Skip to main content

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.