Azaaromatic

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Rfam ID: RF01764 (yjdF RNA)


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Timeline Description Structure&recognition References


Timeline

Start

    2016[1] Discovery of azaaromatic(yjdF) riboswitch

    The genetic regulation mechanism of azaaromatic riboswitch 2018[2]

    2022[3] Its tRNA-like fold generates from SAXS with bingding ligand
2023...



Description

 The azaaromatic riboswitch was named yjdF RNA. The yjdF RNA motif is a conserved RNA structure identified using bioinformatics. Most yjdF RNAs are located in bacteria classified within the phylum Bacillota. A yjdF RNA is found in the presumed 5' untranslated region (5' UTR) of the yjdF gene in Bacillus subtilis, and almost all yjdF RNAs are found in the 5' UTRs of homologs of this gene. yjdF RNAs appear to function as riboswitches that sense azaaromatic compounds, although the precise compound or set of compounds that is sensed by this riboswitch in the cell remains unclear (From Wikipedia).


Gene regulation

Potential mechanism of translation regulation by azaaromatic riboswitch in B. subtilis. RBS denotes ribosome binding site. We present the prototypical mechanism, but not all possible mechanisms[2].
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Structure and Ligand recognition

2D representation

Consensus sequence and secondary structure model for azaaromatic riboswitch[1].


Document
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Ligand recognition

Chemical structures of azaaromatic. The apparent KD of each compound of azaaromatic riboswitch is shown on bottom. Refer to the corresponding references for comprehensive details regarding reaction conditions and species information in measuring the dissociation constant displayed below[1].
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References

[1] The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds.
Li, S., Hwang, X. Y., Stav, S. & Breaker, R. R.
RNA 22, 530–541 (2016).

[2] Genetic regulation mechanism of the yjdF riboswitch.
Gong, S., Wang, Y., Wang, Z., Wang, Y. & Zhang, W.
J. Theor. Biol. 439, 152–159 (2018).

[3] The bacterial yjdF riboswitch regulates translation through its tRNA-like fold.
Trachman, R. J., 3rd, Passalacqua, L. F. M. & Ferré-D’Amaré, A. R.
J. Biol. Chem. 298, 101934 (2022).