YdaO/yuaA leader

ydaO/yuaA leader
	Predicted secondary structure and sequence conservation of ydaO-yuaA
Identifiers
Symbol	ydaO-yuaA
Rfam	RF00379
Other data
RNA type	Cis-reg; riboswitch
Domain(s)	Bacteria
SO	SO:0000233
PDB structures	PDBe

The YdaO/YuaA leader (now called the cyclic di-AMP riboswitch) is a conserved RNA structure found upstream of the ydaO and yuaA genes in Bacillus subtilis and related genes in other bacteria. Its secondary structure and gene associations were predicted by bioinformatics.[1]

These RNAs function as riboswitches, and sense the signaling molecule cyclic di-AMP.[2] The interaction between the riboswitch and c-di-AMP has been revealed in atomic-resolution structures.[3][4][5]

References

Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR (2004). "New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control". Proc. Natl. Acad. Sci. U.S.A. 101 (17): 6421–6426. doi:10.1073/pnas.0308014101. PMC 404060. PMID 15096624.
Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR (2013). "Riboswitches in eubacteria sense the second messenger c-di-AMP". Nat. Chem. Biol. 9 (12): 834–839. doi:10.1038/nchembio.1363. PMC 3830699. PMID 24141192.
Gao A, Serganov A (2014). "Structural insights into recognition of c-di-AMP by the ydaO riboswitch". Nat. Chem. Biol. 10 (9): 787–792. doi:10.1038/nchembio.1607. PMC 4294798. PMID 25086507.
Ren A, Patel DJ (2014). "c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets". Nat. Chem. Biol. 10 (9): 780–786. doi:10.1038/nchembio.1606. PMC 4217635. PMID 25086509.
Jones CP, Ferré-D'Amaré AR (2014). "Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA". EMBO J. 33 (22): 2692–2703. doi:10.15252/embj.201489209. PMC 4282576. PMID 25271255.

External links

Page for ydaO/yuaA leader at Rfam

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[1] Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR (2004). "New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control". Proc. Natl. Acad. Sci. U.S.A. 101 (17): 6421–6426. doi:10.1073/pnas.0308014101. PMC 404060. PMID 15096624.

[2] Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR (2013). "Riboswitches in eubacteria sense the second messenger c-di-AMP". Nat. Chem. Biol. 9 (12): 834–839. doi:10.1038/nchembio.1363. PMC 3830699. PMID 24141192.

[3] Gao A, Serganov A (2014). "Structural insights into recognition of c-di-AMP by the ydaO riboswitch". Nat. Chem. Biol. 10 (9): 787–792. doi:10.1038/nchembio.1607. PMC 4294798. PMID 25086507.

[4] Ren A, Patel DJ (2014). "c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets". Nat. Chem. Biol. 10 (9): 780–786. doi:10.1038/nchembio.1606. PMC 4217635. PMID 25086509.

[5] Jones CP, Ferré-D'Amaré AR (2014). "Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA". EMBO J. 33 (22): 2692–2703. doi:10.15252/embj.201489209. PMC 4282576. PMID 25271255.