Mechanical origin for non-equilibrium ultrasensitivity in the bacterial flagellar motor

Understand this faster with AI
Nature Physics (2026)Cite this article Flagellar motors enable bacteria to navigate their environments by switching rotation direction in response to external cues with high sensitivity. Previous work indicated that the ultrasensitivity of the flagellar motor originates from conformational spread, in which subunits of the switching complex are strongly coupled to their neighbours as in an equilibrium Ising model. However, dynamic single-motor measurements indicated that rotation switching is driven out of equilibrium, and the mechanism for this dissipative driving remains unknown. Here we propose that local mechanical torques on motor subunits can affect their conformation dynamics, based on recent structures observed with cryo-electron microscopy. This gives rise to a tug of war between stator-associated subunits that produces cooperative, non-equilibrium switching responses without requiring nearest-neighbour interactions. Our model predicts that the motor response cooperativity grows with the number of stators driving rotation, which is consistent with published experimental results. Finally, we show that operating out of equilibrium enables motors to achieve high cooperativity with faster responses compared with equilibrium motors. Our results indicate a general role for mechanics in sensitive chemical regulation.This is a preview of subscription content, access via your institution Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value online-access subscription $32.99 / 30 days cancel any timeSubscribe to this journal Receive 12 print issues and online access $259.00 per yearonly $21.58 per issueBuy this articleUSD 39.95Prices may be subject to local taxes which are calculated during checkoutSource data are provided with this paper.Code that can be used to reproduce the main text figures is included as Supplementary Code. The Gillespie simulation code is available via GitHub at https://github.com/hhmattingly/GMC_motor_Gillespie.Armitage, J. P. & Berry, R. M. Assembly and dynamics of the bacterial flagellum. Annu. Rev. Microbiol. 74, 181–200 (2020).Article Google Scholar Wadhwa, N. & Berg, H. C. Bacterial motility: machinery and mechanisms. Nat. Rev. Microbiol. 20, 161–173 (2022).Article Google Scholar Guo, S. & Liu, J. The bacterial flagellar motor: insights into torque generation, rotational switching, and mechanosensing. Front. Microbiol. 13, 911114 (2022).Article Google Scholar Hu, H. et al. Structural basis of torque generation in the bi-directional bacterial flagellar motor. Trends Biochem. Sci. 47, 160–172 (2022).Article Google Scholar Berg, H. C. & Brown, D. A. Chemotaxis in Escherichia coli analysed by three-dimensional tracking. Nature 239, 500–504 (1972).Article ADS Google Scholar Grognot, M. & Taute, K. M. More than propellers: how flagella shape bacterial motility behaviors. Curr. Opin. Microbiol. 61, 73–81 (2021).Article Google Scholar Chen, S. et al. Structural diversity of bacterial flagellar motors. EMBO J. 30, 2972–2981 (2011).Article Google Scholar Zhao, X., Norris, S. J. & Liu, J. Molecular architecture of the bacterial flagellar motor in cells. Biochemistry 53, 4323–4333 (2014).Article Google Scholar Carroll, B. L. & Liu, J. Structural conservation and adaptation of the bacterial flagella motor. Biomolecules 10, 1492–1515 (2020).Article Google Scholar Cluzel, P., Surette, M. & Leibler, S. An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science 287, 1652–1655 (2000).Article ADS Google Scholar Yuan, J. & Berg, H. C. Ultrasensitivity of an adaptive bacterial motor. J. Mol. Biol. 425, 1760–1764 (2013).Article Google Scholar Thomas, D. R., Morgan, D. G. & DeRosier, D. J. Rotational symmetry of the C ring and a mechanism for the flagellar rotary motor. Proc. Natl Acad. Sci. USA 96, 10134–10139 (1999).Article ADS Google Scholar Duke, T. A. J., Le Novère, N. & Bray, D. Conformational spread in a ring of proteins: a stochastic approach to allostery. J. Mol. Biol. 308, 541–553 (2001).Article Google Scholar Bai, F. et al. Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch. Science 327, 685–689 (2010).Article ADS Google Scholar Korobkova, E. A., Emonet, T., Park, H. & Cluzel, P. Hidden stochastic nature of a single bacterial motor. Phys. Rev. Lett. 96, 058105 (2006).Article ADS Google Scholar Wang, F. et al. Non-equilibrium effect in the allosteric regulation of the bacterial flagellar switch. Nat. Phys. 13, 710–714 (2017).Article MathSciNet Google Scholar Tu, Y. Driven to peak. Nat. Phys. 13, 631–632 (2017).Article Google Scholar Tu, Y. The nonequilibrium mechanism for ultrasensitivity in a biological switch: sensing by Maxwell’s demons. Proc. Natl Acad. Sci. USA 105, 11737–11741 (2008).Article ADS Google Scholar Wang, B., Niu, Y., Zhang, R. & Yuan, J. Dynamics of switching at stall reveals nonequilibrium mechanism in the allosteric regulation of the bacterial flagellar switch. Phys. Rev. Lett. 127, 268101 (2021).Article ADS Google Scholar Zhu, S., He, R., Zhang, R. & Yuan, J. Mechanosensitive dose response of the bacterial flagellar motor. Phys. Rev. E 110, 054402 (2024).Article ADS Google Scholar Deme, J. C. et al. Structures of the stator complex that drives rotation of the bacterial flagellum. Nat. Microbiol. 5, 1553–1564 (2020).Article Google Scholar Santiveri, M. et al. Structure and function of stator units of the bacterial flagellar motor. Cell 183, 244–257 (2020).Article Google Scholar Chang, Y. et al. Molecular mechanism for rotational switching of the bacterial flagellar motor. Nat. Struct. Mol. Biol. 27, 1041–1047 (2020).Article Google Scholar Johnson, S. et al. Structural basis of directional switching by the bacterial flagellum. Nat. Microbiol. 9, 1282–1292 (2024).Article Google Scholar Singh, P. K. et al. CryoEM structures reveal how the bacterial flagellum rotates and switches direction. Nat. Microbiol. 9, 1271–1281 (2024).Article Google Scholar Zhou, J., Lloyd, S. A. & Blair, D. F. Electrostatic interactions between rotor and stator in the bacterial flagellar motor. Proc. Natl Acad. Sci. USA 95, 6436–6441 (1998).Article ADS Google Scholar Carroll, B. L. et al. The flagellar motor of Vibrio alginolyticus undergoes major structural remodeling during rotational switching. eLife 9, e61446 (2020).Article Google Scholar Tan, J. et al. Structural basis of the bacterial flagellar motor rotational switching. Cell Res. 34, 788–801 (2024).Article Google Scholar Blair, D. F. & Berg, H. C. Restoration of torque in defective flagellar motors. Science 242, 1678–1681 (1988).Article ADS Google Scholar Lele, P. P., Hosu, B. G. & Berg, H. C. Dynamics of mechanosensing in the bacterial flagellar motor. Proc. Natl Acad. Sci. USA 110, 11839–11844 (2013).Article ADS Google Scholar Tipping, M. J., Delalez, N. J., Lim, R., Berry, R. M. & Armitage, J. P. Load-dependent assembly of the bacterial flagellar motor. mBio 4, e00551–13 (2013).Article Google Scholar Tusk, S. E., Delalez, N. J. & Berry, R. M. Subunit exchange in protein complexes. J. Mol. Biol 430, 4557–4579 (2018).Article Google Scholar Wadhwa, N., Phillips, R. & Berg, H. C. Torque-dependent remodeling of the bacterial flagellar motor. Proc. Natl Acad. Sci. USA 116, 11764–11769 (2019).Article ADS Google Scholar Nirody, J. A., Nord, A. L. & Berry, R. M. Load-dependent adaptation near zero load in the bacterial flagellar motor. J. R. Soc. Interface 16, 20190300 (2019).Article Google Scholar Wadhwa, N., Tu, Y. & Berg, H. C. Mechanosensitive remodeling of the bacterial flagellar motor is independent of direction of rotation. Proc. Natl Acad. Sci. USA 118, e2024608118 (2021).Article Google Scholar Wadhwa, N., Sassi, A., Berg, H. C. & Tu, Y. A multi-state dynamic process confers mechano-adaptation to a biological nanomachine. Nat. Commun. 13, 5327 (2022).Article ADS Google Scholar Reid, S. W. et al. The maximum number of torque-generating units in the flagellar motor of Escherichia coli is at least 11. Proc. Natl Acad. Sci. USA 103, 8066–8071 (2006).Article ADS Google Scholar Ryu, W. S., Berry, R. M. & Berg, H. C. Torque-generating units of the flagellar motor of Escherichia coli have a high duty ratio. Nature 403, 444–447 (2000).Article ADS Google Scholar Yuan, J. & Berg, H. C. Resurrection of the flagellar rotary motor near zero load. Proc. Natl Acad. Sci. USA 105, 1182–1185 (2008).Article ADS Google Scholar Yuan, J., Fahrner, K. A. & Berg, H. C. Switching of the bacterial flagellar motor near zero load. J. Mol. Biol. 390, 394–400 (2009).Article Google Scholar Nakamura, S. et al. Effect of intracellular pH on the torque-speed relationship of bacterial proton-driven flagellar motor. J. Mol. Biol. 386, 332–338 (2009).Article Google Scholar Bell, G. I. Models for the specific adhesion of cells to cells. Science 200, 618–627 (1978).Article ADS Google Scholar Wiita, A. P., Ainavarapu, S. R. K., Huang, H. H. & Fernandez, J. M. Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques. Proc. Natl Acad. Sci. USA 103, 7222–7227 (2006).Article ADS Google Scholar Gardiner, C. Stochastic Methods: A Handbook for the Natural and Social Sciences 4th edn (Springer, 2009).Monod, J., Wyman, J. & Changeux, J.-P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88–118 (1965).Article Google Scholar Gillespie, D. T. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58, 35–55 (2007).Article ADS Google Scholar Zakine, R. & Vanden-Eijnden, E. Minimum-action method for nonequilibrium phase transitions. Phys. Rev. X 13, 041044 (2023).
Google Scholar Hathcock, D., Yu, Q. & Tu, Y. Time-reversal symmetry breaking in the chemosensory array reveals a general mechanism for dissipation-enhanced cooperative sensing. Nat. Commun. 15, 8892 (2024).Article ADS Google Scholar Hill, A. V. The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J. Physiol. 40, 4–7 (1910).
Google Scholar Kullback, S. & Leibler, R. A. On information and sufficiency. Ann. Math. Stat. 22, 79–86 (1951).Article MathSciNet Google Scholar Kawai, R., Parrondo, J. M. R. & den Broeck, C. V. Dissipation: the phase–space perspective. Phys. Rev. Lett. 98, 080602 (2007).Article ADS Google Scholar Yu, Q. & Tu, Y. Energy cost for flocking of active spins: the cusped dissipation maximum at the flocking transition. Phys. Rev. Lett. 129, 278001 (2022).Article ADS MathSciNet Google Scholar Fahrner, K. A., Ryu, W. S. & Berg, H. C. Bacterial flagellar switching under load. Nature 423, 938–938 (2003).Article ADS Google Scholar Yuan, J., Fahrner, K. A., Turner, L. & Berg, H. C. Asymmetry in the clockwise and counterclockwise rotation of the bacterial flagellar motor. Proc. Natl Acad. Sci. USA 107, 12846–12849 (2010).Article ADS Google Scholar Bai, F., Minamino, T., Wu, Z., Namba, K. & Xing, J. Coupling between switching regulation and torque generation in bacterial flagellar motor. Phys. Rev. Lett. 108, 178105 (2012).Article ADS Google Scholar Owen, J. A. & Horowitz, J. M. Size limits the sensitivity of kinetic schemes. Nat. Commun. 14, 1280 (2023).Article ADS Google Scholar Lan, G., Sartori, P., Neumann, S., Sourjik, V. & Tu, Y. The energy-speed-accuracy trade-off in sensory adaptation. Nat. Phys. 8, 422–428 (2012).Article Google Scholar Sartori, P. & Tu, Y. Free energy cost of reducing noise while maintaining a high sensitivity. Phys. Rev. Lett. 115, 118102 (2015).Article ADS Google Scholar Fei, C., Cao, Y., Ouyang, Q. & Tu, Y. Design principles for enhancing phase sensitivity and suppressing phase fluctuations simultaneously in biochemical oscillatory systems. Nat. Commun. 9, 1434 (2018).Article ADS Google Scholar Niu, Y., Zhang, R. & Yuan, J. Flagellar motors of swimming bacteria contain an incomplete set of stator units to ensure robust motility. Sci. Adv. 9, eadi6724 (2023).Article Google Scholar van Albada, S. B., Tănase-Nicola, S. & ten Wolde, P. R. The switching dynamics of the bacterial flagellar motor. Mol. Syst. Biol. 5, 316 (2009).Article Google Scholar Mora, T., Yu, H. & Wingreen, N. S. Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor. Phys. Rev. Lett. 103, 248102 (2009).Article ADS Google Scholar Meacci, G. & Tu, Y. Dynamics of the bacterial flagellar motor with multiple stators. Proc. Natl Acad. Sci. USA 106, 3746–3751 (2009).Article ADS Google Scholar Meacci, G., Lan, G. & Tu, Y. Dynamics of the bacterial flagellar motor: the effects of stator compliance, back steps, temperature, and rotational asymmetry. Biophys. J. 100, 1986–1995 (2011).Article ADS Google Scholar Mandadapu, K. K., Nirody, J. A., Berry, R. M. & Oster, G. Mechanics of torque generation in the bacterial flagellar motor. Proc. Natl Acad. Sci. USA 112, E4381–E4389 (2015).Article ADS Google Scholar Tu, Y. & Cao, Y. Design principles and optimal performance for molecular motors under realistic constraints. Phys. Rev. E 97, 022403 (2018).Article ADS Google Scholar Cao, Y., Li, T. & Tu, Y. Modeling bacterial flagellar motor with new structure information: rotational dynamics of two interacting protein nano-rings. Front. Microbiol. 13, 866141 (2022).Article Google Scholar Delalez, N. J. et al. Signal-dependent turnover of the bacterial flagellar switch protein FliM. Proc. Natl Acad. Sci. USA 107, 11347–11351 (2010).Article ADS Google Scholar Yuan, J., Branch, R. W., Hosu, B. G. & Berg, H. C. Adaptation at the output of the chemotaxis signalling pathway. Nature 484, 233–236 (2012).Article ADS Google Scholar Lele, P. P., Branch, R. W., Nathan, V. S. J. & Berg, H. C. Mechanism for adaptive remodeling of the bacterial flagellar switch. Proc. Natl Acad. Sci. USA 109, 20018–20022 (2012).Article ADS Google Scholar Delalez, N. J., Berry, R. M. & Armitage, J. P. Stoichiometry and turnover of the bacterial flagellar switch protein FliN. mBio 5, e01216–14 (2014).Article Google Scholar Branch, R. W., Sayegh, M. N., Shen, C., Nathan, V. S. J. & Berg, H. C. Adaptive remodelling by FliN in the bacterial rotary motor. J. Mol. Biol. 426, 3314–3324 (2014).Article Google Scholar Antani, J. D. et al. Mechanosensitive recruitment of stator units promotes binding of the response regulator CheY-P to the flagellar motor. Nat. Commun. 12, 5442 (2021).Article ADS Google Scholar Hopfield, J. J. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl Acad. Sci. USA 71, 4135–4139 (1974).Article ADS Google Scholar Hopfield, J. J., Yamane, T., Yue, V. & Coutts, S. M. Direct experimental evidence for kinetic proofreading in amino acylation of tRNAIle. Proc. Natl Acad. Sci. USA 73, 1164–1168 (1976).Article ADS Google Scholar Shelansky, R. et al. Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription. Nat. Commun. 15, 6226 (2024).Article ADS Google Scholar Mahdavi, S. D., Salmon, G. L., Daghlian, P., Garcia, H. G. & Phillips, R. Flexibility and sensitivity in gene regulation out of equilibrium. Proc. Natl Acad. Sci. USA 121, e2411395121 (2024).Article Google Scholar Sharma, S. K., De Los Rios, P., Christen, P., Lustig, A. & Goloubinoff, P. The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase. Nat. Chem. Biol. 6, 914–920 (2010).Article Google Scholar Flatt, S., Busiello, D. M., Zamuner, S. & De Los Rios, P. ABC transporters are billion-year-old Maxwell demons. Commun. Phys. 6, 205 (2023).Article Google Scholar Cao, Y., Wang, H., Ouyang, Q. & Tu, Y. The free-energy cost of accurate biochemical oscillations. Nat. Phys. 11, 772–778 (2015).Article Google Scholar Zhang, D., Cao, Y., Ouyang, Q. & Tu, Y. The energy cost and optimal design for synchronization of coupled molecular oscillators. Nat. Phys. 16, 95–100 (2020).Article Google Scholar Hathcock, D. et al. A nonequilibrium allosteric model for receptor-kinase complexes: the role of energy dissipation in chemotaxis signaling. Proc. Natl Acad. Sci. USA 120, e2303115120 (2023).Article MathSciNet Google Scholar Gross, S. P. Hither and yon: a review of bi-directional microtubule-based transport. Phys. Biol. 1, R1 (2004).Article ADS Google Scholar Welte, M. A. Bidirectional transport along microtubules. Curr. Biol. 14, R525–R537 (2004).Article Google Scholar Hancock, W. O. Bidirectional cargo transport: moving beyond tug of war. Nat. Rev. Mol. Cell Biol. 15, 615–628 (2014).Article Google Scholar Klumpp, S. & Lipowsky, R. Cooperative cargo transport by several molecular motors. Proc. Natl Acad. Sci. USA 102, 17284–17289 (2005).Article ADS Google Scholar Müller, M. J. I., Klumpp, S. & Lipowsky, R. Tug-of-war as a cooperative mechanism for bidirectional cargo transport by molecular motors. Proc. Natl Acad. Sci. USA 105, 4609–4614 (2008).Article ADS Google Scholar Soppina, V., Rai, A. K., Ramaiya, A. J., Barak, P. & Mallik, R. Tug-of-war between dissimilar teams of microtubule motors regulates transport and fission of endosomes. Proc. Natl Acad. Sci. USA 106, 19381–19386 (2009).Article ADS Google Scholar Müller, M. J. I., Klumpp, S. & Lipowsky, R. Bidirectional transport by molecular motors: enhanced processivity and response to external forces. Biophys. J. 98, 2610–2618 (2010).Article ADS Google Scholar Kunwar, A. et al. Mechanical stochastic tug-of-war models cannot explain bidirectional lipid-droplet transport. Proc. Natl Acad. Sci. USA 108, 18960–18965 (2011).Article ADS Google Scholar D’Souza, A. I., Grover, R., Monzon, G. A., Santen, L. & Diez, S. Vesicles driven by dynein and kinesin exhibit directional reversals without regulators. Nat. Commun. 14, 7532 (2023).Article ADS Google Scholar Download referencesWe thank D. Hathcock and Q. Yu for advice on the simulation analysis, M. Leighton for comments on the paper, S. Hanson for help visualizing the motor structures and the Biophysical Modeling Group at the Flatiron Institute for feedback. We also thank J. Yuan and R. He for the experimental measurements of CW bias in Fig. 4.
The Flatiron Institute is a division of the Simons Foundation.Center for Computational Biology, Flatiron Institute, New York, NY, USAHenry H. Mattingly & Yuhai TuCenter for Computational Neuroscience, Flatiron Institute, New York, NY, USAYuhai TuSearch author on:PubMed Google ScholarSearch author on:PubMed Google ScholarH.M. and Y.T. conceived the project, developed the models and wrote the paper. H.M. performed the simulations.Correspondence to Henry H. Mattingly or Yuhai Tu.The authors declare no competing interests.Nature Physics thanks the anonymous reviewers for their contribution to the peer review of this work.Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Supplementary information, derivations and simulation details.Code to reproduce Fig. 2.Code to reproduce Fig. 3.Code to reproduce Fig. 4.Code to reproduce Fig. 5.Code to reproduce Fig. 6. This zip file contains data for all main text figures. Data plotted in Fig. 2 are contained in subfolder Fig. 2.
Source Data Fig. 3 This zip file contains data for all main text figures. Data plotted in Fig. 3 are contained in subfolder Fig. 3.
Source Data Fig. 4 This zip file contains data for all main text figures. Data plotted in Fig. 4 are contained in subfolder Fig. 4.
Source Data Fig. 5 This zip file contains data for all main text figures. Data plotted in Fig. 5 are contained in subfolder Fig. 5.
Source Data Fig. 6 This zip file contains data for all main text figures. Data plotted in Fig. 6 are contained in subfolder Fig. 6.Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.Reprints and permissionsMattingly, H.H., Tu, Y. Mechanical origin for non-equilibrium ultrasensitivity in the bacterial flagellar motor. Nat. Phys. (2026). https://doi.org/10.1038/s41567-025-03105-2Download citationReceived: 04 February 2025Accepted: 21 October 2025Published: 07 January 2026Version of record: 07 January 2026DOI: https://doi.org/10.1038/s41567-025-03105-2Anyone you share the following link with will be able to read this content:Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative
Source Information
Discussion
0 professional contributions
Sign in to join this professional discussion.
Be the first to add a constructive contribution.
