Questions: Bacterial Chemotaxis and Two-Component Signal Transduction

Question 1

An E. coli bacterium swims into a region with uniformly very high attractant concentration and remains there. After the adaptation mechanism has fully reset, what happens to the bacterium's tumbling frequency?

• A. Tumbling frequency remains permanently suppressed because the high attractant concentration continuously inhibits CheA
• B. Tumbling frequency returns to its pre-stimulus baseline, because methylation has restored CheA activity despite the high attractant
• C. Tumbling frequency increases above baseline because high attractant saturates the receptors and disrupts normal signaling
• D. Tumbling frequency stays low only if the bacterium continues to move — once it stops, adaptation occurs

Answer: (B)

This is the key test of whether a student understands adaptation. The bacterium senses the *gradient* (rate of change in concentration), not the absolute concentration. When it enters high attractant, tumbling suppresses. But then CheR continues methylating the MCPs, gradually restoring CheA activity to baseline — and with it, the normal tumbling frequency. After full adaptation, the bacterium behaves exactly as if it were in the original low-attractant environment: it has 'forgotten' the new baseline. Option A (the most tempting wrong answer) confuses maintained inhibition with adaptation — it would predict bacteria can never tumble in high attractant, which would trap them in place rather than allowing continued gradient-following.

Question 2

In the E. coli chemotaxis system, what is the direct effect of phosphorylated CheY (CheY-P) on flagellar rotation?

• A. CheY-P binds the flagellar motor switch complex and promotes counterclockwise rotation, extending runs
• B. CheY-P inhibits CheA autophosphorylation, creating a negative feedback loop that prevents over-tumbling
• C. CheY-P diffuses to the flagellar motor, binds the switch complex, and promotes clockwise rotation, causing tumbling
• D. CheY-P activates CheR to add methyl groups to the MCPs, resetting receptor sensitivity

Answer: (C)

CheY-P is the signal that connects receptor activation to flagellar behavior. When CheA is active (no attractant bound), it phosphorylates CheY; CheY-P diffuses to the flagellar motor switch and promotes clockwise (CW) rotation, causing the flagella to fly apart and the cell to tumble. When attractant binds and inhibits CheA, CheY-P levels drop, and the motor defaults to counterclockwise (CCW) rotation — the run state. The direction of the causal chain is: attractant → inhibit CheA → less CheY-P → CCW rotation → run. Option A reverses the rotational direction. Option D confuses CheY with CheB (which IS activated by phosphorylation and DOES regulate methylation, but as CheB, not CheY).

Question 3

Bacteria navigate chemical gradients by sensing the rate of change (gradient) in attractant concentration rather than its absolute value.

• T. True
• F. False

Answer: True

This is the core insight of bacterial chemotaxis. If bacteria sensed absolute concentration, they would stop tumbling as soon as they entered a favorable zone and would be unable to detect further improvements. Instead, the methylation-based adaptation system allows the bacterium to continuously reset its 'baseline' to the current concentration, so it always compares what it senses now to what it sensed a moment ago. A run is extended when concentration is increasing (getting better); tumbling resumes when concentration plateaus or decreases. This temporal comparison mechanism works over a concentration range spanning five orders of magnitude — far greater than any system based on absolute concentration would achieve.

Question 4

Attractant binding to chemoreceptors directly activates CheA, which then phosphorylates CheY to promote running behavior.

• T. True
• F. False

Answer: False

The logic is inverted. In the *absence* of attractant, CheA is constitutively active, autophosphorylates, and transfers phosphate to CheY — CheY-P promotes clockwise rotation and tumbling. When attractant binds the MCP receptor, a conformational change *inhibits* CheA, reducing CheY-P levels and allowing the motor to default to counterclockwise rotation (running). So attractant → inhibit CheA → less CheY-P → run. This counterintuitive arrangement (the default state is tumbling, not running) is important: it means the system is optimally sensitive to improvements from a baseline of uncertainty, rather than requiring an active 'start moving' signal.

Question 5

How does the methylation-based adaptation mechanism allow bacteria to detect chemical gradients over a concentration range spanning five orders of magnitude?

Model answer: The methylation system acts as a continuously adjustable gain control. CheR constantly adds methyl groups to the MCPs, which gradually restores CheA activity regardless of attractant concentration. CheB (activated by CheA phosphorylation) removes methyl groups. In equilibrium at any given concentration, methylation level reflects the current background — the receptor is effectively 'zeroed out' to the ambient concentration. When concentration suddenly increases (attractant binds), CheA is inhibited, CheY-P drops, and the cell runs. As methyl groups accumulate (CheB is now less active), CheA activity restores and tumbling resumes at the new baseline. Because the reset mechanism is concentration-independent, the system can operate equally well whether the background concentration is 10 nM or 1 mM — it always senses changes relative to the current baseline.

The adaptation mechanism transforms what could only be an absolute-concentration detector into a gradient detector. This is analogous to how the eye adapts to bright or dim light: dark adaptation and light adaptation allow photoreceptors to operate over a ~12-log range of light intensities by continuously adjusting their gain. Chemotaxis achieves the same trick through receptor methylation, and the resulting 5-order-of-magnitude dynamic range is far greater than any simple receptor-ligand system could provide. This is why chemotaxis is described as a nearly perfect sensory system and a model for understanding sensory adaptation in all of biology.