The Architecture of a Prototypical Bacterial Signaling Circuit Enables a Single Point Mutation to Confer Novel Network Properties

English version České info

Even a single mutation can cause a marked change in a protein's properties. When the mutant protein functions within a network, complex phenotypes may emerge that are not intrinsic properties of the protein itself. Network architectures that enable such dramatic changes in function from a few mutations remain relatively uncharacterized. We describe a remarkable example of this versatility in the well-studied PhoQ/PhoP bacterial signaling network, which has an architecture found in many two-component systems. We found that a single point mutation that abolishes the phosphatase activity of the sensor kinase PhoQ results in a striking change in phenotype. The mutant responds to stimulus in a bistable manner, as opposed to the wild-type, which has a graded response. Mutant cells in on and off states have different morphologies, and their state is inherited over many generations. Interestingly, external conditions that repress signaling in the wild-type drive the mutant to the on state. Mathematical modeling and experiments suggest that the bistability depends on positive autoregulation of the two key proteins in the circuit, PhoP and PhoQ. The qualitatively different characteristics of the mutant come at a substantial fitness cost. Relative to the off state, the on state has a lower fitness in stationary phase cultures in rich medium (LB). However, due to the high inheritance of the on state, a population of on cells can be epigenetically trapped in a low-fitness state. Our results demonstrate the remarkable versatility of the prototypical two-component signaling architecture and highlight the tradeoffs in the particular case of the PhoQ/PhoP system.

Vyšlo v časopise: The Architecture of a Prototypical Bacterial Signaling Circuit Enables a Single Point Mutation to Confer Novel Network Properties. PLoS Genet 9(8): e32767. doi:10.1371/journal.pgen.1003706
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003706

Souhrn

Zdroje

1. ShanerNC, CampbellRE, SteinbachPA, GiepmansBN, PalmerAE, et al. (2004) Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22 : 1567–1572.

2. TracewellCA, ArnoldFH (2009) Directed enzyme evolution: climbing fitness peaks one amino acid at a time. Curr Opin Chem Biol 13 : 3–9.

3. PoelwijkFJ, de VosMG, TansSJ (2011) Tradeoffs and optimality in the evolution of gene regulation. Cell 146 : 462–470.

4. BhallaUS, IyengarR (1999) Emergent properties of networks of biological signaling pathways. Science 283 : 381–387.

5. GuetCC, ElowitzMB, HsingW, LeiblerS (2002) Combinatorial synthesis of genetic networks. Science 296 : 1466–1470.

6. GoulianM (2010) Two-component signaling circuit structure and properties. Current Opinion in Microbiology 13 : 184–189.

7. Garcia VescoviE, SonciniFC, GroismanEA (1996) Mg2+ as an extracellular signal: environmental regulation of Salmonella virulence. Cell 84 : 165–174.

8. ProstLR, DaleyME, Le SageV, BaderMW, Le MoualH, et al. (2007) Activation of the bacterial sensor kinase PhoQ by acidic pH. Mol Cell 26 : 165–174.

9. BaderMW, SanowarS, DaleyME, SchneiderAR, ChoU, et al. (2005) Recognition of antimicrobial peptides by a bacterial sensor kinase. Cell 122 : 461–472.

10. GroismanEA (2001) The pleiotropic two-component regulatory system PhoP-PhoQ. J Bacteriol 183 : 1835–1842.

11. CastelliME, Garcia VescoviE, SonciniFC (2000) The phosphatase activity is the target for Mg2+ regulation of the sensor protein PhoQ in Salmonella. J Biol Chem 275 : 22948–22954.

12. BatchelorE, GoulianM (2003) Robustness and the cycle of phosphorylation and dephosphorylation in a two-component regulatory system. Proceedings of the National Academy of Sciences of the United States of America 100 : 691–696.

13. MiyashiroT, GoulianM (2008) High stimulus unmasks positive feedback in an autoregulated bacterial signaling circuit. Proceedings of the National Academy of Sciences of the United States of America 105 : 17457–17462.

14. ShinarG, MiloR, MartinezMR, AlonU (2007) Input-output robustness in simple bacterial signaling systems. Proceedings of the National Academy of Sciences of the United States of America 104 : 19931–19935.

15. SiryapornA, GoulianM (2008) Cross-talk suppression between the CpxA-CpxR and EnvZ-OmpR two-component systems in E. coli. Mol Microbiol 70 : 494–506.

16. HermsenR, EricksonDW, HwaT (2011) Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits. Plos Computational Biology 7: e1002265.

17. HofferSM, WesterhoffHV, HellingwerfKJ, PostmaPW, TommassenJ (2001) Autoamplification of a two-component regulatory system results in “learning” behavior. Journal of Bacteriology 183 : 4914–4917.

18. RayJCJ, IgoshinOA (2010) Adaptable functionality of transcriptional feedback in bacterial two-component systems. Plos Computational Biology 6: e1000676.

19. ShinD, LeeEJ, HuangH, GroismanEA (2006) A positive feedback loop promotes transcription surge that jump-starts Salmonella virulence circuit. Science 314 : 1607–1609.

20. HoyleRB, AvitabileD, KierzekAM (2012) Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. PLoS Comput Biol 8: e1002396.

21. KierzekAM, ZhouL, WannerBL (2010) Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses. Mol Biosyst 6 : 531–542.

22. FerrellJEJr (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14 : 140–148.

23. ElowitzMB, LevineAJ, SiggiaED, SwainPS (2002) Stochastic gene expression in a single cell. Science 297 : 1183–1186.

24. OzbudakEM, ThattaiM, KurtserI, GrossmanAD, van OudenaardenA (2002) Regulation of noise in the expression of a single gene. Nature Genetics 31 : 69–73.

25. KatoA, TanabeH, UtsumiR (1999) Molecular characterization of the PhoP-PhoQ two-component system in Escherichia coli K-12: identification of extracellular Mg2+-responsive promoters. J Bacteriol 181 : 5516–5520.

26. IgoshinOA, AlvesR, SavageauMA (2008) Hysteretic and graded responses in bacterial two-component signal transduction. Molecular Microbiology 68 : 1196–1215.

27. TiwariA, RayJC, NarulaJ, IgoshinOA (2011) Bistable responses in bacterial genetic networks: designs and dynamical consequences. Math Biosci 231 : 76–89.

28. SurekaK, GhoshB, DasguptaA, BasuJ, KunduM, et al. (2008) Positive feedback and noise activate the stringent response regulator rel in mycobacteria. PLoS One 3: e1771.

29. TiwariA, BalazsiG, GennaroML, IgoshinOA (2010) The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Phys Biol 7 : 036005.

30. NovickA, WeinerM (1957) Enzyme Induction as an All-or-None Phenomenon. Proc Natl Acad Sci U S A 43 : 553–566.

31. OzbudakEM, ThattaiM, LimHN, ShraimanBI, Van OudenaardenA (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427 : 737–740.

32. XiongW, FerrellJEJr (2003) A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision. Nature 426 : 460–465.

33. DubnauD, LosickR (2006) Bistability in bacteria. Mol Microbiol 61 : 564–572.

34. LevineJH, FontesME, DworkinJ, ElowitzMB (2012) Pulsed feedback defers cellular differentiation. PLoS Biol 10: e1001252.

35. SuelGM, Garcia-OjalvoJ, LibermanLM, ElowitzMB (2006) An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440 : 545–550.

36. TanC, MarguetP, YouL (2009) Emergent bistability by a growth-modulating positive feedback circuit. Nat Chem Biol 5 : 842–848.

37. RobertL, PaulG, ChenY, TaddeiF, BaiglD, et al. (2010) Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch. Molecular Systems Biology 6 doi: 10.1038/msb.2010.12

38. MiyashiroT, GoulianM (2007) Stimulus-dependent differential regulation in the Escherichia coli PhoQ-PhoP system. Proceedings of the National Academy of Sciences of the United States of America 104 : 16305–16310.

39. Davidson CJ, Surette MG (2008) Individuality in Bacteria. Annual Review of Genetics. pp. 253–268.

40. KussellE, LeiblerS (2005) Phenotypic diversity, population growth, and information in fluctuating environments. Science 309 : 2075–2078.

41. AcarM, BecskeiA, van OudenaardenA (2005) Enhancement of cellular memory by reducing stochastic transitions. Nature 435 : 228–232.

42. ArtyomovMN, DasJ, KardarM, ChakrabortyAK (2007) Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities. Proc Natl Acad Sci U S A 104 : 18958–18963.

43. KitanoH (2007) A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov 6 : 202–210.

44. Miller JH (1992) A short course in bacterial genetics : a laboratory manual and handbook for Escherichia coli and related bacteria. Plainview, N.Y.: Cold Spring Harbor Laboratory Press. 456 p.

45. MiyashiroT, GoulianM (2007) Single-cell analysis of gene expression by fluorescence microscopy. Methods Enzymol 423 : 458–475.

46. Rasband WS (1997–2012) ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, Available: http://imagej.nih.gov/ij/