agent|agent|NN|O  :|:|:|O  Fe|Fe|NNP|Supp 
 antibody|antibody|NN|O  :|:|:|O  9E10|9e10|CD|Anti  Myc|myc|NN|Anti  tag|tag|NN|Anti  antibody|antibody|NN|O 
 antibody|antibody|NN|O  :|:|:|O  Pre-cleared|pre-cleared|JJ|Anti  FNR|fnr|NN|Anti  antibody|antibody|NN|Anti 
 carbon|carbon|NN|O  source|source|NN|O  :|:|:|O  glucose|glucose|NN|Supp 
 Cells|cell|NNS|O  were|be|VBD|O  grown|grow|VBN|O  aerobically|aerobically|RB|O  -LRB-|-lrb-|-LRB-|O  70|70|CD|O  %|%|NN|O  N2|n2|NN|O  ,|,|,|O  25|25|CD|O  %|%|NN|O  O2|o2|CD|O  ,|,|,|O  and|and|CC|O  5|5|CD|O  %|%|NN|O  CO2|co2|NN|O  -RRB-|-rrb-|-RRB-|O  or|or|CC|O  anaerobically|anaerobically|RB|O  -LRB-|-lrb-|-LRB-|O  95|95|CD|O  %|%|NN|O  N2|n2|NN|O  and|and|CC|O  5|5|CD|O  %|%|NN|O  CO2|co2|NN|O  -RRB-|-rrb-|-RRB-|O  until|until|IN|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  -LRB-|-lrb-|-LRB-|O  OD600|od600|NN|OD  of|of|IN|OD  ~|~|NN|OD  0.3-0.35|0.3-0.35|CD|OD  -RRB-|-rrb-|-RRB-|O  .|.|.|O 
 Cells|cell|NNS|O  were|be|VBD|O  grown|grow|VBN|O  aerobically|aerobically|RB|O  -LRB-|-lrb-|-LRB-|O  70|70|CD|O  %|%|NN|O  N2|n2|NN|O  ,|,|,|O  25|25|CD|O  %|%|NN|O  O2|o2|CD|O  ,|,|,|O  and|and|CC|O  5|5|CD|O  %|%|NN|O  CO2|co2|NN|O  -RRB-|-rrb-|-RRB-|O  or|or|CC|O  anaerobically|anaerobically|RB|O  -LRB-|-lrb-|-LRB-|O  95|95|CD|O  %|%|NN|O  N2|n2|NN|O  and|and|CC|O  5|5|CD|O  %|%|NN|O  CO2|co2|NN|O  -RRB-|-rrb-|-RRB-|O  until|until|IN|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  -LRB-|-lrb-|-LRB-|O  OD600|od600|NN|OD  of|of|IN|OD  ~|~|NN|OD  0.3-0.35|0.3-0.35|CD|OD  -RRB-|-rrb-|-RRB-|O  in|in|IN|O  MOPS|MOPS|NNP|Med  minimal|minimal|JJ|Med  glucose|glucose|NN|Med  media|media|NNS|Med  containing|contain|VBG|O  10|10|CD|Supp  µM|µm|NN|Supp  FeSO4|feso4|NN|Supp  .|.|.|O 
 Cells|cell|NNS|O  were|be|VBD|O  grown|grow|VBN|O  with|with|IN|O  16|16|CD|Supp  µM|µm|NN|Supp  IPTG|iptg|NN|Supp  and|and|CC|Supp  300|300|CD|Supp  µL|µl|NN|Supp  Cm20|cm20|NN|Supp  anaerobically|anaerobically|RB|O  -LRB-|-lrb-|-LRB-|O  95|95|CD|O  %|%|NN|O  N2|n2|NN|O  and|and|CC|O  5|5|CD|O  %|%|NN|O  CO2|co2|NN|O  -RRB-|-rrb-|-RRB-|O  until|until|IN|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  -LRB-|-lrb-|-LRB-|O  OD600|od600|NN|OD  of|of|IN|OD  0.3|0.3|CD|OD  -RRB-|-rrb-|-RRB-|O  and|and|CC|O  treated|treat|VBN|O  with|with|IN|O  1|1|CD|O  %|%|NN|O  final|final|JJ|O  volumen|voluman|NNS|O  formaldehyde|formaldehyde|NN|O  for|for|IN|O  ten|ten|CD|O  minutes|minute|NNS|O  .|.|.|O  Sodium|sodium|NN|O  phosphate|phosphate|NN|O  -LRB-|-lrb-|-LRB-|O  1/100|1/100|CD|O  vol|vol|NN|O  .|.|.|O  of|of|IN|O  1M|1m|NN|O  ,|,|,|O  pH|ph|NN|O  7.6|7.6|CD|O  ;|;|:|O  10|10|CD|O  mM|mm|NN|O  final|final|JJ|O  -RRB-|-rrb-|-RRB-|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  the|the|DT|O  mid-log|mid-log|JJ|O  cultures|culture|NNS|O  followed|follow|VBN|O  by|by|IN|O  formaldehyde|formaldehyde|NN|O  to|to|TO|O  1|1|CD|O  %|%|NN|O  final|final|JJ|O  ,|,|,|O  and|and|CC|O  anaerobic|anaerobic|JJ|O  sparging|sparging|NN|O  was|be|VBD|O  continued|continue|VBN|O  for|for|IN|O  10|10|CD|O  min|min|NN|O  .|.|.|O  Cold|Cold|NNP|O  2.5|2.5|CD|O  M|m|NN|O  glycine|glycine|NN|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  100mM|100mm|NN|O  and|and|CC|O  the|the|DT|O  mixture|mixture|NN|O  was|be|VBD|O  incubated|incubate|VBN|O  at|at|IN|O  4|4|CD|O  °C|°c|NN|O  with|with|IN|O  anaerobic|anaerobic|JJ|O  sparging|sparging|NN|O  for|for|IN|O  30|30|CD|O  minutes|minute|NNS|O  to|to|TO|O  stop|stop|VB|O  the|the|DT|O  crosslinking|crosslinking|NN|O  .|.|.|O  Cells|cell|NNS|O  were|be|VBD|O  spun|spin|VBN|O  at|at|IN|O  5000|5000|CD|O  x|x|CC|O  g|g|NN|O  ,|,|,|O  and|and|CC|O  washed|wash|VBN|O  repeatedly|repeatedly|RB|O  with|with|IN|O  phosphate|phosphate|NN|O  buffered|buffer|VBN|O  saline|saline|NN|O  before|before|IN|O  being|be|VBG|O  frozen|freeze|VBN|O  at|at|IN|O  -80|-80|CD|O  °C|°c|NN|O  .|.|.|O 
 chip|chip|NN|O  antibody|antibody|NN|O  :|:|:|O  SeqA|seqa|NN|Anti 
 E.|E.|NNP|O  coli|coli|NN|O  K-12|k-12|NN|O  MG1655|mg1655|NN|O  WT|wt|NN|O  and|and|CC|O  Fur-8-myc|fur-8-myc|NN|O  tagged|tag|VBD|O  strains|strain|NNS|O  were|be|VBD|O  grown|grow|VBN|O  to|to|TO|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  aerobically|aerobically|RB|O  at|at|IN|O  37|37|CD|Temp  °C|°c|NN|Temp  in|in|IN|O  M9|m9|NN|Med  minimal|minimal|JJ|Med  media|media|NNS|Med  supplemented|supplement|VBN|O  with|with|IN|O  0.2|0.2|CD|Supp  %|%|NN|Supp  glucose|glucose|NN|Supp  .|.|.|O  For|for|IN|O  iron|iron|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.1|0.1|CD|O  mM|mm|NN|O  of|of|IN|O  FeCl2|fecl2|NN|O  were|be|VBD|O  treated|treat|VBN|O  from|from|IN|O  the|the|DT|O  beginning|beginning|NN|O  of|of|IN|O  culture|culture|NN|O  ,|,|,|O  and|and|CC|O  for|for|IN|O  DPD|dpd|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.2|0.2|CD|Supp  mM|mm|NN|Supp  of|of|IN|Supp  DPD|dpd|NN|Supp  were|be|VBD|O  added|add|VBN|O  at|at|IN|O  early-log|early-log|JJ|O  phase|phase|NN|O  and|and|CC|O  continued|continue|VBD|O  to|to|TO|O  culture|culture|NN|O  for|for|IN|O  additional|additional|JJ|O  2h|2h|NN|Supp  .|.|.|O  For|for|IN|O  the|the|DT|O  rifampicin-treated|rifampicin-treated|JJ|O  cultures|culture|NNS|O  ,|,|,|O  the|the|DT|O  rifampicin|rifampicin|NN|O  dissolved|dissolve|VBN|O  in|in|IN|O  methanol|methanol|NN|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  a|a|DT|O  final|final|JJ|O  concentration|concentration|NN|O  of|of|IN|O  150|150|CD|O  mg/mL|mg/ml|NN|O  at|at|IN|O  mid-log|mid-log|JJ|O  phase|phase|NN|O  and|and|CC|O  stirred|stir|VBD|O  for|for|IN|O  20|20|CD|O  min|min|NN|O  .|.|.|O 
 E.|E.|NNP|O  coli|coli|NN|O  K-12|k-12|NN|O  MG1655|mg1655|NN|O  WT|wt|NN|O  and|and|CC|O  Fur-8-myc|fur-8-myc|NN|O  tagged|tag|VBD|O  strains|strain|NNS|O  were|be|VBD|O  grown|grow|VBN|O  to|to|TO|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  aerobically|aerobically|RB|O  at|at|IN|O  37|37|CD|Temp  °C|°c|NN|Temp  in|in|IN|O  M9|m9|NN|Med  minimal|minimal|JJ|Med  media|media|NNS|Med  supplemented|supplement|VBN|O  with|with|IN|O  0.2|0.2|CD|Supp  %|%|NN|Supp  glucose|glucose|NN|Supp  .|.|.|O  For|for|IN|O  iron|iron|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.1|0.1|CD|O  mM|mm|NN|O  of|of|IN|O  FeCl2|fecl2|NN|O  were|be|VBD|O  treated|treat|VBN|O  from|from|IN|O  the|the|DT|O  beginning|beginning|NN|O  of|of|IN|O  culture|culture|NN|O  ,|,|,|O  and|and|CC|O  for|for|IN|O  DPD|dpd|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.2|0.2|CD|Supp  mM|mm|NN|Supp  of|of|IN|Supp  DPD|dpd|NN|Supp  were|be|VBD|O  added|add|VBN|O  at|at|IN|O  early-log|early-log|JJ|O  phase|phase|NN|O  and|and|CC|O  continued|continue|VBD|O  to|to|TO|O  culture|culture|NN|O  for|for|IN|O  additional|additional|JJ|O  2h|2h|NN|Supp  .|.|.|O  For|for|IN|O  the|the|DT|O  rifampicin-treated|rifampicin-treated|JJ|O  cultures|culture|NNS|O  ,|,|,|O  the|the|DT|O  rifampicin|rifampicin|NN|Supp  dissolved|dissolve|VBN|Supp  in|in|IN|Supp  methanol|methanol|NN|Supp  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  a|a|DT|O  final|final|JJ|O  concentration|concentration|NN|O  of|of|IN|O  150|150|CD|Supp  mg/mL|mg/ml|NN|Supp  at|at|IN|O  mid-log|mid-log|JJ|O  phase|phase|NN|O  and|and|CC|O  stirred|stir|VBD|O  for|for|IN|O  20|20|CD|Supp  min|min|NN|Supp  .|.|.|O 
 E.|E.|NNP|O  coli|coli|NN|O  K-12|k-12|NN|O  MG1655|mg1655|NN|O  WT|wt|NN|O  and|and|CC|O  Fur-8-myc|fur-8-myc|NN|O  tagged|tag|VBD|O  strains|strain|NNS|O  were|be|VBD|O  grown|grow|VBN|O  to|to|TO|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  aerobically|aerobically|RB|O  at|at|IN|O  37|37|CD|Temp  °C|°c|NN|Temp  in|in|IN|O  M9|m9|NN|Med  minimal|minimal|JJ|Med  media|media|NNS|Med  supplemented|supplement|VBN|O  with|with|IN|O  0.2|0.2|CD|Supp  %|%|NN|Supp  glucose|glucose|NN|Supp  .|.|.|O  For|for|IN|O  iron|iron|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.1|0.1|CD|Supp  mM|mm|NN|Supp  of|of|IN|Supp  FeCl2|fecl2|NN|Supp  were|be|VBD|O  treated|treat|VBN|O  from|from|IN|O  the|the|DT|O  beginning|beginning|NN|O  of|of|IN|O  culture|culture|NN|O  ,|,|,|O  and|and|CC|O  for|for|IN|O  DPD|dpd|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.2|0.2|CD|O  mM|mm|NN|O  of|of|IN|O  DPD|dpd|NN|O  were|be|VBD|O  added|add|VBN|O  at|at|IN|O  early-log|early-log|JJ|O  phase|phase|NN|O  and|and|CC|O  continued|continue|VBD|O  to|to|TO|O  culture|culture|NN|O  for|for|IN|O  additional|additional|JJ|O  2h|2h|NN|Supp  .|.|.|O  For|for|IN|O  the|the|DT|O  rifampicin-treated|rifampicin-treated|JJ|O  cultures|culture|NNS|O  ,|,|,|O  the|the|DT|O  rifampicin|rifampicin|NN|O  dissolved|dissolve|VBN|O  in|in|IN|O  methanol|methanol|NN|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  a|a|DT|O  final|final|JJ|O  concentration|concentration|NN|O  of|of|IN|O  150|150|CD|O  mg/mL|mg/ml|NN|O  at|at|IN|O  mid-log|mid-log|JJ|O  phase|phase|NN|O  and|and|CC|O  stirred|stir|VBD|O  for|for|IN|O  20|20|CD|O  min|min|NN|O  .|.|.|O 
 E.|E.|NNP|O  coli|coli|NN|O  K-12|k-12|NN|O  MG1655|mg1655|NN|O  WT|WT|NNP|O  ,|,|,|O  and|and|CC|O  Δcra|Δcra|NNP|O  were|be|VBD|O  grown|grow|VBN|O  to|to|TO|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  aerobically|aerobically|RB|O  at|at|IN|O  37|37|CD|Temp  °C|°c|NN|Temp  in|in|IN|O  M9|m9|NN|Med  minimal|minimal|JJ|Med  media|media|NNS|Med  supplemented|supplement|VBN|O  with|with|IN|O  0.2|0.2|CD|Supp  %|%|NN|Supp  glucose|glucose|NN|O  ,|,|,|O  fructose|fructose|NN|O  and|and|CC|O  acetate|acetate|NN|O  .|.|.|O 
 E.|E.|NNP|O  coli|coli|NN|O  K-12|k-12|NN|O  MG1655|mg1655|NN|O  WT|wt|NN|O  and|and|CC|O  Δfur|δfur|NN|O  were|be|VBD|O  grown|grow|VBN|O  to|to|TO|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  aerobically|aerobically|RB|O  at|at|IN|O  37|37|CD|Temp  °C|°c|NN|Temp  in|in|IN|O  M9|m9|NN|Med  minimal|minimal|JJ|Med  media|media|NNS|Med  supplemented|supplement|VBN|O  with|with|IN|O  0.2|0.2|CD|Supp  %|%|NN|Supp  glucose|glucose|NN|Supp  .|.|.|O  For|for|IN|O  iron|iron|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.1|0.1|CD|O  mM|mm|NN|O  of|of|IN|O  FeCl2|fecl2|NN|O  were|be|VBD|O  treated|treat|VBN|O  from|from|IN|O  the|the|DT|O  beginning|beginning|NN|O  of|of|IN|O  culture|culture|NN|O  ,|,|,|O  and|and|CC|O  for|for|IN|O  DPD|dpd|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.2|0.2|CD|Supp  mM|mm|NN|Supp  of|of|IN|Supp  DPD|dpd|NN|Supp  were|be|VBD|O  added|add|VBN|O  at|at|IN|O  early-log|early-log|JJ|O  phase|phase|NN|O  and|and|CC|O  continued|continue|VBD|O  to|to|TO|O  culture|culture|NN|O  for|for|IN|O  additional|additional|JJ|O  2h|2h|NN|O  .|.|.|O 
 E.|E.|NNP|O  coli|coli|NN|O  K-12|k-12|NN|O  MG1655|mg1655|NN|O  WT|wt|NN|O  and|and|CC|O  Δfur|δfur|NN|O  were|be|VBD|O  grown|grow|VBN|O  to|to|TO|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  aerobically|aerobically|RB|O  at|at|IN|O  37|37|CD|Temp  °C|°c|NN|Temp  in|in|IN|O  M9|m9|NN|Med  minimal|minimal|JJ|Med  media|media|NNS|Med  supplemented|supplement|VBN|O  with|with|IN|O  0.2|0.2|CD|Supp  %|%|NN|Supp  glucose|glucose|NN|Supp  .|.|.|O  For|for|IN|O  iron|iron|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.1|0.1|CD|Supp  mM|mm|NN|Supp  of|of|IN|Supp  FeCl2|fecl2|NN|Supp  were|be|VBD|O  treated|treat|VBN|O  from|from|IN|O  the|the|DT|O  beginning|beginning|NN|O  of|of|IN|O  culture|culture|NN|O  ,|,|,|O  and|and|CC|O  for|for|IN|O  DPD|dpd|NN|O  treated|treat|VBN|O  cells|cell|NNS|O  ,|,|,|O  0.2|0.2|CD|O  mM|mm|NN|O  of|of|IN|O  DPD|dpd|NN|O  were|be|VBD|O  added|add|VBN|O  at|at|IN|O  early-log|early-log|JJ|O  phase|phase|NN|O  and|and|CC|O  continued|continue|VBD|O  to|to|TO|O  culture|culture|NN|O  for|for|IN|O  additional|additional|JJ|O  2h|2h|NN|O  .|.|.|O 
 E.|E.|NNP|O  coli|coli|NN|O  K-12|k-12|NN|O  MG1655|mg1655|NN|O  WT|WT|NNP|O  ,|,|,|O  GadE-8-myc|gade-8-myc|NN|O  ,|,|,|O  GadW-8-myc|gadw-8-myc|NN|O  ,|,|,|O  and|and|CC|O  GadX-8-myc|gadx-8-myc|NN|O  tagged|tag|VBD|O  strains|strain|NNS|O  were|be|VBD|O  grown|grow|VBN|O  to|to|TO|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  -LRB-|-lrb-|-LRB-|O  OD600|od600|NN|OD 
 Escherichia|escherichia|FW|O  coli|coli|FW|O  ,|,|,|O  expressing|express|VBG|O  NsrR|nsrr|NN|Gtype  with|with|IN|O  a|a|DT|O  C-terminal|c-terminal|JJ|O  Flag-tag|flag-tag|NN|Gtype  ,|,|,|O  was|be|VBD|O  grown|grow|VBN|O  anaerobically|anaerobically|RB|O  in|in|IN|O  L|L|NNP|Med  broth|broth|NN|Med  supplemented|supplement|VBN|O  with|with|IN|O  glucose|glucose|NN|Supp  .|.|.|O 
 Escherichia|escherichia|FW|O  coli|coli|FW|O  MG1655|mg1655|NN|O  K-12|k-12|NN|O  WT|wt|NN|O  and|and|CC|O  ∆|∆|NN|O  fnr|fnr|NN|O  were|be|VBD|O  grown|grow|VBN|O  to|to|TO|O  mid-log|mid-log|JJ|Phase  phase|phase|NN|Phase  -LRB-|-lrb-|-LRB-|O  O.D.|o.d.|NN|OD  600nm|600nm|JJ|OD  0.3|0.3|CD|OD  -RRB-|-rrb-|-RRB-|O  anerobically|anerobically|RB|O  -LRB-|-lrb-|-LRB-|O  95|95|CD|O  %|%|NN|O  N2|n2|NN|O  ,|,|,|O  5|5|CD|O  %|%|NN|O  CO2|co2|NN|O  -RRB-|-rrb-|-RRB-|O  at|at|IN|O  37|37|CD|Temp  °C|°c|NN|Temp  in|in|IN|O  MOPS|MOPS|NNP|Med  +|+|CC|O  0.2|0.2|CD|Supp  %|%|NN|Supp  glucose|glucose|NN|Supp  media|media|NNS|O  -LRB-|-lrb-|-LRB-|O  Ref|ref|NN|O  -RRB-|-rrb-|-RRB-|O  .|.|.|O 
 genotype|genotype|NN|O  :|:|:|O  delta|delta|NN|O  -|-|:|O  cra|cra|NN|Gtype  Knock-out|knock-out|JJ|Gtype  strain|strain|NN|Gtype 
 genotype|genotype|NN|O  :|:|:|O  delta|delta|NN|O  -|-|:|O  crp|crp|NN|Gtype  Knock-out|knock-out|JJ|Gtype  strain|strain|NN|Gtype 
 genotype|genotype|NN|O  :|:|:|O  gadW-8myc|gadw-8myc|NN|Gtype 
 genotype|genotype|NN|O  :|:|:|O  ompR-8myc|ompr-8myc|NN|Gtype 
 genotype|genotype|NN|O  :|:|:|O  PurR-8myc|purr-8myc|NN|Gtype 
 genotype|genotype|NN|O  :|:|:|O  wildtype|wildtype|JJ|Gtype 
 genotype/variation|genotype/variation|NN|O  :|:|:|O  Combined|Combined|NNP|Gtype  input|input|NN|Gtype 
 genotype/variation|genotype/variation|NN|O  :|:|:|O  delta-gadW|delta-gadw|NN|Gtype 
 genotype/variation|genotype/variation|NN|O  :|:|:|O  delta-oxyR|delta-oxyr|NN|Gtype 
 genotype/variation|genotype/variation|NN|O  :|:|:|O  -LCB-|-lcb-|-LRB-|Gtype  delta|delta|NN|Gtype  -RCB-|-rcb-|-RRB-|Gtype  tonB|tonb|NN|Gtype  ,|,|,|Gtype  -LCB-|-lcb-|-LRB-|Gtype  delta|delta|NN|Gtype  -RCB-|-rcb-|-RRB-|Gtype  feoA|feoa|NN|Gtype  ,|,|,|Gtype  -LCB-|-lcb-|-LRB-|Gtype  delta|delta|NN|Gtype  -RCB-|-rcb-|-RRB-|Gtype  zupT|zupt|NN|Gtype  K12|k12|NN|Gtype 
 genotype/variation|genotype/variation|NN|O  :|:|:|O  lacking|lack|VBG|Gtype  the|the|DT|Gtype  small|small|JJ|Gtype  RNA|rna|NN|Gtype  RyhB|ryhb|NN|Gtype 
 genotype/variation|genotype/variation|NN|O  :|:|:|O  oxyR-8myc|oxyr-8myc|NN|Gtype  -|-|:|O  tagged|tag|VBN|O 
 genotype/variation|genotype/variation|NN|O  :|:|:|O  soxS-8myc|soxs-8myc|NN|Gtype  -|-|:|O  tagged|tag|VBN|O 
 growth|growth|NN|O  condition|condition|NN|O  :|:|:|O  16|16|CD|Supp  µM|µm|NN|Supp  IPTG|iptg|NN|Supp 
 growth|growth|NN|O  medium|medium|NN|O  :|:|:|O  MOPS|MOPS|NNP|Med  minimal|minimal|JJ|Med  glucose|glucose|NN|Med  media|media|NNS|Med  containing|contain|VBG|O  10|10|CD|Supp  µM|µm|NN|Supp  FeSO4|feso4|NN|Supp 
 growth|growth|NN|O  medium|medium|NN|O  :|:|:|O  MOPS|MOPS|NNP|Med  minimal|minimal|JJ|Med  glucose|glucose|NN|Med  media|media|NNS|Med  containing|contain|VBG|O  1|1|CD|Supp  µM|µm|NN|Supp  FeSO4|feso4|NN|Supp 
 growth|growth|NN|O  phase|phase|NN|O  :|:|:|O  exponential|exponential|JJ|Phase 
 growth|growth|NN|O  phase|phase|NN|O  :|:|:|O  mid-log|mid-log|NN|Phase 
 growth|growth|NN|OD  phase|phase|NN|OD  :|:|:|OD  stationary|stationary|JJ|Phase 
 ∆|∆|CD|Gtype  fnr|fnr|NN|Gtype  ChIP|chip|NN|O  DNA|dna|NN|O  from|from|IN|O  PK4854|pk4854|NN|Gtype 
 Sequenced|sequence|VBD|O  reads|read|VBZ|O  were|be|VBD|O  mapped|map|VBN|O  onto|onto|IN|O  NC|nc|NN|Gversion  _|_|CD|Gversion  000913|000913|CD|Gversion  reference|reference|NN|O  genome|genome|NN|O  sequence|sequence|NN|O  using|use|VBG|O  bowtie|bowtie|NN|O  v1|v1|NN|O  .0.0|.0.0|CD|O  with|with|IN|O  parameters|parameter|NNS|O  -|-|:|O  X|x|NN|O  1000|1000|CD|O  -|-|:|O  n|n|NN|O  2|2|CD|O  -3|-3|CD|O  3|3|LS|O  -|-|:|O  S|s|NN|O 
 Sodium|sodium|NN|O  phosphate|phosphate|NN|O  -LRB-|-lrb-|-LRB-|O  1/100|1/100|CD|O  vol|vol|NN|O  .|.|.|O  of|of|IN|O  1M|1m|NN|O  ,|,|,|O  pH|ph|NN|O  7.6|7.6|CD|O  ;|;|:|O  10|10|CD|O  mM|mm|NN|O  final|final|JJ|O  -RRB-|-rrb-|-RRB-|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  the|the|DT|O  mid-log|mid-log|NN|Phase  cultures|culture|NNS|O  followed|follow|VBN|O  by|by|IN|O  formaldehyde|formaldehyde|NN|O  to|to|TO|O  1|1|CD|O  %|%|NN|O  final|final|JJ|O  and|and|CC|O  anaerobic|anaerobic|JJ|O  sparging|sparging|NN|O  was|be|VBD|O  continued|continue|VBN|O  for|for|IN|O  10|10|CD|O  min|min|NN|O  .|.|.|O  Cold|Cold|NNP|O  2.5|2.5|CD|O  M|m|NN|O  glycine|glycine|NN|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  100mM|100mm|NN|O  and|and|CC|O  the|the|DT|O  mixture|mixture|NN|O  was|be|VBD|O  incubated|incubate|VBN|O  at|at|IN|O  4|4|CD|O  °C|°c|NN|O  with|with|IN|O  anaerobic|anaerobic|JJ|O  sparging|sparging|NN|O  for|for|IN|O  30|30|CD|O  minutes|minute|NNS|O  to|to|TO|O  stop|stop|VB|O  the|the|DT|O  crosslinking|crosslinking|NN|O  .|.|.|O  Cells|cell|NNS|O  were|be|VBD|O  spun|spin|VBN|O  at|at|IN|O  3500|3500|CD|O  x|x|CC|O  g|g|NN|O  ,|,|,|O  and|and|CC|O  washed|wash|VBN|O  repeatedly|repeatedly|RB|O  with|with|IN|O  phosphate|phosphate|NN|O  buffered|buffer|VBN|O  saline|saline|NN|O  before|before|IN|O  being|be|VBG|O  frozen|freeze|VBN|O  at|at|IN|O  -80|-80|CD|O  °C|°c|NN|O  .|.|.|O  Cell|cell|NN|O  pellets|pellet|NNS|O  -LRB-|-lrb-|-LRB-|O  from|from|IN|O  initial|initial|JJ|O  250|250|CD|O  mL|ml|NN|O  of|of|IN|O  culture|culture|NN|O  -RRB-|-rrb-|-RRB-|O  were|be|VBD|O  thawed|thaw|VBN|O  and|and|CC|O  resuspended|resuspend|VBN|O  in|in|IN|O  250|250|CD|O  μL|μl|NN|O  of|of|IN|O  IP|IP|NNP|O  buffer|buffer|NN|O  -LRB-|-lrb-|-LRB-|O  100|100|CD|O  mM|mm|NN|O  Tris|Tris|NNP|O  pH|ph|NN|O  8|8|CD|O  ,|,|,|O  300|300|CD|O  mM|mm|NN|O  NaCl|nacl|NN|O  ,|,|,|O  1|1|CD|O  %|%|NN|O  TritonX-100|tritonx-100|NN|O  -RRB-|-rrb-|-RRB-|O  and|and|CC|O  sonicated|sonicate|VBN|O  using|use|VBG|O  a|a|DT|O  microtip|microtip|NN|O  sonicator|sonicator|NN|O  set|set|VBN|O  at|at|IN|O  10|10|CD|O  %|%|NN|O  output|output|NN|O  for|for|IN|O  20|20|CD|O  second|second|JJ|O  intervals|interval|NNS|O  with|with|IN|O  periods|period|NNS|O  of|of|IN|O  cooling|cool|VBG|O  in|in|IN|O  between|between|IN|O  .|.|.|O  Cells|cell|NNS|O  were|be|VBD|O  then|then|RB|O  treated|treat|VBN|O  for|for|IN|O  one|one|CD|O  hour|hour|NN|O  at|at|IN|O  4|4|CD|O  °C|°c|NN|O  with|with|IN|O  RNase|rnase|NN|O  A|a|NN|O  -LRB-|-lrb-|-LRB-|O  2|2|CD|O  ng/ml|ng/ml|NN|O  -RRB-|-rrb-|-RRB-|O  ,|,|,|O  micrococcal|micrococcal|JJ|O  nuclease|nuclease|NN|O  -LRB-|-lrb-|-LRB-|O  50|50|CD|O  units|unit|NNS|O  -RRB-|-rrb-|-RRB-|O  ,|,|,|O  20|20|CD|O  μM|μm|NN|O  CaCl2|cacl2|NN|O  ,1.2|,1.2|CD|O  mM|mm|NN|O  KCl|kcl|NN|O  ,|,|,|O  0.3|0.3|CD|O  mM|mm|NN|O  NaCl|nacl|NN|O  ,|,|,|O  6|6|CD|O  mM|mm|NN|O  sucrose|sucrose|NN|O  ,|,|,|O  and|and|CC|O  10|10|CD|O  μM|μm|NN|O  DTT|dtt|NN|O  .|.|.|O  EDTA|edta|NN|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  10|10|CD|O  mM|mm|NN|O  to|to|TO|O  stop|stop|VB|O  the|the|DT|O  micrococcal|micrococcal|JJ|O  nuclease|nuclease|NN|O  and|and|CC|O  the|the|DT|O  samples|sample|NNS|O  were|be|VBD|O  spun|spin|VBN|O  down|down|RP|O  to|to|TO|O  remove|remove|VB|O  cell|cell|NN|O  debris|debris|NN|O  .|.|.|O  The|the|DT|O  lysate|lysate|NN|O  was|be|VBD|O  then|then|RB|O  precleared|preclear|VBN|O  through|through|IN|O  incubation|incubation|NN|O  with|with|IN|O  a|a|DT|O  50/50|50/50|CD|O  slurry|slurry|NN|O  of|of|IN|O  sepharose|sepharose|NN|O  protein|protein|NN|O  A|a|NN|O  beads|bead|NNS|O  in|in|IN|O  IP|IP|NNP|O  buffer|buffer|NN|O  for|for|IN|O  2-3|2-3|CD|O  hours|hour|NNS|O  at|at|IN|O  4|4|CD|O  °C|°c|NN|O  .|.|.|O  The|the|DT|O  beads|bead|NNS|O  were|be|VBD|O  removed|remove|VBN|O  by|by|IN|O  centrifugation|centrifugation|NN|O  and|and|CC|O  antibody|antibody|NN|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  the|the|DT|O  pre-cleared|pre-cleared|JJ|O  lysate|lysate|NN|O  for|for|IN|O  an|a|DT|O  overnight|overnight|JJ|O  incubation|incubation|NN|O  .|.|.|O  The|the|DT|O  next|next|JJ|O  day|day|NN|O  ,|,|,|O  30|30|CD|O  μl|μl|NN|O  of|of|IN|O  a|a|DT|O  50/50|50/50|CD|O  slurry|slurry|NN|O  of|of|IN|O  sepharose|sepharose|NN|O  protein|protein|NN|O  A|a|NN|O  beads|bead|NNS|O  in|in|IN|O  IP|IP|NNP|O  buffer|buffer|NN|O  was|be|VBD|O  added|add|VBN|O  to|to|TO|O  the|the|DT|O  lysate|lysate|NN|O  to|to|TO|O  capture|capture|VB|O  antibody-protein-DNA|antibody-protein-dna|JJ|O  complex|complex|NN|O  for|for|IN|O  one|one|CD|O  hour|hour|NN|O  at|at|IN|O  4|4|CD|O  °C|°c|NN|O  .|.|.|O  Beads|bead|NNS|O  were|be|VBD|O  then|then|RB|O  washed|wash|VBN|O  once|once|RB|O  with|with|IN|O  1|1|CD|O  ml|ml|NN|O  of|of|IN|O  LiCl|licl|NN|O  wash|wash|NN|O  buffer|buffer|NN|O  -LRB-|-lrb-|-LRB-|O  100|100|CD|O  mM|mm|NN|O  Tris|Tris|NNP|O  pH|ph|NN|O  8|8|CD|O  ,|,|,|O  250|250|CD|O  mM|mm|NN|O  LiCl|licl|NN|O  ,|,|,|O  2|2|CD|O  %|%|NN|O  TritonX-100|tritonx-100|NN|O  -RRB-|-rrb-|-RRB-|O  ,|,|,|O  twice|twice|RB|O  with|with|IN|O  600|600|CD|O  mM|mm|NN|O  NaCl|nacl|NN|O  wash|wash|NN|O  buffer|buffer|NN|O  -LRB-|-lrb-|-LRB-|O  100|100|CD|O  mM|mm|NN|O  Tris|Tris|NNP|O  pH|ph|NN|O  8|8|CD|O  ,|,|,|O  600|600|CD|O  mM|mm|NN|O  NaCl|nacl|NN|O  ,|,|,|O  2|2|CD|O  %|%|NN|O  TritonX-100|tritonx-100|NN|O  -RRB-|-rrb-|-RRB-|O  ,|,|,|O  twice|twice|RB|O  with|with|IN|O  300|300|CD|O  mM|mm|NN|O  NaCl|nacl|NN|O  wash|wash|NN|O  buffer|buffer|NN|O  -LRB-|-lrb-|-LRB-|O  100|100|CD|O  mM|mm|NN|O  Tris|Tris|NNP|O  pH|ph|NN|O  8|8|CD|O  ,|,|,|O  300|300|CD|O  mM|mm|NN|O  NaCl|nacl|NN|O  ,|,|,|O  2|2|CD|O  %|%|NN|O  TritonX-100|tritonx-100|NN|O  -RRB-|-rrb-|-RRB-|O  ,|,|,|O  and|and|CC|O  twice|twice|RB|O  with|with|IN|O  TE|te|NN|O  .|.|.|O  Elution|elution|NN|O  buffer|buffer|NN|O  -LRB-|-lrb-|-LRB-|O  50|50|CD|O  mM|mm|NN|O  Tris|Tris|NNP|O  pH|ph|NN|O  8|8|CD|O  ,|,|,|O  10|10|CD|O  mM|mm|NN|O  EDTA|edta|NN|O  ,|,|,|O  1|1|CD|O  %|%|NN|O  SDS|sds|NN|O  -RRB-|-rrb-|-RRB-|O  was|be|VBD|O  added|add|VBN|O  after|after|IN|O  the|the|DT|O  final|final|JJ|O  wash|wash|NN|O  step|step|NN|O  ,|,|,|O  and|and|CC|O  beads|bead|NNS|O  were|be|VBD|O  incubated|incubate|VBN|O  at|at|IN|O  65|65|CD|O  °C|°c|NN|O  for|for|IN|O  30|30|CD|O  minutes|minute|NNS|O  to|to|TO|O  remove|remove|VB|O  the|the|DT|O  crosslinked|crosslink|VBN|O  protein-DNA|protein-dna|JJ|O  complexes|complex|NNS|O  from|from|IN|O  the|the|DT|O  beads|bead|NNS|O  .|.|.|O  After|after|IN|O  centrifugation|centrifugation|NN|O  to|to|TO|O  remove|remove|VB|O  the|the|DT|O  beads|bead|NNS|O  ,|,|,|O  the|the|DT|O  samples|sample|NNS|O  were|be|VBD|O  incubated|incubate|VBN|O  overnight|overnight|RB|O  at|at|IN|O  65|65|CD|O  °C|°c|NN|O  to|to|TO|O  reverse|reverse|VB|O  the|the|DT|O  protein-DNA|protein-dna|JJ|O  formaldehyde|formaldehyde|NN|O  crosslinks|crosslink|NNS|O  .|.|.|O  DNA|dna|NN|O  was|be|VBD|O  purified|purify|VBN|O  using|use|VBG|O  Qiagen|Qiagen|NNP|O  's|'s|POS|O  PCR|pcr|NN|O  Purification|purification|NN|O  kit|kit|NN|O  and|and|CC|O  eluted|elute|VBN|O  to|to|TO|O  a|a|DT|O  final|final|JJ|O  volume|volume|NN|O  of|of|IN|O  50|50|CD|O  μl|μl|NN|O  with|with|IN|O  EB|EB|NNP|O  .|.|.|O 
 strain|strain|NN|O  :|:|:|O  MG1655|mg1655|NN|O  K-12|k-12|NN|O  WT|wt|JJ|Gtype 
 acetate|acetate|NN|Supp 
 The|the|DT|O  cultured|culture|VBN|O  cells|cell|NNS|O  were|be|VBD|O  inoculated|inoculate|VBN|O  with|with|IN|O  1:100|1:100|CD|O  dilution|dilution|NN|O  into|into|IN|O  50|50|CD|O  mL|ml|NN|O  of|of|IN|O  the|the|DT|O  fresh|fresh|JJ|O  M9|m9|NN|O  medium|medium|NN|O  containing|contain|VBG|O  2|2|CD|O  g/L|g/l|NN|O  glucose|glucose|NN|O  in|in|IN|O  either|either|CC|O  the|the|DT|O  presence|presence|NN|O  or|or|CC|O  absence|absence|NN|Supp  of|of|IN|Supp  1|1|CD|Supp  g/L|g/l|NN|Supp  arginine|arginine|NN|Supp  and|and|CC|O  continued|continue|VBD|O  to|to|TO|O  culture|culture|NN|O  at|at|IN|O  37|37|CD|O  °C|°c|NN|O  until|until|IN|O  reaching|reach|VBG|O  an|a|DT|O  appropriate|appropriate|JJ|O  cell|cell|NN|O  density|density|NN|O  -LRB-|-lrb-|-LRB-|O  OD600|od600|NN|O  ≈|≈|CD|O  0.5|0.5|CD|O  -RRB-|-rrb-|-RRB-|O  .|.|.|O 
 The|the|DT|O  cultured|culture|VBN|O  cells|cell|NNS|O  were|be|VBD|O  inoculated|inoculate|VBN|O  with|with|IN|O  1:100|1:100|CD|O  dilution|dilution|NN|O  into|into|IN|O  50|50|CD|O  mL|ml|NN|O  of|of|IN|O  the|the|DT|O  fresh|fresh|JJ|O  M9|m9|NN|Med  medium|medium|NN|Med  containing|contain|VBG|O  2|2|CD|Supp  g/L|g/l|NN|Supp  glucose|glucose|NN|Supp  in|in|IN|O  either|either|CC|O  the|the|DT|O  presence|presence|NN|Supp  or|or|CC|Supp  absence|absence|NN|Supp  of|of|IN|Supp  1|1|CD|Supp  g/L|g/l|NN|Supp  arginine|arginine|NN|Supp  and|and|CC|O  continued|continue|VBD|O  to|to|TO|O  culture|culture|NN|O  at|at|IN|O  37|37|CD|Temp  °C|°c|NN|Temp  until|until|IN|O  reaching|reach|VBG|O  an|a|DT|O  appropriate|appropriate|JJ|O  cell|cell|NN|O  density|density|NN|O  -LRB-|-lrb-|-LRB-|O  OD600|od600|NN|OD  ≈|≈|CD|OD  0.5|0.5|CD|OD  -RRB-|-rrb-|-RRB-|O  .|.|.|O 
 To|to|TO|O  harvest|harvest|VB|O  total|total|JJ|O  RNA|rna|NN|O  samples|sample|NNS|O  ,|,|,|O  overnight|overnight|JJ|O  cultures|culture|NNS|O  of|of|IN|O  wild|wild|JJ|Gtype  type|type|NN|Gtype  MG1655|mg1655|NN|O  grown|grow|VBN|O  in|in|IN|O  LB|lb|NN|O  at|at|IN|O  37|37|CD|O  ˚C|˚c|NN|O  were|be|VBD|O  diluted|dilute|VBN|O  back|back|RB|O  1:500|1:500|CD|O  in|in|IN|O  either|either|CC|O  fresh|fresh|JJ|O  LB|lb|NN|O  or|or|CC|O  M63|m63|NN|O  minimal|minimal|JJ|O  glucose|glucose|NN|O  medium|medium|NN|O  and|and|CC|O  allowed|allow|VBN|O  to|to|TO|O  grow|grow|VB|O  until|until|IN|O  the|the|DT|O  cultures|culture|NNS|O  reached|reach|VBD|O  an|a|DT|O  OD600|od600|NN|O  of|of|IN|O  ~|~|NN|O  0.4|0.4|CD|O  and|and|CC|O  2.0|2.0|CD|O  for|for|IN|O  cultures|culture|NNS|O  grown|grow|VBN|O  in|in|IN|O  LB|lb|NN|O  and|and|CC|O  an|a|DT|O  OD600|od600|NN|O  of|of|IN|O  ~|~|NN|O  0.4|0.4|CD|O  for|for|IN|O  cultures|culture|NNS|O  grown|grow|VBN|O  in|in|IN|O  M63|m63|NN|O  .|.|.|O  For|for|IN|O  samples|sample|NNS|O  grown|grow|VBN|O  to|to|TO|O  OD600|od600|NN|OD  of|of|IN|OD  ~|~|NN|OD  0.4|0.4|CD|OD  a|a|DT|O  total|total|JJ|O  volume|volume|NN|O  of|of|IN|O  25|25|CD|O  ml|ml|NN|O  of|of|IN|O  cells|cell|NNS|O  were|be|VBD|O  harvested|harvest|VBN|O  and|and|CC|O  combined|combine|VBN|O  with|with|IN|O  5|5|CD|O  ml|ml|NN|O  of|of|IN|O  stop|stop|NN|O  solution|solution|NN|O  -LRB-|-lrb-|-LRB-|O  95|95|CD|O  %|%|NN|O  Ethanol|ethanol|NN|O  ,|,|,|O  5|5|CD|O  %|%|NN|O  acid|acid|NN|O  phenol|phenol|NN|O  -RRB-|-rrb-|-RRB-|O  .|.|.|O  For|for|IN|O  samples|sample|NNS|O  grown|grow|VBN|O  to|to|TO|O  OD600|od600|NN|O  of|of|IN|O  2.0|2.0|CD|O  a|a|DT|O  total|total|JJ|O  volume|volume|NN|O  of|of|IN|O  5|5|CD|O  ml|ml|NN|O  of|of|IN|O  cells|cell|NNS|O  were|be|VBD|O  harvested|harvest|VBN|O  and|and|CC|O  combined|combine|VBN|O  with|with|IN|O  1|1|CD|O  ml|ml|NN|O  of|of|IN|O  stop|stop|NN|O  solution|solution|NN|O  .|.|.|O 
 treated|treat|VBN|O  with|with|IN|O  :|:|:|O  250|250|CD|Supp  uM|um|NN|Supp  of|of|IN|Supp  paraquat|paraquat|NN|Supp  at|at|IN|O  mid-log|mid-log|NN|Phase  pahse|pahse|NN|Phase  for|for|IN|O  20|20|CD|Supp  min|min|NN|Supp 
 treatment|treatment|NN|O  :|:|:|O  glucose|glucose|NN|Med  -LRB-|-lrb-|-LRB-|Med  2|2|CD|Med  g/L|g/l|NN|Med  -RRB-|-rrb-|-RRB-|Med  minimal|minimal|JJ|Med  M9|m9|NN|Med  medium|medium|NN|Med  supplemented|supplement|VBN|O  without|without|IN|O  10|10|CD|Supp  mM|mm|NN|Supp  leucine|leucine|NN|Supp  .|.|.|O 
 treatment|treatment|NN|O  :|:|:|O  glucose|glucose|NN|Med  -LRB-|-lrb-|-LRB-|Med  2|2|CD|Med  g/L|g/l|NN|Med  -RRB-|-rrb-|-RRB-|Med  minimal|minimal|JJ|Med  W2|w2|NN|Med  medium|medium|NN|Med  supplemented|supplement|VBN|O  with|with|IN|O  1g/L|1g/l|NN|Supp  arginine|arginine|NN|Supp  .|.|.|O