plasmids used in this study (10)


elife-27455-v3.xml

10.7554/eLife.27455.032Plasmids used in this study.
PlasmidProductSystemIndResSource
pVS52CheZ-5G-YFPpBAD33aracamSourjik and Berg, 2002a
pVS149CheY-5G-mRFP1pTrc99aIPTGampSourjik and Berg, 2002a
pSJAB12CheZ-5G-YFP/CheY-5G-mRFP1PTrc99aIPTGampThis work
pSJAB106CheZ-5G-YFP/CheY-5G-mRFP1PTrc99aIPTGampThis work
pVS91CheBpTrc99aaracamLiberman et al., 2004
pVS97CheB-D56E pBAD33aracamClausznitzer et al., 2010
pVS112CheBc§ pBAD33aracamV. Sourjik
pSJAB 122CheBc-GS4G-mVenuspBAD33aracamThis work
pSJAB 123CheB(D56E)-GS4G-mVenuspBAD33aracamThis work
pSJAB 124CheB-GS4G-mVenuspBAD33aracamThis work
pZR 1FliC*pKG116NaSalcamThis work
pPA114 TsrTsrpPA114NaSalcamAmes et al., 2002

Contains a A206K mutation to enforce monomerity..

expresses WT CheB.

carries a point mutation D56E in CheB.

§expresses only residues 147–349 of CheB, preceded by a start codon (Met).

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


elife-30015-v2.xml

10.7554/eLife.30015.023Plasmids used in this study.
Plasmid #Plasmid nameDescriptionBacterial selectionReference
8pRS316pRS316, cen, Ura3AmpSikorski and Hieter, 1989
10HA-Fzo1 on pRS316HA-Fzo1 on pRS316, Fzo1 prom, cen, Ura3AmpAnton et al. (2013)
14HA-Fzo1-K464R on pRS316HA-Fzo1K464R on pRS316, Fzo1 prom, cen, Ura3AmpAnton et al. (2013)
58YEplac181YEplac181, 2µ, Leu2AmpGietz and Sugino, 1988
59Ubp2-Flag on YEplac181Ubp2-Flag on YEplac181, Adh1 prom, 2µ, Leu2AmpAnton et al. (2013)
60Ubp2-C745S-Flag on YEplac181Ubp2C745S-Flag on YEplac181, Adh1 prom, 2µ, Leu2AmpAnton et al. (2013)
61Ubp12-Flag on YEplac181Ubp2-Flag on YEplac181, Adh1 prom, 2µ, Leu2AmpAnton et al. (2013)
62Ubp12-C372S-Flag on YEplac181Ubp2C372S-Flag on YEplac181, Adh1 prom, 2µ, Leu2AmpAnton et al. (2013)
63YEplac195YEplac195, 2µ, Ura3AmpGietz and Sugino, 1988
65Ubp12C372S on YEplac195Ubp12C372S (non-tagged) on YEplac195, 2µ, Ura3Ampthis study
70mt-GFP on pYX142mt-GFP on pYX142, cen, Leu2AmpWestermann and Neupert, 2000
75Cdc48 wt on pRS313Cdc48 wt on pRS313, cen, His3AmpEsaki and Ogura (2012)
79pRS313pRS313, cen, His3AmpSikorski and Hieter, 1989
150Cdc48-A547T on pRS313Cdc48A547T on pRS313, cen, His3Ampthis study
341Ub on pKT10Ub on pK10, 2µ, Ura3AmpTanaka et al., 1990
342Ub-K48R on pKT10UbK48R on pK10, 2µ, Ura3AmpTanaka et al., 1990
343Ub-K63R on pKT10UbK63R on pK10, 2µ, Ura3AmpTanaka et al., 1990
344Ub-K48R,K63R on pKT10UbK48R,K63R on pK10, 2µ, Ura3AmpTanaka et al., 1990
356Myc-Ub on pRS426pCup1-Myc-Ub on pRS426, 2µ, Ura3AmpLi et al., 2015
375pRS426pRS426, 2µ, Ura3AmpLi et al., 2015

elife-30205-v1.xml

10.7554/eLife.30205.018Plasmids used in this study.
PlasmidDescriptionSource
pMQ307.5 kb mobilizable vector; oriT, sacB, GmR.Shanks et al. (2006)
pAKN69Contains mini-Tn7(Gm)PA1/04/03::eyfp fusion.Lambertsen et al. (2004)
pLD2722GmR, TetR flanked by Flp recombinase target (FRT) sites to resolve out resistance casettes.this study
pFLP2Site-specific excision vector with cI857-controlled FLP recombinase encoding sequence, sacB, ApR.Hoang et al. (1998)
pLD1852ccoN1 PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain InvSc1.this study
pLD1610ccoN2 PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain InvSc1.this study
pLD1616ccoN3 PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain InvSc1.this study
pLD1264ccoN4 PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain InvSc1.this study
pLD1929cco1 cco2 PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain InvSc1.this study
pLD2791hcn PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain InvSc1.this study
pLD1853Full genomic sequence of ccoN4 PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain InvSc1. Verified by sequencing.this study
pLD1966aa3 PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain IncSc1.this study
pLD1967bo3 PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain IncSc1.this study
pLD2044cio PCR fragment introduced into pMQ30 by gap repair cloning in yeast strain IncSc1.this study
pLD2777PCR-amplified cco1 promoter ligated into pSEK103 using SpeI and XhoI.this study
pLD2778PCR-amplified cco2 promoter ligated into pSEK103 using SpeI and XhoI.this study
pLD2779PCR-amplified ccoN4 promoter ligated into pSEK103 using SpeI and XhoI.this study

elife-31250-v2.xml

10.7554/eLife.31250.023Plasmids used in this study
PlasmidDescriptionSource or reference
YCplac111sc LEU2 cloning vector(Gietz and Sugino, 1988)
YEplac181hc LEU2 cloning vector(Gietz and Sugino, 1988)
YCplac22sc TRP1 cloning vector(Gietz and Sugino, 1988)
p3390/pDSO9sc LEU2 TIF11 in YCplac111(Choi et al., 2000)
p5633sc LEU2 tif11-K3E in YCplac111This study
p5635sc LEU2 tif11-K4D in YCplac111This study
p5638sc LEU2 tif11-T6D in YCplac111This study
p5637sc LEU2 tif11-T6R in YCplac111This study
p5640sc LEU2 tif11-ΔG8 in YCplac111This study
p5642sc LEU2 tif11-R13P in YCplac111This study
p5644sc LEU2 tif11-G15D in YCplac111This study
pDH469sc LEU2 tif11-K7A in YCplac111This study
pDH468sc LEU2 tif11- K7D in YCplac111This study
pDH481sc LEU2 tif11-ΔG8ΔG9 in YCplac111This study
pDH471sc LEU2 tif11-K10A in YCplac111This study
pDH470sc LEU2 tif11-K10D in YCplac111This study
pDH473sc LEU2 tif11-R13A in YCplac111This study
pDH472sc LEU2 tif11-R13D in YCplac111This study
pDH475sc LEU2 tif11-R14A in YCplac111This study
pDH474sc LEU2 tif11-R14D in YCplac111This study
pDH478sc LEU2 tif11-K16A in YCplac111This study
pDH476sc LEU2 tif11-K16D in YCplac111This study
p3400/pDSO23hc LEU2 TIF11 in YEplac181(Choi et al., 2000)
pPMB167hc LEU2 tif11-K4D in YEplac181This study
pPMB168hc LEU2 tif11-ΔG8 in YEplac181This study
pPMB169hc LEU2 tif11-ΔG8ΔG9 in YEplac181This study
pPMB170hc LEU2 tif11- K10D in YEplac181This study
p4281/YCpTIF5-G31R-Wsc TRP1 TIF5-G31R in YCplac22(Valásek et al., 2004)
p4280/YCpSUI3-S264Y-Wsc TRP1 SUI3-S264Y in YCplac22(Valásek et al., 2004)
p367sc URA3 HIS4(ATG)-lacZ(Donahue and Cigan, 1988)
p391sc URA3 HIS4(TTG)-lacZ(Donahue and Cigan, 1988)
p180sc URA3 GCN4-lacZ(Hinnebusch, 1985)
pPMB24sc URA3 SUI1-lacZ(Martin-Marcos et al., 2011)
pPMB25sc URA3 SUI1-opt-lacZ(Martin-Marcos et al., 2011)
pPMB28sc URA3 SUI1UUU-lacZ(Martin-Marcos et al., 2011)
pC3502sc URA3 -3AAA−1 el.uORF1 GCN4-lacZ in YCp50(Visweswaraiah et al., 2015)
pC4466sc URA3 -3UAA−1 el.uORF1 GCN4-lacZ in YCp50(Visweswaraiah et al., 2015)
pC3503sc URA3 -3UUU−1 el.uORF1 GCN4-lacZ in YCp50(Visweswaraiah et al., 2015)
pC3505sc URA3 el.uORF1-less GCN4-lacZ in YCp50(Visweswaraiah et al., 2015)
pTYB2-TIF11TIF11 in pTYB2(Acker et al., 2007)
p6013tif11-R13P in pTYB2This study
p6015tif11-K16D in pTYB2This study
pRaugFFuugDual luciferase reporter LUCren(aug)-LUCfirefly (uug) in URA3 vector(Kolitz et al., 2009)
pRaugFFuugDual luciferase reporter LUCren(aug)-LUCfirefly (uug) in URA3 vector(Kolitz et al., 2009)

elife-31981-v2.xml

10.7554/eLife.31981.016Plasmids used in this study
PlasmidDescriptionReference or source
pFL38CEN-ARS (URA3)(Bonneaud et al., 1991)
pFL36CEN-ARS (LEU2)(Bonneaud et al., 1991)
p416 GAL1CEN-ARS GAL1p (URA3)(Mumberg et al., 1994)
pJOD10p416 GAL1p-GAP1-GFP (URA3)(Nikko et al., 2003)
pCJ038p416 GAL1p -GAP1(K9R,K16R)-GFP (URA3)(Lauwers and André, 2006)
pMA065p416 GAL1p -GAP1-126-GFP (URA3)(Merhi et al., 2011)
pMA091p416 GAL1p -GAP1-126-K9R,K16R-GFP (URA3)(Merhi et al., 2011)
pCH500CEN-ARS-GAP1 (URA3)(Hein and André, 1997)
pHcGAP1YEp-HcGAP1 (URA3)(Wipf et al., 2002)
pES103YEp-HA-NPR1 (LEU2)This study
pAS103YEp-HA-NPR1 (URA3)(Schmidt et al., 1998)
pCJ315CEN-ARS (LEU2-HIS3-LYS2)Lab collection
pMYC008YCp-AGP1p-LACZ (HIS3 TRP1 LEU2)Lab collection
pES154YCp-AGP1p-LACZ (HIS3 TRP1)This study
pHl-UYEp-ADH1p-pHluorin (URA3)(Orij et al., 2009; Zimmermannova et al., 2015)
pHl-IYCp-loxP-kanMX-loxP-GPD1p-pHluorin (URA3)(Orij et al., 2009; Zimmermannova et al., 2015)
pCJ366YEp (TRP1-LEU2-HIS3)Lab collection
pPS15-P1YCp-(Sc)PMA1 (LEU2)(Supply et al., 1993)
pPMA4882ochreYEp-PMA1p-(Np)PMA4882ochre (LEU2)(Luo et al., 1999)

elife-32057-v1.xml

10.7554/eLife.32057.033Plasmids used in this study
PlasmidRelevant genotype/markersSource
pGM074pKASBAR-kan (Bottomley et al., 2014) carrying ezra-psmorange under the putative ezrA promoter (amp, kan)G. McVicker
pSNAP-tag (T7)−2E. coli expression plasmid carrying the snap gene under the control of the T7 promoter (amp)New England Biolabs
pOBpGEM3Zf(+) cloning vector containing the erythromycin resistance cassette (amp, ery)(Horsburgh et al., 2002a)
pAISHTetR derivative of pMUTIN4(Aish, 2003)
pKASBAR-EzrA-eYFPpKASBAR-kan containing ezrA-eyfp under the putative ezrA promoter (amp, kan)This study
pKASBAR-EzrA-meYFPpKASBAR-kan containing ezrA-meyfp under the putative ezrA promoter (amp, kan)This study
pKASBAR-EzrA-GFPpKASBAR-kan containing ezrA-gfp under the putative ezrA promoter (amp, kan)This study
pKASBAR-EzrA-SNAPpKASBAR-kan containing ezrA-snap under the putative ezrA promoter (amp, kan)This study
pOB-ΔezrApOB containing the ezrA deletion cassette consisting of a 1.5 kb fragment of the upstream region of S. aureus ezrA, the tetracycline resistance cassette from pAISH and a 1.5 kb fragment of the downstream region of S. aureus ezrA (amp, ery, tet)This study
pSS26bpUC19 encoding snap (amp)Covalys
pSS26bFtsZ-CpSS26b containing ftsZ-snap (amp)This study
pCQ11E. coli-S. aureus shuttle vector containing lacI, Pspac and gfp (amp, ery)(Hardt et al., 2017)
pCQ11-FtsZ-SNAPpCQ11 derivative containing ftsZ-snap under Pspac (amp, ery)This study
pCQ11-FtsZ-eYFPpCQ11-FtsZ-SNAP with eyfp replacement of snap (amp, ery)This study

elife-35588-v2.xml

10.7554/eLife.35588.026Plasmids used in this study.

Genes are human unless otherwise stated

PlasmidBackboneInsertRef
 APX1-GFP1-10APX1super-folder GFPThis study
 CDV-hyPBasepiggpiggyBAC transposase(Yusa et al., 2011)
 NES-EGFP-P4M × 1pEGFP-C1X.leavis map2k1.L(32-44):EGFP:L. pneumophila SidM(546-647)This study
 FKBP-mCherrypmCherry-N1FKBP1A(isoform a, 3–108):mCherryThis study
 SAC1∆TMD-FKBP-mCherrypmCherry-N1SACM1L(1-521):FKBP1A(3-108):mCherryThis study
 SAC1C389S∆TMD-FKBP-mCherrypmCherry-N1SACM1L(C389S; 1–521):FKBP1A(3-108):mCherryThis study
 iRFP-Sec61βpiRFP-C1iRFP:SEC61BThis study
 mKO-ManIIpmKO-N1Kusabira Orange 2:Man2a(1-102)Tamas Balla
 mCherry-VAPBpmCherry-C1mCherry:VAPBThis study
 mCherry-MAPPERpmCherry-C1mCherry:MAPPER(Chang et al., 2013)
 EGFP-MAPPERpEGFP-C1EGFP:MAPPER(Chang et al., 2013)
 GFP-ORP5pEGFP-C1EGFP:OSBPL5(isoform a)(Sohn et al., 2016)
 GFP-E-Syt2pEGFP-C1EGFP:ESYT2(Giordano et al., 2013) Addgene plasmid #66831
 EGFP-SAC1pEGFP-C1EGFP:SACM1L(Sohn et al., 2016)
 mEmerald-N16-CalreticulinpmEmerald-N1mEmerald:CALRMichael Davidson (Addgene plasmid #54023)
 GFP-Sec61βpAcGFP-C1-Sec61βAequorea coerulescens GFP:SEC61B(Voeltz et al., 2006) Addgene plasmid #15108
 EGFP-E-Syt1pEGFP-C1EGFP-ESYT1(Giordano et al., 2013) Addgene plasmid #66830
 EGFP-STIM1pEGFP-C1STIM1(isoform 1 1–22):EGFP:STIM1(23–791)(Várnai et al., 2007)
 EGFP-Nir2pEGFP-N1EGFP:PITPNM1(isoform 2)(Kim et al., 2015)
 EGFP-P4M × 2pEGFP-C1EGFP:L. pneumophila SidM(546-647):SidM(546-647)(Hammond et al., 2014)
 Lyn11-FRB-iRFPpiRFP-N1LYN(1-11):MTOR(2021–2113):iRFP(Hammond et al., 2014)
 mCherry-FKBPpmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG(Hammond et al., 2014)
 mCherry-FKBP-SAC1pmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG:SACM1LThis study
 mCherry-FKBP-SAC1C389SpmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG:SACM1LC389SThis study
 mCherry-SAC1-FKBPpmCherry-C1mCherry:SACM1L:FKBP1A(3-108)This study
 mCherry-SAC1C389S-FKBPpmCherry-C1mCherry:SACM1LC389S:FKBP(3-108)This study
 SAC1∆452-587-FKBP-mCherrypmCherry-N1SACM1L(1-451):FKBP1A(3-108):mCherryThis study
 mCherry-FKBP-SAC1∆TMDpmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG:SACM1L(1-521)This study
 mCherry-FKBP-SAC1-HLx2pmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG::SACM1L(1-520):[EAAAR]2:SACM1L(521-587)This study
 mCherry-FKBP-SAC1-HLx4pmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG::SACM1L(1-520):[EAAAR]4:SACM1L(521-587)This study
 mCherry-FKBP-SAC1-HLx6pmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG:SACM1L(1-520):[EAAAR]6:SACM1L(521-587)This study
 mCherry-FKBP-SAC1-HLx8pmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG:SACM1L(1-520):[EAAAR]8:SACM1L(521-587)This study
 mCherry-FKBP-SAC1-HLx10pmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG:SACM1L(1-520):[EAAAR]10:SACM1L(521-587)This study
 mCherry-FKBP-SAC1C389S-HLx8pmCherry-C1mCherry:FKBP1A(3-108):[GGSA]4GG:SACM1LC389S(1-520):[EAAAR]8:SACM1L(521-587)This study
 mCherrypmCherry-C1mCherry(Hammond et al., 2014)
 mCherry-SAC1pmCherry-C1mCherry:SAC1ML(Sohn et al., 2016)
 mCherry-SAC1-HLx8pmCherry-C1mCherryLSACM1L(1-520):[EAAAR]8:SACM1L(521-587)This study
 mCherry-SAC1C389S-HLx8pmCherry-C1mCherry:SACM1LC389S(1-520):[EAAAR]8:SACM1L(521-587)This study
 mTagBFP2-FKBP-CYB5AtailpmTagBFP2-C1mTagBFP2:FKBP1A(3-108):[GGSA]4GG:CYB5A(100-134)This study

elife-43826-v1.xml

10.7554/eLife.43826.020Plasmids used in this study.
NameDescriptionVector-PromoterAddgene
 P1HA-β2AR-NNES-NanoLuc-15aa linker-AsLOV2(V416L)pAAV-CMV125224
 P2gLuc sp-NanoLuc-HA-β2AR-NNES-AsLOV2(V416L)pAAV-CMV125225
 P3mCherry-GSGS linker-Zdk1pAAV-CMV125226
 P4DRD1-NNES-eLOV-TEVcs-Flag-Gal4-V5pAAV-CMV125227
 P5AVPR2-NNES-eLOV-TEVcs-Flag-Gal4-V5pAAV-CMV104844
 P6β2AR-NNES-eLOV-TEVcs-Flag-Gal4-V5pAAV-CMV104841
 P7NanoLuc-15aa linker-βarrestin2-HA-GS linker-TEVppAAV-CMV125228
 P8UAS-CitrinepAAV-UAS104839
 P9βarrestin2-HA-GS linker-TEVppAAV-CMV104845
 P10UAS-FLucpAAV-UAS104840
 P11IgK sp-HA-CD4-10aa linker-CIBN-NNES-NanoLucpAAV-CMV125229
 P12gLuc sp-NanoLuc-HA-oβ2AR-TS-eLOV-TEVcs-Flag-Gal4pLX208-CMV125230
 P13NanoLuc-15aa linker-βarrestin2-HA-GS linker-TEVppLX208-CMV125231
 P14UAS-CitrinepFPGW-UAS125232
 P15gLuc sp-NanoLuc-15aa linker-ICAM-Nrxn3b-HApLX208-CMV125233
 P16gLuc sp-GS linker-HiBit-Flag-oβ2AR-TS-NNES-eLOV-TEVcs-Flag-Gal4-V5pAAV-CMV125234
 P17NanoLuc-15aa linker-βarrestin2-no HA-GS linker-TEVppAAV-CMV125235
 P18β2AR-NNES-NanoLuc-eLOV-TEVcs-Flag-Gal4-V5pAAV-CMV125236

elife-48215-v2.xml

10.7554/eLife.48215.013Plasmids used in this study.
Plasmid numberGenotypeReference
pSMH145pLIC-Tra His6-TEV-Ctf3; His6-TEV-Mcm16; His6-TEV-Mcm22(Hinshaw et al., 2017)
pSMH1269pFA6a-CTF3-6Gly-3FLAG-KanMX6 (BsiWI/SalI)This study
pSMH1577pFA6a-ctf3-SDD-6Gly-3FLAG-KanMX6 (BsiWI/SalI)This study

elife-56582-v2.xml

Plasmids used in this study.
Protein complexPlasmid nameNames used in this paperProteins expressed*VectorReferences
Mif2Sc_Mf_7Mif2Mif2-linker-(27-392)MBP-6XHis**pLICThis study
pGH52Mif2Mif2-linker-(27-392)MBP**pLICThis study
Sc_Mf_5BΔN-Mif2(41-549)Mif2-linker-(27-392)MBPpLICThis study
OApGH3OAAme1-6XHis, Okp1pST39This study
pGH4OAAme1-FLAG, Okp1pST39This study
pGH42ΔN-OA(21-324)Ame1-FLAG, Okp1pST39This study
pGH15ΔN-OA(21-324)Ame1-6XHis, Okp1pST39This study
MINDpGH632D-MIND6XHis-linker-Nsl1, S240D, S250D-Dsn1, Mtw1, Nnf1pST39This study
pGH622D-MINDFLAG-Nsl1, S240D, S250D-Dsn1, Mtw1, Nnf1pST39This study
pGH46MINDNsl1, FLAG-Dsn1, Mtw1, Nnf1pST39This study
Ndc80cpJT048Part of Ndc80cSpc24-Flag, Spc25pRSFDuetKudalkar et al., 2015
pEM033Part of Ndc80cSpc24-6XHis, Spc25pRSFDuetScarborough et al., 2019
Ndc80/Nuf2Part of Ndc80cNuf2, Ndc80pETDuetWei et al., 2005
Dam1cpJT044Dam1cDad1, Duo1, Spc34-FLAG, Dam1, Hsk3 and Dad4, Dad3, Dad2, Spc19, Ask1pST39Umbreit et al., 2014
CIpGH58CIFLAG-Chl4, Iml3pLICThis study
HistonespScKl2Cse4-NCPK.lactis 6XHis-H2A, K. lactis 6XHis-H2B, Cse4, K. lactis 6XHis-H4pLICMigl et al., 2020
pScKl4H3-NCPH3, 6XHis-H2A, H2B. K.lactis 6XHis-H4pLICMigl et al., 2020
pScHT4Cse4(1-50)6XHis-MBP-(1-50)Cse4pLICThis study