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Molecular Mechanisms

Relevant properties of the chemotaxis pathway

Che-protein localization in the cell

The control of the tumbling frequency of E. coli is achieved by spatially localizing certain elements of the chemotactic network (Che proteins) and thus affecting the activity of their downstream partners. Inside the cell, the chemotactic proteins CheA, CheY and CheZ tend to co-localize with methyl accepting chemotaxis protein MCPs at the membrane. But whereas CheA and CheZ nearly only localize at the MCPs, CheY is also present in significant concentrations in the cytoplasm [1].

Anchor proteins

For spatial localization of the Che-protein complex, three different proteins will be utilized:
1. The tetracyclin repressor tetR anchoring the Che-protein to the DNA by binding to it's operator site tetO [2].
2. The triggor factor binding to the large ribosomal subunit [3].
3. The prokaryotic actin homologue MreB which assembles into helical filaments underneath the cytoplasmic membrane [4].

These anchors should enable to control the tumbling frequency by localizing a Che-protein and therefore interfering with its activity.

Relevant properties of the PhyB/PIF3 module

Properties of holophytochrome

Phytochrome apoproteins (PHYs) are a family of 120-130kD soluble proteins [4, p.105]. They are covalently bound to a linear tetrapyrrole chromophore. The native holoproteins homodimerizes. It is likely that each subunit in the homodimer is phototransformed independently (no co-operative effects) [4, p. 131].

There are two mayor types of phytochromes, type I (PhyA) and type II (PhyB and PhyC) [4, p.142]. The Pfr form of type I proteins is labile (fast degradation, half live between 30min and 2h). Although the Pfr form of type II is also degraded faster than the corresponding Pr form, it is much more stable (half live around 8h). The degradation is temperature dependent and possibly an active process [4, p.142 ff]. On the other hand, the Pr form is very stable (half live of ofer 100h in Cucurbita).

In some plants pyhtochrome type I in the Pfr form sequesters [4, p.146]. The sequestering happens in the timescale of seconds, whereas even when ,deactivated and again and in the Pr form, the half life of the bulk is around 25 min at 25C for etiolated Avena. It is not clear if type II Pfr also sequesteres. It is also possible that the sequestering is part of the active degradation of type I Pfr [4].

References

[1] Sourjik and Berg: Localization of components of the chemotaxis machinery of Escheria coli using fluorescent protein fusions. Molecular Biology. 2000; 37:4.

[2] Bertram and HIllen: The application of Tet repressor in prokaryotic gene regulation and expression. Microbial Biotechnology. 2008; 1:1.

[3] Hesterkamp, Deuerling and Bukau: The Amino-terminal 118 amino acids of Escherichia coli Trigger factor constitute a domain that is necessary and sufficient for binding to ribosomes. The Journal of Biologcial Chemistry. 1997; 272:35.

[4] Kruse, Bork-Jensen and Gerdes: The morphogenetic MreBCD proteins of Escherichia coli form an essential membrane-bound complex. Molecular Microbiology. 2005;55:1.

old references Moritz:

[2]Shiomi, Banno, Homma, and Kawagishi: Stabilization of polar localization of a chemoreceptor via its covalent modifications and its communication with a different chemoreceptor. Journal of Bacteriology. 2005; 187:22.

[3] Shiomi, Zhulin, Homma, and Kawagishi: Dual recognition of the bacterial chemoreceptor by chemotaxis-specific domains of the CheR methyltransferase. The Journal of Biological Chemistry. 2002; 277:44.

[4] Kendrick and Kronenberg: Photomorphogenesis in plants. Kluwer academic publishers, Dordrecht, The Netherlands. 2nd edition, 1994.