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BioMetals

, Volume 32, Issue 2, pp 273–291 | Cite as

Highly conserved nucleotide motifs present in the 5′UTR of the heme-receptor gene shmR are required for HmuP-dependent expression of shmR in Ensifer meliloti

  • Vanesa Amarelle
  • Uriel Koziol
  • Elena FabianoEmail author
Article
  • 76 Downloads

Abstract

Heme may represent a major iron-source for bacteria. In the symbiotic nitrogen-fixing bacterium Ensifer meliloti 1021, iron acquisition from heme depends on the outer-membrane heme-receptor ShmR. Expression of shmR gene is repressed by iron in a RirA dependent manner while under iron-limitation its expression requires the small protein HmuP. In this work, we identified highly conserved nucleotide motifs present upstream the shmR gene. These motifs are widely distributed among Alpha and Beta Proteobacteria, and correlate with the presence of HmuP coding sequences in bacterial genomes. According to data presented in this work, we named these new motifs as HmuP-responsive elements (HPREs). In the analyzed genomes, the HPREs were always present upstream of genes encoding putative heme-receptors. Moreover, in those Alpha and Beta Proteobacteria where transcriptional start sites for shmR homologs are known, HPREs were located in the 5′UTR region. In this work we show that in E. meliloti 1021, HPREs are involved in HmuP-dependent shmR expression. Moreover, we show that changes in sequence composition of the HPREs correlate with changes in a predicted RNA secondary structure element and affect shmR gene expression.

Keywords

Iron homeostasis Heme uptake HmuP Rhizobia Regulation 

Notes

Supplementary material

10534_2019_184_MOESM1_ESM.doc (50 kb)
Supplementary material 1 (DOC 50 kb)
10534_2019_184_MOESM2_ESM.doc (215 kb)
Supplementary material 2 (DOC 215 kb)

References

  1. Allaway D, Schofield NA, Leonard ME, Gilardoni L, Finan TM, Poole PS (2001) Use of differential fluorescence induction and optical trapping to isolate environmentally induced genes. Environ Microbiol 3:397–406.  https://doi.org/10.1046/j.1462-2920.2001.00205.x CrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410.  https://doi.org/10.1016/s0022-2836(05)80360-2 CrossRefGoogle Scholar
  3. Amarelle V, O’Brian MR, Fabiano E (2008) ShmR is essential for utilization of heme as a nutritional iron source in Sinorhizobium meliloti. Appl Environ Microbiol 74:6473–6475.  https://doi.org/10.1128/aem.01590-08 CrossRefGoogle Scholar
  4. Amarelle V, Koziol U, Rosconi F, Noya F, O’Brian MR, Fabiano E (2010) A new small regulatory protein, HmuP, modulates haemin acquisition in Sinorhizobium meliloti. Microbiology 156:1873–1882.  https://doi.org/10.1099/mic.0.037713-0 CrossRefGoogle Scholar
  5. Anderson MT, Armstrong SK (2004) The BfeR regulator mediates enterobactin-inducible expression of Bordetella enterobactin utilization genes. J Bacteriol 186:7302–7311.  https://doi.org/10.1128/jb.186.21.7302-7311.2004 CrossRefGoogle Scholar
  6. Anderson ES, Paulley JT, Roop RM (2008) The AraC-like transcriptional regulator DhbR is required for maximum expression of the 2,3-dihydroxybenzoic acid biosynthesis genes in Brucella abortus 2308 in response to iron deprivation. J Bacteriol 190:1838–1842.  https://doi.org/10.1128/jb.01551-07 CrossRefGoogle Scholar
  7. Andrews SC, Robinson AK, Rodríguez-Quiñones F (2003) Bacterial iron homeostasis. FEMS Microbiol Rev 27:215–237.  https://doi.org/10.1016/s0168-6445(03)00055-x CrossRefGoogle Scholar
  8. Andrews S, Norton I, Salunkhe AS, Goodluck H, Aly WSM, Mourad-Agha H, Cornelis P (2013) Control of iron metabolism in bacteria. Met Ions Life Sci 12:203–239.  https://doi.org/10.1007/978-94-007-5561-1_7 CrossRefGoogle Scholar
  9. Augustus AM, Sage H, Spicer LD (2010) Binding of MetJ repressor to specific and nonspecific DNA and effect of S-adenosylmethionine on these interactions. Biochemistry 49:3289–3295.  https://doi.org/10.1021/bi902011f CrossRefGoogle Scholar
  10. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36Google Scholar
  11. Bailey TL, Gribskov M (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics (Oxford, England) 14:48–54CrossRefGoogle Scholar
  12. Battistoni F, Platero R, Durán R, Cerveñansky C, Battistoni J, Arias A, Fabiano E (2002) Identification of an iron-regulated, hemin-binding outer membrane protein in Sinorhizobium meliloti. Appl Environ Microbiol 68:5877–5881.  https://doi.org/10.1128/aem.68.12.5877-5881.2002 CrossRefGoogle Scholar
  13. Beaumont FC, Kang HY, Brickman TJ, Armstrong SK (1998) Identification and characterization of alcR, a gene encoding an AraC-like regulator of alcaligin siderophore biosynthesis and transport in Bordetella pertussis and Bordetella bronchiseptica. J Bacteriol 180:862–870Google Scholar
  14. Beringer JE (1974) R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 84:188–198Google Scholar
  15. Biville F, Cwerman H, Letoffe S, Rossi M-S, Drouet V, Ghigo JM, Wandersman C (2004) Haemophore-mediated signalling in Serratia marcescens: a new mode of regulation for an extra cytoplasmic function (ECF) sigma factor involved in haem acquisition. Mol Microbiol 53:1267–1277CrossRefGoogle Scholar
  16. Braun V, Mahren S, Ogierman M (2003) Regulation of the FecI-type ECF sigma factor by transmembrane signalling. Curr Opin Microbiol 6:173–180CrossRefGoogle Scholar
  17. Carter RA et al (2002) The vbs genes that direct synthesis of the siderophore vicibactin in Rhizobium leguminosarum: their expression in other genera requires ECF sigma factor RpoI. Mol Microbiol 44:1153–1166CrossRefGoogle Scholar
  18. Chao T-C, Buhrmester J, Hansmeier N, Pühler A, Weidner S (2005) Role of the regulatory gene rirA in the transcriptional response of Sinorhizobium meliloti to iron limitation. Appl Environ Microbiol 71:5969–5982CrossRefGoogle Scholar
  19. Cornelis P (2013) Iron transport systems and iron homeostasis in Pseudomonas. Iron uptake in bacteria with emphasis on E coli and Pseudomonas. Springer, Dordrecht, pp 67–89.  https://doi.org/10.1007/978-94-007-6088-2_3 CrossRefGoogle Scholar
  20. Costa D, Amarelle V, Valverde C, O’Brian MR, Fabiano E (2017) The Irr and RirA proteins participate in a complex regulatory circuit and act in concert to modulate bacterioferritin expression in Ensifer meliloti. Appl Environ Microbiol 83:e00895–17.  https://doi.org/10.1128/aem.00895-17 CrossRefGoogle Scholar
  21. Díaz-Mireles E, Wexler M, Sawers G, Bellini D, Todd JD, Johnston AWB (2004) The Fur-like protein Mur of Rhizobium leguminosarum is a Mn2+-responsive transcriptional regulator. Microbiology 150:1447–1456.  https://doi.org/10.1099/mic.0.26961-0 CrossRefGoogle Scholar
  22. Ditta G, Stanfield S, Corbin D, Helinski DR (1980) Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc Natl Acad Sci USA 77:7347–7351CrossRefGoogle Scholar
  23. Escamilla-Hernández R, O’Brian MR (2012) HmuP is a coactivator of Irr-dependent expression of heme utilization genes in Bradyrhizobium japonicum. J Bacteriol 194:3137–3143.  https://doi.org/10.1128/jb.00071-12 CrossRefGoogle Scholar
  24. Escolar L, Pérez-Martín J, de Lorenzo V (1999) Opening the iron box: transcriptional metalloregulation by the Fur protein. J Bacteriol 181:6223–6229Google Scholar
  25. Fetherston JD, Bearden SW, Perry RD (1996) YbtA, an AraC-type regulator of the Yersinia pestis pesticin/yersiniabactin receptor. Mol Microbiol 22:315–325.  https://doi.org/10.1046/j.1365-2958.1996.00118.x CrossRefGoogle Scholar
  26. Figurski DH, Helinski DR (1979) Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci USA 76:1648–1652CrossRefGoogle Scholar
  27. Finan TM, Hartweig E, LeMieux K, Bergman K, Walker GC, Signer ER (1984) General transduction in Rhizobium meliloti. J Bacteriol 159:120–124Google Scholar
  28. Gaballa A, Helmann JD (2007) Substrate induction of siderophore transport in Bacillus subtilis mediated by a novel one-component regulator. Mol Microbiol 66:164–173.  https://doi.org/10.1111/j.1365-2958.2007.05905.x CrossRefGoogle Scholar
  29. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Res 36:W70–W74.  https://doi.org/10.1093/nar/gkn188 CrossRefGoogle Scholar
  30. Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166:557–580CrossRefGoogle Scholar
  31. Hantke K (2001) Iron and metal regulation in bacteria. Curr Opin Microbiol 4:172–177CrossRefGoogle Scholar
  32. Heinrichs DE, Poole K (1993) Cloning and sequence analysis of a gene (pchR) encoding an AraC family activator of pyochelin and ferripyochelin receptor synthesis in Pseudomonas aeruginosa. J Bacteriol 175:5882–5889CrossRefGoogle Scholar
  33. Hollander A, Mercante AD, Shafer WM, Cornelissen CN (2011) The iron-repressed, AraC-like regulator MpeR activates expression of fetA in Neisseria gonorrhoeae. Infect Immun 79:4764–4776.  https://doi.org/10.1128/iai.05806-11 CrossRefGoogle Scholar
  34. Holmqvist E, Wagner EGH (2017) Impact of bacterial sRNAs in stress responses. Biochem Soc Trans 45:1203–1212.  https://doi.org/10.1042/bst20160363 CrossRefGoogle Scholar
  35. Humann JL et al (2008) Construction and expression of sugar kinase transcriptional gene fusions by using the Sinorhizobium meliloti ORFeome. Appl Environ Microbiol 74:6756–6765.  https://doi.org/10.1128/aem.01468-08 CrossRefGoogle Scholar
  36. Johnston AW, Todd JD, Curson ARJ, Lei S, Nikolaidou-Katsaridou N, Gelfand MS, Rodionov DA (2007) Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other a-proteobacteria. Biometals 20:501–511.  https://doi.org/10.1007/s10534-007-9085-8 CrossRefGoogle Scholar
  37. MacLellan SR, MacLean AM, Finan TM (2006) Promoter prediction in the rhizobia. Microbiology 152:1751–1763.  https://doi.org/10.1099/mic.0.28743-0 CrossRefGoogle Scholar
  38. Meade HM, Long SR, Ruvkun GB, Brown SE, Ausubel FM (1982) Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J Bacteriol 149:114–122Google Scholar
  39. Ngok-Ngam P, Ruangkiattikul N, Mahavihakanont A, Virgem SS, Sukchawalit R, Mongkolsuk S (2009) Roles of Agrobacterium tumefaciens RirA in iron regulation, oxidative stress response, and virulence. J Bacteriol 191:2083–2090.  https://doi.org/10.1128/jb.01380-08 CrossRefGoogle Scholar
  40. Nienaber A, Hennecke H, Fischer H-M (2001) Discovery of a haem uptake system in the soil bacterium Bradyrhizobium japonicum. Mol Microbiol 41:787–800.  https://doi.org/10.1046/j.1365-2958.2001.02555.x CrossRefGoogle Scholar
  41. O’Brian MR (2015) Perception and homeostatic control of iron in the rhizobia and related bacteria. Annu Rev Microbiol 69:229–245CrossRefGoogle Scholar
  42. O’Brian MR, Fabiano E (2010) Mechanisms and regulation of iron homesotasis in the Rhizobia. In: Cornelis P, Andrews SC (eds) Molecular aspects of iron metabolism in pathogenic and symbiotic plant-microbe associations 2012. Caister Academic Press, Norfolk, pp 37–37Google Scholar
  43. Ojeda JF, Martinson DA, Menscher EA, Roop RMI (2012) The bhuQ gene encodes a heme oxygenase that contributes to the ability of Brucella abortus 2308 to use heme as an iron source and is regulated by Irr. J Bacteriol 194:4052–4058.  https://doi.org/10.1128/jb.00367-12 CrossRefGoogle Scholar
  44. Parrow NL, Abbott J, Lockwood AR, Battisti JM, Minnick MF (2009) Function, regulation, and transcriptional organization of the hemin utilization locus of Bartonella quintana. Infect Immun 77:307–316.  https://doi.org/10.1128/iai.01194-08 CrossRefGoogle Scholar
  45. Pellicer Martinez MT et al (2017) Sensing iron availability via the fragile [4Fe-4S] cluster of the bacterial transcriptional repressor RirA. Chem Sci 8:8451–8463.  https://doi.org/10.1039/c7sc02801f CrossRefGoogle Scholar
  46. Platero R, Peixoto L, O’Brian MR, Fabiano E (2004) Fur is involved in manganese-dependent regulation of mntA (sitA) expression in Sinorhizobium meliloti. Appl Environ Microbiol 70:4349–4355.  https://doi.org/10.1128/aem.70.7.4349-4355.2004 CrossRefGoogle Scholar
  47. Rodionov DA, Gelfand MS, Todd JD, Curson ARJ, Johnston AWB (2006) Computational reconstruction of iron- and manganese-responsive transcriptional networks in a-proteobacteria. PLoS Comput Biol 2:e163–e163.  https://doi.org/10.1371/journal.pcbi.0020163 CrossRefGoogle Scholar
  48. Rossi M-S, Paquelin A, Ghigo JM, Wandersman C (2003) Haemophore-mediated signal transduction across the bacterial cell envelope in Serratia marcescens: the inducer and the transported substrate are different molecules. Mol Microbiol 48:1467–1480CrossRefGoogle Scholar
  49. Rudolph G, Hennecke H, Fischer H-M (2006) Beyond the Fur paradigm: iron-controlled gene expression in rhizobia. FEMS Microbiol Rev 30:631–648.  https://doi.org/10.1111/j.1574-6976.2006.00030.x CrossRefGoogle Scholar
  50. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, New YorkGoogle Scholar
  51. Sato T, Nonoyama S, Kimura A, Nagata Y, Ohtsubo Y, Tsuda M (2017) The small protein HemP is a transcriptional activator for the hemin uptake operon in Burkholderia multivorans ATCC 17616. Appl Environ Microbiol 83:e00479–00417.  https://doi.org/10.1128/aem.00479-17 CrossRefGoogle Scholar
  52. Schlüter J-P et al (2010) A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genom 11:245.  https://doi.org/10.1186/1471-2164-11-245 CrossRefGoogle Scholar
  53. Somers WS et al (1994) The Met repressor-operator complex: DNA recognition by b-strands. Ann N Y Acad Sci 726:105–117.  https://doi.org/10.1111/j.1749-6632.1994.tb52802.x CrossRefGoogle Scholar
  54. Stojiljkovic I, Hantke K (1992) Hemin uptake system of Yersinia enterocolitica: similarities with other TonB-dependent systems in Gram-negative bacteria. EMBO J 11:4359–4367CrossRefGoogle Scholar
  55. Todd JD, Wexler M, Sawers G, Yeoman K, Poole P, Johnston AW (2002) RirA, an iron-responsive regulator in the symbiotic bacterium Rhizobium leguminosarum. Microbiology 148:4059–4071.  https://doi.org/10.1099/00221287-148-12-4059 CrossRefGoogle Scholar
  56. van Helden J (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31:3593–3596CrossRefGoogle Scholar
  57. van Hijum SAFT, Medema MH, Kuipers OP (2009) Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev 73:481–509.  https://doi.org/10.1128/mmbr.00037-08 CrossRefGoogle Scholar
  58. Vander Kooi CW (2013) Megaprimer method for mutagenesis of DNA. Methods Enzymol 529:259–269CrossRefGoogle Scholar
  59. Viguier C, OCuiv P, Clarke P, O’Connell M (2005) RirA is the iron response regulator of the rhizobactin 1021 biosynthesis and transport genes in Sinorhizobium meliloti. FEMS Microbiol Lett 246:235–242.  https://doi.org/10.1016/j.femsle.2005.04.012 CrossRefGoogle Scholar
  60. Yang J, Sangwan I, Lindemann A, Hauser F, Hennecke H, Fischer H-M, O’Brian MR (2006) Bradyrhizobium japonicum senses iron through the status of haem to regulate iron homeostasis and metabolism. Mol Microbiol 60:427–437.  https://doi.org/10.1111/j.1365-2958.2006.05101.x CrossRefGoogle Scholar
  61. Yeoman K, May AG, deLuca NG, Stuckey DB, Johnston AW (1999) A putative ECF sigma factor gene, rpol, regulates siderophore production in Rhizobium leguminosarum. Mol Plant-Microbe Interact 12:994–999.  https://doi.org/10.1094/mpmi.1999.12.11.994 CrossRefGoogle Scholar
  62. Yeoman K, Curson ARJ, Todd JD, Sawers G, Johnston AW (2004) Evidence that the Rhizobium regulatory protein RirA binds to cis-acting iron-responsive operators (IROs) at promoters of some Fe-regulated genes. Microbiology 150:4065–4074.  https://doi.org/10.1099/mic.0.27419-0 CrossRefGoogle Scholar

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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Instituto de Investigaciones Biologicas Clemente EstableMontevideoUruguay

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