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. Author manuscript; available in PMC: 2018 Oct 19.
Published in final edited form as: Cell Rep. 2018 Sep 11;24(11):3061–3071.e6. doi: 10.1016/j.celrep.2018.08.023
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit polyclonal anti-PhoB serum This study RRID: AB_2722768
Cy5 Goat anti-rabbit IgG (H+L) ThermoFisher Cat# A10523; Lot #1512070; RRID: AB_2534032
Bacterial and Virus Strains
E. coli DH5a [general cloning strain] ThermoFisher Cat# 18265017
E. coli GM2929 [dam− dcm−, cloning strain] CGSC, Yale University CGSC# 7080
E. coli BW25113 [wild type] Datsenko and Wanner, 2000 N/A
E. coli BW25141 [pir DphoBR580, cloning strain for CRIM integration plasmids] Haldimann and Wanner, 2001 N/A
E. coli RU1616 [LAC, Φ(DphoBp Plac-phoBR) in BW25113] Gao and Stock, 2013b N/A
E. coli RU1621 [ΔphoBR in BW25113 derivative] Gao and Stock, 2013b N/A
E. coli RU1646 [ΔrpoS::kan in BW25113] Gao et al., 2017 N/A
E. coli RU1783 [TRC*, F(ΔphoBp Ptrc-phoBR) attl::pRG378(lacIq)] Gao and Stock, 2015 N/A
E. coli RU1878 [PphoB-phoBR, attHK::pRG390 in RU1621] This paper N/A
E. coli RU1879 [PphoB-rp2-phoBR, attHK::pRG391 in RU1621] This paper N/A
E. coli RU1880 [PphoB-rp2-dn-phoBR, attHK::pRG393 in RU1621] This paper N/A
E. coli RU1881 [PphnC-phoBR, attHK::pRG396 in RU1621] This paper N/A
Chemicals, Peptides, and Recombinant Proteins
Phos-tag Acrylamide AAL-107 Wako Chemicals Cat# 304–93521
E. coli PhoB protein Gao and Stock, 2015 N/A
Oligonucleotides
RG278-f: TCTGACACATAATGACGTCGCA This paper RG278-f
RG279-r: TGCGACGTCATTATGTGTCAGA This paper RG279-r
RG280-f: ATCTGTTCCATAATGTGCTCGCATTA This paper RG280-f
RG281-r: TAATGCGAGCACATTATGGAACAGAT This paper RG281-r
RG282-f: TCTGTTCCATAATGACGTCGCATTA This paper RG282-f
RG283-r: TGCGACGTCATTATGGAACAGATTTATGAC This paper RG283-r
RG293-r:TTGCGATCATTAATGCGAGCACATNATN GAACAGAT This paper RG293-r
RG294-f: GTGCTCGCATTAATGATCGCAACC This paper RG294-f
RG322-f: TGACCACCCTGGCCTCGGCCGTGCAGT GCTTCA-3 This paper RG322-f
RG323-r: AGCACTGCACGGCCGAGGCCAGGGTG GTCACGA This paper RG323-r
Recombinant DNA
pAH144 [CRIM plasmid for integration at attHK site, Spr] Haldimann and Wanner, 2001 pAH144
pRG22 [Multi-cloning site (MCS) in a p15A orgin plasmid, Cmr] Mack et al., 2009 pRG22
pJZG146 [rrnB-MCS-mYFP, Spr] Gao and Stock, 2013a pJZG146
pRG161 [PphoA-mYFP in pJZG146, Spr] Gao and Stock, 2013a pRG161
pJZG202 [PphoB-mYFP in pJZG146, Spr] Gao and Stock, 2015 pJZG202
pRG162 [PphnC-mYFPin pJZG146, Spr] Gao and Stock, 2015 pRG162
pRG252 [Ptet promoter, Ap r] Gao and Stock, 2013a pRG252
pRG367 [PphoB-rp-hi-mYFP in pJZG146, Spr] This paper pRG367
pRG368 [PphoB-rp2-mYFP in pJZG146, Spr] This paper pRG368
pRG369 [PphoB-rp1-mYFP in pJZG146, Spr] This paper pRG369
pRG387 [PphoB-rp2-dn-mYFP in pJZG146, Spr] This paper pRG387
pRG390 [PphoB-phoBR in pAH144, Spr] This paper pRG390
pRG391 [PphoB-rp2-phoBR in pAH144, Spr] This paper pRG391
pRG393 [PphoB-rp2-dn-phoBR in pAH144, Spr] This paper pRG393
pRG396 [PphnC-phoBR in pAH144, Spr] This paper pRG396
pRG411 [Ptet-CFP in pRG22, Cmr] This paper pRG411
pRG426 [Ptet-CFP(T65A W66S G67A) in pRG22, Cmr] This paper pRG426
phoB promoter DNA [for EMSA] This paper N/A
phnC promoter DNA [for EMSA] This paper N/A
Software and Algorithms
MATLAB R2009a MathWorks https://www.mathworks.com/
OriginPro 8 OriginLab https://www.originlab.com/
FIMO tool (MEME suite) Bailey et al., 2009 http://meme-suite.org/tools/fimo
RSAT tool Medina-Rivera et al., 2015 http://embnet.ccg.unam.mx/rsat/
ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/
Thresholding algorithm for colony counting This paper N/A