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Chapter 2 : Genetic Approaches for Signaling Pathways and Proteins

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Genetic Approaches for Signaling Pathways and Proteins, Page 1 of 2

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Abstract:

This chapter discusses some genetic approaches for studying signaling pathways and for elucidating the molecular mechanisms of information processing by modular signaling proteins. Bacteria live in precarious environments. Nutrient and toxin levels, acidity, temperature, osmolarity, humidity, and many other conditions can change rapidly and unexpectedly. Bacterial signaling systems are amenable to detailed genetic and biochemical analyses. In this chapter, some general strategies for using genetic methods to study sensory pathways and signaling proteins are discussed. Many signaling proteins, from both gram-positive and gram-negative bacteria, contain characteristic "transmitters" and "receivers" domains that promote information transfer within and between proteins. Transmitters and receivers are ideally suited as circuit elements for assembling signaling pathways. The only demonstrated mechanisms of transmitter-receiver communication involve phosphorylation and dephosphorylation reactions. With caution, the logic of epistatic analysis can be extended to more elaborate signaling pathways that have branches, feedback loops, and so on. Genetic approaches can provide considerable insight into the operation of signaling pathways and proteins. Even though actual signaling circuits are unlikely to be as simple as the two-component examples in the chapter, the same basic principles should apply.

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2

Key Concept Ranking

Bacterial Proteins
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Signalling Pathway
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Figures

Image of FIGURE 1
FIGURE 1

“Two-component” paradigm for sensory signaling via communication modules. Sensory information flows through noncovalent controls exerted by one domain on another (dashed arrows) and through phosphorylation reactions between transmitter and receiver domains. The convention of representing transmitters by rectangles and receivers by ovals is used in all subsequent figures.

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2
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Image of FIGURE 2
FIGURE 2

Phosphorylation activities of transmitters and receivers. Abbreviations: T, transmitter; R, receiver; H, hisadine; D, aspartic acid; Pi, inorganic phosphate. Details of the phosphorylation reactions are discussed in the text. ATP is required for the “phosphatase” activity exhibited by some transmitters but is not hydrolyzed in the reaction.

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2
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Image of FIGURE 3
FIGURE 3

Signaling transactions in sensor-response regulator circuit, (a) Generation of a conformational change in the sensor input domain on detection of an input signal; (b) modulation of the autophosphorylation-phosphatase activities of the transmitter by the stimulated input domain; (c) communication between transmitter and receiver via specific docking and phosphotransfer; (d) stimulation or inhibition of the response regulator output domain on a change in phosphorylation state of the receiver.

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2
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Image of FIGURE 4
FIGURE 4

Ordering components of signaling pathways by epistasis tests, (a) An activating mutation in the sensor requires a functional response regulator to produce a constitutive output signal, (b) An activating mutation in the response regulator does not require a functional sensor to produce a constitutive output signal.

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2
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Image of FIGURE 5
FIGURE 5

Analyzing intraprotein communication mechanisms by domain surgery, (a) Does ablation of the input domain activate the adjoining output domain? (b) Does scission of input and output domains disrupt signal propagation? (c) Does transplantation of foreign domains disrupt signal propagation?

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2
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Image of FIGURE 6
FIGURE 6

Analyzing transmitter-receiver interactions by domain liberation, (a) Quenching of transmitter signals by liberated receivers; (b) jamming signals from liberated, constitutively active transmitters; (c) shielding of receivers by liberated quiescent transmitters.

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2
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Image of FIGURE 7
FIGURE 7

Structure-function relationships in transmitters and receivers. Sequence motifs characteristic of transmitters and receivers are indicated by black bars whose widths are proportional to the lengths of the motifs. Each sequence tract is labeled with a letter or two indicating their most prominent amino acid residue. Possible functions for some of these structural features are discussed in the text.

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2
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Image of FIGURE 8
FIGURE 8

Functional suppression of signaling defects. The starting circuit has a missense mutation in the transmitter that interrupts the signal pathway. Three different suppression mechanisms that may be represented among phenotypic revertants are shown: (a) mutations within the mutant domain that compensate for a defect in folding, stability, or signaling function; (b) mutations in another domain of the same protein that restore normal communication with the mutant domain; (c) mutations in another signaling component that restore normal communication with the mutant protein.

Citation: Parkinson J. 1995. Genetic Approaches for Signaling Pathways and Proteins, p 9-23. In Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch2
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References

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1. Ames, P.,, and J. S. Parkinson. 1994. Constitutively signaling fragments of Tsr, the E. coli serine chemoreceptor. J. Bacteriol. 176:63406348.
2. Baumgartner, J. W.,, C. Kim,, R. R. Brissette,, M. Inouye,, C. Park,, and G. L. Hazelbauer. 1994. Transmembrane signalling by a hybrid protein: communication from the domain of chemoreceptor Trg that recognizes sugar-binding proteins to kinase/phosphatase domain of osmosensor EnvZ. J. Bacteriol. 176:11571163.
3. Bourret, R. B.,, K. A. Borkovich,, and M. I. Simon. 1991. Signal transduction pathways involving protein phosphorylation in prokaryotes. Annu. Rev. Biochem. 60:401441.
4. Morrison, T. B.,, and J. S. Parkinson. 1994. Liberation of an interaction domain from the phosphotransfer region of CheA, a signaling kinase of E. coli. Proc. Natl. Acad. Set. USA 91:54855489.
5. Nakashima, K.,, K. Kanamaru,, H. Aiba,, and T. Mizuno. 1991. Osmoregulatory expression of the porin genes in Escherichia coli: evidence for signal titration in the signal transduction through EnvZ-OmpR phosphotransfer. FEMS Microbiol. Lett. 66:4347.
6. Parkinson, J. S. 1993. Signal transduction schemes of bacteria. Cell 73:857871.
7. Parkinson, J. S.,, and E. C. Kofoid. 1992. Communication modules in bacterial signaling proteins. Annu. Rev. Genet. 26:71112.
8. Stock, J. B.,, A. M. Stock,, and J. M. Mottonen. 1990. Signal transduction in bacteria. Nature 344:395400.
9. Utsumi, R.,, R. E. Brissette,, A. Rampersaud,, S. A. Forst,, K. Oosawa,, and M. Inouye. 1989. Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate. Science 245:12461249.

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