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SAM riboswitch (S box leader)
Encyclopedia
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. The predicted secondary structure
consists of a complex stem-loop
region followed by a single stem-loop terminator region. An alternative and mutually exclusive form involves bases in the 3' segment of helix 1 with those in the 5' region of helix 5 to form a structure termed the anti-terminator form. However, many SAM riboswitches are likely to regulate gene expression at the level of translation.
The structure of the SAM riboswitch has been determined with X-ray crystallography
. The SAM riboswitch
is organized about a four way junction, with two sets of coaxially stacked helices arranged side-by-side. These stacks are held together by a pseudoknot
formed between the loop on the end of stem P2 and the J3/4 joining region. The formation of the pseudoknot is facilitated by a protein-independent kink turn that induces a 100o bend into P2. Ribosomal proteins, known to bind kink-turns in the ribosome, favor SAM aptamer folding by interacting with P2 kink-turn motif. Both the kink-turn and the pseudoknot are critical to the establishment of the global fold and productive binding. The binding pocket is split between conserved, tandem AU pairs in stem P1, the conserved G in the J1/2 joining region, and the conserved asymmetric bulge in stem P3. The adenosyl and methionine main-chain moieties of S-Adenosyl methionine
(SAM) are recognized through hydrogen-bonding into the bulge in P3 and the conserved G in J1/2. The methyl group is recognized indirectly through the charged sulfur, which forms an electrostatic interaction with the negative surface potential created by the tandem AU pairs in the minor groove of P1. These pairs are highly conserved and alterations to the orientation of these pairs, as well the identity of the bases in the pairs (i.e., GC pairs instead of AU pairs) result in reduced affinity for SAM. Affinity for SAH, however, is unaffected by changes to the P1 sequence, further supporting the idea that the interaction between SAM and the P1 helix is electrostatic in nature.
Other structural classes of SAM-binding riboswitches have been found that are entirely different from that of the SAM-I riboswitch. These unrelated SAM-binding riboswitches are SAM-II riboswitches, SAM-III riboswitches
and SAM-SAH riboswitch
es. The details of these riboswitches are covered in their articles.
There are also classes of SAM-binding riboswitches that are structurally related to SAM-I riboswitches. SAM-IV riboswitch
es, appears to share a similar ligand
-binding site with that of SAM-I riboswitches, but in the context of a discreet distinct scaffold. In SAM-IV, the P4 stem is located downstream of the P1 stem and interacts, by a second pseudoknot, with P3, while the kink turn is absent. SAM-I/IV variant riboswitches combine features of SAM-I and SAM-IV riboswitches. For example, they have the P4 outside of the multistem junction, like SAM-IV riboswitches, but also often have a SAM-I-like P4 within the multistem junction. However, unlike SAM-I and SAM-IV riboswitches, the variant riboswitches entirely lack an internal loop in P2. As noted above, this internal loop in SAM-I riboswitches forms a kink turn motif that allows the RNA to form a pseudoknot. The variant riboswitches lack an internal loop that might allow such a turn, and also show no signs of forming the SAM-I-like pseudoknot.
Methionine
Methionine is an α-amino acid with the chemical formula HO2CCHCH2CH2SCH3. This essential amino acid is classified as nonpolar. This amino-acid is coded by the codon AUG, also known as the initiation codon, since it indicates mRNA's coding region where translation into protein...
or cysteine
Cysteine
Cysteine is an α-amino acid with the chemical formula HO2CCHCH2SH. It is a non-essential amino acid, which means that it is biosynthesized in humans. Its codons are UGU and UGC. The side chain on cysteine is thiol, which is polar and thus cysteine is usually classified as a hydrophilic amino acid...
biosynthesis in Gram-positive
Gram-positive
Gram-positive bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink...
bacteria. Two SAM riboswitches in Bacillus subtilis
Bacillus subtilis
Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium commonly found in soil. A member of the genus Bacillus, B. subtilis is rod-shaped, and has the ability to form a tough, protective endospore, allowing the organism to tolerate...
that were experimentally studied act at the level of transcription termination
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
control. The predicted secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
consists of a complex 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,...
region followed by a single stem-loop terminator region. An alternative and mutually exclusive form involves bases in the 3' segment of helix 1 with those in the 5' region of helix 5 to form a structure termed the anti-terminator form. However, many SAM riboswitches are likely to regulate gene expression at the level of translation.
Structure organization
X-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 SAM 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 organized about a four way junction, with two sets of coaxially stacked helices arranged side-by-side. These stacks are held together by a pseudoknot
Pseudoknot
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 mosaic virus in 1982...
formed between the loop on the end of stem P2 and the J3/4 joining region. The formation of the pseudoknot is facilitated by a protein-independent kink turn that induces a 100o bend into P2. Ribosomal proteins, known to bind kink-turns in the ribosome, favor SAM aptamer folding by interacting with P2 kink-turn motif. Both the kink-turn and the pseudoknot are critical to the establishment of the global fold and productive binding. The binding pocket is split between conserved, tandem AU pairs in stem P1, the conserved G in the J1/2 joining region, and the conserved asymmetric bulge in stem P3. The adenosyl and methionine main-chain moieties of S-Adenosyl methionine
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) are recognized through hydrogen-bonding into the bulge in P3 and the conserved G in J1/2. The methyl group is recognized indirectly through the charged sulfur, which forms an electrostatic interaction with the negative surface potential created by the tandem AU pairs in the minor groove of P1. These pairs are highly conserved and alterations to the orientation of these pairs, as well the identity of the bases in the pairs (i.e., GC pairs instead of AU pairs) result in reduced affinity for SAM. Affinity for SAH, however, is unaffected by changes to the P1 sequence, further supporting the idea that the interaction between SAM and the P1 helix is electrostatic in nature.
Other structural classes of SAM-binding riboswitches have been found that are entirely different from that of the SAM-I riboswitch. These unrelated SAM-binding riboswitches are SAM-II riboswitches, SAM-III riboswitches
SMK box riboswitch
The SMKbox riboswitch 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...
and SAM-SAH riboswitch
SAM-SAH riboswitch
The 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...
es. The details of these riboswitches are covered in their articles.
There are also classes of SAM-binding riboswitches that are structurally related to SAM-I riboswitches. SAM-IV riboswitch
SAM-IV riboswitch
SAM-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...
es, appears to share a similar ligand
Ligand
In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
-binding site with that of SAM-I riboswitches, but in the context of a discreet distinct scaffold. In SAM-IV, the P4 stem is located downstream of the P1 stem and interacts, by a second pseudoknot, with P3, while the kink turn is absent. SAM-I/IV variant riboswitches combine features of SAM-I and SAM-IV riboswitches. For example, they have the P4 outside of the multistem junction, like SAM-IV riboswitches, but also often have a SAM-I-like P4 within the multistem junction. However, unlike SAM-I and SAM-IV riboswitches, the variant riboswitches entirely lack an internal loop in P2. As noted above, this internal loop in SAM-I riboswitches forms a kink turn motif that allows the RNA to form a pseudoknot. The variant riboswitches lack an internal loop that might allow such a turn, and also show no signs of forming the SAM-I-like pseudoknot.
See also
- SAM-II riboswitch
- SAM-III riboswitchSMK box riboswitchThe SMKbox riboswitch 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...
- 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...