extensively used for RNA folding to neutralize negative charges of
the RNA backbone [33] and promote close contacts between RNA
regions. The M-box riboswitch contains several Mg
2+
-binding
pockets, which facilitate the formation of the riboswitch structure.
Three of these regions are particularly important for forming tertiary long-distance interactions and allosteric transitions that cause
alternative folding of the riboswitch [56, 57] (Fig. 3a). Structural
and biochemical studies suggest that two of these sites (cores 2 and
3) initially bind several Mg
2+ ligands and induce a conformational
change that brings together two RNA regions that form the third
Mg
2+ binding region, core 1, thus allowing for long-distance tertiary interactions to form. These interactions induce formation of
the regulatory helix P1 of the riboswitch, thereby preventing formation of the transcription antiterminator hairpin and facilitating
folding of the transcription terminator in the downstream region.
Thus, Mg
2+ binding to the riboswitch modulates transcription of
the downstream gene, which is related to Mg
2+ transport, and
ensures an adequate amount of the Mg
2+ transporter in the cell.
Although cooperative binding has not been explicitly demonstrated
for the M-box riboswitch, allosteric modulations upon Mg
2+ binding undoubtedly indicate involvement of cooperativity in the formation of the ligand-bound state of this RNA.
Recent studies revealed that riboswitches can specifically recognize metals aside from Mg
2+ cations. One of the most interesting
metal-binding riboswitches resides upstream of a manganese (Mn
2+
)
efflux pump gene [59, 60]. This RNA forms two distant cationbinding sites, one for a Mg
2+ cation and another for a Mn
2+ cation.
Since the concentration of Mg
2+ cations in cells is high, the riboswitch initially binds a Mg
2+ cation. This interaction induces an
allosteric change in the RNA structure and facilitates binding of a
Mn
2+ cation, if the concentration of Mn
2+ in the cell exceeds the
threshold. Cooperative binding of two metals directs RNA folding
such that the riboswitch adopts a conformation that precludes formation of the transcription terminator and allows transcription of
the gene.
Metal cations are not the only ligands that are able to bind
riboswitches in a cooperative fashion and induce large allosteric
changes. Tetrahydrofolate (THF)-sensing riboswitch recognizes
two THF molecules in a single domain using two very similar
ligand-binding sites [58]. Although the two sites are separated by
ä
Fig. 3 (continued) is required to form an adjacent transcription terminator
instead of an antiterminator [58]. (c) Thermodynamic cycle for formation of the
S15-S6-S18-rRNA complex in the central domain of the 30S ribosomal subunit
[8]. The rRNA fragment is shown in black lines and proteins are shown in color.
The schematic depicts structural transitions in RNA upon protein binding and
these transitions are the basis for cooperativity in the system
266
Alla Peselis and Alexander Serganov
the RNA backbone [33] and promote close contacts between RNA
regions. The M-box riboswitch contains several Mg
2+
-binding
pockets, which facilitate the formation of the riboswitch structure.
Three of these regions are particularly important for forming tertiary long-distance interactions and allosteric transitions that cause
alternative folding of the riboswitch [56, 57] (Fig. 3a). Structural
and biochemical studies suggest that two of these sites (cores 2 and
3) initially bind several Mg
2+ ligands and induce a conformational
change that brings together two RNA regions that form the third
Mg
2+ binding region, core 1, thus allowing for long-distance tertiary interactions to form. These interactions induce formation of
the regulatory helix P1 of the riboswitch, thereby preventing formation of the transcription antiterminator hairpin and facilitating
folding of the transcription terminator in the downstream region.
Thus, Mg
2+ binding to the riboswitch modulates transcription of
the downstream gene, which is related to Mg
2+ transport, and
ensures an adequate amount of the Mg
2+ transporter in the cell.
Although cooperative binding has not been explicitly demonstrated
for the M-box riboswitch, allosteric modulations upon Mg
2+ binding undoubtedly indicate involvement of cooperativity in the formation of the ligand-bound state of this RNA.
Recent studies revealed that riboswitches can specifically recognize metals aside from Mg
2+ cations. One of the most interesting
metal-binding riboswitches resides upstream of a manganese (Mn
2+
)
efflux pump gene [59, 60]. This RNA forms two distant cationbinding sites, one for a Mg
2+ cation and another for a Mn
2+ cation.
Since the concentration of Mg
2+ cations in cells is high, the riboswitch initially binds a Mg
2+ cation. This interaction induces an
allosteric change in the RNA structure and facilitates binding of a
Mn
2+ cation, if the concentration of Mn
2+ in the cell exceeds the
threshold. Cooperative binding of two metals directs RNA folding
such that the riboswitch adopts a conformation that precludes formation of the transcription terminator and allows transcription of
the gene.
Metal cations are not the only ligands that are able to bind
riboswitches in a cooperative fashion and induce large allosteric
changes. Tetrahydrofolate (THF)-sensing riboswitch recognizes
two THF molecules in a single domain using two very similar
ligand-binding sites [58]. Although the two sites are separated by
ä
Fig. 3 (continued) is required to form an adjacent transcription terminator
instead of an antiterminator [58]. (c) Thermodynamic cycle for formation of the
S15-S6-S18-rRNA complex in the central domain of the 30S ribosomal subunit
[8]. The rRNA fragment is shown in black lines and proteins are shown in color.
The schematic depicts structural transitions in RNA upon protein binding and
these transitions are the basis for cooperativity in the system
266
Alla Peselis and Alexander Serganov