YybP-ykoY leader explained

yybP-ykoY leader
Symbol:	yybP-ykoY
Altsymbols:	SraF
Rfam:	RF00080
Rna Type:	Cis-reg; riboswitch
Tax Domain:	Bacteria

The yybP-ykoY leader RNA element was originally discovered in E. coli during a large scale screen and was named SraF.^[1] This family was later found to exist upstream of related families of protein genes in many bacteria, including the yybP and ykoY genes in B. subtilis. The specific functions of these proteins are unknown, but this structured RNA element may be involved in their genetic regulation as a riboswitch.^[2] The yybP-ykoY element was later proposed to be manganese-responsive after another associated family of genes, YebN/MntP, was shown to encode Mn²⁺ efflux pumps in several bacteria.^{[3] [4] [5]} Genetic data and a crystal structure confirmed that yybp-ykoY is a manganese riboswitch that directly binds Mn^{2+[6] [7]}

Notes and References

1. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S . Novel small RNA-encoding genes in the intergenic regions of Escherichia coli . Current Biology . 11 . 12 . 941–950 . June 2001 . 11448770 . 10.1016/S0960-9822(01)00270-6 . free .
2. Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR . New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control . Proceedings of the National Academy of Sciences of the United States of America . 101 . 17 . 6421–6426 . April 2004 . 15096624 . 404060 . 10.1073/pnas.0308014101 . 2004PNAS..101.6421B . free .
3. Waters LS, Sandoval M, Storz G . The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis . Journal of Bacteriology . 193 . 21 . 5887–5897 . November 2011 . 21908668 . 3194919 . 10.1128/jb.05872-11 .
4. Li C, Tao J, Mao D, He C . A novel manganese efflux system, YebN, is required for virulence by Xanthomonas oryzae pv. oryzae . PLOS ONE . 6 . 7 . e21983 . 2011 . 21789199 . 3136493 . 10.1371/journal.pone.0021983 . 2011PLoSO...621983L . free .
5. Veyrier FJ, Boneca IG, Cellier MF, Taha MK . A novel metal transporter mediating manganese export (MntX) regulates the Mn to Fe intracellular ratio and Neisseria meningitidis virulence . PLOS Pathogens . 7 . 9 . e1002261 . September 2011 . 21980287 . 10.1371/journal.ppat.1002261 . 3182930 . free .
6. Price IR, Gaballa A, Ding F, Helmann JD, Ke A . Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches . Molecular Cell . 57 . 6 . 1110–1123 . March 2015 . 25794619 . 4703321 . 10.1016/j.molcel.2015.02.016 .
7. Dambach M, Sandoval M, Updegrove TB, Anantharaman V, Aravind L, Waters LS, Storz G . The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element . Molecular Cell . 57 . 6 . 1099–1109 . March 2015 . 25794618 . 4376352 . 10.1016/j.molcel.2015.01.035 .