E. coli K-12 (MG1655)
The non-pathogenic laboratory workhorse. K-12 strains have lost the ability to colonize the human gut and are the reference BSL-1 host for genetic engineering, with the deepest tooling of any bacterial chassis.
Identity
- Species
- Escherichia coli
- Strain
- K-12 MG1655
- NCBI taxid
- 511145
- Genome
- NC_000913.3
Safety
- Biosafety level
- BSL-1
- Pathogenic
- No
- GRAS
- No
- Biocontainment
- Auxotrophic and synthetic-amino-acid kill-switch systems are well characterized in K-12.
- BSL-1 basis
- ABSA/NIH Risk Group 1; E. coli K-12 derivatives are exempt host-vector systems under NIH Guidelines Appendix C.
K-12 lacks the O-antigen and many colonization factors; it is the standard 'safe' cloning host.
Traits
- Gram
- negative
- Oxygen
- facultative
- Optimal temp
- 37 °C
- Doubling time
- ~20 min
- Spore-forming
- No
- Transformable
- Yes
Engineering
- CRISPR tooling
- dCas9/CRISPRi and CRISPRa extensively characterized in E. coli.
- Common promoters
- pTac, pBAD (araBAD), pLac, Anderson series (J23xxx)
- Selection markers
- AmpR, KanR, CmR
- Toolkits
- SEVA, Anderson promoter collection, Marionette sensor library
Biosensors using this chassis
Arsenic AND mercury gate (dual heavy-metal)
A two-input AND gate that fires only when BOTH arsenic and mercury are present — reducing false positives and flagging co-contaminated water. ArsR drives the sgRNA and MerR drives dCas9, so CRISPRi repression (and the readout) needs both metals.
Arsenic ratiometric quantifier
Quantifies arsenic with two reporters: an arsenic-driven green channel over a constitutive red channel. The green/red ratio cancels out cell number, growth, and instrument variation — giving a robust, self-normalizing readout for field quantitation.
Arsenic water sensor (ArsR + CRISPRi)
Detects arsenite in drinking water. The validated ArsR/Pars sensing module gates an sgRNA that, with dCas9, represses a constitutive sfGFP reporter (CRISPRi inverter). Built in safe E. coli K-12.
Bacterial contamination sensor (AI-2 + CRISPRi)
Flags general bacterial contamination by sensing autoinducer-2 (AI-2), the inter-species quorum signal made by most bacteria. The LsrR/AI-2 system gates a CRISPRi circuit driving a visible pigment, in safe E. coli K-12.
Cholera sensor (CAI-1 + CRISPRa)
Detects Vibrio cholerae by sensing its species-specific quorum signal CAI-1. The CqsS receptor gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12 — no live pathogen required.
Explosives/landmine sensor (YqjF + CRISPRa)
Detects buried explosives by sensing DNT vapour (a TNT degradation product that leaks from landmines). The YqjF sensor gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12.
Nickel/cobalt sensor (RcnR + CRISPRi)
Detects nickel and cobalt in water. The native E. coli RcnR metal-responsive repressor gates a CRISPRi circuit driving a visible chromoprotein, in safe E. coli K-12.
Nitrate sensor (NarL + CRISPRi)
Detects nitrate in water and food. The native E. coli NarX/NarL nitrate two-component system gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12.
P. aeruginosa quorum sensor (LasR + CRISPRi)
Flags contamination by Pseudomonas aeruginosa by sensing its quorum-sensing signal 3-oxo-C12-HSL. The LasR sensor gates a CRISPRi inverter driving a pigment reporter, in safe E. coli K-12.
Salicylate sensor (NahR + CRISPRi)
Detects salicylate (a naphthalene-degradation marker and drug metabolite). The NahR LysR-family activator gates a CRISPRi circuit driving a visible pigment, in safe E. coli K-12.
Tetracycline sensor (TetR + CRISPRi)
Detects tetracycline antibiotic contamination in water and food. The classic TetR sensor gates a CRISPRi circuit driving a visible pigment, in safe E. coli K-12.
Theophylline sensor (riboswitch + CRISPRa)
Detects theophylline, an asthma drug with a narrow therapeutic window. The well-characterized synthetic theophylline riboswitch gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12 — a model for low-cost therapeutic drug monitoring.
Vanillate sensor (VanR + CRISPRa)
Detects vanillate/vanillin (lignin-degradation and food/flavour marker). The Marionette VanR sensor gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12.
Vibrio sensor (LuxR/3OC6-HSL + CRISPRa)
Detects Vibrio-type contamination via the 3-oxo-C6-homoserine-lactone quorum signal. The classic LuxR receptor gates a CRISPRa circuit driving a luminescent reporter, in safe E. coli K-12.
Zinc band-pass sensor (healthy-window)
Fires only when zinc sits within a target concentration window — not too low, not too high — using an incoherent feed-forward loop. Useful for flagging deviations from a healthy/optimal range rather than mere presence.