HMP-PP

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Rfam ID: nan (nan)


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Timeline Description Structure&recognition References


Timeline

Start

    2019[2] Discovery of HMP-PP riboswitch by genome-wide search

    Bioinformatic and biochemical validation of the ligand for the HMP-PP riboswitch 2019[3]
2023...



Description

 HMP-PP riboswitches are a class of homologous RNAs in certain bacteria that function as sensors of the thiamin precursor HMP-PP, which is fused with HET-P ultimately to form the final active coenzyme thiamin pyrophosphate (TPP). The HMP-PP riboswitch was initially named as the ‘thiS motif' because of its frequent association with a gene coding for the ThiS protein, which delivers sulfur to form the thiazole moiety of the thiamin precursor HET-P, which was firstly reported by using a computational approach to identify new riboswitches in bacteria in 2019. Unlike with many other riboswitches,the small ligand sensing aptamer of the HMP-PP riboswitch was embedded within a terminator, rather than being a separate entity. The 3D structure of the HMP-PP riboswitch has not been solved yet[2-3].


Gene association

Typical biosynthetic pathways of Clostridium species for the pyrimidine and thiazole moieties of thiamin, and their eventual conversion into the enzyme cofactor thiamin pyrophosphate (TPP). Genes coding for the enzymes involved in HET transport and catalysis of various biosynthetic steps are showed. The genes colored in red are associated with the HMP-PP riboswitch[1-3].
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Gene regulation

Potential mechanism of transcription termination regulation for the Clostridium species HMP-PP riboswitch. The shaded nucleotides highlight possible base-pairs of the predicted pseudoknot. Complementary sequences and alternate base-pairing are shown in blue. We present the prototypical mechanism, but not all possible mechanisms[3].
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Structure and Ligand recognition

2D representation

Top: The consensus models and two possible secondary structure models based on 400 representatives for the HMP-PP riboswitch. Bottom: Sequence and predicted secondary structure of the HMP-PP riboswitch of Clostridium species. The structural model is depicted in its presumed ‘ON' state, where the shaded nucleotides highlight possible base-pairs of the predicted pseudoknot. Red nucleotides are >97% conserved as depicted in the HMP-PP riboswitch consensus model[2-3].

nan (Sequence from bottom structure )


Ligand recognition

Chemical structures of hydroxymethyl-pyrimidine pyrophosphate (HMP-PP) and its precursors. The apparent KD of each compound 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. Refer to the corresponding references for comprehensive details regarding reaction conditions and species information in measuring the dissociation constant displayed below[3].
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References

[1] Thiamin biosynthesis in prokaryotes.
Begley, T. P. et al.
Arch. Microbiol. 171, (1999).

[2] Genome-wide discovery of structured noncoding RNAs in bacteria.
Stav, S. et al.
BMC Microbiol. 19, (2019).

[3] A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer.
Atilho, R. M., Mirihana, A. G., Greenlee, E. B., Knecht, K. M. & Breaker, R. R.
Elife 8, (2019).