SAM-SAH riboswitch
Encyclopedia
The SAM-SAH riboswitch is a conserved RNA structure in certain bacteria
that binds S-adenosylmethionine
(SAM) and S-adenosylhomocysteine
(SAH) 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. The binding affinities for both compounds are similar, but binding for SAH is at least somewhat stronger. SAM-SAH riboswitches are exclusively found in Rhodobacterales
, an order
of alphaproteobacteria
. They are always found in the apparent 5' untranslated regions of metK genes, which encode the enzyme (Methionine adenosyltransferase
) that synthesizes SAM.
Given this gene association, it was proposed that SAM-SAH riboswitches more likely function as SAM-sensing RNAs. SAM-SAH riboswitches are relatively small among known riboswitches, which might relate to their inability to discriminate against SAH. However, the ability to reject SAH as a ligand might not be important under physiological conditions, because the cellular concentration of SAM is higher.
A region of the conserved structure of SAM-SAH riboswitches includes a predicted Shine-Dalgarno sequence
(ribosome
-binding site) of the downstream metK genes. These nucleotides are required for optimal binding to the ligand and might form a pseudoknot with the terminal loop within the main stem-loop
structure. Occlusion of the Shine-Dalgarno sequence might be the mechanism by which SAM-SAH riboswitches regulate expression of the downstream genes.
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...
that binds S-adenosylmethionine
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...
(SAM) and S-adenosylhomocysteine
S-adenosyl-L-homocysteine
S-Adenosyl-L-homocysteine is an amino acid derivative used in several metabolic pathways in most organisms. It is an intermediate in the synthesis of cysteine and adenosine....
(SAH) and is therefore presumed to be a 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...
. SAM-SAH riboswitches do not share any apparent structural resemblance to known riboswitches that bind SAM or SAH. The binding affinities for both compounds are similar, but binding for SAH is at least somewhat stronger. SAM-SAH riboswitches are exclusively found in Rhodobacterales
Rhodobacterales
In taxonomy, the Rhodobacterales are an order of the Alphaproteobacteria.Gene transfer agents are viruslike elements produced by Rhodobacterales which transfer DNA and may be an important factor in their evolution.-External links:...
, an order
Order (biology)
In scientific classification used in biology, the order is# a taxonomic rank used in the classification of organisms. Other well-known ranks are life, domain, kingdom, phylum, class, family, genus, and species, with order fitting in between class and family...
of alphaproteobacteria
Alphaproteobacteria
Alphaproteobacteria is a class of Proteobacteria. Like all Proteobacteria, they are Gram-negative.-Characteristics:The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds , symbionts of plants and animals, and a group of pathogens, the...
. They are always found in the apparent 5' untranslated regions of metK genes, which encode the enzyme (Methionine adenosyltransferase
Methionine adenosyltransferase
Methionine adenosyltransferase is an enzyme which catalyses the synthesis of S-adenosylmethionine from methionine and ATP.-External links:...
) that synthesizes SAM.
Given this gene association, it was proposed that SAM-SAH riboswitches more likely function as SAM-sensing RNAs. SAM-SAH riboswitches are relatively small among known riboswitches, which might relate to their inability to discriminate against SAH. However, the ability to reject SAH as a ligand might not be important under physiological conditions, because the cellular concentration of SAM is higher.
A region of the conserved structure of SAM-SAH riboswitches includes a predicted 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;...
(ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
-binding site) of the downstream metK genes. These nucleotides are required for optimal binding to the ligand and might form a pseudoknot with the terminal loop within the main stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
structure. Occlusion of the Shine-Dalgarno sequence might be the mechanism by which SAM-SAH riboswitches regulate expression of the downstream genes.