| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| Escherichia coli EcNR2 | Addgene | Addgene #26931 |
| Chemicals, peptides, and recombinant proteins | ||
| LB growth medium | AmericanBio | N/A |
| Solid chemicals: amino acids (phenylalanine, tryptophan, tyrosine), antibiotics (carbenicillin, spectinomycin), inducers (anhydrotetracycline, vanillic acid), trace minerals (Table S2), vitamins (Table S2) | SigmaAldrich | N/A |
| Colicin E1 for tolC counterselections | This paper | N/A |
| Experimental models: Organisms/strains | ||
| E. coli EcNR2.ΔpheA, ΔtrpDE, ΔtyrA, ΔpheA.ΔtrpDE, ΔtrpDE.ΔtyrA, ΔtyrA.ΔpheA, ΔpheA.ΔtrpDE.ΔtyrA, ΔpheA.ΔtrpDE.ΔtyrA.entA | This paper | CFH748-755 |
| Oligonucleotides | ||
| MAGE oligo for aroF-FIM: T∗T∗CAGTTGTTCCGGAGTCATTAAAACCTGTTCGTCG GTAATATGTACTTTATTCAGCGCGTCTTTTTGcatGATG GCGATCCTGTTTAT |
This paper | oCFH007 |
| MAGE oligo for aroG-FIM: T∗G∗CGCCCCAGCTCATCAGGTCAGCGAGATATTGT GGGGTGATCATGTTGAGAAACTCACCTGCCGCTGG CAGACCGCTGTCGTTAATATC |
This paper | oCFH008 |
| Primers for cloning pPAF-v5 and pGFP-RFP | This paper | rCFH404-415 |
| MAGE oligos for knockout of tolC insertions at pheA, trpDE, tyrA, and entA | This paper | oCFH026-29 |
| Primers for amplifying tolC cassettes to recombiner into pheA, trpDE, tyrA, entA, and tyrR | This paper | rCFH334-337, 344-347, 511-512 |
| Recombinant DNA | ||
| pPAF-v5 | This paper | CFH489 |
| pGFP-RFP | This paper | CFH496 |
| papBAC synthetic genes | GenScript | N/A |
| Software and algorithms | ||
| Python scripts for OptForce simulations | This paper | https://doi.org/10.5281/zenodo.6569900 |
| Python v2.7.11 for Unix | Python Software Foundation | www.python.org |
| MATLAB r2019a for doubling time calculations | MathWorks Inc | https://www.mathworks.com |
| Gurobi Optimizer v9.0.0 | Gurobi Optimization | https://www.gurobi.com |
| COBRApy Toolbox v0.9.1 | cobrapy - constraint-based metabolic modeling in Python | https://opencobra.github.io/cobrapy/ |
| Other | ||
| SCC Shared Computing Cluster, SCC1, 2 fourteen-core 2.4 GHz Intel Xeon E5-2680v4, 256 Gb RAM, 2 nodes | Boston University Research Computing, Massachusetts Green High Performance Computing Center (MGHPCC), Holyoke, MA | https://www.bu.edu/tech/support/research/computing-resources/scc/ |
| Yale West Campus Analytical Core | Yale University | https://wcac.yale.edu |
| Experimental data and MATLAB analysis code for Figure 1, Figure 3 and 3 | This paper | https://doi.org/10.5281/zenodo.6569900 |