Skip to main content

Advertisement

Table 1 Mutations discovered in genome resequencing of evolved isobutanol tolerant E. coli clones

From: Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

Clone Gene Gene Description Biological Process Cellular Location Genomic Coordinate Nucleotide Change Protein Change
G3.2/G3.6 phoQ sensory histidine kinase in two-component regulatory system with PhoP Signal transduction Inner membrane 1197581 A→G L209P
  acrB multidrug efflux system protein Transport Inner and outer membrane 480665 G→A P988L
  queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC:5.-.-.-) Translation Cytoplasm 425270 A→G N346D
  secA preprotein translocase subunit, ATPase Protein secretion Inner membrane 108975 T→C S233P
  cadA lysine decarboxylase 1 (EC:4.1.1.18) Amino acid metabolism Cytoplasm 4363790 A→G I686T
  groL Cpn60 chaperonin GroEL, large subunit of GroESL Protein folding Cytoplasm 4378650 A→C K132N
  mutL methyl-directed mismatch repair protein Mismatch repair Cytoplasm 4405650 -19 bp Frameshift
  pstC phosphate transporter subunit Transport Inner membrane 3917582 T→C D16G
  rph defective ribonuclease PH RNA processing Cytoplasm 3823229 +4:GGTC Frameshift
  yiaK 2,3-diketo-L-gulonate dehydrogenase, NADH-dependent (EC:1.1.1.-) Carbohydrate metabolism Cytoplasm 3750540 T→C L193P
  gltD glutamate synthase, 4Fe-4S protein, small subunit (EC:1.4.1.13) Amino acid, Nitrogen metabolism Cytoplasm 3367270 +1:G Frameshift
  mdh malate dehydrogenase, NAD(P)-binding (EC:1.1.1.37) Tricarboxylic acid cycle Membrane peripheral 3390726 -1:C Frameshift
  nlpI lipoprotein involved in cell division Cell cycle Inner membrane 3316213 T→C Non-coding region; Possible effect on terminator before nlpI
  glnE fused deadenylyltransferase/adenylyltransferase for glutamine Nitrogen metabolism Cytoplasm 3205272 IS186 insertion Disruption
  hybB predicted hydrogenase 2 cytochrome b type component Electron transport chain Inner membrane 3150318 A→G V359A
  gatZ D-tagatose 1,6-bisphosphate aldolase 2, subunit (EC:4.1.2.40) Carbohydrate metabolism Cytoplasm 2182915 -1:C Frameshift
  yeeE predicted inner membrane protein - Inner membrane 2092513 A→G S333P
  lepB leader peptidase (signal peptidase I) (EC:3.4.21.89) Transport Inner membrane 2711902 G→A P213S
  hfq HF-I, host factor for RNA phage Q β replication Translation Cytoplasm 4407505 -7:AGGAAAA Non-coding region; Ribosome binding site deletion
  marC conserved protein; predicted transporter - Inner membrane 1625925 IS1 insertion Disruption
G3.266.7 groL Cpn60 chaperonin GroEL, large subunit of GroESL Protein folding Cytoplasm 4378650 A→C K132N
  rph defective ribonuclease PH RNA processing Cytoplasm 3823229 +4:GGTC Frameshift
  gltB-yhcE - - - - -9.9 kb ΔgltBDF, ΔyhcADE
  mdh malate dehydrogenase, NAD(P)-binding (EC:1.1.1.37) Tricarboxylic acid cycle Membrane peripheral 3390726 -1:C Frameshift
  glnE fused deadenylyltransferase/adenylyltransferase for glutamine Nitrogen metabolism Cytoplasm 3205272 IS186 insertion Disruption
  hfq HF-I, host factor for RNA phage Q β replication Translation Cytoplasm 4407505 -7:AGGAAAA Non-coding region; Ribosome binding site deletion
  ycfK e14 prophage; predicted protein - - 1216432 -1688 bp ΔycfK
  marC conserved protein; predicted transporter - Inner membrane 1625925 IS1 insertion Disruption
X3.5 acrA multidrug efflux system protein Transport Inner and outer membrane 483735 +1:A Frameshift
  rpsB 30S ribosomal subunit protein S2 Translation Cytoplasm 190557 +1:A Frameshift
  rph defective ribonuclease PH RNA processing Cytoplasm   -1:C Frameshift
  mdh malate dehydrogenase, NAD(P)-binding (EC:1.1.1.37) Tricarboxylic acid cycle Membrane peripheral 3390936 +5:AACCT Frameshift
  deaD DEAD-box RNA helicase Translation Cytoplasm 3314027 +4:AGAC Frameshift
  yfgO predicted inner membrane protein - Inner membrane 2623022 C→T G30D
  gatC galactitol-specific enzyme IIC component of PTS Transport Inner membrane 2180640 C→T E290K
  plsX fatty acid/phospholipid synthesis protein Fatty acid metabolism Cytoplasm 1493514 A→G E216G
  hrpA ATP-dependent helicase RNA processing Cytoplasm 1493514 C→T L1075L
  mdtJ-tqsA MdtJ SMR protein; transporter of quorum signal AI-2 Transporter/Transporter Inner membrane 1681114 IS5 insertion Non-coding region; mdtJ and tqsA promoter region
  marC conserved protein; predicted transporter - Inner membrane 1626081 IS1 insertion Disruption
  1. Clonal isolates from isobutanol tolerant E. coli EcNR1 populations were sequenced with the Illumina platform to identify mutations. Clones G3.2 and G3.6 were taken from the G3 end point population, which developed a mutator phenotype via a 19 bp deletion in mutL. These clones thus each have a large number of mutations, so for brevity we show here the subset of mutations shared between G3.2/G3.6 (full mutation lists available in Additional file 1). All mutations shown above were verified by Sanger sequencing. Mutation entries that are bold and italic denote loci that were mutated in all sequenced clones from end populations. The mutation positions are listed as absolute genomic coordinates in the E. coli EcNR1 reference sequence (available in Additional file 2). SNPs are indicated by base transition/transversion. Small insertions are indicated by a '+', with the size (number of bp) of the insertion and sequence of inserted bases. Small deletions are designated by '-' with a format similar to that for small insertions; for large deletions, the sequence of deleted bases is excluded. Transposons are indicated by the insertion sequence (IS) identity.