(A) Schematic of open-loop system driving expression of constitutively open KcsA* bacterial potassium channel. Activator IacR and repressor MarR (tagged with ODC degron; Takeuchi et al., 2008) are …
Source data for Figure 1H, I.
Galactose-inducible activator (IacR) and repressor (MarR) constructs are shown. The potassium channel (KcsA*) plasmid contains a synthetic minimal promoter with IacR and MarR operator sites.
Screenshots from microscopy imaging of yeast after 24 hr in different KCl concentrations, and quantification of mean ThT (A), DIBAC4(3) (B), and Dis-C3(3) (C) fluorescence (upper panels) for …
Source data for Figure 1—figure supplement 2A–C.
(A) Cumulative autocorrelation of ThT traces in control strain averaged across n = 33 (yeast communities) trapping regions show noisy, non-synchronized pattern. (B) Weak autocorrelation of ThT …
Source data for Figure 1—figure supplement 3C–E.
Related to Figure 1D. Left panel, differential interference contrast (DIC), middle panel, ThT (cyan), and right panel, ThT color coded in heat map colors (blue [low signal], red [high signal]) of …
Related to Figure 1F. Left panel, differential interference contrast (DIC), middle panel, ThT (cyan), and right panel, ThT color coded in heat map colors (blue [low signal], red [high signal]) of …
(A) Schematic of dual-feedback circuit controlling downstream expression of bacterial potassium channel KcsA*. All components of the system are controlled by the same promoter to allow integration …
Source data for Figure 2H, I.
Computer simulations of a dual-feedback circuit model (upper panel) and corresponding phase portraits with nullclines (lower panel) for the different ratio of IacR–MarR receptor turnover (1:1 (A), …
Activator (IacR), repressor (MarR), and destabilized reporter (dGFP) constructs are shown. All components are controlled from the same synthetic promoter containing IacR and MarR operator sites. The …
A heat map of circuit response recorder with dEGFP reporter (upper panel) to chemical gradients (lower panel). Note a precise control of circuit output is possible by using a dual phytohormone …
dEGFP fluorescence normalized to OD600 (upper panel) and OD600 absorbance (lower panel) for 24-hr measurements using graded changes of phytohormones was used to analyze the excitable potential of …
(A–E) Left panel, dEGFP time evolutions from all traps recorded in the microfluidic device. Right panel, the heat map of dEGFP fluorescence for each of the recorded trapping regions corresponds to …
(A) A distribution of dGFP periods for three different frequencies of stimuli, as marked with corresponding colors. (B) Violin plot of peak amplitude distribution in all recorded yeast communities …
Source data for Figure 2—figure supplement 6A–C.
(A) Time evolution of KcsA-EGFP reporter traces under indicated pulses of phytohormones (3-hr period). An average trace of n = 25 yeast communities is shown in black. (B) Kymograph (heat map) of …
Source data for Figure 2—figure supplement 7D–G.
Related to Figure 2E. Left panel, dfferential interference contrast (DIC), middle panel, dEGFP (cyan) and mCherry (cell marker), and right panel, dEGFP color coded in heat map colors (blue [low …
Left panel, differential interference contrast (DIC), middle panel, dEGFP (cyan) and mCherry (cell marker), and right panel, dEGFP color coded in heat map colors (blue [low signal], red [high …
(A) Representative time traces of Thioflavin T (ThT) fluorescence per community (n = 56 yeast communities) under 2-hr hormone stimuli. Average trend is shown in black. SA and IAA peaks are shown as …
Source data for Figure 3D, E.
Time evolutions of ThT fluorescence across communities in 3 hr (A) and 1 hr (B) lasting phytohormone stimuli. Average traces are shown in black (C, D), kymographs related to (A) and (B) for n = 27 …
Source data for Figure 3—figure supplement 1F–H.
(A) Cumulative autocorrelation analysis of cumulative trend across all measured communities for 2 hr (black line) shows coherent oscillations in Thioflavin T (ThT) fluorescence. Peak amplitudes (B), …
Source data for Figure 3—figure supplement 2B–E.
Related to Figure 3A. Left panel, differential interference contrast (DIC), middle panel, ThT (cyan), and right panel, ThT color coded in heat map colors (blue [low signal], red [high signal]) of …
Related to Figure 3—figure supplement 1A. Left panel, differential interference contrast (DIC), middle panel, ThT (cyan), and right panel, ThT color coded in heat map colors (blue [low signal], red …
Related to Figure 3—figure supplement 1B. Left panel, differential interference contrast (DIC), middle panel, ThT (cyan), and right panel, ThT color coded in heat map colors (blue [low signal], red …
Related to Figure 3G. Left panel, differential interference contrast (DIC), middle panel, ThT (cyan), and right panel, ThT color coded in heat map colors (blue [low signal], red [high signal]) of …
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 (Saccharomyces cerevisiae) | sRedM | Pérez-García et al., 2021 | BY4741 pGK1:: mCherry | Selection: KanMX (G418) |
Strain, sRedM (Saccharomyces cerevisiae) | cLPdGFP | This study | sRedM pMarOIacO:: IacR-VP64 (pEX1004, ADDGENE_194950) pMarOIacO::MarR-RD (pEX1005, ADDGENE_ 194951) pMarOIacO::dEGFP (UbG76V-EGFP) (pEX1006, ADDGENE_194952) | Selection: KanMX (G418) -Leu, -Ura, -His |
Strain, BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 (Saccharomyces cerevisiae) | oLPKcsA* | This study | BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pGal7:: IacR-VP64 (pEX1001, ADDGENE_ 194713) pGal7::MarR-RD (pEX1002 ADDGENE_ 194714) pMarOIacO::KcsA*(pEX1003, ADDGENE_194949) | Selection: -Leu, -Ura, -His |
Strain, BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 (Saccharomyces cerevisiae) | sEmpty (control strain) | This study | BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 Empty insert plasmids pGADT7 (Takara Bio) backbone with auxotrophic markers | Selection: -Leu, -Ura, -His |
Strain, BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 (Saccharomyces cerevisiae) | cLPKcsA* | This study | sRedM pMarOIacO:: IacR-VP64 (pEX1004, ADDGENE_194950) pMarOIacO::MarR-RD (pEX1005, ADDGENE_ 194951) pMarOIacO::KcsA*(pEX1003, ADDGENE_194949) | Selection: -Leu, -Ura, -His |
Strain, BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 (Saccharomyces cerevisiae) | cLPTOK1* | This study | pMarOIacO:: IacR-VP64 (pEX1004, ADDGENE_194950) pMarOIacO::MarR-RD (pEX1005, ADDGENE_ 194951) pMarOIacO::TOK1*(pEX1008, ADDGENE_194954) | Selection: -Leu, -Ura, -His |
Strain, BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 (Saccharomyces cerevisiae) | cLPKcsA-EGFP* | This study | sRedM pMarOIacO:: IacR-VP64 (pEX1004, ADDGENE_194950) pMarOIacO::MarR-RD (pEX1005, ADDGENE_ 194951) pMarOIacO::KcsA- GFP*(pEX1007, ADDGENE_194953) | Selection: KanMX (G418) -Leu, -Ura, -His |
Other, PMP dye: Thioflavin T | ThT | Fisher Scientific, Thermo Scientific | CAS: 2390-54-7 | |
Other, PMP dye: Bis-(1,3-Dibutylbarbituric Acid)Trimethine Oxonol | DIBAC4(3) | VWR INTERNATIONAL EUROLAB, S.L | CAS: 70363-83-6 | |
Other, PMP dye: 3,3'-di-n-propylthiacarbocyanine iodide | DIS-C3(3) | FISHER SCIENTIFIC | CAS: 53336-12-2 |
Oligos and synthetic DNA sequences used in this study.
Computer model parameters.