Table 1.
Bacterial strains, plasmids and primers used in this study
| Strain, plasmid, or primer | Genotype, phenotype, or sequence of primer (5' to 3') | Reference |
|---|---|---|
| E. coli | ||
| K-12 | K-12 MG1655 Wild-type strain | |
| DH5α | F- ψ80dlacZΔM15 Δ(lacZYA-argF) U169 recA1 endA1 hsdR17(rk-, mk+) phoA supE44 λ- thi-1 gyrA96 relA1 | Novagen |
| DB3.1 | F- gyrA462 endA1Δ(sr1-recA) mcrB mrr hsdS20(rB-, mB-) supE44 ara-14 galK2 lacY1 proA2 rpsL20(SmR) xyl-5λ-leu mtl1 | Invitrogen |
| WM3064 | thrB1004 pro thi rpsL hsdS lacZΔM15 RP4-1360 Δ(araBAD)567 ΔdapA1341::[erm pir] | W. Metcalf |
| BL21(DE3) | F- ompT hsdSB(rB-mB-) gal dcm (DE3) | Invitrogen |
| Z. mobilis | ||
| ZM4 | ATCC31821 | ATCC |
| AcR | ZM4 acetate tolerant strain generated by random mutagenesis | [13] |
| AcRIM0347 | hfq::pKm-0347, insertional mutant of AcR hfq gene ZMO0347 | This study |
| AcRIM0347 (p42-0347) | AcRIM0347 containing plasmid p42-0347 | This study |
| ZM4(p42-0347) | ZM4 containing plasmid p42-0347 | This study |
| AcR (p42-0347) | AcR containing plasmid p42-0347 | This study |
| S. cerevisiae | ||
| BY4741 | MATa his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 - s288c background | Open Biosystems |
| YSC1021-554440 | Yeast: Yeast Knock Out Strain (YKO_LSM1) Clone Id: 1301; Accession: YJL124C (Lsm1) |
Open Biosystems |
| YSC1021-552226 | Yeast: Yeast Knock Out Strain (YKO_LSM6) Clone Id: 4214; Accession: YDR378C (Lsm6) |
Open Biosystems |
| YSC1021-556031 | Yeast: Yeast Knock Out Strain (YKO_LSM7) Clone Id: 7383; Accession: YNL147W (Lsm7) |
Open Biosystems |
| YSC1021-552677 | Yeast: Yeast Knock Out Strain (YKO_LSM9) Clone Id: 3501; Accession: YCR020C-A (Mak31P, Lsm9) |
Open Biosystems |
| YSC1021-552563 | Yeast: Yeast Knock Out Strain (YKO_LSM12) Clone Id: 1949; Accession: YHR121W (Lsm12) |
Open Biosystems |
| YSC1021-553518 | Yeast: Yeast Knock Out Strain (YKO_LSM13) Clone Id: 5544; Accession: YPR129W (Lsm13) |
Open Biosystems |
| YSC1021-552280 | Yeast: Yeast Knock Out Strain (YKO_LSM16) Clone Id: 255; Accession: YEL015W (Lsm16) |
Open Biosystems |
| YSC4515-98807049 | Yeast GST-Tagged Strain (GST_LSM1) Clone Id: YJL124C; Accession: YJL124C (lsm1) |
Open Biosystems |
| YSC4515-98811389 | Yeast GST-Tagged Strain (GST_LSM6) Clone Id: YDR378C; Accession: YDR378C (Lsm6) |
Open Biosystems |
| YSC4515-98805426 | Yeast GST-Tagged Strain (GST_LSM9) Clone Id: YCR020C-A; Accession: YCR020C-A (Mak31P, Lsm9) |
Open Biosystems |
| YSC4515-98806813 | Yeast GST-Tagged Strain (GST_LSM12) Clone Id: YHR121W; Accession: YHR121W (Lsm12) |
Open Biosystems |
| YSC4515-98808930 | Yeast GST-Tagged Strain (GST_LSM13) Clone Id: YPR129W; Accession: YPR129W (Lsm13) |
Open Biosystems |
| YSC4515-98809076 | Yeast GST-Tagged Strain (GST_LSM16) Clone Id: YEL015W; Accession: YEL015W (Lsm16) |
Open Biosystems |
| Plasmids | ||
| pKNOCK-Km | Kmr, mob, broad host range suicide cloning vector, 1.8 kb | [26] |
| pET-DEST42 | Apr, Cmr, C-terminal 6×His and V5 epitope | Invitrogen |
| pDONR221 | Kmr, gateway entry vector Gmr, N-terminal GST | Invitrogen |
| pBBR1MCS-3 | Tcr, mob, broad host range cloning vector | [36] |
| pBBR3DEST42 | Cmr Tcr, C-terminal 6×His and V5 epitope | This study |
| pKm-0347 | pKnock-Km containing 262-bp hfq internal fragment for insertional mutant construction | This study |
| p42-0347 | pBBR3DEST42 containing ZM4 gene ZMO0347 | This study |
| PCR Primers | ||
| hfq_MF | cggagagatggtcagtcaca | 262-bp |
| hfq_MR | ttcttgctgctgcataatcg | |
| hfq_CF | ggggacaagtttgtacaaaaaagcaggcttcgaaggagatagaATGGCCGAAAAGGTCAACAATC | 483-bp |
| hfq_CR | ggggaccactttgtacaagaaagctgggtcATCCTCGTCTCGGCTTTCTG | |
| hfq_OCF | Caaagcttgagctcgaattcatttttgccgtggtagttgc | 1050-bp |
| hfq_OCR | caggtacctctagaattcaccactcaatcctcgtctcg | |
hfq_MF and hfq_MR are primers used for insertional mutant construction using pKnock mutagenesis system. Hfq_OCF and Hfq_OCR are primers for mutant confirmation. Hfq_CF and Hfq_CR are primers used to clone the hfq gene into low copy number Gate-Way compatible plasmid pBBR3DEST42 for complementation, which results in a plasmid called p42-0347.