Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates

engineering-non-exponential-proliferation-in-escherichia-coli-using-functionalized-protein-aggregates
Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates

References

  1. Nyström, T. Stationary-phase physiology. Annu. Rev. Microbiol. 58, 161–181 (2004).

    Google Scholar 

  2. Meunier, A., Cornet, F. & Campos, M. Bacterial cell proliferation: from molecules to cells. FEMS Microbiol. Rev. 45, fuaa046 (2021).

    Google Scholar 

  3. Gonzalez, J. M. & Aranda, B. Microbial growth under limiting conditions—future perspectives. Microorganisms 11, 1641 (2023).

    Google Scholar 

  4. Chan, C. T. Y., Lee, J. W., Cameron, D. E., Bashor, C. J. & Collins, J. J. Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment. Nat. Chem. Biol. 12, 82–86 (2016).

    Google Scholar 

  5. Stirling, F. et al. Rational design of evolutionarily stable microbial kill switches. Mol. Cell 68, 686–697.e3 (2017).

    Google Scholar 

  6. Mandell, D. J. et al. Biocontainment of genetically modified organisms by synthetic protein design. Nature 518, 55–60 (2015).

    Google Scholar 

  7. VanArsdale, E. et al. Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis. Biotechnol. Bioeng. 120, 1366–1381 (2023).

    Google Scholar 

  8. Huang, S. et al. Coupling spatial segregation with synthetic circuits to control bacterial survival. Mol. Syst. Biol. 12, MSB156567 (2016).

    Google Scholar 

  9. Logsdon, M. M. & Aldridge, B. B. Stable regulation of cell cycle events in mycobacteria: Insights from inherently heterogeneous bacterial populations. Front. Microbiol. 9, 514 (2018).

    Google Scholar 

  10. Aldridge, B. B. et al. Asymmetry and aging of mycobacterial cells lead to variable growth and antibiotic susceptibility. Science 335, 100–104 (2011).

    Google Scholar 

  11. Oh, D. et al. Asymmetric polar localization dynamics of the serine chemoreceptor protein Tsr in Escherichia coli. PLoS ONE 13, e0195887 (2018).

    Google Scholar 

  12. Ebersbach, G., Briegel, A., Jensen, G. J. & Jacobs-Wagner, C. A self-associating protein critical for chromosome attachment, division, and polar organization in Caulobacter. Cell 134, 956–968 (2008).

    Google Scholar 

  13. Lindner, A. B., Madden, R., Demarez, A., Stewart, E. J. & Taddei, F. Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation. Proc. Natl. Acad. Sci. USA. 105, 3076–3081 (2008).

    Google Scholar 

  14. Mushnikov, N. V., Fomicheva, A., Gomelsky, M. & Bowman, G. R. Inducible asymmetric cell division and cell differentiation in a bacterium. Nat. Chem. Biol. 15, 925–931 (2019).

    Google Scholar 

  15. Lin, D. W. et al. Construction of intracellular asymmetry and asymmetric division in Escherichia coli. Nat. Commun. 12, 888 (2021).

  16. Hong, J. C. et al. Localized proteolysis for the construction of intracellular asymmetry in Escherichia coli. ACS Synth. Biol. 10, 1830–1836 (2021).

    Google Scholar 

  17. Görke, B. & Stülke, J. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat. Rev. Microbiol. 6, 613–624 (2008).

    Google Scholar 

  18. Saier, M. H. Multiple mechanisms controlling carbon metabolism in bacteria. Biotechnol. Bioeng. 58, 170–174 (1998).

    Google Scholar 

  19. Karimova, G., Pidoux, J., Ullmann, A. & Ladant, D. A bacterial two-hybrid system based on a reconstituted signal transduction pathway. Proc. Natl. Acad. Sci. USA 95, 5752–5756 (1998).

    Google Scholar 

  20. Battesti, A. & Bouveret, E. The bacterial two-hybrid system based on adenylate cyclase reconstitution in Escherichia coli. Methods 58, 325–334 (2012).

    Google Scholar 

  21. Bindels, D. S. et al. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat. Methods 14, 53–56 (2016).

    Google Scholar 

  22. Markwardt, M. L. et al. An improved cerulean fluorescent protein with enhanced brightness and reduced reversible photoswitching. PLoS ONE 6, e17896 (2011).

  23. Govers, S. K., Mortier, J., Adam, A. & Aertsen, A. Protein aggregates encode epigenetic memory of stressful encounters in individual Escherichia Coli cells. PLoS Biol. 16, e2003853 (2018).

  24. Lee, S., Sowa, M. E., Choi, J. M. & Tsai, F. T. F. The ClpB/Hsp104 molecular chaperone—a protein disaggregating machine. J. Struct. Biol. 146, 99–105 (2004).

    Google Scholar 

  25. Doyle, S. M. & Wickner, S. Hsp104 and ClpB: protein disaggregating machines. Trends Biochem. Sci. 34, 40–48 (2009).

    Google Scholar 

  26. Katikaridis, P., Bohl, V. & Mogk, A. Resisting the heat: bacterial disaggregases rescue cells from devastating protein aggregation. Front. Mol. Biosci. 8, 681439 (2021).

    Google Scholar 

  27. Lewis, M. Allostery and the lac operon. J. Mol. Biol. 425, 2309–2316 (2013).

    Google Scholar 

  28. Perlman, R. et al. The regulation of lac operon transcription by cyclic adenosine 3’, 5’-monophosphate. In Proc. Cold Spring Harbor Symposia on Quantitative Biology Vol. 35, 419–423 (Cold Spring Harbor Laboratory Press, 1970).

  29. Maser, A., Peebo, K., Vilu, R. & Nahku, R. Amino acids are key substrates to Escherichia coli BW25113 for achieving high specific growth rate. Res. Microbiol. 171, 185–193 (2020).

    Google Scholar 

  30. Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).

    Google Scholar 

  31. Wiktor, J. et al. RecA finds homologous DNA by reduced dimensionality search. Nature 597, 426–429 (2021).

    Google Scholar 

  32. Kremers, G. J., Goedhart, J., Van Munster, E. B. & Gadella, T. W. J. Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET förster radius. Biochemistry 45, 6570–6580 (2006).

    Google Scholar 

  33. Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J. & Voigt, C. A. Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nat. Chem. Biol. 15, 196–204 (2019).

    Google Scholar 

  34. Chen, Y. J. et al. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat. Methods 10, 659–664 (2013).

    Google Scholar 

  35. Passaris, I., Tadesse, W. M., Gayán, E. & Aertsen, A. Construction and validation of the Tn5-PLtetO-1-msfGFP transposon as a tool to probe protein expression and localization. J. Microbiol. Methods 161, 56–62 (2019).

    Google Scholar 

  36. Aurélia Battesti, E. B. Improvement of bacterial two-hybrid vectors for detection of fusion proteins and transfer to pBAD-tandem affinity purification, calmodulin binding peptide, or 6-histidine tag vectors. Proteomics 8, 4768–4771 (2008).

    Google Scholar 

  37. Mortier, J. et al. Gene erosion can lead to gain-of-function alleles that contribute to bacterial fitness. mBio 12, e01129-21 (2021).

    Google Scholar 

  38. Hopp, T. P. et al. A short polypeptide marker sequence useful for recombinant protein identification and purification. Bio/Technology 6, 1204–1210 (1988).

    Google Scholar 

  39. Chen, X., Zaro, J. L. & Shen, W. C. Fusion protein linkers: property, design and functionality. Adv. Drug Deliv. Rev. 65, 1357–1369 (2013).

    Google Scholar 

  40. Elowitz, M. B. & Leibler, S. A. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).

    Google Scholar 

  41. Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA. 97, 6640–6645 (2000).

    Google Scholar 

  42. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).

  43. Schindelin, J. et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Google Scholar 

  44. Serif (Europe) Ltd. Affinity Designer v 1.9.1.979. https://www.affinity.studio/ (2019).

  45. Berg, S. et al. ilastik: interactive machine learning for (bio)image analysis. Nat. Methods 16, 1226–1232 (2019).

    Google Scholar 

  46. Todorov, H., Miguel Trabajo, T. & van der Meer, J. R. STrack: a tool to simply track bacterial cells in microscopy time-lapse images. mSphere 8, e00658-22 (2023).

  47. RStudio Team. RStudio: integrated development environment for R. RStudio, PBC. http://www.rstudio.com/ (2025).

  48. Mortier, J. et al. Protein aggregates act as a deterministic disruptor during bacterial cell size homeostasis. Cell. Mol. Life Sci. 80, 360 (2023).

    Google Scholar 

  49. Truncated violin plots, scatter plots (and quadratic curve fitting), bar graphs and bulk growth curves were made using GraphPad Prism version 10.3.1 for Windows (64-bit), GraphPad Software. www.graphpad.com.

  50. Van Eyken, R., Oome, D., Broux, K., Jordens, S., & Aertsen, A. Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates. Zenodo, https://doi.org/10.5281/zenodo.15195477 (2026).

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