Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells

Burak Okumus, Dirk Landgraf, Ghee Chuan Lai, Somenath Bakhsi, Juan Carlos Arias-Castro, Sadik Yildiz, Dann Huh, Raul Fernandez-Lopez, Celeste N. Peterson, Erdal Toprak, Meriem El Karoui, Johan Paulsson

Research output: Contribution to journalArticlepeer-review

36 Scopus citations


Many key regulatory proteins in bacteria are present in too low numbers to be detected with conventional methods, which poses a particular challenge for single-cell analyses because such proteins can contribute greatly to phenotypic heterogeneity. Here we develop a microfluidics-based platform that enables single-molecule counting of low-abundance proteins by mechanically slowing-down their diffusion within the cytoplasm of live Escherichia coli (E. coli) cells. Our technique also allows for automated microscopy at high throughput with minimal perturbation to native physiology, as well as viable enrichment/retrieval. We illustrate the method by analysing the control of the master regulator of the E. coli stress response, RpoS, by its adapter protein, SprE (RssB). Quantification of SprE numbers shows that though SprE is necessary for RpoS degradation, it is expressed at levels as low as 3-4 molecules per average cell cycle, and fluctuations in SprE are approximately Poisson distributed during exponential phase with no sign of bursting.

Original languageEnglish (US)
Article number11641
JournalNature communications
StatePublished - May 18 2016

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)


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