Microbes as Biosensors (Inda and Lu)

[SarahHagg]

Microbes as Biosensors

Maria Eugenia Inda and Timothy K. Lu https://doi.org/10.1146/annurev-micro-022620-081059

this is a super good overview!

Key parts of engineered sense-compute-and-respond genetic circuits:

• sensors (encoded proteins or RNAs) that sense chemical or physical inputs from inside or outside the cell and then transduce this information to downstream
• compute elements (genetic circuitry that processes information and then translates it into outputs based on a defined input-output relationship)
• outputs: e.g. gene transcription or translation, posttranscriptional modification, metabolic pathway activation, and protein secretion

benefits of microbial biosensors:

• robustnesses can be engineered (e.g. gene clusters that encode acid-resistance systems (e.g., AR1, AR2, and AR3 from E. coli), or osmoyolerant mutants)
• evolvability
• high sensitivity
• specificity
• continuous sensing
• noninvasiveness
• scalability

Synthetic gene networks:

• simple open-loop circuits (linear output)
• feedforward circuit (input affects output through indirect nodes): -> e.g. pulse-generating network ('concentration of the output has a strong, transient response to a change in the input, which is then dampened to a new steady state through the delayed action of the inhibitor') -> e.g. incoherent feedforward loop circuit that reduced unwanted cross talk between two stress-responsive promoters (environmental stress-responsive system with increased specificity)
• positive feedback circuit -> increased steady-state levels of expressed gene (amplification) -> faster response kinetics -> increased sensitivity -> expand the input dynamic range of a circuit (low-copy/high-copy plasmid system with AraC ...TESEC strains!)
• negative feedback circuit -> reduces cell-to-cell fluctuations in the steady-state level of the transcription factor -> speed up responses by reducing rise time
• 'double-negative feedback loop has been used to implement the toggle switch, a synthetic memory circuit'

Memory Circuits

• toggle switches
• recombinases (recognize specific sequences of DNA and can invert them or cut them out, leaving long-lasting changes in DNA that serve as memories of past events) -> e.g. to evaluate order in which biological events occur (what happened first?)

CRISPR-Cas9-Based Memory targeted, dynamic, recurring modifications of DNA in living cells -> distinct DNA memory states (information retrieved by sequencing, turning ON or OFF reporter expression, or measuring signal intensity)

• precise writers: base editor is fused to dead Cas9; complementary guide RNA to target site
• pseudorandom writers (stochastic mutations): Cas1-Cas2 writing system (chronological order of spacer addition events is preserved within the CRISPR array configuration) -> record temporal order of signals

[SarahHagg]

[SarahHagg]

[SarahHagg]