Protein Dynamics in Phosphoryl-Transfer Signaling Mediated by Two-Component Systems

  • Felipe Trajtenberg
  • Alejandro BuschiazzoEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2077)


The ability to perceive the environment, an essential attribute in living organisms, is linked to the evolution of signaling proteins that recognize specific signals and execute predetermined responses. Such proteins constitute concerted systems that can be as simple as a unique protein, able to recognize a ligand and exert a phenotypic change, or extremely complex pathways engaging dozens of different proteins which act in coordination with feedback loops and signal modulation. To understand how cells sense their surroundings and mount specific adaptive responses, we need to decipher the molecular workings of signal recognition, internalization, transfer, and conversion into chemical changes inside the cell. Protein allostery and dynamics play a central role. Here, we review recent progress on the study of two-component systems, important signaling machineries of prokaryotes and lower eukaryotes. Such systems implicate a sensory histidine kinase and a separate response regulator protein. Both components exploit protein flexibility to effect specific conformational rearrangements, modulating protein–protein interactions, and ultimately transmitting information accurately. Recent work has revealed how histidine kinases switch between discrete functional states according to the presence or absence of the signal, shifting key amino acid positions that define their catalytic activity. In concert with the cognate response regulator’s allosteric changes, the phosphoryl-transfer flow during the signaling process is exquisitely fine-tuned for proper specificity, efficiency and directionality.

Key words

Bacterial signaling Protein phosphorylation Allostery Histidine kinase Response regulator 



This work was partially funded by grant # FCE 1_2017_1_136291 (ANII, Uruguay). We wish to thank Alberto Marina for discussions and useful suggestions.


  1. 1.
    Gao R, Stock AM (2017) Quantitative kinetic analyses of shutting off a two-component system. MBio 8(3):e00412–17PubMedPubMedCentralCrossRefGoogle Scholar
  2. 2.
    Hart Y, Alon U (2013) The utility of paradoxical components in biological circuits. Mol Cell 49(2):213–221PubMedCrossRefPubMedCentralGoogle Scholar
  3. 3.
    Stock AM, Robinson VL, Goudreau PN (2000) Two-component signal transduction. Annu Rev Biochem 69:183–215CrossRefGoogle Scholar
  4. 4.
    Parkinson JS, Hazelbauer GL, Falke JJ (2015) Signaling and sensory adaptation in Escherichia coli chemoreceptors: 2015 update. Trends Microbiol 23(5):257–266PubMedPubMedCentralCrossRefGoogle Scholar
  5. 5.
    Dupre E, Lesne E, Guerin J, Lensink MF, Verger A, de Ruyck J, Brysbaert G, Vezin H, Locht C, Antoine R, Jacob-Dubuisson F (2015) Signal transduction by BvgS sensor kinase: binding of modulator nicotinate affects the conformation and dynamics of the entire periplasmic moiety. J Biol Chem 290(38):23307–23319PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Neiditch MB, Federle MJ, Pompeani AJ, Kelly RC, Swem DL, Jeffrey PD, Bassler BL, Hughson FM (2006) Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell 126(6):1095–1108PubMedPubMedCentralCrossRefGoogle Scholar
  7. 7.
    Zschiedrich CP, Keidel V, Szurmant H (2016) Molecular mechanisms of two-component signal transduction. J Mol Biol 428(19):3752–3775PubMedPubMedCentralCrossRefGoogle Scholar
  8. 8.
    Casino P, Miguel-Romero L, Marina A (2014) Visualizing autophosphorylation in histidine kinases. Nat Commun 5:3258PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Mechaly AE, Sassoon N, Betton JM, Alzari PM (2014) Segmental helical motions and dynamical asymmetry modulate histidine kinase autophosphorylation. PLoS Biol 12(1):e1001776PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    Pontiggia F, Pachov DV, Clarkson MW, Villali J, Hagan MF, Pande VS, Kern D (2015) Free energy landscape of activation in a signalling protein at atomic resolution. Nat Commun 6:7284PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Bhate MP, Molnar KS, Goulian M, DeGrado WF (2015) Signal transduction in histidine kinases: insights from new structures. Structure 23(6):981–994PubMedPubMedCentralCrossRefGoogle Scholar
  12. 12.
    Gao R, Stock AM (2010) Molecular strategies for phosphorylation-mediated regulation of response regulator activity. Curr Opin Microbiol 13(2):160–167PubMedPubMedCentralCrossRefGoogle Scholar
  13. 13.
    Galperin MY (2006) Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol 188(12):4169–4182PubMedPubMedCentralCrossRefGoogle Scholar
  14. 14.
    Bergerat A, de Massy B, Gadelle D, Varoutas PC, Nicolas A, Forterre P (1997) An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 386(6623):414–417PubMedCrossRefGoogle Scholar
  15. 15.
    Cock PJ, Whitworth DE (2007) Evolution of prokaryotic two-component system signalling pathways: gene fusions and fissions. Mol Biol Evol 24(11):2355–2357PubMedCrossRefGoogle Scholar
  16. 16.
    Wuichet K, Cantwell BJ, Zhulin IB (2010) Evolution and phyletic distribution of two-component signal transduction systems. Curr Opin Microbiol 13(2):219–225PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Lou YC, Weng TH, Li YC, Kao YF, Lin WF, Peng HL, Chou SH, Hsiao CD, Chen C (2015) Structure and dynamics of polymyxin-resistance-associated response regulator PmrA in complex with promoter DNA. Nat Commun 6:8838PubMedPubMedCentralCrossRefGoogle Scholar
  18. 18.
    Narayanan A, Kumar S, Evrard AN, Paul LN, Yernool DA (2014) An asymmetric heterodomain interface stabilizes a response regulator-DNA complex. Nat Commun 5:3282PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Gushchin I, Melnikov I, Polovinkin V, Ishchenko A, Yuzhakova A, Buslaev P, Bourenkov G, Grudinin S, Round E, Balandin T, Borshchevskiy V, Willbold D, Leonard G, Büldt G, Popov A, Gordeliy V (2017) Mechanism of transmembrane signalling by sensor histidine kinases. Science 356(6342):eaah6345PubMedCrossRefGoogle Scholar
  20. 20.
    Marina A, Waldburger CD, Hendrickson WA (2005) Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein. EMBO J 24(24):4247–4259PubMedPubMedCentralCrossRefGoogle Scholar
  21. 21.
    Rivera-Cancel G, Ko W-h, Tomchick DR, Correa F, Gardner KH (2014) Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation. Proc Natl Acad Sci 111:17839–17844PubMedCrossRefGoogle Scholar
  22. 22.
    Albanesi D, Martin M, Trajtenberg F, Mansilla MC, Haouz A, Alzari PM, de Mendoza D, Buschiazzo A (2009) Structural plasticity and catalysis regulation of a thermosensor histidine kinase. Proc Natl Acad Sci U S A 106(38):16185–16190PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Stock JB, Ninfa AJ, Stock AM (1989) Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiol Rev 53(4):450–490PubMedPubMedCentralGoogle Scholar
  24. 24.
    Hess JF, Oosawa K, Matsumura P, Simon MI (1987) Protein phosphorylation is involved in bacterial chemotaxis. Proc Natl Acad Sci 84:7609–7613PubMedCrossRefGoogle Scholar
  25. 25.
    Dutta R, Inouye M (2000) GHKL, an emergent ATPase/kinase superfamily. Trends Biochem Sci 25(1):24–28PubMedCrossRefGoogle Scholar
  26. 26.
    Grebe TW, Stock JB (1999) The histidine protein kinase superfamily. Adv Microb Physiol 41:139–227PubMedCrossRefGoogle Scholar
  27. 27.
    Parkinson JS, Kofoid EC (1992) Communication modules in bacterial signalling proteins. Annu Rev Genet 26:71–112CrossRefGoogle Scholar
  28. 28.
    Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44(Database issue):D279–D285PubMedCrossRefGoogle Scholar
  29. 29.
    Galperin MY, Nikolskaya AN (2007) Identification of sensory and signal-transducing domains in two-component signalling systems. Methods Enzymol 422:47–74PubMedPubMedCentralCrossRefGoogle Scholar
  30. 30.
    Ulrich LE, Zhulin IB (2010) The MiST2 database: a comprehensive genomics resource on microbial signal transduction. Nucleic Acids Res 38(Database issue):D401–D407PubMedCrossRefPubMedCentralGoogle Scholar
  31. 31.
    Srivastava SK, Rajasree K, Fasim A, Arakere G, Gopal B (2014) Influence of the AgrC-AgrA complex on the response time of Staphylococcus aureus quorum sensing. J Bacteriol 196(15):2876–2888PubMedPubMedCentralCrossRefGoogle Scholar
  32. 32.
    Herrou J, Crosson S, Fiebig A (2017) Structure and function of HWE/HisKA2-family sensor histidine kinases. Curr Opin Microbiol 36:47–54PubMedPubMedCentralCrossRefGoogle Scholar
  33. 33.
    Anantharaman V, Balaji S, Aravind L (2006) The signalling helix: a common functional theme in diverse signalling proteins. Biol Direct 1:25PubMedPubMedCentralCrossRefGoogle Scholar
  34. 34.
    Singh M, Berger B, Kim PS, Berger JM, Cochran AG (1998) Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. Proc Natl Acad Sci U S A 95(6):2738–2743PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Trajtenberg F, Imelio JA, Machado MR, Larrieux N, Marti MA, Obal G, Mechaly AE, Buschiazzo A (2016) Regulation of signalling directionality revealed by 3D snapshots of a kinase:regulator complex in action. eLife 5:e21422PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Saita E, Abriata LA, Tsai YT, Trajtenberg F, Lemmin T, Buschiazzo A, Dal Peraro M, de Mendoza D, Albanesi D (2015) A coiled coil switch mediates cold sensing by the thermosensory protein DesK. Mol Microbiol 98(2):258–271PubMedCrossRefPubMedCentralGoogle Scholar
  37. 37.
    Purcell EB, McDonald CA, Palfey BA, Crosson S (2010) An analysis of the solution structure and signalling mechanism of LovK, a sensor histidine kinase integrating light and redox signals. Biochemistry 49(31):6761–6770PubMedPubMedCentralCrossRefGoogle Scholar
  38. 38.
    Monzel C, Unden G (2015) Transmembrane signalling in the sensor kinase DcuS of Escherichia coli: a long-range piston-type displacement of transmembrane helix 2. Proc Natl Acad Sci U S A 112(35):11042–11047PubMedPubMedCentralCrossRefGoogle Scholar
  39. 39.
    Yusuf R, Nguyen TL, Heininger A, Lawrence RJ, Hall BA, Draheim RR (2018) In vivo cross-linking and transmembrane helix dynamics support a bidirectional non-piston model of signalling within E. coli EnvZ. bioRxiv.
  40. 40.
    Wang LC, Morgan LK, Godakumbura P, Kenney LJ, Anand GS (2012) The inner membrane histidine kinase EnvZ senses osmolality via helix-coil transitions in the cytoplasm. EMBO J 31(11):2648–2659PubMedPubMedCentralCrossRefGoogle Scholar
  41. 41.
    Wang X, Vallurupalli P, Vu A, Lee K, Sun S, Bai WJ, Wu C, Zhou H, Shea JE, Kay LE, Dahlquist FW (2014) The linker between the dimerization and catalytic domains of the CheA histidine kinase propagates changes in structure and dynamics that are important for enzymatic activity. Biochemistry 53(5):855–861PubMedPubMedCentralCrossRefGoogle Scholar
  42. 42.
    Bhatnagar J, Borbat PP, Pollard AM, Bilwes AM, Freed JH, Crane BR (2010) Structure of the ternary complex formed by a chemotaxis receptor signalling domain, the CheA histidine kinase, and the coupling protein CheW as determined by pulsed dipolar ESR spectroscopy. Biochemistry 49(18):3824–3841PubMedPubMedCentralCrossRefGoogle Scholar
  43. 43.
    Gushchin I, Gordeliy V (2018) Transmembrane signal transduction in two-component systems: piston, scissoring, or helical rotation? BioEssays 40(2):1700197. Scholar
  44. 44.
    Moglich A, Ayers RA, Moffat K (2009) Design and signalling mechanism of light-regulated histidine kinases. J Mol Biol 385(5):1433–1444PubMedCrossRefGoogle Scholar
  45. 45.
    Huynh TN, Noriega CE, Stewart V (2013) Missense substitutions reflecting regulatory control of transmitter phosphatase activity in two-component signalling. Mol Microbiol 88(3):459–472PubMedPubMedCentralCrossRefGoogle Scholar
  46. 46.
    Bhate MP, Lemmin T, Kuenze G, Mensa B, Ganguly S, Peters J, Schmidt N, Pelton JG, Gross C, Meiler J, DeGrado WF (2018) Structure and function of the transmembrane domain of NsaS, an antibiotic sensing histidine kinase in S. aureus. J Am Chem Soc 140(24):7471–7485PubMedPubMedCentralCrossRefGoogle Scholar
  47. 47.
    Casino P, Rubio V, Marina A (2009) Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction. Cell 139(2):325–336PubMedCrossRefGoogle Scholar
  48. 48.
    Volkman BF, Lipson D, Wemmer DE, Kern D (2001) Two-state allosteric behavior in a single-domain signalling protein. Science 291(5512):2429–2433PubMedCrossRefGoogle Scholar
  49. 49.
    Minato Y, Ueda T, Machiyama A, Iwai H, Shimada I (2017) Dynamic domain arrangement of CheA-CheY complex regulates bacterial thermotaxis, as revealed by NMR. Sci Rep 7(1):16462PubMedPubMedCentralCrossRefGoogle Scholar
  50. 50.
    Jiang P, Peliska JA, Ninfa AJ (2000) Asymmetry in the autophosphorylation of the two-component regulatory system transmitter protein nitrogen regulator II of Escherichia coli. Biochemistry 39(17):5057–5065PubMedCrossRefGoogle Scholar
  51. 51.
    Trajtenberg F, Grana M, Ruetalo N, Botti H, Buschiazzo A (2010) Structural and enzymatic insights into the ATP binding and autophosphorylation mechanism of a sensor histidine kinase. J Biol Chem 285(32):24892–24903PubMedPubMedCentralCrossRefGoogle Scholar
  52. 52.
    Bauer J, Reiss K, Veerabagu M, Heunemann M, Harter K, Stehle T (2013) Structure-function analysis of Arabidopsis thaliana histidine kinase AHK5 bound to its cognate phosphotransfer protein AHP1. Mol Plant 6(3):959–970PubMedCrossRefGoogle Scholar
  53. 53.
    Bell CH, Porter SL, Strawson A, Stuart DI, Armitage JP (2010) Using structural information to change the phosphotransfer specificity of a two-component chemotaxis signalling complex. PLoS Biol 8(2):e1000306PubMedPubMedCentralCrossRefGoogle Scholar
  54. 54.
    Mo G, Zhou H, Kawamura T, Dahlquist FW (2012) Solution structure of a complex of the histidine autokinase CheA with its substrate CheY. Biochemistry 51(18):3786–3798PubMedPubMedCentralCrossRefGoogle Scholar
  55. 55.
    Varughese KI, Tsigelny I, Zhao H (2006) The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state. J Bacteriol 188(13):4970–4977PubMedPubMedCentralCrossRefGoogle Scholar
  56. 56.
    Willett JW, Herrou J, Briegel A, Rotskoff G, Crosson S (2015) Structural asymmetry in a conserved signalling system that regulates division, replication, and virulence of an intracellular pathogen. Proc Natl Acad Sci U S A 112(28):E3709–E3718PubMedPubMedCentralCrossRefGoogle Scholar
  57. 57.
    Zhao X, Copeland DM, Soares AS, West AH (2008) Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog. J Mol Biol 375(4):1141–1151PubMedCrossRefGoogle Scholar
  58. 58.
    Yamada S, Sugimoto H, Kobayashi M, Ohno A, Nakamura H, Shiro Y (2009) Structure of PAS-linked histidine kinase and the response regulator complex. Structure 17(10):1333–1344PubMedCrossRefGoogle Scholar
  59. 59.
    Capra EJ, Perchuk BS, Skerker JM, Laub MT (2012) Adaptive mutations that prevent crosstalk enable the expansion of paralogous signalling protein families. Cell 150(1):222–232PubMedPubMedCentralCrossRefGoogle Scholar
  60. 60.
    Villanueva M, Garcia B, Valle J, Rapun B, Ruiz de Los Mozos I, Solano C, Marti M, Penades JR, Toledo-Arana A, Lasa I (2018) Sensory deprivation in Staphylococcus aureus. Nat Commun 9(1):523PubMedPubMedCentralCrossRefGoogle Scholar
  61. 61.
    Willett JW, Tiwari N, Muller S, Hummels KR, Houtman JC, Fuentes EJ, Kirby JR (2013) Specificity residues determine binding affinity for two-component signal transduction systems. MBio 4(6):e00420–13PubMedPubMedCentralCrossRefGoogle Scholar
  62. 62.
    Skerker JM, Prasol MS, Perchuk BS, Biondi EG, Laub MT (2005) Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biol 3(10):e334PubMedPubMedCentralCrossRefGoogle Scholar
  63. 63.
    Podgornaia AI, Casino P, Marina A, Laub MT (2013) Structural basis of a rationally rewired protein-protein interface critical to bacterial signalling. Structure 21(9):1636–1647PubMedCrossRefGoogle Scholar
  64. 64.
    Skerker JM, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O, Goulian M, Laub MT (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133(6):1043–1054PubMedPubMedCentralCrossRefGoogle Scholar
  65. 65.
    Podgornaia AI, Laub MT (2015) Protein evolution. Pervasive degeneracy and epistasis in a protein-protein interface. Science 347(6222):673–677PubMedCrossRefGoogle Scholar
  66. 66.
    Imelio JA, Larrieux N, Mechaly AE, Trajtenberg F, Buschiazzo A (2017) Snapshots of the signalling complex DesK:DesR in different functional states using rational mutagenesis and X-ray crystallography. Bio-Protocol 7(16):e2510CrossRefGoogle Scholar
  67. 67.
    Huynh TN, Stewart V (2011) Negative control in two-component signal transduction by transmitter phosphatase activity. Mol Microbiol 82(2):275–286PubMedPubMedCentralCrossRefGoogle Scholar
  68. 68.
    Pazy Y, Motaleb MA, Guarnieri MT, Charon NW, Zhao R, Silversmith RE (2010) Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate. Proc Natl Acad Sci U S A 107(5):1924–1929PubMedPubMedCentralCrossRefGoogle Scholar
  69. 69.
    Huynh TN, Noriega CE, Stewart V (2010) Conserved mechanism for sensor phosphatase control of two-component signalling revealed in the nitrate sensor NarX. Proc Natl Acad Sci U S A 107(49):21140–21145PubMedPubMedCentralCrossRefGoogle Scholar
  70. 70.
    Kamberov ES, Atkinson MR, Chandran P, Ninfa AJ (1994) Effect of mutations in Escherichia coli glnL (ntrB), encoding nitrogen regulator II (NRII or NtrB), on the phosphatase activity involved in bacterial nitrogen regulation. J Biol Chem 269(45):28294–28299PubMedPubMedCentralGoogle Scholar
  71. 71.
    Dutta R, Inouye M (1996) Reverse phosphotransfer from OmpR to EnvZ in a kinase−/phosphatase+ mutant of EnvZ (EnvZ.N347D), a bifunctional signal transducer of Escherichia coli. J Biol Chem 271(3):1424–1429PubMedCrossRefPubMedCentralGoogle Scholar
  72. 72.
    Hsing W, Silhavy TJ (1997) Function of conserved histidine-243 in phosphatase activity of EnvZ, the sensor for porin osmoregulation in Escherichia coli. J Bacteriol 179(11):3729–3735PubMedPubMedCentralCrossRefGoogle Scholar
  73. 73.
    Tindall MJ, Porter SL, Maini PK, Armitage JP (2010) Modeling chemotaxis reveals the role of reversed phosphotransfer and a bi-functional kinase-phosphatase. PLoS Comput Biol 6(8):e1000896PubMedPubMedCentralCrossRefGoogle Scholar
  74. 74.
    Pena-Sandoval GR, Kwon O, Georgellis D (2005) Requirement of the receiver and phosphotransfer domains of ArcB for efficient dephosphorylation of phosphorylated ArcA in vivo. J Bacteriol 187(9):3267–3272PubMedPubMedCentralCrossRefGoogle Scholar
  75. 75.
    Uhl MA, Miller JF (1996) Central role of the BvgS receiver as a phosphorylated intermediate in a complex two-component phosphorelay. J Biol Chem 271(52):33176–33180PubMedCrossRefPubMedCentralGoogle Scholar
  76. 76.
    Kenney LJ (2010) How important is the phosphatase activity of sensor kinases? Curr Opin Microbiol 13(2):168–176PubMedPubMedCentralCrossRefGoogle Scholar
  77. 77.
    Batchelor E, Goulian M (2003) Robustness and the cycle of phosphorylation and dephosphorylation in a two-component regulatory system. Proc Natl Acad Sci U S A 100(2):691–696PubMedPubMedCentralCrossRefGoogle Scholar
  78. 78.
    Siryaporn A, Goulian M (2008) Cross-talk suppression between the CpxA-CpxR and EnvZ-OmpR two-component systems in E. coli. Mol Microbiol 70(2):494–506PubMedPubMedCentralCrossRefGoogle Scholar
  79. 79.
    Mechaly AE, Soto Diaz S, Sassoon N, Buschiazzo A, Betton JM, Alzari PM (2017) Structural coupling between autokinase and phosphotransferase reactions in a bacterial histidine kinase. Structure 25(6):939–944PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Laboratory of Molecular and Structural MicrobiologyInstitut Pasteur de MontevideoMontevideoUruguay
  2. 2.Département de MicrobiologieInstitut PasteurParisFrance

Personalised recommendations