Skip to main content

Table 4 Bacterial strains, plasmids, primers and oligonucleotides used in this study.

From: Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensisMR-1

Strain/plasmid/primer/Probe

Relevant genotype or sequencea,b

Source

Escherichia coli K-12

  

   β2155

DAP auxotroph

[61]

Shewanella oneidensis

  

   MR-1 (ATCC 700550T)

wild type

[62]

   EtrA7-1

As MR-1 but ΔetrA::loxP

This study

   EtrA7-1 complement

EtrA7-1 complemented with the etrA gene (SO2356) cloned into

This study

 

pCM62

 

   EtrA7-1 with pCM62

EtrA7-1 harboring the pCM62 as a negative control for complementation

This study

Plasmids

  

   pCM62

Tcr; traJ' trfA oriT oriV

[63]

   pCM157

Tcr; trfA oriT oriV ColE1 ori; lacZp-cre

[46]

   pCM184

Apr Tcr; loxP-kan-loxP

[46]

   pKNOCK-Gm

Gmr; oriR6K oriTRP4

[64]

   pCCG02

As pKNOCK-Gm but etrA'-loxP-kan-loxP-'etrA

This study

   pCCG03

As pCM62 but lacZp-etrA

This study

Primersc

  

   etrAN Fwd

GCCGCGGTCATGTCGGTTCTCAAGT

 

   etrAN Rev

CGAGCTCCGACAGCTATCTGTTAGTCT

 

   etrAC Fwd

CGAATTCAAATCACCGCTTTTAACTTG

 

   etrAC Rev

GCATATGCCAGATAAATCACACCTTTT

 

   etrAScreenout

AATTCTTCAGGCATTTGACTCG

 

   Fwd

  

   etrAScreenout

GGCCGTATCTTGAGTTATACCC

 

   Rev

  

   etrAcomp Fwd

GGATCCAGGTGTGATTTATCTGGCG

 

   etrAcomp Rev

GAATTCCCGACATGACAATAGAGCAGA

 

   23SRT Fwd

TAGCGAAATTCCTTGTCGGG

 

   23SRT Rev

GAGACAGCGTGGCCATCATT

 

   23Stemp Rev

GTATCAGTTAGCTCAACGCCTC

 

   napART Fwd

AGAAAGCCCTGTTAACCGTGG

 

   napART Rev

TCATCCGCAGCAATGGTGT

 

   napAtemp Rev

GATCGAAGCTACGGTTCTCG

 

   nrfART Fwd

GCCACATGTATGCCGTGACT

 

   nrfART Rev

TTTACAGCTCCAGCAAGCCA

 

   nrfAtemp Rev

ACGTTTCATACTCGGGATGC

 

Probes

  

   23SRTProbe

AGTTCCGACCTGCACGAATGGCG

 

   napARTProbe

CTGTATTAAAGGTTACTTCCTGTCGAAAATCATGTACGG

 

   nrfARTProbe

CGTAATACCTTGCGTACTGGCGCGC

 
  1. a The sequence for the primers is written from the 5'end to the 3'end.
  2. b Primers were designed using putative gene sequences of S. oneidensis MR-1.
  3. c For primer sequences, the restriction sites incorporated are underlined. CATATG, NdeI; GAATTC, EcoRI; GAGCTC, SacI; CCGCGG, SacII.