Table 1.
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 |
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.