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Table 1 Confirmed mutations discovered in eleven endpoint strains of MG1655 adapted to growth in lactate minimal media

From: Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

Endpoint Gene Product/duplication Class Nucleotide Codon Protein change
LactA crp cAMP response protein Regulator t452a CTG->CAG L151Q
  hfq RNA binding protein Regulator c28t CCG->TCG P10S
  ydjO Predicted protein - t138g GGT->GGG G46G
   ~87 kb duplication (3946000-4033000)     
LactB gcvT Glycine cleavage system Metabolic Δ1 bp (971) Frameshift  
   ~44 kb duplication (1248300-1292200)     
LactC rph-pyrE RNase PH/orotate phosphoribosyltransferase Metabolic Δ82bp Frameshift  
  cya Adenylate cyclase Regulator c547t CTT->TTT L183F
  infC IF-3 Translation g283a GAA->AAA E95K
LactD rph-pyrE RNase PH/orotate phosphoribosyltransferase Metabolic Δ82 bp Frameshift  
  ppsA Phosphoenolpyruvate synthase Metabolic c288a ATC->ATA I96I
  atoS AtoS/AtoC two component regulatory system Regulator a1367c CAA->CCA Q456P
  relA ppGpp synthetase Regulator a956c TAT->TCT Y319S
  rho Transcription termination factor Regulator c304t CGC->TGC R102C
  hepA RNAP recycling factor Regulator c2665t CAA->TAA Q889(stop)
  kdtA KDO transferase Cell envlp. t701a GTA->GAA V234E
LactE ppsA Phosphoenolpyruvate synthase Metabolic c17t TCG->TTG S6L
  acpP Acyl carrier protein Metabolic g50t GGC->GTC G17V
  hfq RNA binding protein Regulator c28t CCG->TCG P10S
  crp cAMP response protein Regulator t497c ATC->ACC I166T
  ydcI Putative transcriptional regulator - g41a CGC->CAC R14H
  yjbM Predicted protein - g141a ATG->ATA M47I
   ~140 kb duplication (3620000-3760000), ~87 kb duplication (3946000-4033000)     
LactF rph-pyrE RNase PH/orotate phosphoribosyltransferase Metabolic Δ82 bp Frameshift  
  kdtA KDO transferase Cell envlp. g292a GGG->AGG G98R
  rpoC RNA polymerase Regulator c2524t CGT->TGT R842C
  argS Arginyl-tRNA synthetase Translation g110c GGC->GCC G37A
   ~12 kb duplication (1774000-1786000)     
LactG rph-pyrE RNase PH/orotate phosphoribosyltransferase Metabolic Δ82 bp Frameshift  
  trpB Tryptophan synthase Metabolic g462t GCG->GCT A154A
  nadB NAD biosynthesis Metabolic c405t GCC->GCT A135A
  rpoB RNA polymerase Regulator a1664c TAC->TCC Y555S
  rpoS σS Regulator Δ1 bp (609) Frameshift  
  kdtA KDO transferase Cell envlp. g292a GGG->AGG G98R
  osmF ABC transporter involved in osmoprotection Cell envlp. ins T after 873 AAA->TAA K292(stop)
  proQ Predicted structural transport element Cell envlp. g(-8)t Promoter  
LactH rph-pyrE RNase PH/orotate phosphoribosyltransferase Metabolic Δ82 bp Frameshift  
  pdxB Erythronate-4-phosphate dehydrogenase Metabolic g286t GTG->TTG V96L
  ilvG_1 Acetolactate synthase II (pseudogene) Metabolic Δ1 bp (977) Frameshift  
  rpoB RNA polymerase Regulator Δ1 bp (4006) Frameshift  
  kdtA KDO transferase Cell envlp. g292a GGG->AGG G98R
  wcaA Glycosyl transferase Cell envlp. Δ4 bp (506509) Frameshift  
LactI rph-pyrE RNase PH/orotate phosphoribosyltransferase Metabolic Δ82 bp Frameshift  
  relA ppGpp synthetase Regulator g4c GTT->CTT V2L
  proQ Predicted structural transport element Cell envlp. ins T after 15 Frameshift, AAG->TAA K6(stop)
LactJ rph-pyrE RNase PH/orotate phosphoribosyltransferase Metabolic Δ82 bp Frameshift  
  mrdA Peptidoglycan synthetase, PBP2 Cell envlp. c157a CGC->AGC R53S
  rpsA 30S ribosomal subunit Translation a490t AAC->TAC N164Y
  kgtP Á-ketoglutarate MFS transporter Cell envlp. g1083a AAG->AAA K361K
  kgtP    Δ1 bp (1212) Frameshift  
   Intergenic   g3630812t   
LactK ppsA Phosphoenolpyruvate synthase Metabolic g61a GTA->ATA V21I
  rpoC RNA polymerase Regulator Δ9 bp (36113619) In frame V1204G
  ryhA Small RNA that interacts with Hfq Regulator c(-9)t Promoter  
  treA Trehalase Osmotic g676a GCG->ACG A226T
  secE Sec protein secretion complex Cell envlp. g350a CGC->CAC R117H
  secF Sec protein secretion complex Cell envlp. g109a GCT->ACT A37T
   ~40 kb duplication (1253000-1294000)     
  1. DNA from single colonies isolated from the endpoints of the 11 strains adapted to growth on lactate M9 minimal media were screened for mutations using Nimblegen CGS and Solexa technologies. Mutations (except for large duplications) were confirmed by Sanger sequencing of the DNA isolated from the single colonies using primers flanking the mutated site. Nucleotide changes refer to position within the respective gene, deletions are indicated by the Δ symbol, and insertions are marked by 'ins'. The rph-pyrE Δ82 bp mutation is described in Figure 3. Genomic coordinates of large duplications are shown in parentheses. Cell envlp., cell envelope.