Skip to main content

Table 1 Bacterial strains, plasmids and primers used in this study

From: The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors

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- 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

  

   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

 
  1. 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.