RyhB
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 Wasserman 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]
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 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. doi:10.1093/nar/gkl356. PMC 1464411. PMID 16717284.
- ↑ 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. doi:10.1016/S0960-9822(01)00270-6. PMID 11448770.
- 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. doi:10.1101/gad.901001. PMC 312727. PMID 11445539.
- ↑ 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. doi:10.1073/pnas.032066599. PMC 123697. PMID 11917098.
- ↑ 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. doi:10.1073/pnas.1303248110. PMC 3773804. PMID 23980183.
- ↑ 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. doi:10.1093/nar/gkl1040. PMC 1807950. PMID 17264113.
- ↑ 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. doi:10.1038/emboj.2009.116. PMC 2693151. PMID 19407815.
- ↑ 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. doi:10.1073/pnas.0403423101. PMC 470753. PMID 15210934.
Further reading
- Salvail H, Lanthier-Bourbonnais P, Sobota JM, Caza M, Benjamin JA, Mendieta ME, Lépine F, Dozois CM, Imlay J, Massé E; Lanthier-Bourbonnais; Sobota; Caza; Benjamin; Mendieta; Lépine; Dozois; Imlay; Massé (2010). "A small RNA promotes siderophore production through transcriptional and metabolic remodeling". Proc Natl Acad Sci U S A 107 (34): 15223–8. doi:10.1073/pnas.1007805107. PMC 2930555. PMID 20696910.
- Nandal, A.; Huggins, C. C. O.; Woodhall, M. R.; McHugh, J.; Rodríguez-Quiñones, F.; Quail, M. A.; Guest, J. R.; Andrews, S. C. (2010). "Induction of the ferritin gene (ftnA) ofEscherichia coliby Fe2+-Fur is mediated by reversal of H-NS silencing and is RyhB independent". Molecular Microbiology 75 (3): 637–57. doi:10.1111/j.1365-2958.2009.06977.x. PMID 20015147.
- Bollinger, C. J. T.; Kallio, P. T. (2007). "Impact of the small RNA RyhB on growth, physiology and heterologous protein expression inEscherichia coli". FEMS Microbiology Letters 275 (2): 221–228. doi:10.1111/j.1574-6968.2007.00880.x. PMID 17784860.
- Prévost, K.; Salvail, H.; Desnoyers, G.; Jacques, J-F.; Phaneuf, É.; Massé, E. (2007). "The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis". Molecular Microbiology 64 (5): 1260–73. doi:10.1111/j.1365-2958.2007.05733.x. PMID 17542919.
- Murphy, E. R.; Payne, S. M. (2007). "RyhB, an Iron-Responsive Small RNA Molecule, Regulates Shigella dysenteriae Virulence". Infection and Immunity 75 (7): 3470–3477. doi:10.1128/IAI.00112-07. PMC 1932958. PMID 17438026.
- Večerek, B.; Moll, I.; Bläsi, U. (2007). "Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding". The EMBO Journal 26 (4): 965–975. doi:10.1038/sj.emboj.7601553. PMC 1852835. PMID 17268550.
- Jacques, J. F. �O.; Jang, S.; Prévost, K.; Desnoyers, G.; Desmarais, M.; Imlay, J.; Massé, E. (2006). "RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli". Molecular Microbiology 62 (4): 1181–1190. doi:10.1111/j.1365-2958.2006.05439.x. PMID 17078818. replacement character in
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at position 7 (help) - Oglesby, A. G.; Murphy, E. R.; Iyer, V. R.; Payne, S. M. (2005). "Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP". Molecular Microbiology 58 (5): 1354–67. doi:10.1111/j.1365-2958.2005.04920.x. PMID 16313621.
- Massé, E.; Vanderpool, K.; Gottesman, S. (Oct 2005). "Effect of RyhB small RNA on global iron use in Escherichia coli" (Free full text). Journal of Bacteriology 187 (20): 6962–6971. doi:10.1128/JB.187.20.6962-6971.2005. ISSN 0021-9193. PMC 1251601. PMID 16199566.
- Mey, A. R.; Craig, S. A.; Payne, S. M. (2005). "Characterization of Vibrio cholerae RyhB: the RyhB Regulon and Role of ryhB in Biofilm Formation". Infection and Immunity 73 (9): 5706–5719. doi:10.1128/IAI.73.9.5706-5719.2005. PMC 1231101. PMID 16113288.
- Davis, B. M.; Quinones, M.; Pratt, J.; Ding, Y.; Waldor, M. K. (2005). "Characterization of the Small Untranslated RNA RyhB and Its Regulon in Vibrio cholerae". Journal of Bacteriology 187 (12): 4005–4014. doi:10.1128/JB.187.12.4005-4014.2005. PMC 1151736. PMID 15937163.
- Gottesman, S (2005). "Micros for microbes: non-coding regulatory RNAs in bacteria". Trends Genet 21 (7): 399–404. doi:10.1016/j.tig.2005.05.008. PMID 15913835.
- Afonyushkin, T.; Vecerek, B.; Moll, I.; Blasi, U.; Kaberdin, V. R. (2005). "Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB". Nucleic Acids Research 33 (5): 1678–1689. doi:10.1093/nar/gki313. PMC 1069011. PMID 15781494.
- Oglesby-Sherrouse, A. G.; Murphy, E. R. (2013). "Iron-responsive bacterial small RNAs: Variations on a theme". Metallomics 5: 276. doi:10.1039/c3mt20224k. PMID 23340911.
- Tanabe, T.; Funahashi, T.; Nakao, H.; Maki, J.; Yamamoto, S. (2013). "The Vibrio parahaemolyticus small RNA RyhB promotes production of the siderophore vibrioferrin by stabilizing the polycistronic mRNA". Journal of Bacteriology 195 (16): 3692–703. doi:10.1128/JB.00162-13. PMID 23772063.
- Bos, J.; Duverger, Y.; Thouvenot, B. T.; Chiaruttini, C.; Branlant, C.; Springer, M.; Charpentier, B.; Barras, F. D. R. (2013). Cascales, Eric, ed. "The sRNA RyhB Regulates the Synthesis of the Escherichia coli Methionine Sulfoxide Reductase MsrB but Not MsrA". PLoS ONE 8 (5): e63647. doi:10.1371/journal.pone.0063647. PMC 3650055. PMID 23671689.
- Deng, Z; Liu, Z; Bi, Y; Wang, X; Zhou, D; Yang, R; Han, Y (2014). "Rapid Degradation of Hfq-Free RyhB in Yersinia pestis by PNPase Independent of Putative Ribonucleolytic Complexes.". BioMed research international 2014: 798918. doi:10.1155/2014/798918. PMC 4003864. PMID 24818153.
- Li, F; Wang, Y; Gong, K; Wang, Q; Liang, Q; Qi, Q (Jan 2014). "Constitutive expression of RyhB regulates the heme biosynthesis pathway and increases the 5-aminolevulinic acid accumulation in Escherichia coli.". FEMS microbiology letters 350 (2): 209–15. doi:10.1111/1574-6968.12322. PMID 24188714.
- Porcheron, G; Habib, R; Houle, S; Caza, M; Lépine, F; Daigle, F; Massé, E; Dozois, CM (Sep 22, 2014). "The small RNA RyhB contributes to siderophore production and virulence of uropathogenic Escherichia coli". Infection and immunity 82: 5056–68. doi:10.1128/IAI.02287-14. PMID 25245805.
- Calderón, PF; Morales, EH; Acuña, LG; Fuentes, DN; Gil, F; Porwollik, S; McClelland, M; Saavedra, CP; Calderón, IL (Jul 18, 2014). "The small RNA RyhB homologs from Salmonella typhimurium participate in the response to S-nitrosoglutathione-induced stress". Biochemical and Biophysical Research Communications 450 (1): 641–5. doi:10.1016/j.bbrc.2014.06.031. PMID 24937451.