YkoK leader

ykoK leader
	Predicted secondary structure and sequence conservation of ykoK
Identifiers
Symbol	ykoK
Rfam	RF00380
Other data
RNA type	Cis-reg; riboswitch
Domain(s)	Bacteria
SO	SO:0000233
PDB structures	PDBe

The Ykok leader or M-box is a Mg²⁺-sensing RNA structure that controls the expression of Magnesium ion transport proteins in bacteria. It is a distinct structure to the Magnesium responsive RNA element.

The Ykok leader was originally described as a conserved sequence with potential riboswitch function found upstream of the B. subtilis ykoK gene and genes with related functions in other bacteria.[1] Examples of the conserved M-box RNA structure occur upstream of each of the three major families of Mg²⁺ transporters (CorA, MgtE and MgtA/MgtB) in various bacterial species.[2]

The molecular structure of the M-box example upstream of the B. subtilis ykoK gene includes six bound Mg²⁺ ions. Biochemical studies indicate that this M-Box RNA compacts in the presence of Mg²⁺ and other divalent ions. This folding process appears to disrupt an antiterminator structure, and thereby allow a transcription terminator structure to form. As expected from this model, B. subtilis cells repress expression of a downstream reporter gene when grown in the presence of Mg²⁺. Therefore, the M-box appears to function as a genetic "off" switch that is important for maintaining Mg²⁺ homeostasis in bacteria.

A 3D representation of the Ykok leader. Structure of the M-box riboswitch aptamer domain from Bacillus subtilis.[2]

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 USA. 101 (17): 6421–6426. doi:10.1073/pnas.0308014101. PMC 404060. PMID 15096624.
Dann CE, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winkler WC (2007). "Structure and mechanism of a metal-sensing regulatory RNA". Cell. 130 (5): 878–892. doi:10.1016/j.cell.2007.06.051. PMID 17803910.

External links

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[Barrick-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 USA. 101 (17): 6421–6426. doi:10.1073/pnas.0308014101. PMC 404060. PMID 15096624.

[pmid17803910-2] Dann CE, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winkler WC (2007). "Structure and mechanism of a metal-sensing regulatory RNA". Cell. 130 (5): 878–892. doi:10.1016/j.cell.2007.06.051. PMID 17803910.