PreQ1-III riboswitch

PreQ1-III riboswitches are a class of riboswitches that bind pre-queuosine₁ (PreQ₁), a precursor to the modified nucleoside queuosine.[1] PreQ₁-III riboswitches are the third class of riboswitches to be discovered that sense this ligand, and are structurally distinct from preQ₁-I and preQ₁-II riboswitches. Most sequenced examples of preQ₁-III riboswitches are obtained from uncultivated metagenome samples, but the few examples in cultivated organisms are present in strains that are known to or suspected to be Faecalibacterium prausnitzii, a species of Gram-positive Clostridia. Known examples of preQ₁-III riboswitches are found upstream of queT genes, which are expected to encode transporters of a queuosine derivative. The other two known classes of preQ₁ riboswitches are also commonly found upstream of queT genes.

Consensus secondary structure of PreQ₁-III riboswitches, based on earlier data than a previously published depiction.[1] The structural significance of the pairing interaction labeled "pseudoknot or alternate stem" is currently unknown. The P1 stem is unusually rich in A and U nucleotides, but is supported by experimental data.

The atomic-resolution structure of a preQ1-III riboswitch has been solved by X-ray crystallography.[2]

References

McCown PJ, Liang JJ, Weinberg Z, Breaker RR (2014). "Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes". Chem. Biol. 21 (7): 880–889. doi:10.1016/j.chembiol.2014.05.015. PMC 4145258. PMID 25036777.
Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE (2015). "Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics". Proc. Natl. Acad. Sci. USA. 112 (27): E3485–3494. doi:10.1073/pnas.1503955112. PMC 4500280. PMID 26106162.

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[McCown2014-1] McCown PJ, Liang JJ, Weinberg Z, Breaker RR (2014). "Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes". Chem. Biol. 21 (7): 880–889. doi:10.1016/j.chembiol.2014.05.015. PMC 4145258. PMID 25036777.

[2] Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE (2015). "Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics". Proc. Natl. Acad. Sci. USA. 112 (27): E3485–3494. doi:10.1073/pnas.1503955112. PMC 4500280. PMID 26106162.