Advertisement

BioMetals

, 20:467 | Cite as

Bioinformatic analysis of the TonB protein family

  • Byron C. H. Chu
  • R. Sean Peacock
  • Hans J. VogelEmail author
Original Paper

Abstract

TonB is a protein prevalent in a large number of Gram-negative bacteria that is believed to be responsible for the energy transduction component in the import of ferric iron complexes and vitamin B12 across the outer membrane. We have analyzed all the TonB proteins that are currently contained in the Entrez database and have identified nine different clusters based on its conserved 90-residue C-terminal domain amino acid sequence. The vast majority of the proteins contained a single predicted cytoplasmic transmembrane domain; however, nine of the TonB proteins encompass a ∼90 amino acid N-terminal extension homologous to the MecR1 protein, which is composed of three additional predicted transmembrane helices. The periplasmic linker region, which is located between the N-terminal domain and the C-terminal domain, is extremely variable both in length (22–283 amino acids) and in proline content, indicating that a Pro-rich domain is not a required feature for all TonB proteins. The secondary structure of the C-terminal domain is found to be well preserved across all families, with the most variable region being between the second α-helix and the third β-strand of the antiparallel β-sheet. The fourth β-strand found in the solution structure of the Escherichia coli TonB C-terminal domain is not a well conserved feature in TonB proteins in most of the clusters. Interestingly, several of the TonB proteins contained two C-terminal domains in series. This analysis provides a framework for future structure-function studies of TonB, and it draws attention to the unusual features of several TonB proteins.

Keywords

Gram-negative bacteria Iron transport TonB Multiple sequence alignment 

Abbreviations

CTD

carboxy-terminal domain

DSS

2,2-dimethyl-2-silapentane-5-sulfonate

HSQC

Heteronuclear single quantum coherence

MSA

multiple sequence alignment

NTD

amino-terminal domain

NOE

nuclear overhauser effect

OMT

outer membrane transporter

Notes

Acknowledgements

This work was supported by an operating grant from the Canadian Institutes for Health Research (CIHR) to H.J.V.. R.S.P. was supported by Studentship awards from the Alberta Heritage Foundation for Medical Research (AHFMR) and the National Science and Engineering Research Council (NSERC). HJV holds a Scientist award from AHFMR. The NMR equipment used was obtained through grants from the Canada Foundation for Innovation, the Alberta Science and Research Authority (ASRA) and AHFMR. Maintenance of the Bio-NMR centre is supported by CIHR and the University of Calgary.

References

  1. Altschul SF, Madden TL, Schaffer AA et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedGoogle Scholar
  2. Beddek AJ, Sheehan BJ, Bosse JT et al. (2004) Two TonB systems in Actinobacillus pleuropneumoniae: their roles in iron acquisition and virulence. Infect Immun 72:701–708CrossRefPubMedGoogle Scholar
  3. Berger-Bachi B, Rohrer S (2002) Factors influencing methicillin resistance in staphylococci. Arch Microbiol 178:165–171CrossRefPubMedGoogle Scholar
  4. Birck C, Cha JY, Cross J et al. (2004) X-ray crystal structure of the acylated beta-lactam sensor domain of BlaR1 from Staphylococcus aureus and the mechanism of receptor activation for signal transduction. J Am Chem Soc 126:13945–13947CrossRefPubMedGoogle Scholar
  5. Braun V, Braun M (2002) Active transport of iron and siderophore antibiotics. Curr Opin Microbiol 5:194–201CrossRefPubMedGoogle Scholar
  6. Brewer S, Tolley M, Trayer IP et al. (1990) Structure and function of X-Pro dipeptide repeats in the TonB proteins of Salmonella typhimurium and Escherichia coli. J Mol Biol 216:883–895CrossRefPubMedGoogle Scholar
  7. Carter DM, Gagnon JN, Damlaj M et al. (2006a) Phage display reveals multiple contact sites between FhuA, an outer membrane receptor of Escherichia coli, and TonB. J Mol Biol 357:236–251CrossRefGoogle Scholar
  8. Carter DM, Miousse IR, Gagnon JN et al. (2006b) Interactions between TonB from Escherichia coli and the periplasmic protein FhuD. J Biol ChemGoogle Scholar
  9. Chang C, Mooser A, Pluckthun A, Wlodawer A (2001) Crystal structure of the dimeric C-terminal domain of TonB reveals a novel fold. J Biol Chem 276:27535–27540CrossRefPubMedGoogle Scholar
  10. Chimento DP, Kadner RJ, Wiener MC (2005) Comparative structural analysis of TonB-dependent outer membrane transporters: implications for the transport cycle. Proteins 59:240–251CrossRefPubMedGoogle Scholar
  11. Cuff JA, Barton GJ (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40:502–511CrossRefPubMedGoogle Scholar
  12. Delaglio F, Grzesiek S, Vuister GW et al. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293CrossRefPubMedGoogle Scholar
  13. Eisenhauer HA, Shames S, Pawelek PD, Coulton JW (2005) Siderophore transport through Escherichia coli outer membrane receptor FhuA with disulfide-tethered cork and barrel domains. J Biol Chem 280:30574–30580CrossRefPubMedGoogle Scholar
  14. Evans JS, Levine BA, Trayer IP, Dorman CJ, Higgins CF (1986) Sequence-imposed structural constraints in the TonB protein of E. coli. FEBS Lett 208:211–216CrossRefPubMedGoogle Scholar
  15. Ghosh J, Postle K (2004) Evidence for dynamic clustering of carboxy-terminal aromatic amino acids in TonB-dependent energy transduction. Mol Microbiol 51:203–213CrossRefPubMedGoogle Scholar
  16. Hanique S, Colombo ML, Goormaghtigh E et al. (2004) Evidence of an intramolecular interaction between the two domains of the BlaR1 penicillin receptor during the signal transduction. J Biol Chem 279:14264–14272CrossRefPubMedGoogle Scholar
  17. Hardt K, Joris B, Lepage S et al. (1997) The penicillin sensory transducer, BlaR, involved in the inducibility of beta-lactamase synthesis in Bacillus licheniformis is embedded in the plasma membrane via a four-alpha-helix bundle. Mol Microbiol 23:935–944CrossRefPubMedGoogle Scholar
  18. Higgs PI, Larsen RA, Postle K (2002) Quantification of known components of the Escherichia coli TonB energy transduction system: TonB, ExbB, ExbD and FepA. Mol Microbiol 44:271–281CrossRefPubMedGoogle Scholar
  19. Johnson BA, Blevins RA (1994) NMRView–a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614CrossRefGoogle Scholar
  20. Jurado RL (1997) Iron, infections, and anemia of inflammation. Clin Infect Dis 25:888–895CrossRefPubMedGoogle Scholar
  21. Kampfenkel K, Braun V (1992) Membrane topology of the Escherichia coli ExbD protein. J Bacteriol 174:5485–5487PubMedGoogle Scholar
  22. Kampfenkel K, Braun V (1993) Topology of the ExbB protein in the cytoplasmic membrane of Escherichia coli. J Biol Chem 268:6050–6057PubMedGoogle Scholar
  23. Karlsson M, Hannavy K, Higgins CF (1993) A sequence-specific function for the N-terminal signal-like sequence of the TonB protein. Mol Microbiol 8:379–388CrossRefPubMedGoogle Scholar
  24. Kay LE, Torchia DA, Bax A (1989) Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28:8972–8979CrossRefPubMedGoogle Scholar
  25. Khursigara CM, De Crescenzo G, Pawelek PD, Coulton JW (2004) Enhanced binding of TonB to a ligand-loaded outer membrane receptor: role of the oligomeric state of TonB in formation of a functional FhuA-TonB complex. J Biol Chem 279:7405–7412CrossRefPubMedGoogle Scholar
  26. Khursigara CM, De Crescenzo G, Pawelek PD, Coulton JW (2005) Deletion of the proline-rich region of TonB disrupts formation of a 2:1 complex with FhuA, an outer membrane receptor of Escherichia coli. Protein Sci 14:1266–1273CrossRefPubMedGoogle Scholar
  27. Klebba PE (2003) Three paradoxes of ferric enterobactin uptake. Front Biosci 8:s1422–s1436CrossRefPubMedGoogle Scholar
  28. Koedding J, Howard P, Kaufmann L et al. (2004) Dimerization of TonB is not essential for its binding to the outer membrane siderophore receptor FhuA of Escherichia coli. J Biol Chem 279:9978–9986CrossRefPubMedGoogle Scholar
  29. Koedding J, Killig F, Polzer P et al. (2005) Crystal structure of a 92-residue C-terminal fragment of TonB from Escherichia coli reveals significant conformational changes compared to structures of smaller TonB fragments. J Biol Chem 280:3022–3028CrossRefGoogle Scholar
  30. Larsen RA, Letain TE, Postle K (2003) In vivo evidence of TonB shuttling between the cytoplasmic and outer membrane in Escherichia coli. Mol Microbiol 49:211–218CrossRefPubMedGoogle Scholar
  31. Larsen RA, Postle K (2001) Conserved residues Ser(16) and His(20) and their relative positioning are essential for TonB activity, cross-linking of TonB with ExbB, and the ability of TonB to respond to proton motive force. J Biol Chem 276:8111–8117CrossRefPubMedGoogle Scholar
  32. Larsen RA, Wood GE, Postle K (1993) The conserved proline-rich motif is not essential for energy transduction by Escherichia coli TonB protein. Mol Microbiol 10:943–953CrossRefPubMedGoogle Scholar
  33. Letain TE, Postle K (1997) TonB protein appears to transduce energy by shuttling between the cytoplasmic membrane and the outer membrane in Escherichia coli. Mol Microbiol 24:271–283CrossRefPubMedGoogle Scholar
  34. Lubkowski J, Hennecke F, Pluckthun A, Wlodawer A (1999) Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. Structure Fold Des 7:711–722CrossRefPubMedGoogle Scholar
  35. Nierman WC, Feldblyum TV, Laub MT et al. (2001) Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci USA 98:4136–4141CrossRefPubMedGoogle Scholar
  36. Pawelek PD, Croteau N, Ng-Thow-Hing C et al. (2006) Structure of TonB in complex with FhuA, E. coli outer membrane receptor. Science 312:1399–1402CrossRefPubMedGoogle Scholar
  37. Peacock RS, Weljie AM, Howard SP, Price FD, Vogel HJ (2005) The solution structure of the C-terminal domain of TonB and interaction studies with TonB box peptides. J Mol Biol 345:1185–1197CrossRefGoogle Scholar
  38. Postle K, Kadner RJ (2003) Touch and go: tying TonB to transport. Mol Microbiol 49:869–882CrossRefPubMedGoogle Scholar
  39. Ratledge C, Dover LG (2000) Iron metabolism in pathogenic bacteria. Annu Rev Microbiol 54:881–941CrossRefPubMedGoogle Scholar
  40. Roof SK, Allard JD, Bertrand KP, Postle K (1991) Analysis of Escherichia coli TonB membrane topology by use of PhoA fusions. J Bacteriol 173:5554–5557PubMedGoogle Scholar
  41. Sauter A, Howard SP, Braun V (2003) In vivo evidence for TonB dimerization. J Bacteriol 185:5747–5754CrossRefPubMedGoogle Scholar
  42. Seliger SS, Mey AR, Valle AM, Payne SM (2001) The two TonB systems of Vibrio cholerae: redundant and specific functions. Mol Microbiol 39:801–812CrossRefPubMedGoogle Scholar
  43. Shultis DD, Purdy MD, Banchs CN, Wiener MC (2006) Outer membrane active transport: structure of the BtuB:TonB complex. Science 312:1396–1399CrossRefPubMedGoogle Scholar
  44. Stork M, Di Lorenzo M, Mourino S et al. (2004) Two tonB systems function in iron transport in Vibrio anguillarum, but only one is essential for virulence. Infect Immun 72:7326–7329CrossRefPubMedGoogle Scholar
  45. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedGoogle Scholar
  46. Torres AG, Redford P, Welch RA, Payne SM (2001) TonB-dependent systems of uropathogenic Escherichia coli: aerobactin and heme transport and TonB are required for virulence in the mouse. Infect Immun 69:6179–6185CrossRefPubMedGoogle Scholar
  47. Weinberg ED (1984) Iron withholding: a defense against infection and neoplasia. Physiol Rev 64:65–102PubMedGoogle Scholar
  48. Wiener MC (2005) TonB-dependent outer membrane transport: going for Baroque? Curr Opin Struct Biol 15:394–400CrossRefPubMedGoogle Scholar
  49. Witty M, Sanz C, Shah A et al. (2002) Structure of the periplasmic domain of Pseudomonas aeruginosa TolA: evidence for an evolutionary relationship with the TonB transporter protein. EMBO J 21:4207–4218CrossRefPubMedGoogle Scholar
  50. Zhai Y, Saier MH Jr. (2001) A web-based program for the prediction of average hydropathy, average amphipathicity and average similarity of multiply aligned homologous proteins. J Mol Microbiol Biotechnol 3:285–286PubMedGoogle Scholar
  51. Zhao Q, Poole K (2002) Mutational analysis of the TonB1 energy coupler of Pseudomonas aeruginosa. J Bacteriol 184:1503–1513CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Byron C. H. Chu
    • 1
  • R. Sean Peacock
    • 1
  • Hans J. Vogel
    • 1
    Email author
  1. 1.Structural Biology Research Group, Department of Biological SciencesUniversity of CalgaryCalgaryCanada

Personalised recommendations