Strain, plasmid, or primer | Genotype, phenotype, or sequence of primer (5' to 3') | Reference |
---|---|---|
E. coli | Â | Â |
   K-12 | K-12 MG1655 Wild-type strain |  |
   DH5α | F- ψ80dlac ZΔM15 Δ(lac ZYA-arg F) U169 rec A1 end A1 hsd R17(rk-, mk+) pho A sup E44 λ- thi-1 gyr A96 rel A1 | Novagen |
   DB3.1 | F- gyr A462 end A1Δ(sr1-rec A) mcr B mrr hsd S20(rB-, mB-) sup E44 ara-14 gal K2 lac Y1 pro A2 rps L20(SmR) xyl-5λ-leu mtl 1 | Invitrogen |
   WM3064 | thrB1 004 pro thi rpsL hsdS lacZ ΔM15 RP4-1360 Δ(araBAD)567 ΔdapA 1341::[erm pir] | W. Metcalf |
   BL21(DE3) | F- omp T hsd SB(rB-mB-) gal dcm (DE3) | Invitrogen |
Z. mobilis | Â | Â |
   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 | Â | Â |
   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 | Â | Â |
   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 | Â | Â |
   hfq_MF | cggagagatggtcagtcaca | 262-bp |
   hfq_MR | ttcttgctgctgcataatcg |  |
   hfq_CF | ggggacaagtttgtacaaaaaagcaggcttcgaaggagatagaATGGCCGAAAAGGTCAACAATC | 483-bp |
   hfq_CR | ggggaccactttgtacaagaaagctgggtcATCCTCGTCTCGGCTTTCTG |  |
   hfq_OCF | Caaagcttgagctcgaattcatttttgccgtggtagttgc | 1050-bp |
   hfq_OCR | caggtacctctagaattcaccactcaatcctcgtctcg |  |