Fibro-purF RNA motif

Fibro-purF
Fibro-purF
	Consensus secondary structure and sequence conservation of Fibro-purF RNA
Identifiers
Symbol	Fibro-purF
Rfam	RF02974
Other data
RNA type	Cis-reg
SO	SO:0005836
PDB structures	PDBe

Last updated October 07, 2024

The Fibro-purF RNA motif is a conserved RNA structure that was discovered by bioinformatics.^[1] Fibro-purF motif RNAs are found in Fibrobacterota, a group of bacteria that are common in cow rumen. Additionally, the RNAs are found in metagenomic sequences of DNA isolated from cow rumen.

Fibro-purF motif RNAs likely function as cis-regulatory elements, in view of their positions upstream of protein-coding genes. In fact, instances of the Fibro-purF RNA motif are often located nearby to the predicted Shine-Dalgarno sequence of the downstream gene. This arrangement is consistent with a model of cis-regulation where the RNA allosterically controls access to the Shine-Dalgarno sequence, thus regulating the gene translationally.

All known Fibro-purF RNAs are found upstream of purF genes, which encode amidophosphoribosyltransferase, which participates in the biosynthesis of biological purine molecules. The Fibro-purF motif is found only in closely related organisms. As a result, the RNAs do not exhibit a high degree of mutations when compared, and it was difficult^[1] to study the RNA's secondary structure by covariation methods. As a result, the predicted secondary structure is uncertain in some places.

The Fibro-purF RNA motif was considered^[1] a potential candidate riboswitch, but no ligand has been established, as of 2022. However, experiments have confirmed that the RNA motif corresponds to a regulatory element and in vitro experiments corroborate the predicted structure.^[2] Due to the instability of the proposed ligand,^[2]^[1] 5-phospho-D-ribosylamine, direct experiments to confirm this ligand have not yet been conducted.

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References

1 2 3 4 Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR (October 2017). "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids Res. 45 (18): 10811–10823. doi:10.1093/nar/gkx699. PMC 5737381 . PMID 28977401.
1 2 Malkowski SN, Atilho RM, Greenlee EB, Weinberg CE, Breaker RR (December 2020). "A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine". RNA. 26 (12): 1838–1846. doi:10.1261/rna.077313.120. PMC 7668255 . PMID 32843366.

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[Weinberg2017b-1] 1 2 3 4 Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR (October 2017). "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids Res. 45 (18): 10811–10823. doi:10.1093/nar/gkx699. PMC 5737381 . PMID 28977401.

[Malkowski2020-2] 1 2 Malkowski SN, Atilho RM, Greenlee EB, Weinberg CE, Breaker RR (December 2020). "A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine". RNA. 26 (12): 1838–1846. doi:10.1261/rna.077313.120. PMC 7668255 . PMID 32843366.

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