Researchers reveal novel mechanisms for decoding bacterial frequency modulation in signal processing

Bacteria employ complex signaling networks for adaptive gene control in changing environments. Bacterial second messenger molecules such as cyclic AMP (cAMP) relay external environmental signals into intracellular responses by employing both amplitude modulation (AM) and frequency modulation (FM) strategies. AM has been well studied, but the mechanisms by which cells decode frequency-encoded signals remain largely unknown.

In a study published in Nature Physics, a team led by Prof. JIN Fan from the Shenzhen Institutes of Advanced Technology of the Chinese Academy of Sciences (CAS), along with Prof. YANG Shuai from the National Science Library (Chengdu) of CAS, revealed the fundamental physical principles underlying bacterial FM signal processing, and demonstrated that FM decoding mechanisms enable bacteria to increase information entropy by approximately 2 bits compared to traditional AM in three-gene regulatory systems.

The researchers reconstructed a simplified cAMP signaling pathway in Pseudomonas aeruginosa by replacing endogenous cAMP synthesis machinery with a light-controlled system and native promoters with constitutive ones. This created a precisely controllable frequency-decoding cAMP circuit (FDCC) for quantitative monitoring.

Through time-scale analysis, the researchers discovered that the FDCC system naturally exhibited hierarchical signal processing across three functional modules: a wave converter that operates on second-to-minute timescales to transform periodic light inputs into sawtooth cAMP concentration patterns; a thresholding filter acting on millisecond-to-second timescales via cooperative Vfr-cAMP binding; and an integrator functioning on minute-to-hour timescales to convert dynamic frequency signals into stable protein expression levels.

Moreover, the researchers developed complementary theoretical frameworks including detailed chemical reaction network (CRN) models and analytical theory. Mathematical analysis revealed a critical dimensionless threshold parameter that controls the phase transition between high-pass and low-pass filtering behaviors, and the system's frequency selectivity was primarily determined by this threshold.

Using an automated high-throughput experimental platform supported by the Shenzhen Synthetic Biology Infrastructure, the researchers validated their theoretical predictions. Quantitative analysis revealed that FM significantly expands accessible state space beyond AM alone. In two-gene systems, AM accessed 19 distinct states, while FM enabled 38 states. In three-gene systems, there was a nearly four-fold increase in distinguishable expression patterns.

This work establishes fundamental principles of frequency-based signal processing in bacterial networks, offering valuable insights into the rational design of synthetic biological circuits.