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A genetically incorporated crosslinker reveals chaperone cooperation in acid resistance

Nature Chemical Biology volume 7, pages 671–677 (2011)Cite this article

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Abstract

Acid chaperones are essential factors in preserving the protein homeostasis for enteric pathogens to survive in the extremely acidic mammalian stomach (pH 1–3). The client proteins of these chaperones remain largely unknown, primarily because of the exceeding difficulty of determining protein-protein interactions under low-pH conditions. We developed a genetically encoded, highly efficient protein photocrosslinking probe, which enabled us to profile the in vivo substrates of a major acid-protection chaperone, HdeA, in Escherichia coli periplasm. Among the identified HdeA client proteins, the periplasmic chaperones DegP and SurA were initially found to be protected by HdeA at a low pH, but they subsequently facilitated the HdeA-mediated acid recovery of other client proteins. This unique, ATP-independent chaperone cooperation in the ATP-deprived E. coli periplasm may support the acid resistance of enteric bacteria. The crosslinker would be valuable in unveiling the physiological interaction partners of any given protein and thus their functions under normal and stress conditions.

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Figure 1: Development of the DiZPK protein photocrosslinker.
Figure 2: Identifying the native client proteins of HdeA under acid stress.
Figure 3: The cooperative mode between HdeA and SurA/DegP during acid stress and recovery.
Figure 4: A chaperone-cooperation model for bacterial acid resistance.

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Acknowledgements

We thank the Nara Institute of Science and Technology (Ikoma, Nara, Japan) for E. coli strains BW25113 and JWK3478 and P. Schultz for the aminoacyl-tRNA synthetase and tRNA expression vectors. We are grateful to W. Hong, Y. Liu and C. Liu for valuable discussions. We would also like to thank T. Kellie of the Graduate University of the Chinese Academy of Sciences for his editorial assistance. This work was supported by research grants from the National Natural Science Foundation of China (91013005 and 21001010 to P.R.C., 30570355 and 30670022 to Z.C.) and the National Key Basic Research Foundation of China (2010CB912300 to P.R.C., 2006CB806508 and 2006CB910300 to Z.C.).

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  1. Meng Zhang and Shixian Lin: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China

    Meng Zhang, Xinwen Song, Xi Ge, Xinmiao Fu & Zengyi Chang

  2. Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China

    Meng Zhang, Shixian Lin, Jun Liu & Peng R Chen

  3. Department of Chemistry, University of Chicago, Chicago, Illinois, USA

    Ye Fu

  4. Center for Protein Science, Peking University, Beijing, China

    Xinmiao Fu, Zengyi Chang & Peng R Chen

  5. Peking-Tsinghua Center for Life Sciences, Beijing, China

    Peng R Chen

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  1. Meng Zhang
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Contributions

M.Z. and S.L. performed most of the experiments and interpreted data. X.S., J.L. and X.G. provided reagents and helped on part of the experiments. Y.F. helped on the initial synthesis of the photocrosslinker compound. X.F. interpreted data. P.R.C. and Z.C. conceived the study, designed experiments, interpreted data and wrote the manuscript with input from all authors.

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Correspondence to Zengyi Chang or Peng R Chen.

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Zhang, M., Lin, S., Song, X. et al. A genetically incorporated crosslinker reveals chaperone cooperation in acid resistance. Nat Chem Biol 7, 671–677 (2011). https://doi.org/10.1038/nchembio.644

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