RyhB

Secondary structure for the RyhB RNA. The Sm-like protein Hfq binds to the AU-rich unstructured region of RyhB as indicated. Below the secondary structure, the primary sequence of RyhB is shown along with its putative binding interaction to the target mRNA sodB. The start codon for sodB is underlined. RyhB nucleotides that participate in the interaction are in bold.[1]

RyhB RNA is a 90 nucleotide non-coding RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur (Ferric uptake regulator).

Discovery

This ncRNA gene was independently identified in two screens, named RyhB by Wassarman et al. and called SraI by Argaman et al. and was found to be expressed only in stationary phase.[2][3]

Function and regulation

RyhB RNA levels are inversely correlated with mRNA levels for the sdhCDAB operon, encoding succinate dehydrogenase, as well as five other genes previously shown to be positively regulated by Fur by an unknown mechanism. These include two other genes encoding enzymes in the tricarboxylic acid cycle, acnA and fumA, two ferritin genes, ftnA and bfr, and a gene for superoxide dismutase, sodB.[4] A number of other genes have been predicted computationally and verified as targets by microarray analysis: napF, sodA, cysE, yciS, acpS, nagZ and dadA.[1] RyhB is bound by the Hfq protein, that increases its interaction with its target messages.

A comparative genomics target prediction approach suggests that the mRNAs of eleven additional iron containing proteins are controlled by RyhB in Escherichia coli. Two of those (erpA, nirB) and two additional targets that are not directly related to iron (nagZ, marA) were verified with a GFP reporter system.[5][6]

It has been shown that RyhB has a role in targeting the polycistronic transcript iscRSUA for differential degradation. RyhB binds to the second cistron of iscRSUA, which encodes machinery for biosynthesis of Fe-S clusters. This binding promotes cleavage of the downstream iscSUA transcript. This cleavage leaves the 5' IscR transcript which is a transcriptional regulator responsible regulating several genes that depend on cellular Fe-S level.[7]

RyhB is an analog of the sRNA PrrF RNA found in Pseudomonas aeruginosa [8], to HrrF RNA in Haemophilus species [9] and to IsaR1 in cyanobacteria.[10]

Naming

The RyhB gene name is an acronym composed of R for RNA, y for unknown function (after the protein naming convention), with the h representing the ten-minute-interval section of the E. coli map the gene is found in. The B comes from the fact that this was one of two RNA genes identified in this interval.[3] Other RNAs using this nomenclature include RydB RNA, RyeB RNA, RyeE RNA and RyfA RNA.

References

  1. 1 2 Tjaden B, Goodwin SS, Opdyke JA, et al. (2006). "Target prediction for small, noncoding RNAs in bacteria". Nucleic Acids Res. 34 (9): 2791–802. PMC 1464411 Freely accessible. PMID 16717284. doi:10.1093/nar/gkl356.
  2. ↑ Argaman, L; Hershberg R; Vogel J; Bejerano G; Wagner EG; Margalit H; Altuvia S (2001). "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli". Curr Biol. 11 (12): 941–950. PMID 11448770. doi:10.1016/S0960-9822(01)00270-6.
  3. 1 2 Wassarman, K. M.; Repoila, F.; Rosenow, C.; Storz, G.; Gottesman, S. (2001). "Identification of novel small RNAs using comparative genomics and microarrays". Genes & Development. 15 (13): 1637–1651. PMC 312727 Freely accessible. PMID 11445539. doi:10.1101/gad.901001.
  4. ↑ Masse, E; Gottesman S (2002). "A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli". Proc Natl Acad Sci USA. 99 (7): 4620–4625. PMC 123697 Freely accessible. PMID 11917098. doi:10.1073/pnas.032066599.
  5. ↑ Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J; Richter; Papenfort; Mann; Vogel; Hess; Backofen; Georg (2013). "Comparative genomics boosts target prediction for bacterial small RNAs". Proc Natl Acad Sci U S A. 110 (37): E3487–E3496. PMC 3773804 Freely accessible. PMID 23980183. doi:10.1073/pnas.1303248110.
  6. ↑ Urban JH, Vogel J; Vogel (2007). "Translational control and target recognition by Escherichia coli small RNAs in vivo". Nucleic Acids Res. 35 (3): 1018–37. PMC 1807950 Freely accessible. PMID 17264113. doi:10.1093/nar/gkl1040.
  7. ↑ Desnoyers G, Morissette A, Prévost K, Massé E; Morissette; Prévost; Massé (June 2009). "Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA". EMBO J. 28 (11): 1551–61. PMC 2693151 Freely accessible. PMID 19407815. doi:10.1038/emboj.2009.116.
  8. ↑ Wilderman, PJ; Sowa NA; FitzGerald DJ; FitzGerald PC; Gottesman S; Ochsner UA; Vasil ML (2004). "Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis". Proc Natl Acad Sci USA. 101 (26): 9792–9797. PMC 470753 Freely accessible. PMID 15210934. doi:10.1073/pnas.0403423101.
  9. ↑ Santana, Estevan A.; Harrison, Alistair; Zhang, Xinjun; Baker, Beth D.; Kelly, Benjamin J.; White, Peter; Liu, Yunlong; Munson, Robert S. (2014-01-01). "HrrF is the Fur-regulated small RNA in nontypeable Haemophilus influenzae". PloS One. 9 (8): e105644. ISSN 1932-6203. PMC 4144887 Freely accessible. PMID 25157846. doi:10.1371/journal.pone.0105644.
  10. ↑ Georg J, Kostova G, Vuorijoki L, Schön V, Kadowaki T, Huokko T, Baumgartner D, Müller M, Klähn S, Allahverdiyeva Y, Hihara Y, Futschik ME, Aro EM, Hess WR (2017). "Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1". Curr Biol. 27 (10): 1425–1436.e7. PMID 28479323. doi:10.1016/j.cub.2017.04.010.

Further reading

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