leader)The SAM riboswitch is found upstream of a number of genes which code for proteins involved in methionine or cysteine biosynthesis in Gram-positive bacteria. Two SAM riboswitches in Bacillus subtilis that were experimentally studied act at the level of transcription termination control...
- SAM-II riboswitch
- SAM-IV riboswitchSAM-IV riboswitchSAM-IV riboswitches are a kind of riboswitch that specifically binds S-adenosylmethionine , a cofactor used in many methylation reactions. Originally identified by bioinformatics , SAM-IV riboswitches are largely confined to the Actinomycetales, an order of Bacteria...
- SAM-V riboswitchSAM-V riboswitchSAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine . It was first discovered in the marine organism Candidatus Pelagibacter ubique and can also be found in marine metagenomes. SAM-V features a similar consensus sequence and secondary structure as the binding site of SAM-II...
- SAM-Chlorobi RNA motifSAM-Chlorobi RNA motifThe 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 Chlorobi. These RNAs are always in the 5' untranslated regions of operons that contain metK and ahcY genes...
- SAM-SAH riboswitchSAM-SAH riboswitchThe SAM-SAH riboswitch is a conserved RNA structure in certain bacteria that binds S-adenosylmethionine and S-adenosylhomocysteine and is therefore presumed to be a riboswitch. SAM-SAH riboswitches do not share any apparent structural resemblance to known riboswitches that bind SAM or SAH...