1932

Abstract

Adaptation refers to the biological phenomenon where living systems change their internal states in response to changes in their environments in order to maintain certain key functions critical for their survival and fitness. Adaptation is one of the most ubiquitous and arguably one of the most fundamental properties of living systems. It occurs throughout all biological scales, from adaptation of populations of species over evolutionary time to adaptation of a single cell to different environmental stresses during its life span. In this article, we review some of the recent progress made in understanding molecular mechanisms of cellular-level adaptation. We take the minimalist (or the physicist) approach and study the simplest systems that exhibit generic adaptive behaviors, namely chemotaxis in bacterium cells () and eukaryotic cells (). We focus on understanding the basic biochemical interaction networks that are responsible for adaptation dynamics. By combining theoretical modeling with quantitative experimentation, we demonstrate universal features in adaptation as well as important differences in different cellular systems. Future work in extending the modeling framework to study adaptation in more complex systems such as sensory neurons is also discussed.

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2018-03-10
2024-06-24
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Literature Cited

  1. Ma W, Trusina A, El-Samad H, Lim WA, Tang C. 1.  2009. Cell 138:760–73 [Google Scholar]
  2. Berg HC, Brown DA. 2.  1972. Nature 239:500–4 [Google Scholar]
  3. Kollmann M, Lvdok L, Bartholom K, Timmer J, Sourjik V. 3.  2005. Nature 438:504–7 [Google Scholar]
  4. Hazelbauer G, Falke J, Parkinson J. 4.  2008. Trends Biochem. Sci. 33:9–19 [Google Scholar]
  5. Maddock J, Shapiro L. 5.  1993. Science 259:1717 [Google Scholar]
  6. Tu Y. 6.  2013. Annu. Rev. Biophys. 42:337–59 [Google Scholar]
  7. Spiro PA, Parkinson JS, Othmer HG. 7.  1997. PNAS 94:7263–68 [Google Scholar]
  8. Barkai N, Leibler S. 8.  1997. Nature 387:913–17 [Google Scholar]
  9. Mello BA, Tu Y. 9.  2003.a Biophys. J. 84:2943–56 [Google Scholar]
  10. Sourjik V, Berg HC. 10.  2002. PNAS 99:123–27 [Google Scholar]
  11. Sourjik V. 11.  2004. Trends Microbiol 12:12569–76 [Google Scholar]
  12. Mello B, Tu Y. 12.  2005. PNAS 102:17354 [Google Scholar]
  13. Keymer JE, Endres RG, Skoge M, Meir Y, Wingreen NS. 13.  2006. PNAS 103:1786–91 [Google Scholar]
  14. Duke T, Bray D. 14.  1999. PNAS 96:10104 [Google Scholar]
  15. Mello B, Tu Y. 15.  2003.b PNAS 100:8223 [Google Scholar]
  16. Mello B, Shaw L, Tu Y. 16.  2004. Biophys. J. 87:1578–95 [Google Scholar]
  17. Shimizu TS, Delalez N, Pichler K, Berg H. 17.  2006. PNAS 103:2093–97 [Google Scholar]
  18. Shimizu T, Tu Y, Berg H. 18.  2010. Mol. Syst. Biol. 6:382 [Google Scholar]
  19. Yi TM, Huang Y, Simon MI, Doyle J. 19.  2000. PNAS 97:4649–53 [Google Scholar]
  20. Tu Y, Shimizu T, Berg H. 20.  2008. PNAS 105:14855 [Google Scholar]
  21. Block S, Segall J, Berg H. 21.  1983. J. Bacteriol. 154:312–23 [Google Scholar]
  22. Jiang L, Ouyang Q, Tu Y. 22.  2010. PLOS Comput. Biol. 6:e1000735 [Google Scholar]
  23. Si G, Wu T, Ouyang Q, Tu Y. 23.  2012. Phys. Rev. Lett. 109:048101 [Google Scholar]
  24. Kalinin Y, Jiang L, Tu Y, Wu M. 24.  2009. Biophys. J. 96:2439–48 [Google Scholar]
  25. Zhu X, Si G, Deng N, Ouyang Q, Wu T. 25.  et al. 2012. Phys. Rev. Lett. 108:128101 [Google Scholar]
  26. Li Z, Cai Q, Zhang X, Si G, Ouyang Q. 26.  et al. 2017. Phys. Rev. Lett. 118:098101 [Google Scholar]
  27. Ridley AJ, Schwartz MA, Burridge K, Firtel RA, Ginsberg MH. 27.  et al. 2003. Science 302:1704–9 [Google Scholar]
  28. Levine H, Rappel WJ. 28.  2013. Phys. Today 66:210.1063/PT.3.1884 [Google Scholar]
  29. Iglesias PA. 29.  2012. Sci. Signal. 5:pe8 [Google Scholar]
  30. Clark R. 30.  1996. The Molecular and Cellular Biology of Wound Repair New York: Plenum [Google Scholar]
  31. Yu TW, Bargmann CI. 31.  2001. Nat. Neurosci. 4:1169–76 [Google Scholar]
  32. Montell DJ. 32.  2003. Nat. Rev. Mol. Cell Biol. 4:13–24 [Google Scholar]
  33. Condeelis J, Singer RH, Segall JE. 33.  2005. Annu. Rev. Cell Dev. Biol. 21:695–718 [Google Scholar]
  34. Swaney KF, Huang CH, Devreotes PN. 34.  2010. Annu. Rev. Biophys. 39:265–89 [Google Scholar]
  35. Graziano BR, Weiner OD. 35.  2014. Curr. Opin. Cell Biol. 30:60–67 [Google Scholar]
  36. Insall RH. 36.  2010. Nat. Rev. Mol. Cell Biol. 11:453–58 [Google Scholar]
  37. van Es S, Devreotes PN. 37.  1999. Cell. Mol. Life Sci. 55:1341–51 [Google Scholar]
  38. Jin T, Xu X, Fang J, Isik N, Yan J. 38.  et al. 2009. Immunol. Res. 43:118–27 [Google Scholar]
  39. Artemenko Y, Lampert TJ, Devreotes PN. 39.  2014. Cell. Mol. Life Sci. 71:3711–47 [Google Scholar]
  40. Kessin RH. 40.  2001. Dictyostelium: The Evolution, Cell Biology, and Development of a Social Organism Cambridge, UK: Cambridge Univ. Press [Google Scholar]
  41. Loomis WF. 41.  1982. The Development of Dictyostelium discoideum New York: Academic [Google Scholar]
  42. Chang H, Levchenko A. 42.  2013. Philos. Trans. R. Soc. B 368:20130117 [Google Scholar]
  43. Iglesias PA, Shi C. 43.  2014. IET Syst. Biol. 8:268–81 [Google Scholar]
  44. Lauffenburger DA, Horwitz AF. 44.  1996. Cell 84:359–69 [Google Scholar]
  45. Pollard TD, Borisy GG. 45.  2003. Cell 112:453–55 [Google Scholar]
  46. Allen WE, Zicha D, Ridley AJ, Jones GE. 46.  1998. J. Cell Biol. 141:1147–57 [Google Scholar]
  47. Monypenny J, Zicha D, Higashida C, Oceguera-Yanez F, Narumiya S, Watanabe N. 47.  2009. Mol. Cell. Biol. 29:2730–47 [Google Scholar]
  48. Jeon NL, Baskaran H, Dertinger SK, Whitesides GM, de Water LV, Toner M. 48.  2002. Nat. Biotechnol. 20:826–30 [Google Scholar]
  49. Wessels D, Soll DR, Knecht D, Loomis WF, De Lozanne A Spudich J. 49.  1988. Dev. Biol. 128:164–77 [Google Scholar]
  50. Bourne HR, Weiner O. 50.  2002. Nature 419:21 [Google Scholar]
  51. Haastert PJV, Devreotes PN. 51.  2004. Nat. Rev. Mol. Cell Biol. 5:626–34 [Google Scholar]
  52. Skoge M, Adler M, Groisman A, Levine H, Loomis WF, Rappel W-J. 52.  2010. Integr. Biol. (Camb.) 2:11–12659–68 [Google Scholar]
  53. Shi Y, Zhang J, Mullin M, Dong B, Alberts AS, Siminovitch KA. 53.  2009. J. Immunol. 182:3837–45 [Google Scholar]
  54. Herzmark P, Campbell K, Wang F, Wong K, El-Samad H. 54.  et al. 2007. PNAS 104:13349–54 [Google Scholar]
  55. Fisher PR, Merkl R, Gerisch G. 55.  1989. J. Cell Biol. 108:973–84 [Google Scholar]
  56. Song L, Nadkarni SM, Bödeker HU, Beta C, Bae A. 56.  et al. 2006. Eur. J. Cell Biol. 85:981–89 [Google Scholar]
  57. Parent CA, Devreotes PN. 57.  1999. Science 284:765–70 [Google Scholar]
  58. Levchenko A, Iglesias PA. 58.  2002. Biophys. J. 82:50–63 [Google Scholar]
  59. Ming Gl, Wong ST, Henley J, Yuan Xb, Song Hj. 59.  et al. 2002. Nature 417:411–18 [Google Scholar]
  60. Janetopoulos C, Jin T, Devreotes P. 60.  2001. Science 291:2408–11 [Google Scholar]
  61. Zigmond SH, Sullivan SJ. 61.  1979. J. Cell Biol. 82:517–27 [Google Scholar]
  62. van Haastert PJM, van der Heijden PR. 62.  1983. J. Cell. Biol. 96:347–53 [Google Scholar]
  63. Xu X, Meier-Schellersheim M, Jiao X, Nelson LE, Jin T. 63.  2005. Mol. Biol. Cell 16:676–88 [Google Scholar]
  64. Xu X, Meier-Schellersheim M, Yan J, Jin T. 64.  2007. J. Cell Biol. 178:141–53 [Google Scholar]
  65. Sasaki AT, Chun C, Takeda K, Firtel RA. 65.  2004. J. Cell Biol. 167:505–18 [Google Scholar]
  66. Irimia D, Geba DA, Toner M. 66.  2006. Anal. Chem. 78:3472–77 [Google Scholar]
  67. Skoge M, Yue H, Erickstad M, Bae A, Levine H. 67.  et al. 2014. PNAS 111:14448–53 [Google Scholar]
  68. Takeda K, Shao D, Adler M, Charest PG, Loomis WF. 68.  et al. 2012. Sci. Signal. 5:ra2 [Google Scholar]
  69. Rappel WJ, Firtel RA. 69.  2012. Cell Cycle 11:1051–52 [Google Scholar]
  70. Wang CJ, Bergmann A, Lin B, Kim K, Levchenko A. 70.  2012. Sci. Signal. 5:ra17 [Google Scholar]
  71. Goldbeter A, Koshland DE. 71.  1981. PNAS 78:6840–44 [Google Scholar]
  72. Levine H, Loomis WF, Rappel WJ. 72.  2010. New Perspectives in Mathematical Biology S Sivaloganathan Fields Inst. Commun.1–20 Providence, RI: Am. Math. Soc. [Google Scholar]
  73. Xiong Y, Huang CH, Iglesias PA, Devreotes PN. 73.  2010. PNAS 107:17079–86 [Google Scholar]
  74. Iglesias PA, Devreotes PN. 74.  2012. Curr. Opin. Cell Biol. 24:245–53 [Google Scholar]
  75. Arrieumerlou C, Meyer T. 75.  2005. Dev. Cell 8:215–27 [Google Scholar]
  76. Whitelam S, Bretschneider T, Burroughs NJ. 76.  2009. Phys. Rev. Lett. 102:198103 [Google Scholar]
  77. Hecht I, Kessler DA, Levine H. 77.  2010. Phys. Rev. Lett. 104:158301 [Google Scholar]
  78. Cooper RM, Wingreen NS, Cox EC. 78.  2012. PLOS ONE 7:e33528 [Google Scholar]
  79. Postma M, Roelofs J, Goedhart J, Gadella TW, Visser AJ, Haastert PJV. 79.  2003. Mol. Biol. Cell 14:5019–27 [Google Scholar]
  80. Nishikawa M, Horning M, Ueda M, Shibata T. 80.  2014. Biophys. J. 106:723–34 [Google Scholar]
  81. Shoval O, Goentoro L, Hart Y, Mayo A, Sontag E, Alon U. 81.  2010. PNAS 107:15995–6000 [Google Scholar]
  82. Shoval O, Alon U, Sontag E. 82.  2011. SIAM J. Appl. Dyn. Syst. 10:857–96 [Google Scholar]
  83. Kamino K, Kondo Y. 83.  2016. PLOS ONE 11:e0164674 [Google Scholar]
  84. Lazova MD, Ahmed T, Bellomo D, Stocker R, Shimizu TS. 84.  2011. PNAS 108:13870–75 [Google Scholar]
  85. Skataric M, Sontag ED. 85.  2012. PLOS Comput. Biol. 8:e1002748 [Google Scholar]
  86. Cao LH, Jing BY, Yang D, Zeng X, Shen Y. 86.  et al. 2016. PNAS 113:E902–11 [Google Scholar]
  87. Van Kampen NG. 87.  2007. Stochastic Processes in Physics and Chemistry. North-Holland Personal Library Amsterdam: Elsevier Sci. , 3rd ed.. [Google Scholar]
  88. Lan G, Sartori P, Neumann S, Sourjik V, Tu Y. 88.  2012. Nat. Phys. 8:422–28 [Google Scholar]
  89. Lan G, Tu Y. 89.  2013. J. R. Soc. Interface 10:20130489 [Google Scholar]
  90. Sartori P, Tu Y. 90.  2015. Phys. Rev. Lett. 115:118102 [Google Scholar]
  91. Yuan J, Brand RW, Basarab GH, Berg H. 91.  2012. Nature 484:233–36 [Google Scholar]
  92. Tu Y, Berg HC. 92.  2012. J. Mol. Biol. 423:782–88 [Google Scholar]
  93. Muzzey D, Gomez-Uribe CA, Mettetal JT, van Oudenaarden A. 93.  2009. Cell 138:160–71 [Google Scholar]
  94. Kurahashi T, Menini A. 94.  1997. Nature 385:725–29 [Google Scholar]
  95. Matthews HR, Reisert J. 95.  2003. Curr. Opin. Neurobiol. 13:469–75 [Google Scholar]
  96. Nakatani K, Tamura T, Yau KW. 96.  1991. J. Gen. Physiol. 97:413–35 [Google Scholar]
  97. Fain GL, Matthews HR, Cornwall MC, Koutalos Y. 97.  2001. Physiol. Rev. 81:117–51 [Google Scholar]
  98. Burns M, Baylor DA. 98.  2001. Ann. Rev. Neurosci. 24:779–805 [Google Scholar]
  99. Peng AW, Effertz T, Ricci AJ. 99.  2013. Neuron 80:4960–72 [Google Scholar]
  100. Corns LF, Johnsona SL, Krosb CJ, Marcotti W. 100.  2014. PNAS 111:14918–23 [Google Scholar]
  101. El-Samad H, Goff JP, Khammash M. 101.  2002. J. Theor. Biol. 214:17–29 [Google Scholar]
  102. Boyden ES, Zhang F, Bamberg E, Nagel G, Deisseroth K. 102.  2005. Nat. Neurosci. 8:1263–68 [Google Scholar]
  103. Levskaya A, Weiner OD, Lim WA, Voigt CA. 103.  2009. Nature 461:997–1001 [Google Scholar]
  104. Toettcher JE, Weiner OD, Lim WA. 104.  2013. Cell 155:1422–34 [Google Scholar]
  105. Toettcher JE, Voigt CA, Weiner OD, Lim WA. 105.  2011. Nat. Methods 8:35–38 [Google Scholar]
  106. Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I. 106.  et al. 2009. Nature 461:104–8 [Google Scholar]
  107. Fuller D, Chen W, Adler M, Groisman A, Levine H. 107.  et al. 2010. PNAS 107:9656–59 [Google Scholar]
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