### AND ### #Sugars %agent: arabinose(Loc~ex~in,c) %agent: xylose(Loc~ex~in,c) #Sugar transporter %agent: araE_gene(bs) %agent: araE_mrna() %agent: araE(Ex_pore,In_pore) #Degradation proteins %agent: araA_gene(bs) %agent: araA_mrna() %agent: araA(x) %agent: xylA_gene(bs) %agent: xylA_mrna() %agent: xylA(x) #Repressors %agent: xylR_gene(bs) %agent: xylR_mrna() %agent: xylR(ms,x) %agent: araR_gene(bs) %agent: araR_mrna() %agent: araR(ms,x) #constitutive repressors %agent: xylReC-araC_gene() %agent: xylReC-araC_mrna() %agent: araC(ms,x) #Activators %agent: TF(ms,x) %agent: P4_gene(bs1,bs2) %agent: P4_mrna() %agent: P4_AND() # reporter %agent: RFP_mrna() %agent: RFP_AND() # ###################################### ## Sugar concentration # OutSystem InFlux #'in.flux.ara' -> arabinose(Loc~ex,c) @ 'fluxRate' #'in.flux.xyl' -> xylose(Loc~ex,c) @ 'fluxRate' # Influx of arabinose through araE 'ara.araE' arabinose(Loc~ex), araE(Ex_pore) -> arabinose(Loc~ex!1),araE(Ex_pore!1) @ 'GeneralBinding' 'ara[ex-in]' arabinose(Loc~ex!1), araE(Ex_pore!1,In_pore) -> arabinose(Loc~in!2), araE(Ex_pore,In_pore!2) @ 'GeneralTransportRate' 'ara..araE' arabinose(Loc~in!2),araE(In_pore!2) -> arabinose(Loc~in),araE(In_pore) @ 'GeneralUnbinding' #'arabinose.araE' arabinose(Loc~ex), araE() -> araE(), arabinose(Loc~in) @ 'GeneralTransportRate' # degradation of arabinose through araA 'ara.araA' arabinose(Loc~in), araA(x) -> arabinose(Loc~in!1),araA(x!1) @ 'GeneralBinding' 'araDeg' arabinose(Loc~in!1), araA(x!1) -> araA(x) @ 'araAdegRate' #'arabinose.araA' arabinose(Loc~in), araA() -> araA() @ # Influx of xylose through araE 'xyl.araE' xylose(Loc~ex), araE(Ex_pore) -> xylose(Loc~ex!1),araE(Ex_pore!1) @ 'GeneralBinding' 'xyl[ex-in]' xylose(Loc~ex!1), araE(Ex_pore!1,In_pore) -> xylose(Loc~in!2), araE(Ex_pore,In_pore!2) @ 'GeneralTransportRate' 'xyl..araE' xylose(Loc~in!2),araE(In_pore!2) -> xylose(Loc~in),araE(In_pore) @ 'GeneralUnbinding' # degradation of arabinose through xylA 'xyl.xylA' xylose(Loc~in), xylA(x) -> xylose(Loc~in!1),xylA(x!1) @ 'GeneralBinding' 'xylDeg' xylose(Loc~in!1), xylA(x!1) -> xylA(x) @ 'araAdegRate' # ###################################### ## transporters & degProteins # araE regulation t&t 'araR-araE_on-off' araE_gene(bs),araR(x) <-> araE_gene(bs!2),araR(x!2) @ 'TF_onRate', 'TF_offRate' 'araR-araE-arabinose_off' araE_gene(bs!2), araR(ms,x!2), arabinose(Loc~in,c) -> araE_gene(bs),arabinose(Loc~in,c) @ 'mBindingRate' 'araE-transc' araE_gene(bs) -> araE_gene(bs),araE_mrna() @ 'araEtcRate' 'araE-transl' araE_mrna() -> araE_mrna(), araE() @ 'araEtlRate' # araA regulation t&t 'araR-araA_on-off' araA_gene(bs),araR(x) <-> araA_gene(bs!2),araR(x!2) @ 'TF_onRate', 'TF_offRate' 'araR-araA-arabinose_off' araA_gene(bs!2), araR(ms,x!2), arabinose(Loc~in,c) -> araA_gene(bs),arabinose(Loc~in,c) @ 'mBindingRate' 'araA-transc' araA_gene(bs) -> araA_gene(bs),araA_mrna() @ 'araAtcRate' 'araA-transl' araA_mrna() -> araA_mrna(), araA() @ 'araAtlRate' # xylA regulation t&t 'xylR-xylA_on-off' xylA_gene(bs),xylR(x) <-> xylA_gene(bs!2),xylR(x!2) @ 'TF_onRate', 'TF_offRate' 'xylR-xylA-xylose_off' xylA_gene(bs!2), xylR(ms,x!2), xylose(Loc~in,c) -> xylA_gene(bs),xylose(Loc~in,c) @ 'mBindingRate' 'xylA-transc' xylA_gene(bs) -> xylA_gene(bs), xylA_mrna() @ 'araAtcRate' 'xylA-transl' xylA_mrna() -> xylA_mrna(), xylA() @ 'araAtlRate' # ###################################### ## Repressors # xylR regulation ##transc & transl 'TF-xylose_activation' TF(ms,x), xylose(Loc~in,c) <-> TF(ms!3,x), xylose(Loc~in,c!3) @ 'GeneralBinding', 'GeneralUnbinding' 'TF-xylR_on-off' xylR_gene(bs),TF(ms!3,x),xylose(Loc~in,c!3) <-> xylR_gene(bs!1),TF(ms!3,x!1),xylose(Loc~in,c!3) @ 'TF_onRate','TF_offRate' 'xylR-transc' xylR_gene() -> xylR_gene(),xylR_mrna() @ 'xylRtcRate' 'xylR-transc_a' xylR_gene(bs!1), TF(ms!3,x!1), xylose(Loc~in,c!3) -> xylR_gene(bs!1),TF(ms!3,x!1),xylose(Loc~in,c!3),xylR_mrna() @ 'xylRtcRate_a' 'xylR-transl' xylR_mrna() -> xylR_mrna(), xylR() @ 'xylRtlRate' # araR t&t 'araR-NAR_on-off' araR_gene(bs),araR(x) <-> araR_gene(bs!2),araR(x!2) @ 'TF_onRate', 'TF_offRate' 'araR-NAR-arabinose_off' araR_gene(bs!2), araR(ms,x!2), arabinose(Loc~in,c) -> araR_gene(bs),arabinose(Loc~in,c) @ 'mBindingRate' 'araR-transc' araR_gene(bs) -> araR_gene(bs),araR_mrna() @ 'araRtcRate' 'araR-transl' araR_mrna() -> araR_mrna(), araR() @ 'araRtlRate' # araC & xylReC 'xylReC-araC_tcConstEx' xylReC-araC_gene() -> xylReC-araC_gene(), xylReC-araC_mrna() @ 'tcConstEx' 'xylReC-araC_tlConstEx' xylReC-araC_mrna() ->xylReC-araC_mrna(), xylR(), araC() @ 'tlConstEx' # ###################################### ## ACTIVATORs ### P4_AND ### #AND arabinose regulation 'araC-P4_on-off' P4_gene(bs1),araC(x) <-> P4_gene(bs1!7),araC(x!7) @ 'TF_onRate', 'TF_offRate' 'araC-P4-arabinose_off' P4_gene(bs1!7),araC(ms,x!7),arabinose(Loc~in,c) -> P4_gene(bs1),arabinose(Loc~in,c) @ 'mBindingRate' #AND xylose regulation 'xylR-P4_on' P4_gene(bs2), xylR(x) <-> P4_gene(bs2!8), xylR(x!8) @ 'TF_onRate', 'TF_offRate' 'xylR-P4-xylose_off' P4_gene(bs2!8),xylR(ms,x!8),xylose(Loc~in,c) -> P4_gene(bs2),xylose(Loc~in,c) @ 'mBindingRate' # t&t &dim 'P4-transc' P4_gene(bs1,bs2) -> P4_gene(bs1,bs2),P4_mrna(),RFP_mrna() @ 'P4tcRate' 'P4-transl' P4_mrna() -> P4_mrna(),P4_AND() @ 'P4tlRate' #decay 'araE_mrna-dec' araE_mrna() -> @ 'mrna-decRate' 'araE-dec' araE() -> @ 'prot-decRate' 'araA_mrna-dec' araA_mrna() -> @ 'mrna-decRate' 'araA-dec' araA() -> @ 'prot-decRate' 'xylA_mrna-dec' xylA_mrna() -> @ 'mrna-decRate' 'xylA-dec' xylA() -> @ 'prot-decRate' 'xylR_mrna-dec' xylR_mrna() -> @ 'mrna-decRate' 'xylR-dec' xylR() -> @ 'prot-decRate' 'araR_mrna-dec' araR_mrna() -> @ 'mrna-decRate' 'araR-dec' araR() -> @ 'prot-decRate' 'xylReC-araC_mrna-dec' xylReC-araC_mrna() -> @ 'mrna-decRate' 'araC-dec' araC() -> @ 'prot-decRate' 'P4_mrna-dec' P4_mrna()-> @ 'mrna-decRate' 'P4_AND-dec' P4_AND()-> @ 'prot-decRate' 'RFP_mrna-dec' RFP_mrna()-> @ 'mrna-decRate' 'RFP_AND-dec' RFP_AND()-> @ 'prot-decRate' ###Rates %var: 'mBindingRate' 1.0 %var: 'GeneralBinding' 0.003 # per molecules per second %var: 'GeneralUnbinding' 0.3 %var: 'GeneralTransportRate' 1.0 %var: 'TF_onRate' 0.001 %var: 'TF_offRate' 0.4 %var: 'araAdegRate' 0.1 %var: 'xylAdegRate' 0.1 %var: 'araEtcRate' 0.06 %var: 'araAtcRate' 0.053 %var: 'araRtcRate' 0.069 %var: 'xylRtcRate' 0.008 %var: 'xylRtcRate_a' 0.075 %var: 'xylAtcRate' 0.06 %var: 'tcConstEx' 0.1 %var: 'P4tcRate' 0.1 %var: 'araEtlRate' 0.04 %var: 'araAtlRate' 0.04 %var: 'araRtlRate' 0.05 %var: 'xylRtlRate' 0.055 %var: 'xylAtlRate' 0.044 %var: 'tlConstEx' 0.02 %var: 'P4tlRate' 0.02 %var: 'mrna-decRate' 0.0041 %var: 'prot-decRate' 0.0002 ##init %init: 600 araE() %init: 1200 araR() %init: 2400 araC() %init: 2850 xylR() %init: 590 araA() %init: 300 xylA() %init: 1 araA_gene() %init: 1 araE_gene() %init: 1 araR_gene() %init: 1 xylA_gene() %init: 1 xylR_gene() %init: 1 xylReC-araC_gene() %init: 1 P4_gene() #obs #%obs: 'araIN' arabinose(Loc~in?) #%obs: 'araOUT' arabinose(Loc~ex?) #%obs: 'xylIn' xylose(Loc~in?) #%obs: 'xylOUT' xylose(Loc~ex?) #%obs: 'xylReC-araC_mrna' xylReC-araC_mrna() %obs: 'araC' araC() #%obs: 'araA_mrna' araA_mrna() %obs: 'araA' araA() #%obs: 'araE_mrna' araE_mrna() %obs: 'araE' araE() #%obs: 'araR_mrna' araR_mrna() %obs: 'araR' araR() #%obs: 'xylR_mrna' xylR_mrna() %obs: 'xylR' xylR() #%obs: 'xylA_mrna' xylA_mrna() %obs: 'xylA' xylA() #%obs: 'P4_mrna' P4_mrna() %obs: 'P4' P4_AND() #%mod: [T] > 5 do $UPDATE 'fluxRate' 10000.0 #%mod: [T] > 2000 do $ADD 25000 arabinose(Loc~ex,c) #%mod: [T] > 2000 do $ADD 25000 xylose(Loc~ex)