Archives of Microbiology

, Volume 194, Issue 4, pp 305–313 | Cite as

Global analysis of the Nitrosomonas europaea iron starvation stimulon

  • Neeraja Vajrala
  • Luis A. Sayavedra-Soto
  • Peter J. Bottomley
  • Daniel J. Arp
Short Communication


The importance of iron to the metabolism of the ammonia-oxidizing bacterium Nitrosomonas europaea is well known. However, the mechanisms by which N. europaea acquires iron under iron limitation are less well known. To obtain insight into these mechanisms, transcriptional profiling of N. europaea was performed during growth under different iron availabilities. Of 2,355 N. europaea genes on DNA microarrays, transcripts for 247 genes were identified as differentially expressed when cells were grown under iron limitation compared to cells grown under iron-replete conditions. Genes with higher transcript levels in response to iron limitation included those with confirmed or assigned roles in iron acquisition. Genes with lower transcript levels included those encoding iron-containing proteins. Our analysis identified several potentially novel iron acquisition systems in N. europaea and provided support for the primary involvement of a TonB-dependent heme receptor gene in N. europaea iron homeostasis. We demonstrated that hemoglobin can act as an iron source under iron-depleted conditions for N. europaea. In addition, we identified a hypothetical protein carrying a lipocalin-like domain that may have the ability to chelate iron for growth in iron-limited media.


Nitrosomonas europaea Fe Iron limitation Microarrays Lipocalin Hemoglobin 



This research was supported by grant DE-FG03-01ER63149 to D. J. A. and the Oregon Agricultural Experiment Station.

Supplementary material

203_2011_778_MOESM1_ESM.doc (296 kb)
Supplementary material 1 (DOC 296 kb)


  1. Akerstrom B, Flower DR, Salier JP (2000) Lipocalins: unity in diversity. Biochim Biophys Acta 1482:1–8PubMedCrossRefGoogle Scholar
  2. Al-Karadaghi S, Franco R, Hansson M, Shelnutt JA, Isaya G, Ferreira GC (2006) Chelatases: distort to select? Trends Biochem Sci 31:135–142PubMedCrossRefGoogle Scholar
  3. Andrews SC, Robinson AK, Rodriguez-Quinones F (2003) Bacterial iron homeostasis. FEMS Microbiol Rev 27:215–237PubMedCrossRefGoogle Scholar
  4. Archibald F (1983) Lactobacillus plantarum, an organism not requiring iron. FEMS Microbiol Lett 19:29–32CrossRefGoogle Scholar
  5. Arciero DM, Hooper AB (1993) Hydroxylamine oxidoreductase from Nitrosomonas europaea is a multimer of an octa-heme subunit. J Biol Chem 268:14645–14654PubMedGoogle Scholar
  6. Arsene F, Tomoyasu T, Bukau B (2000) The heat shock response of Escherichia coli. Int J Food Microbiol 55:3–9PubMedCrossRefGoogle Scholar
  7. Bishop RE (2000) The bacterial lipocalins. Biochim Biophys Acta 1482:73–83PubMedCrossRefGoogle Scholar
  8. Bracken CS, Baer MT, Abdur-Rashid A, Helms W, Stojiljkovic I (1999) Use of heme-protein complexes by the Yersinia enterocolitica HemR receptor: histidine residues are essential for receptor function. J Bacteriol 181:6063–6072PubMedGoogle Scholar
  9. Braun VHK, Koster W (1998) Bacterial iron transport: mechanisms, genetics and regulation. In: Sigel A, Sigel H (eds) Metal ions in biological systems. Iron transport and storage in microorganisms, plants and animals. Marcel Dekker, New York, pp 67–145Google Scholar
  10. Brown DC, Collins KD (1991) Dihydroorotase from Escherichia coli. Substitution of Co(II) for the active site Zn(II). J Biol Chem 266:1597–1604PubMedGoogle Scholar
  11. Chain P et al (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol 185:2759–2773PubMedCrossRefGoogle Scholar
  12. Eggleson KK, Duffin KL, Goldberg DE (1999) Identification and characterization of falcilysin, a metallopeptidase involved in hemoglobin catabolism within the malaria parasite Plasmodium falciparum. J Biol Chem 274:32411–32417PubMedCrossRefGoogle Scholar
  13. Ensign SA, Hyman MR, Arp DJ (1993) In vitro activation of ammonia monooxygenase from Nitrosomonas europaea by copper. J Bacteriol 175:1971–1980PubMedGoogle Scholar
  14. Escolar L, Perez-Martin J, de Lorenzo V (1999) Opening the iron box: transcriptional metalloregulation by the Fur protein. J Bacteriol 181:6223–6229PubMedGoogle Scholar
  15. Flower DR (2000) Beyond the superfamily: the lipocalin receptors. Biochim Biophys Acta 1482:327–336PubMedCrossRefGoogle Scholar
  16. Fluckinger M, Haas H, Merschak P, Glasgow BJ, Redl B (2004) Human tear lipocalin exhibits antimicrobial activity by scavenging microbial siderophores. Antimicrob Agents Chemother 48:3367–3372PubMedCrossRefGoogle Scholar
  17. Goetz DH, Holmes MA, Borregaard N, Bluhm ME, Raymond KN, Strong RK (2002) The neutrophil lipocalin NGAL is a bacteriostatic agent that interferes with siderophore-mediated iron acquisition. Mol Cell 10:1033–1043PubMedCrossRefGoogle Scholar
  18. Grifantini R et al (2003) Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis of Neisseria meningitidis group B. Proc Natl Acad Sci USA 100:9542–9547PubMedCrossRefGoogle Scholar
  19. Guerinot ML (1994) Microbial iron transport. Annu Rev Microbiol 48:743–772PubMedCrossRefGoogle Scholar
  20. Hassett RF, Romeo AM, Kosman DJ (1998) Regulation of high affinity iron uptake in the yeast Saccharomyces cerevisiae. Role of dioxygen and Fe. J Biol Chem 273:7628–7636PubMedCrossRefGoogle Scholar
  21. Herbik A, Bolling C, Buckhout TJ (2002) The involvement of a multicopper oxidase in iron uptake by the green algae Chlamydomonas reinhardtii. Plant Physiol 130:2039–2048PubMedCrossRefGoogle Scholar
  22. Holmes K et al (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur. Microbiology 151:243–257PubMedCrossRefGoogle Scholar
  23. Jacques JF et al (2006) RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli. Mol Microbiol 62:1181–1190PubMedCrossRefGoogle Scholar
  24. Letoffe S, Heuck G, Delepelaire P, Lange N, Wandersman C (2009) Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact. Proc Natl Acad Sci USA 106:11719–11724PubMedCrossRefGoogle Scholar
  25. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402–408PubMedCrossRefGoogle Scholar
  26. Markossian KA, Kurganov BI (2003) Copper chaperones, intracellular copper trafficking proteins. Function, structure, and mechanism of action. Biochemistry (Mosc) 68:827–837CrossRefGoogle Scholar
  27. McHugh JP et al (2003) Global iron-dependent gene regulation in Escherichia coli. A new mechanism for iron homeostasis. J Biol Chem 278:29478–29486PubMedCrossRefGoogle Scholar
  28. Mey AR, Craig SA, Payne SM (2005a) Characterization of Vibrio cholerae RyhB: the RyhB regulon and role of ryhB in biofilm formation. Infect Immun 73:5706–5719PubMedCrossRefGoogle Scholar
  29. Mey AR, Wyckoff EE, Kanukurthy V, Fisher CR, Payne SM (2005b) Iron and fur regulation in Vibrio cholerae and the role of fur in virulence. Infect Immun 73:8167–8178PubMedCrossRefGoogle Scholar
  30. Neilands JB (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270:26723–26726PubMedGoogle Scholar
  31. Palma M, Worgall S, Quadri LE (2003) Transcriptome analysis of the Pseudomonas aeruginosa response to iron. Arch Microbiol 180:374–379PubMedCrossRefGoogle Scholar
  32. Palumaa P, Kangur L, Voronova A, Sillard R (2004) Metal-binding mechanism of Cox17, a copper chaperone for cytochrome c oxidase. Biochem J 382:307–314PubMedCrossRefGoogle Scholar
  33. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45PubMedCrossRefGoogle Scholar
  34. Stearman R, Yuan DS, Yamaguchi-Iwai Y, Klausner RD, Dancis A (1996) A permease-oxidase complex involved in high-affinity iron uptake in yeast. Science 271:1552–1557PubMedCrossRefGoogle Scholar
  35. Stein LY, Arp DJ (1998) Loss of ammonia monooxygenase activity in Nitrosomonas europaea upon exposure to nitrite. Appl Environ Microbiol 64:4098–4102PubMedGoogle Scholar
  36. Taylor AB, Stoj CS, Ziegler L, Kosman DJ, Hart PJ (2005) The copper-iron connection in biology: structure of the metallo-oxidase Fet3p. Proc Natl Acad Sci USA 102:15459–15464PubMedCrossRefGoogle Scholar
  37. Tindale AE, Mehrotra M, Ottem D, Page WJ (2000) Dual regulation of catecholate siderophore biosynthesis in Azotobacter vinelandii by iron and oxidative stress. Microbiology 146(Pt 7):1617–1626PubMedGoogle Scholar
  38. Upadhyay AK, Petasis DT, Arciero DM, Hooper AB, Hendrich MP (2003) Spectroscopic characterization and assignment of reduction potentials in the tetraheme cytochrome C554 from Nitrosomonas europaea. J Am Chem Soc 125:1738–1747PubMedCrossRefGoogle Scholar
  39. Vajrala N, Sayavedra-Soto LA, Bottomley PJ, Arp DJ (2010) Role of Nitrosomonas europaea NitABC iron transporter in the uptake of Fe(3+)-siderophore complexes. Arch Microbiol 192:899–908PubMedCrossRefGoogle Scholar
  40. Vajrala N, Sayavedra-Soto LA, Bottomley PJ, Arp DJ (2011) Role of a Fur homolog in iron metabolism in Nitrosomonas europaea. BMC Microbiol 11:37PubMedCrossRefGoogle Scholar
  41. Wei X, Vajrala N, Hauser L, Sayavedra-Soto LA, Arp DJ (2006) Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea. Arch Microbiol 186:107–118PubMedCrossRefGoogle Scholar
  42. Wei X, Sayavedra-Soto LA, Arp DJ (2007) Characterization of the ferrioxamine uptake system of Nitrosomonas europaea. Microbiology 153:3963–3972PubMedCrossRefGoogle Scholar
  43. Whittaker M, Bergmann D, Arciero D, Hooper AB (2000) Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea. Biochim Biophys Acta 1459:346–355PubMedCrossRefGoogle Scholar
  44. Wilderman PJ et al (2004) Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc Natl Acad Sci USA 101:9792–9797PubMedCrossRefGoogle Scholar
  45. Zhu W, Wilks A, Stojiljkovic I (2000) Degradation of heme in gram-negative bacteria: the product of the hemO gene of Neisseriae is a heme oxygenase. J Bacteriol 182:6783–6790PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Neeraja Vajrala
    • 1
  • Luis A. Sayavedra-Soto
    • 1
  • Peter J. Bottomley
    • 2
  • Daniel J. Arp
    • 1
  1. 1.Department of Botany and Plant PathologyOregon State UniversityCorvallisUSA
  2. 2.Department of MicrobiologyOregon State UniversityCorvallisUSA

Personalised recommendations