2

Supplementary Table 1. Bacterial strains.

Strain / Genotypea / Pedigreeb / Sourcec
BW25113 / rrnB3 ΔlacZ4787 hsdR514 ΔaraBAD567 ΔrhaBAD568 rph-1 / BD792 via BW25083 / (Haldimann and Wanner, 2001)
BW25141 / rrnB3 ΔlacZ4787 ΔphoBR580 hsdR514 ΔaraBAD567 ΔrhaBAD568 galU95 ΔendA9 ΔuidA3::pir+ rph-1 recA1 / BD792 via BW25140 / (Haldimann and Wanner, 2001)
BW32395 / rph+ lacZ4788 lacZp4105(UV5)-lacY
/ MG1655via BW30270 / Datsenko and Wanner., unpublished
BW35696 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ)d / BD792 via BW32395 / Integration of pSJ143
BW36522d / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) cvpA101::Ez-Tn5 / BD792 via BW35696 / Ez-Tn5TM mutagenesis
BW37265 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔcvpA724::kan / BD792 via BW35696 / KmR with P1kc on Keio 63F4
(Baba et al., 2006)
BW37266 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurF723::kan / BD792 via BW35696 / KmR with P1kc on Keio 53B4
BW37275 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔubiX732::kan / BD792 via BW35696 / KmR with P1kc on Keio 43E6
BW37550 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurD776::kan / BD792 via BW35696 / KmR with P1kc on Keio 53C6
BW37543 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurT774::kan / BD792 via BW35696 / KmR with P1kc on Keio 53B3
BW37549 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurN748::kan / BD792 via BW35696 / KmR with P1kc on Keio 53F4
BW37542 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurU741::kan / BD792 via BW35696 / KmR with P1kc on Keio 49F7
BW37545 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurL731::kan / BD792 via BW35696 / KmR with P1kc on Keio 53H4
BW37548 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurM747::kan / BD792 via BW35696 / KmR with P1kc on Keio 53E4
BW37541 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurE736::kan / BD792 via BW35696 / KmR with P1kc on Keio 49D6
BW37540 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurK735::kan / BD792 via BW35696 / KmR with P1kc on Keio 49C6
BW37544 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurC725::kan / BD792 via BW35696 / KmR with P1kc on Keio 85F4
BW37547 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurH777::kan / BD792 via BW35696 / KmR with P1kc on Keio 85C5
BW37546 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurA727::kan / BD792 via BW35696 / KmR with P1kc on Keio 53D6
BW37552 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔguaA::kan / BD792 via BW35696 / KmR with P1kc on Keio 85G4
BW37553 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔguaB::kan / BD792 via BW35696 / KmR with P1kc on Keio 69A4
BW37551 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) Δndk::kan / BD792 via BW35696 / KmR with P1kc on Keio 85F5
BW37269 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpurR746::kan / BD792 via BW35696 / KmR with P1kc on Keio 1H7
BW38089 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔthiC::kan / BD792 via BW35696 / KmR with P1kc on Keio 43D9
BW38092 / Like BW32395 except att::pSJ143 (ppkPEc::lacZ) ΔpyrE::kan / BD792 via BW35696 / KmR with P1kc on Keio 53A6

a. A ll known mutations are shown.

b. The parental strain from another lab and its most immediate ancestor in this lab are given.

c. See Materials and Methods. KmR, kanamycin-resistant; CmR, chloramphenicol-resistant; KmS, kanamycin-sensitive.

d. BW36522 has EZ::TN5 within cvpA 198-bp before its C-terminus with kan in the same orientation as the cvpA and downsteam purF coding regions.


Supplementary Table 2. Plasmids.

Plasmid / Genotypea / Template
Vector / Derivation and/or Reference(s)
pAH125 / -lacZ oriRγ attλ kan / (Haldimann and Wanner, 2001)
pLZ13 / ppkPEc-lacZ oriRγ cat / L. Zhou and B. L. W., unpublished data; pAH125 containing PstI-BamHI 194-bp ppkPEc PCR product generated with P855 and P856 on E. coli K-12 BW25113 as template
pLZ31 / oriRg attλ KmR / (Zhou et al., 2003)
pKD307 / araBp-lacZ oriRg attλ KmR / Kirill A. Datsenko and B. L. W., unpublished data
pLA22 / araBp-phoB oriRg Att80n CmR / Larisa Avramova
pSJ88-1 / ppkPEc-lacZ oriRγ attλ cat / Ligation of BsaI to NotI ppkPEc fragment of pLZ13 into pLA22 backbone
pSJ127 / araBp-lacZ oriRg Att80n CmR / pKD307
pLA22 / Ligation of pLA22 cut NheI..1669 to BsaI..20 into pKD307 cut BsaI..20 to NheI..4535 rotated to position 6450
pSJ132 / ppkpEc::lacZ oriRg Att80n CmR / pSJ127 / ppk PCR fragment (79bp) was generated using P2806/P2861 and E. coli K-12 BW25113 as a template, which are cloned into pSJ127 using PstI and NdeI
pSJ133 / Ppkpst::lacZ oriRg Att80n CmR / pSJ127 / ppk PCR fragment (189bp) was generated using P2810/P2862 and S. enterica (v12417) as a template, which are cloned into pSJ127 using PstI and NdeI
pSJ141 / ppkpEc::lacZ oriRg attλ CmR / pSJ88-1
pSJ132 / Promoter region form pSJ132 was cut using PstI and NheI and ligated into pSJ88-1.
pSJ142 / ppkpSt::lacZ oriRg attλ CmR / pSJ88-1
pSJ133 / ppk PCR fragment (189bp) was generated using P2810/P2935 and S. enterica LT2 MS1868 as a template, which are cloned into pSJ127 using PstI and NdeI
pSJ143 / ppkpEc::lacZ oriRg attλ CmR / pSJ142 / ppk PCR fragment (199bp) was generated using P2806/P2934 and E. coli (BW25113) as a template, which are cloned into pSJ141 using PstI and NdeI
pSJ144 / ppkpSt::lacZ oriRg attλ CmR / pSJ141 / ppk PCR fragment (209bp) was generated using P2810/P2935 and S. enterica (v12417) as a template, which are cloned into pSJ141 using PstI and NdeI
pLZ102 / ppkpKp::lacZ oriRg attλ KmR / pLZ31 / ppk PCR fragment (194bp) was generated using P2061/P2062 and K. pneumoniae (v32184) as a template, which are cloned into pLZ31 using PstI and BamHI
pLZ128 / ppkpADP1::lacZ oriRg attλ KmR / pLZ31 / ppk PCR fragment (293bp) was generated using P2562/P2563 and ADP1 (v34237) as a template, which are cloned into pLZ31 using PstI and BamHI
pLZ135 / ppkpVc::lacZ oriRg attλ KmR / pLZ31 / ppk PCR fragment (238bp) was generated using P2640/2641and V. cholerae (v36016) as a template, which are cloned into pLZ31 using XhoI
F'-CAS7 / pLZ119 attλ attHK attφ80TetR / Zhou and Wanner, Unpublished data
pSJ176 / F'-CAS7 ::pSJ143 TetR CatR / F'-CAS7 / Integration of pSJ143 into F'-CAS7
pSJ177 / F'-CAS7 ::pSJ144 TetR CatR / F'-CAS7 / Integration of pSJ144 into F'-CAS7
pSJ179 / F'-CAS7 ::pLZ102 TetR KmR / F'-CAS7 / Integration of pLZ102 into F'-CAS7
pSJ180 / F'-CAS7 ::pLZ128 TetR KmR / F'-CAS7 / Integration of pLZ128 into F'-CAS7
pSJ181 / F'-CAS7 ::pLZ135 TetR KmR / F'-CAS7 / Integration of pLZ135 into F'-CAS7

a. All fragments amplified by PCR were verified by DNA sequencing after cloning. Primers are described in Supplementary Table 3.

Supplementary Table 3. Oligonucleotide primers.

Primera / Sequenceb
P2806 / ppkPEc-5', GCACTGCAGGACGAGTAATACCCCCGTAAT
P2934 / ppkPEc-3', GGAATTCCATATGCACTTTTACTCCGTTTTATTCAC
P2810 / ppkPST-5', GCACTGCAGAATATGTCATCGGACAGGACT
P2935 / ppkPST-3', GGAATTCCATATGTACCTATACTCCGTTTTATTCAC
P855 / ppkPEc-5' AACTGCAGGACTCGAGTCATACCCCCGTAATTAAAGCG
P856 / ppkPEc-3' CGGGATCCGACTCGAGTCACTTTTACTCCGTTTTATTC
P2861 / ppkPSt-5' GGAATTCCATATGTACCACTTTTACTCCGTTTTATTC
P2862 / ppkPST-3' GGAATTCCATATGTACTACCTATACTCCGTTTTATTCAC
P2963 / lacZ-5', CAAATCAGCGATTTCCATGTTG
P2964 / lacZ-3', TCTGAACTTCAGCCTCCAGTACAG
P2979 / ppk-5', TAGCGAAGAACAAGGCTCCAA
P2980 / ppk-3', CGTTGTAGAGGCCGTCGAAT
P2965 / gnd-5', CGGTGAACCATGCGTTACC
P2966 / gnd-3', CCGTTGTGAACCATCTTCACATA

a. Laboratory primer identification (I. D.).

b. Restriction sites are italicized. Bases complementary to the template are underlined.