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Research Article

Kinetics of DNA uptake during transformation provide evidence for a translocation ratchet mechanism

Christof Hepp and Berenike Maier
  1. aDepartment of Physics, University of Cologne, 50539 Cologne, Germany

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PNAS first published October 17, 2016; https://doi.org/10.1073/pnas.1608110113
Christof Hepp
aDepartment of Physics, University of Cologne, 50539 Cologne, Germany
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Berenike Maier
aDepartment of Physics, University of Cologne, 50539 Cologne, Germany
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  • For correspondence: berenike.maier@uni-koeln.de
  1. Edited by Steven M. Block, Stanford University, Stanford, CA, and approved September 13, 2016 (received for review May 20, 2016)

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Significance

Transport of macromolecules through nanometer-sized membrane pores is a ubiquitous theme in cell biology. Examples include the linear import of precurser proteins into mitochondria and DNA transport during bacterial gene transfer. However, little is known about the biophysical mechanisms that bias the direction of macromolecular movement within membrane pores. Here, we used a single-molecule approach for studying a key step of bacterial gene transfer, the import of macromolecular DNA from the environment into the periplasm of the bacterial pathogen Neisseria gonorrhoeae. We show that the force-dependent kinetics of DNA uptake are in remarkable agreement with a translocation ratchet model, whereby the periplasmic ComE protein acts as a chaperone that rectifies DNA diffusion through the outer membrane by reversible binding.

Abstract

Horizontal gene transfer can speed up adaptive evolution and support chromosomal DNA repair. A particularly widespread mechanism of gene transfer is transformation. The initial step to transformation, namely the uptake of DNA from the environment, is supported by the type IV pilus system in most species. However, the molecular mechanism of DNA uptake remains elusive. Here, we used single-molecule techniques for characterizing the force-dependent velocity of DNA uptake by Neisseria gonorrhoeae. We found that the DNA uptake velocity depends on the concentration of the periplasmic DNA-binding protein ComE, indicating that ComE is directly involved in the uptake process. The velocity–force relation of DNA uptake is in very good agreement with a translocation ratchet model where binding of chaperones in the periplasm biases DNA diffusion through a membrane pore in the direction of uptake. The model yields a speed of DNA uptake of 900 bp⋅s−1 and a reversal force of 17 pN. Moreover, by comparing the velocity–force relation of DNA uptake and type IV pilus retraction, we can exclude pilus retraction as a mechanism for DNA uptake. In conclusion, our data strongly support the model of a translocation ratchet with ComE acting as a ratcheting chaperone.

  • molecular motor
  • translocation ratchet
  • bacterial transformation
  • gene transfer

Footnotes

  • ↵1To whom correspondence should be addressed. Email: berenike.maier{at}uni-koeln.de.
  • Author contributions: C.H. and B.M. designed research; C.H. performed research; C.H. and B.M. analyzed data; and C.H. and B.M. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1608110113/-/DCSupplemental.

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Kinetics of DNA uptake
Christof Hepp, Berenike Maier
Proceedings of the National Academy of Sciences Oct 2016, 201608110; DOI: 10.1073/pnas.1608110113

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Kinetics of DNA uptake
Christof Hepp, Berenike Maier
Proceedings of the National Academy of Sciences Oct 2016, 201608110; DOI: 10.1073/pnas.1608110113
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