Skip to main content
SpringerLink
Log in

Expression, Purification and Characterization of a ZIP Family Transporter from Desulfovibrio vulgaris

  • Published:
The Protein Journal Aims and scope Submit manuscript

Abstract

The ZIP family transport zinc ions from the extracellular medium across the plasma membrane or from the intracellular compartments across endomembranes, which play fundamental roles in metal homeostasis and are broadly involved in physiological and pathological processes. Desulfovibrio is the predominant sulphate-reducing bacteria in human colonic microbiota, but also a potential choice for metal bioremediation. while, there are no published studies describing the zinc transporters from Desulfovibrio up to now. In this study, we obtained for the first time a heterologously expressed ZIP homolog from Desulfovibrio vulgaris, termed dvZip. The purified dvZip was reconstituted into proteoliposomes, and confirmed its zinc transport ability in vitro. By combining topology prediction, homology modeling and phylogenetic approaches, we also noticed that dvZip belongs to the GufA and probably have 8 transmembrane α-helical segments (TM 1–8) in which both termini are located on the extracellular, with TM2, 4, 5 and 7 create an inner bundle. We believe that purification and characterization of zinc (probably also cadmium) transporters from Desulfovibrio vulgaris such as dvZip could shed light on understanding of metal homeostasis of Desulfovibrio and provided protein products for future detailed function and structural studies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Data Availability

The PDB file of dvZip model is available from the corresponding author on reasonable request. All the remaining data are included in this article and its supplementary information files.

References

  1. de Luis DA, Izaola O, Aller R, Armentia A, Cuellar L (2003) Antioxidant and fat intake in patients with polinic asthma. Med Clin 121:653–654

    Article  Google Scholar 

  2. Ho E, Quan N, Tsai YH, Lai W, Bray TM (2001) Dietary zinc supplementation inhibits NFkappaB activation and protects against chemically induced diabetes in CD1 mice. Exp Biol Med (Maywood) 226:103–111. https://doi.org/10.1177/153537020122600207

    Article  CAS  Google Scholar 

  3. Lang C, Murgia C, Leong M, Tan LW, Perozzi G, Knight D, Ruffin R, Zalewski P (2007) Anti-inflammatory effects of zinc and alterations in zinc transporter mRNA in mouse models of allergic inflammation. Am J Physiol Lung Cell Mol Physiol 292:L577-584. https://doi.org/10.1152/ajplung.00280.2006

    Article  CAS  PubMed  Google Scholar 

  4. Sekler I, Sensi SL, Hershfinkel M, Silverman WF (2007) Mechanism and regulation of cellular zinc transport. Mol Med 13:337–343. https://doi.org/10.2119/2007-00037.Sekler

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Soutar A, Seaton A, Brown K (1997) Bronchial reactivity and dietary antioxidants. Thorax 52:166–170. https://doi.org/10.1136/thx.52.2.166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Terres-Martos C, Navarro-Alarcon M, Martin-Lagos F, LopezPerez-Valero GdlSHV, Lopez-Martinez MC (1998) Serum zinc and copper concentrations and Cu/Zn ratios in patients with hepatopathies or diabetes. J Trace Elem Med Biol 12:44–49. https://doi.org/10.1016/s0946-672x(98)80020-5

    Article  CAS  PubMed  Google Scholar 

  7. Hantke K (2001) Bacterial zinc transporters and regulators. Biometals 14:239–249. https://doi.org/10.1023/a:1012984713391

    Article  CAS  PubMed  Google Scholar 

  8. Pinilla-Tenas JJ, Sparkman BK, Shawki A, Illing AC, Mitchell CJ, Zhao N, Liuzzi JP, Cousins RJ, Knutson MD, Mackenzie B (2011) Zip14 is a complex broad-scope metal-ion transporter whose functional properties support roles in the cellular uptake of zinc and nontransferrin-bound iron. Am J Physiol Cell Physiol 301:C862-871. https://doi.org/10.1152/ajpcell.00479.2010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Wang CY, Jenkitkasemwong S, Duarte S, Sparkman BK, Shawki A, Mackenzie B, Knutson MD (2012) ZIP8 is an iron and zinc transporter whose cell-surface expression is up-regulated by cellular iron loading. J Biol Chem 287:34032–34043. https://doi.org/10.1074/jbc.M112.367284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Lichten LA, Cousins RJ (2009) Mammalian zinc transporters: nutritional and physiologic regulation. Annu Rev Nutr 29:153–176. https://doi.org/10.1146/annurev-nutr-033009-083312

    Article  PubMed  Google Scholar 

  11. Zhao H, Eide D (1996) The yeast ZRT1 gene encodes the zinc transporter protein of a high-affinity uptake system induced by zinc limitation. Proc Natl Acad Sci U S A 93:2454–2458. https://doi.org/10.1073/pnas.93.6.2454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Grotz N, Fox T, Connolly E, Park W, Guerinot ML, Eide D (1998) Identification of a family of zinc transporter genes from Arabidopsis that respond to zinc deficiency. Proc Natl Acad Sci U S A 95:7220–7224. https://doi.org/10.1073/pnas.95.12.7220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Taylor KM, Morgan HE, Johnson A, Hadley LJ, Nicholson RI (2003) Structure-function analysis of LIV-1, the breast cancer-associated protein that belongs to a new subfamily of zinc transporters. Biochem J 375:51–59. https://doi.org/10.1042/Bj20030478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lin W, Chai J, Love J, Fu D (2010) Selective electrodiffusion of zinc ions in a Zrt-, Irt-like protein, ZIPB. J Biol Chem 285:39013–39020. https://doi.org/10.1074/jbc.M110.180620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Bin BH, Fukada T, Hosaka T, Yamasaki S, Ohashi W, Hojyo S, Miyai T, Nishida K, Yokoyama S, Hirano T (2011) Biochemical characterization of human ZIP13 protein: a homo-dimerized zinc transporter involved in the spondylocheiro dysplastic Ehlers-Danlos syndrome. J Biol Chem 286:40255–40265. https://doi.org/10.1074/jbc.M111.256784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Gupta S, Merriman C, Petzold CJ, Ralston CY, Fu D (2019) Water molecules mediate zinc mobility in the bacterial zinc diffusion channel ZIPB. J Biol Chem 294:13327–13335. https://doi.org/10.1074/jbc.RA119.009239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Zhang T, Liu J, Fellner M, Zhang C, Sui D, Hu J (2017) Crystal structures of a ZIP zinc transporter reveal a binuclear metal center in the transport pathway. Sci Adv 3:e1700344. https://doi.org/10.1126/sciadv.1700344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Eide DJ (2004) The SLC39 family of metal ion transporters. Pflug Arch 447:796–800. https://doi.org/10.1007/s00424-003-1074-3

    Article  CAS  Google Scholar 

  19. Zhou JZ, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou AF, He ZL, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP (2011) How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol 9:452–466. https://doi.org/10.1038/nrmicro2575

    Article  CAS  PubMed  Google Scholar 

  20. Biswas KC, Woodards NA, Xu H, Barton LL (2009) Reduction of molybdate by sulfate-reducing bacteria. Biometals 22:131–139. https://doi.org/10.1007/s10534-008-9198-8

    Article  CAS  PubMed  Google Scholar 

  21. Cabrera G, Perez R, Gomez JM, Abalos A, Cantero D (2006) Toxic effects of dissolved heavy metals on Desulfovibrio vulgaris and Desulfovibrio sp. strains. J Hazard Mater 135:40–46. https://doi.org/10.1016/j.jhazmat.2005.11.058

    Article  CAS  PubMed  Google Scholar 

  22. Chardin B, Dolla A, Chaspoul F, Fardeau ML, Gallice P, Bruschi M (2002) Bioremediation of chromate: thermodynamic analysis of the effects of Cr(VI) on sulfate-reducing bacteria. Appl Microbiol Biotechnol 60:352–360. https://doi.org/10.1007/s00253-002-1091-8

    Article  CAS  PubMed  Google Scholar 

  23. Goulhen F, Gloter A, Guyot F, Bruschi M (2006) Cr(VI) detoxification by Desulfovibrio vulgaris strain Hildenborough: microbe-metal interactions studies. Appl Microbiol Biotechnol 71:892–897. https://doi.org/10.1007/s00253-005-0211-7

    Article  CAS  PubMed  Google Scholar 

  24. Humphries AC, Nott KP, Hall LD, Macaskie LE (2004) Continuous removal of Cr(VI) from aqueous solution catalysed by palladised biomass of Desulfovibrio vulgaris. Biotechnol Lett 26:1529–1532. https://doi.org/10.1023/B:BILE.0000044457.80314.4d

    Article  CAS  PubMed  Google Scholar 

  25. Klonowska A, Clark ME, Thieman SB, Giles BJ, Wall JD, Fields MW (2008) Hexavalent chromium reduction in Desulfovibrio vulgaris Hildenborough causes transitory inhibition of sulfate reduction and cell growth. Appl Microbiol Biotechnol 78:1007–1016. https://doi.org/10.1007/s00253-008-1381-x

    Article  CAS  PubMed  Google Scholar 

  26. Ma C, Hao Z, Huysmans G, Lesiuk A, Bullough P, Wang Y, Bartlam M, Phillips SE, Young JD, Goldman A, Baldwin SA, Postis VL (2015) A versatile strategy for production of membrane proteins with diverse topologies: application to investigation of bacterial homologues of human divalent metal ion and nucleoside transporters. PLoS ONE 10:e0143010. https://doi.org/10.1371/journal.pone.0143010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296–W303. https://doi.org/10.1093/nar/gky427

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Davis IW, Murray LW, Richardson JS, Richardson DC (2004) MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32:W615-619. https://doi.org/10.1093/nar/gkh398

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, Richardson DC (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-383. https://doi.org/10.1093/nar/gkm216

    Article  PubMed  PubMed Central  Google Scholar 

  30. Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12–21. https://doi.org/10.1107/S0907444909042073

    Article  CAS  PubMed  Google Scholar 

  31. Janson G, Zhang C, Prado MG, Paiardini A (2017) PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL. Bioinformatics 33:444–446. https://doi.org/10.1093/bioinformatics/btw638

    Article  CAS  PubMed  Google Scholar 

  32. Guex N, Peitsch MC, Schwede T (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis 30(Suppl 1):S162-173. https://doi.org/10.1002/elps.200900140

    Article  PubMed  Google Scholar 

  33. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691–699. https://doi.org/10.1093/oxfordjournals.molbev.a003851

    Article  CAS  PubMed  Google Scholar 

  34. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282. https://doi.org/10.1093/bioinformatics/8.3.275

    Article  CAS  PubMed  Google Scholar 

  35. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x

    Article  PubMed  Google Scholar 

  36. Postis VLG, Deacon SE, Roach PCJ, Wright GSA, Xia X, Ingram JC, Hadden JM, Henderson PJF, Phillips SEV, McPherson MJ, Baldwin SA (2008) A high-throughput assay of membrane protein stability. Mol Membr Biol 25:617–624. https://doi.org/10.1080/09687680802530469

    Article  CAS  PubMed  Google Scholar 

  37. Chao Y, Fu D (2004) Kinetic study of the antiport mechanism of an Escherichia coli zinc transporter, ZitB. J Biol Chem 279:12043–12050. https://doi.org/10.1074/jbc.M313510200

    Article  CAS  PubMed  Google Scholar 

  38. Guerinot ML (2000) The ZIP family of metal transporters. Biochim Biophys Acta 1465:190–198. https://doi.org/10.1016/s0005-2736(00)00138-3

    Article  CAS  PubMed  Google Scholar 

  39. Bernsel A, Viklund H, Hennerdal A, Elofsson A (2009) TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res 37:W465-468. https://doi.org/10.1093/nar/gkp363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Viklund H, Elofsson A (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci 13:1908–1917. https://doi.org/10.1110/ps.04625404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580. https://doi.org/10.1006/jmbi.2000.4315

    Article  CAS  PubMed  Google Scholar 

  42. Jones DT (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23:538–544. https://doi.org/10.1093/bioinformatics/btl677

    Article  CAS  PubMed  Google Scholar 

  43. Gong CX, Ma C (2020) Detergents properties and their applications in membrane protein structural biology. Chin J Biochem Mol Biol 36:14–20

    CAS  Google Scholar 

  44. Lu M, Chai J, Fu D (2009) Structural basis for autoregulation of the zinc transporter YiiP. Nat Struct Mol Biol 16:1063-U1081. https://doi.org/10.1038/nsmb.1662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wei YN, Fu D (2006) Binding and transport of metal ions at the dimer interface of the Escherichia coli metal transporter YiiP. J Biol Chem 281:23492–23502. https://doi.org/10.1074/jbc.M602254200

    Article  CAS  PubMed  Google Scholar 

  46. Lopez-Redondo ML, Coudray N, Zhang ZN, Alexopoulos J, Stokes DL (2018) Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP. Proc Natl Acad Sci USA 115:3042–3047. https://doi.org/10.1073/pnas.1715051115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Dr Gerard Huysmans and other colleges for their kind supervision during this study and other related studies. As a friend of Prof. Steve Baldwin, I dedicate this paper to him in memoriam.

Funding

This work was originally supported by funds from Prof. Steve Baldwin, University of Leeds, UK. To complete this work, it was latter supported by grants from the Zhejiang Province Science and Technology Plan of Traditional Chinese Medicine [grant number 2020ZQ031], the Natural Science Foundation of China [grant number 32000707], and Zhejiang University [grant number SJS202014].

Author information

Authors and Affiliations

  1. Protein Facility, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China

    Cheng Ma

  2. Department of Geriatrics, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China

    Caixia Gong

Authors
  1. Cheng Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Caixia Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

CM designed the project, did the experiments, and performed the analysis. CM drafted the manuscript. CXG optimized the manuscript and provided partial funding support.

Corresponding author

Correspondence to Cheng Ma.

Ethics declarations

Conflict of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ma, C., Gong, C. Expression, Purification and Characterization of a ZIP Family Transporter from Desulfovibrio vulgaris. Protein J 40, 776–785 (2021). https://doi.org/10.1007/s10930-021-10008-7

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10930-021-10008-7

Keywords

Search

Navigation