strains used in this study (7)

elife-27455-v3.xml

10.7554/eLife.27455.031

Table 2.Strains used in this study.

Background			Plasmids
Strain	Source	Relevant genotype	Plasmid 1	Plasmid 2
VS115	V. Sourjik	ΔYZ ΔFliC	pSJAB106	pZR1
VS104	Sourjik and Berg, 2002a	ΔCheYZ	pSJAB12	pBAD33
TSS58	this work	ΔRBYZ ΔFliC	pSJAB106	pZR1
VS149	Sourjik and Berg, 2004	ΔRBYZ	pVS12	pVS33
VS124	Clausznitzer et al., 2010	ΔCheBYZ	pSJAB12	pVS112
VS124		ΔCheBYZ	pSJAB12	pVS97
VS124		ΔCheBYZ	pSJAB12	pVS91
UU2567	Kitanovic et al., 2015	ΔCheRBYZ,ΔMCP^†	pSJAB106	pPA114 Tsr
TSS1964	this work	ΔCheRBYZ,ΔMCP FliC*	pSJAB106	pPA114 Tsr
UU2614	J.S. Parkinson	CheB Δ(4-345)	pTrc99a	pVS91,97,112

All strains are descendants of E. coli K-12 HCB33 (RP437). In all FRET experiments, strains carry two plasmids and therefore confer resistance to chloramphenicol and ampicillin.

^†all five chemoreceptor genes tar tsr tap trg aer deleted.

*expresses sticky FliC filament (Scharf et al., 1998)

elife-30205-v1.xml

10.7554/eLife.30205.016

Table 1.Strains used in this study.

Strain	Number	Description	Source
Pseudomonas aeruginosa strains
UCBPP-PA14		Clinical isolate UCBPP-PA14.	Rahme et al. (1995)
PA14 ∆phz	LD24	PA14 with deletions in phzA1-G1 and phzA2-G2 operons.	Dietrich et al., 2006a
PA14 ∆ccoN1	LD1784	PA14 with deletion in PA14_44370.	this study
PA14 ∆ccoN2	LD1614	PA14 with deletion in PA14_44340.	this study
PA14 ∆ccoN3	LD1620	PA14 with deletion in PA14_40510.	this study
PA14 ∆ccoN4	LD2833	PA14 with deletion in PA14_10500.	this study
PA14 ∆ccoN1 ∆ccoN2	LD1888	PA14 with deletions in PA14_44370 and PA14_44340. Made by mating pLD1610 into LD1784.	this study
PA14 ∆ccoN1 ∆ccoN4	LD1951	PA14 with deletions in PA14_44370 and PA14_10500. Made by mating pLD1264 into LD1784.	this study
PA14 ∆ccoN2 ∆ccoN4	LD1692	PA14 with deletions in PA14_44340 and PA14_10500. Made by mating pLD1264 into LD1614.	this study
PA14 ∆ccoN3 ∆ccoN4	LD1649	PA14 with deletions in PA14_40510 and PA14_10500. Made by mating pLD1264 into LD1620.	this study
PA14 ∆ccoN1 ∆ccoN2 ∆ccoN3	LD1977	PA14 with deletions in PA14_443470, PA14_44340, and PA14_40510. Made by mating pLD1616 into LD1888.	this study
PA14 ∆ccoN1 ∆ccoN2 ∆ccoN4	LD1976	PA14 with deletions in PA14_443470, PA14_44340, and PA14_10500. Made by mating pLD1264 into LD1888.	this study
PA14 ∆ccoN1 ∆ccoN2 ∆ccoN4 ∆ccoN3	LD2020	PA14 with deletions in PA14_443470, PA14_44340, PA14_10500, and PA14_40510. Made by mating pLD1264 into LD1977.	this study
PA14 ∆cco1cco2	LD1933	PA14 with both cco operons (PA14_44340-PA14_44400) deleted simultaneously.	this study
PA14 ∆cox ∆cyo ∆cio	LD2587	PA14 with deletions in PA14_01290–01320 (cox/aa3 operon), PA14_47150–47210 (cyo/bo3 operon), and PA14_13030–13040 (cio operon). Made by mating pLD1966, pLD1967, and pLD2044, in that order, to PA14.	this study
PA14 ∆hcn	LD2827	PA14 with deletion in hcnABC operon (PA14_36310–36330).	this study
PA14 ∆phz ∆hcn	LD2828	PA14 with deletions in phzA1-G1, phzA2-G2, and hcnABC operons. Made by mating pLD2791 into LD24.	this study
PA14 ∆ccoN4 ∆hcn	LD2829	PA14 with deletions in PA14_10500 and hcnABC operon. Made by mating pLD2791 into LD2833.	this study
PA14 ∆ccoN1 ∆ccoN2 ∆hcn	LD2830	PA14 with deletions in PA14_44370, PA14_44340, and hcnABC operon. Made by mating pLD2791 into LD1888.	this study
PA14 ∆ccoN1 ∆ccoN2 ∆ccoN4 ∆hcn	LD2831	PA14 with deletions in PA14_44370, PA14_44340, PA14_10500 and hcnABC operon. Made by mating pLD2791 into LD1976.	this study
Pseudomonas aeruginosa strains
PA14 ∆cco1cco2 ∆hcn	LD2832	PA14 with deletions in cco1, cco2, and hcnABC operons. Made by mating pLD2791 into LD1933.	this study
PA14 gacA::Tn	LD1560	MAR2xT7 transposon insertion into PA14_30650.	Liberati et al. (2006)
PA14 ∆ccoN4::ccoN4	LD1867	PA14 ∆ccoN4 strain with wild-type ccoN4 complemented back into the site of deletion. Made by mating pLD1853 into LD2833.	this study
PA14 ∆ccoN1 ∆ccoN2 ∆ccoN4::ccoN4	LD2576	PA14 ∆ccoN1 ∆ccoN2 ∆ccoN4 strain with wild-type ccoN4 complemented back into the site of deletion. Made by mating pLD1853 into LD1976.	this study
PA14 MCS-gfp	LD2820	PA14 without a promoter driving gfp expression.	this study
PA14 Pcco-1-gfp	LD2784	PA14 with promoter of cco1 operon driving gfp expression.	this study
PA14 Pcco-2-gfp	LD2786	PA14 with promoter of cco2 operon driving gfp expression.	this study
PA14 PccoN4-gfp	LD2788	PA14 with promoter of ccoN4Q4 operon driving gfp expression.	this study
PA14-yfp	LD2780	WT PA14 constitutively expressing eyfp.	this study
PA14 ∆ccoN1 ∆ccoN2-yfp	LD2013	PA14 ∆ccoN1 ∆ccoN2 constitutively expressing eyfp. Made by mating pAKN69 into LD1888.	this study
PA14 ∆ccoN4-yfp	LD2834	PA14 ∆ccoN4 constitutively expressing eyfp. Made by mating pAKN69 into LD2833.	this study
PA14 ∆ccoN1 ∆ccoN2 ∆ccoN4-yfp	LD2136	PA14 ∆ccoN1 ∆ccoN2 ∆ccoN4 constitutively expressing eyfp. Made by mating pAKN69 into LD1976.	this study
PA14 ∆cco1cco2-yfp	LD2012	PA14 ∆cco1cco2 constitutively expressing eyfp. Made by mating pAKN69 into LD1933.	this study
Escherichia coli strains
UQ950	LD44	E. coli DH5 λpir strain for cloning. F-∆(argF- lac) 169φ80 dlacZ58(∆M15) glnV44(AS) rfbD1 gyrA96(NaIR) recA1 endA1 spoT thi-1 hsdR17 deoR λpir+	D. Lies, Caltech
BW29427	LD661	Donor strain for conjugation. thrB1004 pro thi rpsL hsdS lacZ ∆M15RP4-1360 ∆(araBAD)567 ∆dapA1314::[erm pir(wt)]	W. Metcalf, University of Illinois
β2155	LD69	Helper strain. thrB1004 pro thi strA hsdsS lacZ∆M15 (F’lacZ∆M15 lacIq traD36 proA + proB + ) ∆dapA::erm (Ermr)pir::RP4 [::kan (Kmr) from SM10]	Dehio and Meyer (1997)
S17-1	LD2901	StrR, TpR, F− RP4-2-Tc::Mu aphA::Tn7 recA λpir lysogen	Simon et al. (1983)
Saccharomyces cerevisiae strains
InvSc1	LD676	MATa/MATalpha leu2/leu2 trp1-289/trp1-289 ura3−52/ura3-52 his3-∆1/his3-∆1	Invitrogen

elife-32057-v1.xml

10.7554/eLife.32057.032

Appendix 1—table 1.Strains used in this study.

Strain	Relevant Genotype/markers	Source
SH1000	Functional rsbU⁺ derivative of 8325–4	(Horsburgh et al., 2002b)
RN4220	Restriction deficient transformation recipient	(Kreiswirth et al., 1983)
CYL316	S. aureus RN4220 pCL112Δ19 (cm)	(Lee et al., 1991)
JGL227	S. aureus SH1000 ezrA-gfp+ (ery)	(Steele et al., 2011)
SH4386	S. aureus SH1000 ezrA-eyfp (kan)	This study
SH4388	S. aureus SH1000 ezrA-eyfp ΔezrA (kan, tet)	This study
SH4603	S. aureus SH1000 ezrA-meyfp (kan)	This study
SH4604	S. aureus SH1000 ezrA-meyfp ΔezrA (kan, tet)	This study
SH4639	S. aureus SH1000 ezrA-gfp (kan)	This study
SH4640	S. aureus SH1000 ezrA-gfp ΔezrA (kan, tet)	This study
SH4641	S. aureus SH1000 ezrA-snap (kan)	This study
SH4642	S. aureus SH1000 ezrA-snap ΔezrA (kan, tet)	This study
SH4652	S. aureus SH1000 ezrA-eyfp ΔezrA pCQ11-FtsZ-SNAP (kan, tet, ery)	This study
SH4665	S. aureus SH1000 pCQ11-FtsZ-eYFP (ery)	This study
NE679	S. aureus JE2 with transposon insertion in pbp4 (ery)	(Fey et al., 2013)
SH4425	S. aureus SH1000 pbp4 (ery)	This study
N315	Methicillin-resistant S. aureus	(Kuroda et al., 2001)
SU492	B. subtilis SU5 P_xyl-ftsZ-yfp (spec)	(Monahan et al., 2014)

elife-34878-v1.xml

10.7554/eLife.34878.007

Table 1.Strains used in this study.

Strain Abbreviation*	Ancestor (source)^†	Genotype	# UAG Codons^‡	RF1 Status^§	Ribosomal rescue gene deletion	ssrA tag Status^#	Investigated in
GRO.DD.prfA+	GRO.AA (this study)	ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla]	0	+RF1	n/a	DD	GFP expression for mass spectrometry (Figure 2)
GRO.DD	GRO.AA (this study)	ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC	0	∆RF1	n/a	DD	GFP expression for mass spectrometry (Figure 2)
ECNR2.AA	E. coli MG1655 (Wang et al., 2009)	MG1655 ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla]	321	+RF1	n/a	AA	Fitness, conjugation, and viral infection (Figures 3 and 4)
GRO.AA	ECNR2.AA (Lajoie et al., 2013b)	ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC	0	∆RF1	n/a	AA	Fitness, conjugation, and viral infection (Figures 3 and 4)
GRO.AA.∆ssrA	GRO.AA (this study)	ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC	0	∆RF1	∆ssrA	AA	Fitness, conjugation, and viral infection (Figures 3 and 4)
GRO.AA.∆arfA	GRO.AA (this study)	ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC	0	∆RF1	∆arfA	AA	Fitness, conjugation, and viral infection (Figures 3 and 4)
GRO.AA.∆arfB	GRO.AA (this study)	ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC	0	∆RF1	∆arfB	AA	Fitness, conjugation, and viral infection (Figures 3 and 4)
GRO.AA.∆ssrA.∆arfB	GRO.AA (this study)	ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC	0	∆RF1	∆ssrA, ∆arfB	AA	Fitness, conjugation, and viral infection (Figures 3 and 4)
GRO.AA.∆arfA. ∆arfB	GRO.AA (this study)	ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC	0	∆RF1	∆arfA, ∆arfB	AA	Fitness, conjugation, and viral infection (Figures 3 and 4)

*All strains derived from ECNR2, as described in Wang et al. (2009).

†See Key Resources Table for additional information on strains and sources. The GenBank accession number for E. coli MG1655 is U00096, and the GenBank accession number for GRO.AA is CP006698.

‡ Out of a total of 321 in the original ECNR2 strain.

§RF1 terminates translation at UAG and UAA. Deletion of RF1 eliminates recognition of UAG during translation; translational termination continues through RF2, which recognizes UAA and UGA.

#The ssrA gene encodes the tmRNA, which appends the ssrA degradation tag to stalled ribosomes. The wild-type sequence is AANDENYALAA; mutation of the C-terminus to AANDENYALDD slows degradation of peptides to enable detection by mass spectrometry.

elife-48508-v2.xml

10.7554/eLife.48508.027

Table 1.Strains used in this study.

‘Aggregation’ was determined as ‘yes’ if the majority of cells (>~50%) were observed in clusters of more than five individual cells, and ‘no’ otherwise. Survival level was estimated as follows: ‘low’: almost no survival (<3% of cells); ‘medium’: survival of 3% to 50% of the cells; ‘high’:>50% of all cells survived.

Genus	Species	Strain	Gram +/-	Major habitat	Aggregation	Survival at 24 hr	Gifted from
Pseudomonas	syringae	B728a	-	phyllosphere	No	low	S. Lindow
Pseudomonas	syringae	DC3000	-	phyllosphere	No	low	O. Bahar
Pseudomonas	fluorescens	A506	-	phyllosphere	Yes	medium	S. Lindow
Pseudomonas	fluorescens	NT133	-	rhizosphere	Yes	low	D. Minz
Pseudomonas	putida	KT2440	-	soil	Yes	medium	Purchased from ATCC
Pseudomonas	putida	KT2442	-	soil	Yes	medium	Y. Friedman
Pseudomonas	putida	IsoF101	-	soil	Yes	medium	L. Eberl
Pseudomonas	citronellolis	13674 (ATCC)	-	soil	Yes	low	Y. Friedman
Pseudomonas	aurantiaca	33663 (ATCC)	-	soil	Yes	medium	Y. Friedman
Pseudomonas	veronii	700474 (ATCC)	-	water	Yes	high	Y. Friedman
Pantoea	agglomerans	299 r	-	phyllosphere	No	low	S. Lindow
Pantoea	agglomerans	BRT98	-	soil	Yes	high	Z. Cardon
Escherichia	coli	K-12 MG1655	-	human gut	No	medium	Y. Helman
Xanthomoas	campestris	85–10	-	phyllosphere	No	low	G. Sessa
Burkholderia	cenocepacia	H111	-	human	Yes	low	Y. Helman
Acidovorax	citrulli	M6	-	phyllosphere	No	low	S. Burdman
Bacillus	subtilis	3610	+	soil	No	low	Y. Helman
Clavibacter	michiganensis		+	soil	Yes	low	S. Burdman

elife-50749-v1.xml

Table 4.Strains used in this study.

DDY2733*	MATa his3-∆200 leu2-3, 112 lys2-801 ura3-52 ABP1-GFP::HIS3
DDY2734*	MATa his3-∆200 leu2-3, 112 lys2-801 ura3-52 SLA1-GFP::HIS3
DDY2735*	MATα his3-∆200 leu2-3, 112 lys2-801 ura3-52 PAN1-GFP::HIS3
DDY2795*	MATa his3-∆200 leu2-3, 112 lys2-801 ura3-52 SLA2-GFP::HIS3
DDY2736*	MATa his3-∆200 leu2-3, 112 lys2-801 ura3-52 LAS17-GFP::HIS3
DDY3201*	MATa his3-∆200 leu2-3, 112 lys2-801 ura3-52 VRP1-GFP::HIS3
DDY2752*	MATα his3-∆200 leu2-3, 112 lys2-801 ura3-52 ARC15-GFP::HIS3
DDY2960*	MATα his3-∆200 leu2-3, 112 lys2-801 ura3-52 SAC6-GFP::HIS3
YSY4303	MATα his3-∆200 leu2-3, 112 lys2-801 ura3-52 LAS17-sfGFP::HIS3
YSY4305	MATα his3-∆200 leu2-3, 112 lys2-801 ura3-52 MYO5-sfGFP::HIS3
YSY4307	MATα his3-∆200 leu2-3, 112 lys2-801 ura3-52 SLA1-sfGFP::HIS3
YSY4315	MATα his3-∆200 leu2-3, 112 lys2-801 ura3-52 CSE4-sfGFP::HIS3
YSY4218	MATα his3-∆200 leu2-3, 112 lys2-801 ura3-52 MYO3-GFP::HIS3
YSY4299	MAT a his3-∆200 leu2-3, 112 lys2-801 ura3-52 MYO3-GFP::HIS, ABP1-RFP::HygMX
YSY4300	MAT α his3-∆200 leu2-3, 112 lys2-801 ura3-52 MYO5-GFP::HIS, ABP1-RFP::HygMX
YSY4125	MAT a his3-∆200 leu2-3, 112 lys2-801 ura3-52 GFP-LAS17::KanMX6, ABP1-RFP::HygMX
YSY4126	MAT α his3-∆200 leu2-3, 112 lys2-801 ura3-52 GFP-LAS17::KanMX6, MYO5-RFP::HIS
YSY4291	MAT α his3-∆200 leu2-3, 112 lys2-801 ura3-52 Myo5-GFP::KanMX6, MYO3-GFP::HIS
YSY4120	MAT α his3-∆200 leu2-3, 112 lys2-801 ura3-52 GFP-LAS17::KanMX6
YSY4257	h+ leu1-32 ura4-D18 his3-D1 ade6-M210 pan1-mEGFP-kanMX6 fim1mcherry-natRMX6
YSY4266	h- or h+ leu1-32 ura4-D18 his3-D1 ade6 kanMX6- Pwsp1-mEGFP-wsp1 fim1mcherry-natRMX6
YSY4269	h- or h+ leu1-32 ura4-D18 his3-D1 ade6 kanMX6- Pmyo1-mEGFP-myo1 fim1mcherry-natRMX6
YSY4335	h+ leu1-32 ura4-D18 his3-D1 ade6-M210 fim1mcherry-natRMX6 wsp1-CA∆-GFP-kanMX6
YSY4345	h- or h+ leu1-32 ura4-D18 his3-D1 ade6-M210 myo1-ca∆-GFP-kanMX6 fim1-mcherry-natRMX6
YSY4346	h- leu1-32 ura4-D18 his3-D1 ade6-M210 fim1mcherry-natRMX6, hob1-GFP-kanMX6
YSY4346	h+ leu1-32 ura4-D18 his3-D1 ade6-M210 hob1-GFP-kanMX6
TP401**	h+ leu1-32 ura4-D18 his3-D1 ade6-M210 pan1-mEGFP-kanMX6
TP398**	h+ leu1-32 ura4-D18 his3-D1 ade6-M210 end4-mEGFP-kanMX6
TP203**	h- leu1-32 ura4-D18 his3-D1 ade6-M210 kanMX6- Pwsp1-mEGFP-wsp1
TP186**	h- or h+ leu1-32 ura4-D18 his3-D1 ade6-M210 vrp1-EGFP-kanMX6
TP198**	h- leu1-32 ura4-D18 his3-D1 ade6-M210 kanMX6-myo1-mEGFP
TP226**	h- leu1-32 ura4-D18 his3-D1 ade6-M210 arpc5-mEGFP-kanMX6
TP347**	h- leu1-32 ura4-D18 ade6-M210 fim1-mEGFP-kanMX
*	from Kaksonen et al. (2003) or Sun et al. (2006)
**	from Sirotkin et al. (2005) or Wu and Pollard (2005)
otherwise	This study

elife-52482-v2.xml

Table 2.Strains used in this study.

Strain	Genotype/description	Construction	Reference
LSH100	Wild-type: mouse-adapted G27 derivative	-	Lowenthal et al., 2009
LSH141 (Δcsd2)	LSH100 csd2::cat	-	Sycuro et al., 2010
TSH17 (Δcsd6)	LSH100 csd6::cat	-	Sycuro et al., 2013
LSH108	LSH100 rdxA::aphA3sacB	-	Sycuro et al., 2010
HMJ_Ec_pLC292-KU	E. coli TOP10 pLC292-KU	Transformation of TOP10 with pLC292-KU	This study
HJH1	LSH100 rdxA::amgKmurU	Integration of pLC292-KU into LSH108	This study
IM4	LSH100 mcGee:mreB	Integration of pIM04into LSH100	This study
JTH3	LSH100 ccmA:2X-FLAG:aphA3	-	Blair et al., 2018
JTH5	LSH100 ccmA:2X-FLAG:aphA3 rdxA::amgKmurU	Natural transformation of HJH1 with JTH3 genomic DNA	This study
KGH10	NSH57 ccmA::catsacB	-	Sycuro et al., 2010
LSH117	LSH100 ccmA::catsacB	Natural transformation of LSH100 with KGH10 genomic DNA	This study
SSH1	LSH100 ccmA^I55A	Natural transformation with ccmA I55A PCR product	This study
SSH2	LSH100 ccmA^L110S	Natural transformation with ccmA L110S PCR product	This study
LSH142 (ΔccmA)	LSH100 ccmA::cat	-	Sycuro et al., 2010
JTH6	LSH100 rdxA::amgKmurU ccmA::cat	Natural transformation of HJH1 with LSH142 genomic DNA	This study