strains and plasmids used in this study (4)

elife-27396-v2.xml

10.7554/eLife.27396.017

Table 1.Strains and plasmids used in this study

Strain/plasmid	Description/genotype	Reference/source
S. cerevisiae strains
DKY6281	MATα pho8∆::TRP1 leu2-3,112 ura3-52 his3-200 trp1-901 lys2-801 suc2-9
BJ3505	MATα pep4∆::HIS3 prb1-∆1.6R ura3-52 his3-200 trp1-∆101 lys2-801 can1 gal2	(Jones, 2002)
BY4741	MATa his3∆one leu2∆0 met15∆0 ura3∆0	ATCC
	BY4741 vam7∆::KAN	Invitrogen
AMY1018	BY4741 VAM7::NAT (Qc-wt knock-in; control wt strain)	This study
AMY1022	BY4741 vam7(1-289)::NAT (Qc-1∆ knock-in)	This study
AMY1021	BY4741 vam7(1-295)::NAT (Qc-3∆ knock-in)	This study
AMY1020	BY4741 vam7(1-302)::NAT (Qc-5∆ knock-in)	This study
AMY1019	BY4741 vam7(1-309)::NAT (Qc-7∆ knock-in)	This study
DNY588	BY4741 VAM7::NAT yck3∆::KAN	This study
DNY591	BY4741 vam7(1-289)::NatR yck3∆::KAN	This study
DNY589	BY4741 vam7(1-295)::NatR yck3∆::KAN	This study
DNY590	BY4741 vam7(1-302)::NatR yck3∆::KAN	This study
GOY23	MATα pep4∆::LEU2 prb1∆::LEU2 leu2-3,112 ura3-52 his3-200 trp1-901 lys2-801 suc2-9	(Odorizzi et al., 1998)
AMY87	BJ3505 vam3∆	Merz Lab collection
RSY269	sec17-1	(Novick et al., 1981)
Yeast plasmids
pDN516	Ap^R 2µ URA3	(Nickerson et al., 2012)
pDN313	pDN516::SEC18	(Lobingier et al., 2014)
pDN314	pDN516::SEC17	(Lobingier et al., 2014)
pDN315	pDN516::SEC17 SEC18	(Lobingier et al., 2014)
pDN365	pDN516::sec17-(F21S, M22S — ‘FSMS’)	This study
pDN366	pDN516::sec17-(L291A, L292A —‘LALA’)	This study
pRS416	Ap^R CEN URA3	(Sikorski and Hieter, 1989)
pRS426	Ap^R 2µ URA3	(Sikorski and Hieter, 1989)
pMS120	VAM7 (pRS426; Qc-wt overproduction)	This study
pMS121	vam7(1-289) (pRS426; Qc-1∆ overproduction)	This study
pMS122	vam7(1-295) (pRS426; Qc-3∆ overproduction)	This study
pMS123	vam7(1-302) (pRS426; Qc-5∆ overproduction)	This study
pMS124	vam7(1-309) (pRS426; Qc-7∆ overproduction)	This study
pMS125	VAM7 (pAG25)	This study
AMP1492	pRS416::SEC17	This study
AMP1774	pRS416::sec17-K159E
AMP1774	pRS416::sec17-K163E	This study
AMP1774	pRS416::sec17-K159E,K163E (‘KEKE’)	This study
E. coli plasmids
AMP356	pET41::His₆-TEV-VAM7-intein-CBD	(Schwartz and Merz, 2009)
AMP359	pET41::His₆-TEV-VAM7(1–289, 1∆)-intein-CBD	(Schwartz and Merz, 2009)
AMP1809	pET41::His₆-TEV-VAM7(1–291, 2∆)-intein-CBD	This study
AMP358	pET41::His₆-TEV-VAM7(1–295, 3∆)-intein-CBD	(Schwartz and Merz, 2009)
AMP1810	pET41::His₆-TEV-VAM7(1–299, 4∆)-intein-CBD	This study
AMP357	pET41::His₆-TEV-VAM7(1–302, 5∆)-intein-CBD	(Schwartz and Merz, 2009)
AMP1806	pET41::His₆-TEV-VAM7(1–302, AR-5∆)-intein-CBD	This study
AMP1807	pET41::His₆-TEV-VAM7(1–302, RA-5∆)-intein-CBD	This study
AMP1808	pET41::His₆-TEV-VAM7(1–302, AA-5∆)-intein-CBD	This study
AMP360	pET41::His₆-TEV-VAM7(1–309, 7∆)-intein-CBD	(Schwartz and Merz, 2009)
AMP1547	pTYB12::intein-CBD-SEC17	(Schwartz and Merz, 2009)
AMP1547	pTYB12::intein-CBD-SEC17 (F21R, M22S, L24S, F25R)	This study
AMP1548	pTYB12::intein-CBD-SEC17 (F21R, F25R)	This study
AMP1549	pTYB12::intein-CBD-SEC17 (∆21–25)	This study
AMP1550	pTYB12::intein-CBD-SEC17 (F21S, M22S — ‘FSMS’)	This study
AMP1551	pTYB12::intein-CBD-SEC17 (∆1–26)	This study
AMP1777	pTYB12::intein-CBD-SEC17 (K159E)	This study
AMP1778	pTYB12::intein-CBD-SEC17 (K163E)	This study
AMP1779	pTYB12::intein-CBD-SEC17 (K159E, K163E — ‘KEKE’)	This study

elife-28683-v2.xml

10.7554/eLife.28683.030

Table 2.Strains and plasmids used in this study

Bacterium	Strain	Relevant characteristics	Reference/source
E. coli	DH5α	F recA lacZM15	Bethesda research laboratory
	DH5α λpir	F recA lacZM15 λpir	HP Schweizer
C. taiwanensis	LMG19424	Wild-type strain isolated from Mimosa pudica in Taiwan	(Chen et al., 2001)
	CBM832	LMG19424 derivative resistant to Streptomycin, Str^R	M. Hynes
	CBM2568	CBM832 deleted in nifH, Str^R	This study
	CBM2700	CBM832 carrying a Pps-GFP fusion downstream glmS, Str^R	This study
	CBM2701	CBM2568 carrying a Pps-GFP fusion downstream glmS, Str^R	This study
	CBM2707	CBM2568 carrying a Pps-mCherry fusion downstream glmS, Str^R	This study
	CBM2708	CBM832 carrying a Pps-mCherry fusion downstream glmS, Str^R	This study
Plasmids	Name	Relevant characteristics	Reference/source
	pGPI-SceI	ori_R6K, mob⁺, carries a I-SceI site, Tri^R	(Flannagan et al., 2008)
	pDAI-SceI	ori_pBBR1, mob⁺, carries the I-SceI gene, Tet^R	(Flannagan et al., 2008)
	pRCK-Pps-GFP	Plasmid carrying the psbA promoter region fused to GFP, Kan^R	M. Valls
	pRCK-Pps-mCherry	Plasmid carrying the psbA promoter region fused to mCherry, Kan^R	M. Valls
	pCBM156	pGPI-SceI carrying the nifH 5’ and 3’ regions, Tri^R	This study
	pCBM161	pGPI-SceI carrying the glmS-Ralta_A0206 intergenic region interrupted by a Pps-GFP fusion, Tri^R	This study
	pCBM162	pGPI-SceI carrying the glmS-Ralta_A0206 intergenic region interrupted by a Pps-mCherry fusion, Tri^R	This study
	pRK2013	Helper plasmid, Kan^R	(Figurski and Helinski, 1979)

Str, spreptomycin; Tri, trimethoprim; Tet, tetracycline; Kan, kanamycin.

elife-46735-v2.xml

10.7554/eLife.46735.024

Table 2.Strains and plasmids used in this study.

Strain/genotype	Information	Source/reference
Wild-type (WT)	YBC16G1, prototrophic sigma1278b, MAT a	Isolate via Fink Lab
WT (pPCK1-mCherry)	Wild-type strain with gluconeogenesis reporter plasmid (mCherry with PCK1 promoter)	this study
WT (pHXK1-mCherry)	Wild-type strain with constitutive reporter plasmid (mCherry with HXK1 promoter)	this study
WT (pTKL1-mCherry)	Wild-type strain with pentose phosphate pathway reporter plasmid (mCherry with TKL1 promoter)	this study
PCK1-flag	MAT a PCK1-3xFLAG::natNT2	this study
FBP1-flag	MAT a FBP1-3xFLAG::natNT2	this study
ICL1-flag	MAT a ICL1-3xFLAG::natNT2	this study
MAL11-flag	MAT a MAL11-3xFLAG::natNT2	this study
NTH1-flag	MAT a NTH1-3xFLAG::natNT2	this study
∆nth1	MAT a nth1::kanMX6	this study
∆mal11	MAT a mal11::kanMX6	this study
∆nth1 (pPCK1-mCherry)	∆nth1 strain with gluconeogenesis reporter plasmid (mCherry with PCK1 promoter)	this study
∆mal11 (pPCK1-mCherry)	∆mal11 strain with gluconeogenesis reporter plasmid (mCherry with PCK1 promoter)	this study
∆nth1 (pTKL1-mCherry)	∆nth1 strain with pentose phosphate pathway reporter plasmid (mCherry with TKL1 promoter)	this study
∆mal11 (pTKL1-mCherry)	∆mal11 strain with pentose phosphate pathway reporter plasmid (mCherry with TKL1 promoter)	this study
Plasmid	Information	Source/reference
pPCK1-mCherry	mCherry under the PCK1 promoter and CYC1 termin- ator. p417 centromeric plasmid backbone, G418^R.	this study
pHXK1-mCherry	mCherry under the HXK1 promoter and CYC1 termin- ator. p417 centromeric plasmid backbone, G418^R.	this study
pTKL1-mCherry	mCherry under the TKL1 promoter and CYC1 termin- ator. p417 centromeric plasmid backbone, G418^R.	this study

elife-57915-v2.xml

Table 1.Strains and plasmids used in this study.

Strains or plasmids	Relevant genotype or phenotype	References
E. coli
DH5αλpir	endA1 hsdR17 glnV44 (=supE44) thi-1 recA1 gyrA96 relA1 φ80dlacΔ(lacZ)M15 Δ(lacZYA-argF)U169 zdg-232::Tn10 uidA::pir+	Platt et al., 2000
P. putida UWC1	plasmid-free derivative ofP. putida KT2440 (Rif)	McClure et al., 1989
UWCGC	Single copy integration of lacI-less P_tac promoter controlling echerry expression (Gm)	Miyazaki and van der Meer, 2011b
ICEclc	ICEclc copy integrated into tRNA^gly-5 (3-CBA)	Miyazaki and van der Meer, 2011b
ICEclc ∆tciR	tciR (orf17162) derivative mutant of ICEclc (3-CBA)	Pradervand et al., 2014
ICEclc ∆bisR	bisR (orf101284) derivative mutant of ICEclc (3-CBA)	This work
ICEclc ∆bisD	bisD (orf98147) derivative mutant of ICEclc (3-CBA)	This work
miniTn7::P_inR-egfp	Single copy chromosomal integration of P_inR promoter fused to egfp (Gm)	This work
miniTn7::P_alpA-egfp	Single copy chromosomal integration of P_alpA promoter fused to egfp (Gm)	This work
miniTn5:: P_bisR-egfp	Single copy chromosomal integration of P_bisR promoter fused to egfp (Kn)	This work
miniTn5:: P_int-echerry/P_inR egfp (C)	Single copy chromosomal integration of a dual reporter P_int and P_inR promoter fused to echerry and egfp, respectively (Kn)	Minoia et al., 2008
miniTn7::P_tac-bisR (A)	Single copy chromosomal integration of P_tac promoter fused to bisR (Gm)	This work
miniTn7::P_tac-echerry	Single copy chromosomal integration of P_tac promoter fused to echerry (Gm)	This work
Plasmids
pME6032	pVS1-p15A shuttle vector carrying the lacI^q-P_tac expression system (Tc)	Heeb et al., 2000
pMEtciR	pME6032 derivative allowing IPTG-controlled expression of tciR (Tc)	This work
pMEbisR	pME6032 derivative allowing IPTG-controlled expression of bisR (Tc)	This work
pMEbisC	pME6032 derivative allowing IPTG-controlled expression of bisC (Tc)	This work
pMEbisD	pME6032 derivative allowing IPTG-controlled expression of bisD (Tc)	Reinhard et al., 2013
pMEbisDC	pME6032 derivative allowing IPTG-controlled expression of bisCD (Tc)	This work
pMEparA	pME6032 derivative allowing IPTG-controlled expression of parA (Tc)	Reinhard et al., 2013
pMEparA-shi-bisD	pME6032 derivative allowing IPTG-controlled expression ofparA, shi and bisD (Tc)	Reinhard et al., 2013
pMEbisC96	pME6032 derivative allowing IPTG-controlled expression of bisC and 96323 (Tc)	This work
pMEalpA	pME6032 derivative allowing IPTG-controlled expression of alpA (Tc)	This work
pMEinrR	pME6032 derivative allowing IPTG-controlled expression of inrR (Tc)	This work
pMEreg	pME6032 derivative allowing IPTG-controlled expression of the alpA-inrR loci (Tc)	This work
pMEreg∆alpA	pME6032 derivative allowing IPTG-controlled expression of the parA-inrR loci (Tc)	This work
pMEreg∆alpA∆P	pMEreg∆alpA derivative lacking 3’ half of 96323, 95213 and inrR (Tc)	This work
pMEreg∆alpA∆A	pMEreg∆alpA derivative lacking the bisC, 96323, 95213 and inrR (Tc)	This work
pMEreg∆P	pMEreg derivative lacking 3’ half of 96323, 95213 and inrR (Tc)	This work
pMEreg∆A	pMEreg derivative lacking the bisC, 96323, 95213 and inrR (Tc)	This work
pMEbg	lacI^q-P_tac-less pME6032 derivative carrying the P_alpA-inrR loci (Tc)	This work
pMEbg_short (comp B)	pMEbg derivative lacking 96323, 95213 and inrR (Tc)	This work
pUX-BF13	helper plasmid for integration of Tn7 (Ap)	Heeb et al., 2000

3-chlorobenzoate (3-CBA); Ampicillin (Ap); gentamycin (Gm); kanamycin (Kn); rifampicin (Rf); tetracycline (Tc).

(A), (B) and (C) refer to components of the reconstituted bistability generator.

For strain numbers, see Supplementary file 1.