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Bioinformatic analysis of the TonB protein family

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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.

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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

References

  • 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 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Beddek AJ, Sheehan BJ, Bosse JT et al. (2004) Two TonB systems in Actinobacillus pleuropneumoniae: their roles in iron acquisition and virulence. Infect Immun 72:701–708

    Article  PubMed  CAS  Google Scholar 

  • Berger-Bachi B, Rohrer S (2002) Factors influencing methicillin resistance in staphylococci. Arch Microbiol 178:165–171

    Article  PubMed  CAS  Google Scholar 

  • 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 126:13945–13947

    Article  PubMed  CAS  Google Scholar 

  • Braun V, Braun M (2002) Active transport of iron and siderophore antibiotics. Curr Opin Microbiol 5:194–201

    Article  PubMed  CAS  Google Scholar 

  • 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 216:883–895

    Article  PubMed  CAS  Google Scholar 

  • 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 357:236–251

    Article  CAS  Google Scholar 

  • Carter DM, Miousse IR, Gagnon JN et al. (2006b) Interactions between TonB from Escherichia coli and the periplasmic protein FhuD. J Biol Chem

  • 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 276:27535–27540

    Article  PubMed  CAS  Google Scholar 

  • Chimento DP, Kadner RJ, Wiener MC (2005) Comparative structural analysis of TonB-dependent outer membrane transporters: implications for the transport cycle. Proteins 59:240–251

    Article  PubMed  CAS  Google Scholar 

  • Cuff JA, Barton GJ (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40:502–511

    Article  PubMed  CAS  Google Scholar 

  • Delaglio F, Grzesiek S, Vuister GW et al. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293

    Article  PubMed  CAS  Google Scholar 

  • 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 280:30574–30580

    Article  PubMed  CAS  Google Scholar 

  • Evans JS, Levine BA, Trayer IP, Dorman CJ, Higgins CF (1986) Sequence-imposed structural constraints in the TonB protein of E. coli. FEBS Lett 208:211–216

    Article  PubMed  CAS  Google Scholar 

  • Ghosh J, Postle K (2004) Evidence for dynamic clustering of carboxy-terminal aromatic amino acids in TonB-dependent energy transduction. Mol Microbiol 51:203–213

    Article  PubMed  CAS  Google Scholar 

  • 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 279:14264–14272

    Article  PubMed  CAS  Google Scholar 

  • 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 23:935–944

    Article  PubMed  CAS  Google Scholar 

  • 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 44:271–281

    Article  PubMed  CAS  Google Scholar 

  • Johnson BA, Blevins RA (1994) NMRView–a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614

    Article  CAS  Google Scholar 

  • Jurado RL (1997) Iron, infections, and anemia of inflammation. Clin Infect Dis 25:888–895

    Article  PubMed  CAS  Google Scholar 

  • Kampfenkel K, Braun V (1992) Membrane topology of the Escherichia coli ExbD protein. J Bacteriol 174:5485–5487

    PubMed  CAS  Google Scholar 

  • Kampfenkel K, Braun V (1993) Topology of the ExbB protein in the cytoplasmic membrane of Escherichia coli. J Biol Chem 268:6050–6057

    PubMed  CAS  Google Scholar 

  • Karlsson M, Hannavy K, Higgins CF (1993) A sequence-specific function for the N-terminal signal-like sequence of the TonB protein. Mol Microbiol 8:379–388

    Article  PubMed  CAS  Google Scholar 

  • 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 28:8972–8979

    Article  PubMed  CAS  Google Scholar 

  • 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 279:7405–7412

    Article  PubMed  CAS  Google Scholar 

  • 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 14:1266–1273

    Article  PubMed  CAS  Google Scholar 

  • Klebba PE (2003) Three paradoxes of ferric enterobactin uptake. Front Biosci 8:s1422–s1436

    Article  PubMed  CAS  Google Scholar 

  • 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 279:9978–9986

    Article  PubMed  CAS  Google Scholar 

  • 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 280:3022–3028

    Article  CAS  Google Scholar 

  • Larsen RA, Letain TE, Postle K (2003) In vivo evidence of TonB shuttling between the cytoplasmic and outer membrane in Escherichia coli. Mol Microbiol 49:211–218

    Article  PubMed  CAS  Google Scholar 

  • 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 276:8111–8117

    Article  PubMed  CAS  Google Scholar 

  • 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 10:943–953

    Article  PubMed  CAS  Google Scholar 

  • 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 24:271–283

    Article  PubMed  CAS  Google Scholar 

  • 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 7:711–722

    Article  PubMed  CAS  Google Scholar 

  • Nierman WC, Feldblyum TV, Laub MT et al. (2001) Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci USA 98:4136–4141

    Article  PubMed  CAS  Google Scholar 

  • Pawelek PD, Croteau N, Ng-Thow-Hing C et al. (2006) Structure of TonB in complex with FhuA, E. coli outer membrane receptor. Science 312:1399–1402

    Article  PubMed  CAS  Google Scholar 

  • 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 345:1185–1197

    Article  CAS  Google Scholar 

  • Postle K, Kadner RJ (2003) Touch and go: tying TonB to transport. Mol Microbiol 49:869–882

    Article  PubMed  CAS  Google Scholar 

  • Ratledge C, Dover LG (2000) Iron metabolism in pathogenic bacteria. Annu Rev Microbiol 54:881–941

    Article  PubMed  CAS  Google Scholar 

  • Roof SK, Allard JD, Bertrand KP, Postle K (1991) Analysis of Escherichia coli TonB membrane topology by use of PhoA fusions. J Bacteriol 173:5554–5557

    PubMed  CAS  Google Scholar 

  • Sauter A, Howard SP, Braun V (2003) In vivo evidence for TonB dimerization. J Bacteriol 185:5747–5754

    Article  PubMed  CAS  Google Scholar 

  • Seliger SS, Mey AR, Valle AM, Payne SM (2001) The two TonB systems of Vibrio cholerae: redundant and specific functions. Mol Microbiol 39:801–812

    Article  PubMed  CAS  Google Scholar 

  • Shultis DD, Purdy MD, Banchs CN, Wiener MC (2006) Outer membrane active transport: structure of the BtuB:TonB complex. Science 312:1396–1399

    Article  PubMed  CAS  Google Scholar 

  • 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 72:7326–7329

    Article  PubMed  CAS  Google Scholar 

  • 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 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • 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 69:6179–6185

    Article  PubMed  CAS  Google Scholar 

  • Weinberg ED (1984) Iron withholding: a defense against infection and neoplasia. Physiol Rev 64:65–102

    PubMed  CAS  Google Scholar 

  • Wiener MC (2005) TonB-dependent outer membrane transport: going for Baroque? Curr Opin Struct Biol 15:394–400

    Article  PubMed  CAS  Google Scholar 

  • 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 21:4207–4218

    Article  PubMed  CAS  Google Scholar 

  • 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 3:285–286

    PubMed  CAS  Google Scholar 

  • Zhao Q, Poole K (2002) Mutational analysis of the TonB1 energy coupler of Pseudomonas aeruginosa. J Bacteriol 184:1503–1513

    Article  PubMed  CAS  Google Scholar 

Download references

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.

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Authors and Affiliations

  1. Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4

    Byron C. H. Chu, R. Sean Peacock & Hans J. Vogel

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  1. Byron C. H. Chu
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  2. R. Sean Peacock
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  3. Hans J. Vogel
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Correspondence to Hans J. Vogel.

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Byron C. H. Chu and R. Sean Peacock contributed equally to this work.

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Chu, B.C.H., Peacock, R.S. & Vogel, H.J. Bioinformatic analysis of the TonB protein family. Biometals 20, 467–483 (2007). https://doi.org/10.1007/s10534-006-9049-4

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