TABLE 1.
E. coli strains and plasmids
| Strain or plasmid | Relevant genotype or descriptiona | Constructionb or reference |
|---|---|---|
| Strains | ||
| MG1655 | a.k.a. NCM3105; see text and Table 7 | E. coli Genetic Stock Center (CGSC 6300) |
| MG1655 | a.k.a. NCM3628; see text | American Type Culture Collection (ATCC 47076) |
| MG1655 | a.k.a. NCM3430; see text | Mitchell Singer and Carol Gross |
| MG1655 | a.k.a. NCM3629; see text | Frederick Blattner |
| CAG12080 | F− λ−rph-1 mhpC281::Tn10 | E. coli Genetic Stock Center |
| CAG12163 | F− λ−rph-1 zib-207::Tn10 | E. coli Genetic Stock Center |
| W2244c | ΔlacZ39 rpsL110 (strR) | E. coli Genetic Stock Center (8) |
| M7044 | lacY328(Am) relA1 rpsL150 (Strr) spoT1 | E. coli Genetic Stock Center (38) |
| AD110 | Δ(lac-pro) supE thi malF::Tn10 F′ (traD36 proAB lacIqlacZΔM15) | H. Nikaido |
| AD111 | Δ(lac-pro) supE thi malG::Tn10 F′ (traD36 proAB lacIqlacZΔM15) | H. Nikaido |
| pop4062 | F−araD139 Δ(argF-lac)U169 rpsL150 relAI flbB5301 deoC1 ptsF25 rbsR malT::Tn10 | O. Danot |
| GM15 | malS::Tn10 malE::Kanr | W. Boos |
| TE2680 | F− λ− IN(rrnD-rrnE)1 ΔlacX74 rpsL galK2 recD1903::Tn10d-Tet trpDC700::putPA1303::[Kans-Camr-lac] | 11 |
| IBPC534 | nagA::Tetr | 45 |
| IBPC536 | nagC::Tetr | 45 |
| IBPC540 | nagD::Tetr | 45 |
| IBPC542 | nagE::Kanr | 45 |
| IBPC546 | nagB::Kanr | 45 |
| IBPC571 | nagB2 zbf-507::Tn10 asnB::Tn5 | 44 |
| IBPC590 | Δnag(EBACD)::Tetr | 44 |
| VH1000 | ΔlacIZ | V. J. Hernandez via C. L. Turnbough |
| RK4353 | fnr+ | 55 |
| RK4942 | ycj-630::Tn10 | 55 |
| RK5279 | fnr-250 | 55 |
| NCM3350 | malF::Tn10 | P1(AD110) → NCM3105d |
| NCM3351 | malG::Tn10 | P1(AD111) → NCM3105d |
| NCM3364 | malT::Tn10 | P1(pop4062) → NCM3105d |
| NCM3384 | mhpC281::Tn10 | P1(CAG12080) → NCM3105d |
| NCM3385c | ΔlacZ39 mhpC281::Tn10 | P1(NCM3384) → W2244d,e,f |
| NCM3386 | lacY328(Am) mhpC281::Tn10 | P1(NCM3384) → M7044d,g,h |
| NCM3387c | mhpC281::Tn10 ΔlacZ39 | P1(NCM3385) → NCM3105d,e,f |
| NCM3388 | mhpC281::Tn10 lacY328(Am) | P1(NCM3386) → NCM3105d,g,h |
| NCM3410 | malE::Kanr | P1(GM15) → NCM3105i |
| NCM3414 | Δlac1Z zib-207::Tn10 | P1(CAG12163) → VH1000d |
| NCM3415j | rph-1 zib-207::Tn10 | P1(NCM3414) → NCM3105d |
| NCM3416j | zib-207::Tn10 | P1(NCM3414) → NCM3105d |
| NCM3426 | recD1903::Tn10d-Tet | P1(TE2680) → NCM3105d |
| NCM3467 | recD1903::Tn10d-Tet ΔycjT::Kanr | See Materials and Methods |
| NCM3468 | ΔycjT::Kanr | P1(NCM3467) → NCM3105i |
| NCM3556 | Galactose fast-grower, LacZ− Lac(Con) | See Materials and Methods and Results |
| NCM3558 | Galactose fast-grower | See Materials and Methods |
| NCM3559 | Galactose fast-grower, Lac(Con) | See Materials and Methods |
| NCM3560 | Galactose fast-grower, Lac(Con) | See Materials and Methods |
| NCM3601 | seq404 (UTI isolate) | See Materials and Methods |
| NCM3610 | seq915 (UTI isolate) | See Materials and Methods |
| NCM3611 | 10002-006 (intestinal commensal) | See Materials and Methods |
| NCM3722 | E. coli K-12 prototroph | See Materials and Methods |
| NCM3748 | lacA::Kanr | See Materials and Methods |
| NCM3749 | mhpC281::Tn10 lacA::Kanr | P1(NCM3748) → NCM3384g,i |
| NCM3750c | mhpC281::Tn10 ΔlacZ39 lacA::Kanr | P1(NCM3748) → NCM3387e,f,i |
| NCM3786 | nagA::Tetr | P1(IBPC534) → NCM3105d,k |
| NCM3787 | nagC::Tetr | P1(IBPC536) → NCM3105d |
| NCM3789 | nagE::Kanr | P1(IBPC542) → NCM3105i |
| NCM3817 | nagB::Kanr | P1(IBPC546) → NCM3105i,l |
| NCM3818 | zbf-507::Tn10 asnB::Tn5 nagB2 | P1(IBPC571) → NCM3105d,l |
| NCM3819 | zbf-507::Tn10 asnB::Tn5 | P1(IBPC571) → NCM3105d,m |
| NCM3820 | Δnag(EBACD)::Tetr | P1(IBPC590) → NCM3105d,l |
| NCM3821 | nagD::Tetr | P1(IBPC540) → NCM3105d |
| NCM3845 | Galactose fast-grower, NagA− | See Materials and Methodsk |
| NCM3851 | nagE::KanrnagA::Tetr | P1(IBPC534) → NCM3789d,i,k |
| NCM3852 | nagE::KanrnagC::Tetr | P1(IBPC536) → NCM3789d,i |
| NCM3954 | eut+ | See Materials and Methods |
| NCM3955 | eut+ | See Materials and Methods/PICK> |
| Plasmids | ||
| pNoTA/T7 | PCR cloning vector | 5′ → 3′ Inc. |
| pUC4K | pUC4 carrying a kanamycin resistance cassette | Amersham-Pharmacia Biotech |
| pK03 | Gene replacement vector; repAts, cat, sacB | 33 |
| pJES1333 | PCR fragment containing ycjUTS in pBluescript-KS | See Materials and Methods |
| pJES1336 | pBluescript-KS containing ycjU′-ΔycjT::Kanr-′ycjS | See Materials and Methods |
| pJES1411 | PCR fragment containing lacA in pNoTA/T7 | See Materials and Methods |
| pJES1413 | EcoRI-SacI deleted from polylinker of pJES1411 | See Materials and Methods |
| pJES1415 | pJES1413 containing lacA::Kanr | See Materials and Methods |
| pJES1506 | pK03 containing lacA::Kanr | See Materials and Methods |
| pBR(NagA) | pBR322 containing nagA | 45 |
| pBR(NagC) | pBR322 containing nagC | 45 |
a
a.k.a., also known as.
b
For strains constructed by phage P1vir-mediated transduction, the donor is listed after P1vir and the recipient is listed after the arrow.
c
The length of the in-frame deletion in lacZ was estimated by PCR to be approximately 1,100 to 1,200 bp. The unique restriction sites for EcoRV, DraIII, AvaII, and SacI, all of which are approximately in the middle of the lacZ gene, are absent.
d
Selected for tetracycline resistance.
e
Screened for white colonies (lacZ null mutants) on X-Gal and IPTG.
g
Screened for blue colonies (lacZ+) on X-Gal and IPTG.
h
Screened for failure to grow on melibiose at 42°C (lacY) (36).
i
Selected for kanamycin resistance.
j
rph allele checked by sequence analysis.
k
Tested for the ability to grow on glucosamine but not N-acetylglucosamine as the sole carbon source.
l
Tested for failure to grow on glucosamine and N-acetylglucosamine as the sole carbon sources.
m
Screened for growth on glucosamine and N-acetylglucosamine as the sole carbon sources (Nag+).