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An in vitro microfluidic approach to generating protein-interaction networks

Abstract

We developed an in vitro protein expression and interaction analysis platform based on a highly parallel and sensitive microfluidic affinity assay, and used it for 14,792 on-chip experiments, which exhaustively measured the protein-protein interactions of 43 Streptococcus pneumoniae proteins in quadruplicate. The resulting network of 157 interactions was denser than expected based on known networks. Analysis of the network revealed previously undescribed physical interactions among members of some biochemical pathways.

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Figure 1: Experimental design.
Figure 2: On-chip protein expression.
Figure 3: Analysis of protein-protein interactions.
Figure 4: S. pneumoniae interaction network represented by a hairball graph created with Cytoscape 2.4.

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References

  1. Arifuzzaman, M. et al. Genome Res. 16, 686–691 (2006).

    Article  CAS  Google Scholar 

  2. Parrish, J.R. et al. Genome Biol. 8, R130 (2007).

    Article  Google Scholar 

  3. Shimoda, Y. et al. DNA Res. 15, 13–23 (2008).

    Article  CAS  Google Scholar 

  4. Hyde, T.B. et al. J. Am. Med. Assoc. 286, 1857–1862 (2001).

    Article  CAS  Google Scholar 

  5. Fields, S. & Song, O. Nature 340, 245–246 (1989).

    Article  CAS  Google Scholar 

  6. Aloy, P. & Russell, R.B. Trends Biochem. Sci. 27, 633–638 (2002).

    Article  CAS  Google Scholar 

  7. Parrish, J.R., Gulyas, K.D. & Finley, R.L. Jr. Curr. Opin. Biotechnol. 17, 387–393 (2006).

    Article  CAS  Google Scholar 

  8. Cusick, M.E., Klitgord, N., Vidal, M. & Hill, D.E. Hum. Mol. Genet. 14 (Special issue 2), R171–R181 (2005).

    Article  CAS  Google Scholar 

  9. Lee, C., Chang, J.H., Lee, H.S. & Cho, Y. Genes Dev. 16, 3199–3212 (2002).

    Article  CAS  Google Scholar 

  10. Yu, H. et al. Science 322, 104–110 (2008).

    Article  CAS  Google Scholar 

  11. Deshaies, R.J. et al. Mol. Cell. Proteomics 1, 3–10 (2002).

    Article  CAS  Google Scholar 

  12. Rigaut, G. et al. Nat. Biotechnol. 17, 1030–1032 (1999).

    Article  CAS  Google Scholar 

  13. Ho, Y. et al. Nature 415, 180–183 (2002).

    Article  CAS  Google Scholar 

  14. Butland, G. et al. Nature 433, 531–537 (2005).

    Article  CAS  Google Scholar 

  15. Zhu, H. et al. Science 293, 2101–2105 (2001).

    Article  CAS  Google Scholar 

  16. Tarassov, K. et al. Science 320, 1465–1470 (2008).

    Article  CAS  Google Scholar 

  17. Maerkl, S.J. & Quake, S.R. Science 315, 233–237 (2007).

    Article  CAS  Google Scholar 

  18. Ramachandran, N. et al. Science 305, 86–90 (2004).

    Article  CAS  Google Scholar 

  19. Einav, S. et al. Nat. Biotechnol. 26, 1019–1027 (2008).

    Article  CAS  Google Scholar 

  20. Edwards, A.M. et al. Trends Genet. 18, 529–536 (2002).

    Article  CAS  Google Scholar 

  21. Curnow, A.W., Tumbula, D.L., Pelaschier, J.T., Min, B. & Soll, D. Proc. Natl. Acad. Sci. USA 95, 12838–12843 (1998).

    Article  CAS  Google Scholar 

  22. Gancedo, C. & Flores, C.L. Microbiol. Mol. Biol. Rev. 72, 197–210 (2008).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank members of the Stanford microfluidics foundry for help with device fabrication. This work was supported in part by the US National Institutes of Health Director's Pioneer award (to S.R.Q.) and a Fulbright award (to D.G.).

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Correspondence to Stephen R Quake.

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S.R.Q. and S.J.M. are authors on a pending patent based on the results of this research.

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Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1–4, Supplementary Methods (PDF 826 kb)

Supplementary Data

Protein interaction list in MIMIx format (XLS 33 kb)

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Gerber, D., Maerkl, S. & Quake, S. An in vitro microfluidic approach to generating protein-interaction networks. Nat Methods 6, 71–74 (2009). https://doi.org/10.1038/nmeth.1289

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