1887

Abstract

We describe a hybrid transcriptomic and modelling analysis of the dynamics of a bacterial response to stress, namely the addition of 200 µM Zn to growing in severely Zn-depleted medium and of cells growing at different Zn concentrations at steady state. Genes that changed significantly in response to the transition were those reported previously to be associated with zinc deficiency (, , ) or excess (, , ). Cellular Zn levels were confirmed by ICP-AES to be 14- to 28-fold greater after Zn addition but there was also 6- to 8-fold more cellular Fe 30 min after Zn addition. Statistical modelling of the transcriptomic data generated from the Zn shift focused on the role of ten key regulators; ArsR, BaeR, CpxR, CusR, Fur, OxyR, SoxS, ZntR, ZraR and Zur. The data and modelling reveal a transient change in the activity of the iron regulator Fur and of the oxidative stress regulator SoxS, neither of which is evident from the steady-state transcriptomic analyses. We hypothesize a competitive binding mechanism that combines these observations and existing data on the physiology of Zn and Fe uptake. Formalizing the mechanism in a differential equation model shows that it can reproduce qualitatively the behaviour seen in the data. This gives new insights into the interplay of these two fundamental metal ions in gene regulation and bacterial physiology, as well as highlighting the importance of dynamic studies to reverse-engineer systems behaviour.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.053843-0
2012-01-01
2019-12-11
Loading full text...

Full text loading...

/deliver/fulltext/micro/158/1/284.html?itemId=/content/journal/micro/10.1099/mic.0.053843-0&mimeType=html&fmt=ahah

References

  1. Asif H. M. S., Rolfe M. D., Green J., Lawrence N. D., Rattray M., Sanguinetti G.. ( 2010;). TFInfer: a tool for probabilistic inference of transcription factor activities. . Bioinformatics 26:, 2635–2636. [CrossRef][PubMed]
    [Google Scholar]
  2. Bagai I., Rensing C., Blackburn N. J., McEvoy M. M.. ( 2008;). Direct metal transfer between periplasmic proteins identifies a bacterial copper chaperone. . Biochemistry 47:, 11408–11414. [CrossRef][PubMed]
    [Google Scholar]
  3. Beard S. J., Hashim R., Membrillo-Hernández J., Hughes M. N., Poole R. K.. ( 1997;). Zinc(II) tolerance in Escherichia coli K-12: evidence that the zntA gene (o732) encodes a cation transport ATPase. . Mol Microbiol 25:, 883–891. [CrossRef][PubMed]
    [Google Scholar]
  4. Berducci G., Mazzetti A. P., Rotilio G., Battistoni A.. ( 2004;). Periplasmic competition for zinc uptake between the metallochaperone ZnuA and Cu,Zn superoxide dismutase. . FEBS Lett 569:, 289–292. [CrossRef][PubMed]
    [Google Scholar]
  5. Berg J. M., Shi Y.. ( 1996;). The galvanization of biology: a growing appreciation for the roles of zinc. . Science 271:, 1081–1085. [CrossRef][PubMed]
    [Google Scholar]
  6. Blencowe D. K., Morby A. P.. ( 2003;). Zn(II) metabolism in prokaryotes. . FEMS Microbiol Rev 27:, 291–311. [CrossRef][PubMed]
    [Google Scholar]
  7. Bull A. T.. ( 2010;). The renaissance of continuous culture in the post-genomics age. . J Ind Microbiol Biotechnol 37:, 993–1021. [CrossRef][PubMed]
    [Google Scholar]
  8. Danese P. N., Silhavy T. J.. ( 1998;). CpxP, a stress-combative member of the Cpx regulon. . J Bacteriol 180:, 831–839.[PubMed]
    [Google Scholar]
  9. Dian C., Vitale S., Leonard G. A., Bahlawane C., Fauquant C., Leduc D., Muller C., de Reuse H., Michaud-Soret I., Terradot L.. ( 2011;). The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites. . Mol Microbiol 79:, 1260–1275. [CrossRef][PubMed]
    [Google Scholar]
  10. Edgar R., Domrachev M., Lash A. E.. ( 2002;). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. . Nucleic Acids Res 30:, 207–210. [CrossRef][PubMed]
    [Google Scholar]
  11. Fleischer R., Heermann R., Jung K., Hunke S.. ( 2007;). Purification, reconstitution, and characterization of the CpxRAP envelope stress system of Escherichia coli.. J Biol Chem 282:, 8583–8593. [CrossRef][PubMed]
    [Google Scholar]
  12. Franke S., Grass G., Rensing C., Nies D. H.. ( 2003;). Molecular analysis of the copper-transporting efflux system CusCFBA of Escherichia coli.. J Bacteriol 185:, 3804–3812. [CrossRef][PubMed]
    [Google Scholar]
  13. Fraústo da Silva J. J. R., Williams R. J. P.. ( 2001;). The Biological Chemistry of the Elements: the Inorganic Chemistry of Life, , 2nd edn.. Oxford:: Oxford University Press;.
    [Google Scholar]
  14. Gabbianelli R., Scotti R., Ammendola S., Petrarca P., Nicolini L., Battistoni A.. ( 2011;). Role of ZnuABC and ZinT in Escherichia coli O157 : H7 zinc acquisition and interaction with epithelial cells. . BMC Microbiol 11:, 36. [CrossRef][PubMed]
    [Google Scholar]
  15. Garland P. B., Randle P. J.. ( 1962;). A rapid enzymatic assay for glycerol. . Nature 196:, 987–988. [CrossRef][PubMed]
    [Google Scholar]
  16. Graham A. I., Hunt S., Stokes S. L., Bramall N., Bunch J., Cox A. G., McLeod C. W., Poole R. K.. ( 2009;). Severe zinc depletion of Escherichia coli: roles for high affinity zinc binding by ZinT, zinc transport and zinc-independent proteins. . J Biol Chem 284:, 18377–18389. [CrossRef][PubMed]
    [Google Scholar]
  17. Grass G., Fan B., Rosen B. P., Franke S., Nies D. H., Rensing C.. ( 2001;). ZitB (YbgR), a member of the cation diffusion facilitator family, is an additional zinc transporter in Escherichia coli.. J Bacteriol 183:, 4664–4667. [CrossRef][PubMed]
    [Google Scholar]
  18. Grass G., Franke S., Taudte N., Nies D. H., Kucharski L. M., Maguire M. E., Rensing C.. ( 2005a;). The metal permease ZupT from Escherichia coli is a transporter with a broad substrate spectrum. . J Bacteriol 187:, 1604–1611. [CrossRef][PubMed]
    [Google Scholar]
  19. Grass G., Otto M., Fricke B., Haney C. J., Rensing C., Nies D. H., Munkelt D.. ( 2005b;). FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress. . Arch Microbiol 183:, 9–18. [CrossRef][PubMed]
    [Google Scholar]
  20. Gu M., Imlay J. A.. ( 2011;). The SoxRS response of Escherichia coli is directly activated by redox-cycling drugs rather than by superoxide. . Mol Microbiol 79:, 1136–1150. [CrossRef][PubMed]
    [Google Scholar]
  21. Hagiwara D., Yamashino T., Mizuno T.. ( 2004;). A genome-wide view of the Escherichia coli BasS-BasR two-component system implicated in iron-responses. . Biosci Biotechnol Biochem 68:, 1758–1767. [CrossRef][PubMed]
    [Google Scholar]
  22. Halliwell B., Gutteridge J.. ( 2007;). Free Radicals in Biology and Medicine, , 4th edn.. Oxford:: OUP Oxford;.
    [Google Scholar]
  23. Hayes A., Zhang N., Wu J., Butler P. R., Hauser N. C., Hoheisel J. D., Lim F. L., Sharrocks A. D., Oliver S. G.. ( 2002;). Hybridization array technology coupled with chemostat culture: tools to interrogate gene expression in Saccharomyces cerevisiae.. Methods 26:, 281–290. [CrossRef][PubMed]
    [Google Scholar]
  24. Hoskisson P. A., Hobbs G.. ( 2005;). Continuous culture–making a comeback?. Microbiology 151:, 3153–3159. [CrossRef][PubMed]
    [Google Scholar]
  25. Hughes M. N., Poole R. K.. ( 1989;). Metals and Microorganisms. London:: Springer;.
    [Google Scholar]
  26. Lee L. J., Barrett J. A., Poole R. K.. ( 2005;). Genome-wide transcriptional response of chemostat-cultured Escherichia coli to zinc. . J Bacteriol 187:, 1124–1134. [CrossRef][PubMed]
    [Google Scholar]
  27. Macomber L., Imlay J. A.. ( 2009;). The iron-sulfur clusters of dehydratases are primary intracellular targets of copper toxicity. . Proc Natl Acad Sci U S A 106:, 8344–8349. [CrossRef][PubMed]
    [Google Scholar]
  28. Mills S. A., Marletta M. A.. ( 2005;). Metal binding characteristics and role of iron oxidation in the ferric uptake regulator from Escherichia coli.. Biochemistry 44:, 13553–13559. [CrossRef][PubMed]
    [Google Scholar]
  29. Niles B. J., Clegg M. S., Hanna L. A., Chou S. S., Momma T. Y., Hong H., Keen C. L.. ( 2008;). Zinc deficiency-induced iron accumulation, a consequence of alterations in iron regulatory protein-binding activity, iron transporters, and iron storage proteins. . J Biol Chem 283:, 5168–5177. [CrossRef][PubMed]
    [Google Scholar]
  30. Outten C. E., O’Halloran T. V.. ( 2001;). Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis. . Science 292:, 2488–2492. [CrossRef][PubMed]
    [Google Scholar]
  31. Pagani M. A., Casamayor A., Serrano R., Atrian S., Ariño J.. ( 2007;). Disruption of iron homeostasis in Saccharomyces cerevisiae by high zinc levels: a genome-wide study. . Mol Microbiol 65:, 521–537. [CrossRef][PubMed]
    [Google Scholar]
  32. Panina E. M., Mironov A. A., Gelfand M. S.. ( 2003;). Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. . Proc Natl Acad Sci U S A 100:, 9912–9917. [CrossRef][PubMed]
    [Google Scholar]
  33. Partridge J. D., Sanguinetti G., Dibden D. P., Roberts R. E., Poole R. K., Green J.. ( 2007;). Transition of Escherichia coli from aerobic to micro-aerobic conditions involves fast and slow reacting regulatory components. . J Biol Chem 282:, 11230–11237. [CrossRef][PubMed]
    [Google Scholar]
  34. Patzer S. I., Hantke K.. ( 1998;). The ZnuABC high-affinity zinc uptake system and its regulator Zur in Escherichia coli.. Mol Microbiol 28:, 1199–1210. [CrossRef][PubMed]
    [Google Scholar]
  35. Patzer S. I., Hantke K.. ( 2000;). The zinc-responsive regulator Zur and its control of the znu gene cluster encoding the ZnuABC zinc uptake system in Escherichia coli.. J Biol Chem 275:, 24321–24332. [CrossRef][PubMed]
    [Google Scholar]
  36. Petrarca P., Ammendola S., Pasquali P., Battistoni A.. ( 2010;). The Zur-regulated ZinT protein is an auxiliary component of the high-affinity ZnuABC zinc transporter that facilitates metal recruitment during severe zinc shortage. . J Bacteriol 192:, 1553–1564. [CrossRef][PubMed]
    [Google Scholar]
  37. Piper M. D., Daran-Lapujade P., Bro C., Regenberg B., Knudsen S., Nielsen J., Pronk J. T.. ( 2002;). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae.. J Biol Chem 277:, 37001–37008. [CrossRef][PubMed]
    [Google Scholar]
  38. Pullan S. T., Monk C. E., Lee L., Poole R. K.. ( 2008;). Microbial responses to nitric oxide and nitrosative stress: growth, “omic,” and physiological methods. . Methods Enzymol 437:, 499–519. [CrossRef][PubMed]
    [Google Scholar]
  39. Puškárová A., Ferianc P., Kormanec J., Homerová D., Farewell A., Nyström T.. ( 2002;). Regulation of yodA encoding a novel cadmium-induced protein in Escherichia coli.. Microbiology 148:, 3801–3811.[PubMed]
    [Google Scholar]
  40. Sanguinetti G., Lawrence N. D., Rattray M.. ( 2006;). Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities. . Bioinformatics 22:, 2775–2781. [CrossRef][PubMed]
    [Google Scholar]
  41. Sheikh M. A., Taylor G. L.. ( 2009;). Crystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals insights into metal co-ordination. . Mol Microbiol 72:, 1208–1220. [CrossRef][PubMed]
    [Google Scholar]
  42. Sigdel T. K., Easton J. A., Crowder M. W.. ( 2006;). Transcriptional response of Escherichia coli to TPEN. . J Bacteriol 188:, 6709–6713. [CrossRef][PubMed]
    [Google Scholar]
  43. Tai S. L., Daran-Lapujade P., Walsh M. C., Pronk J. T., Daran J. M.. ( 2007;). Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. . Mol Biol Cell 18:, 5100–5112. [CrossRef][PubMed]
    [Google Scholar]
  44. Zhou X., Keller R., Volkmer R., Krauss N., Scheerer P., Hunke S.. ( 2011;). Structural basis for two-component system inhibition and pilus sensing by the auxiliary CpxP protein. . J Biol Chem 286:, 9805–9814. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.053843-0
Loading
/content/journal/micro/10.1099/mic.0.053843-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error