Table 1 Mutations that occurred in the evolved PB13 strain during the ALE process

(A) JM101 vs PB13 Non-synonymous point mutations (WG)

Hypothetical/putative/unknown function genes

 wzyE

Predicted Wzy protein involved in ECA polysaccharide chain elongation

GCG

GtG

221

74 A-V

 ydiM

Predicted transporter of the major facilitator superfamily (MFS) of transporters

TTC

cTC

982

328 F-L

 ydaF

Predicted protein

ACT

AaT

116

39 T-N

Metabolism and transport

 bglA

One of several 6-phospho-β-glucosidases in E. coli

CCG

CtG

839

280 P-L

 deoB

Phosphodeoxyribomutase; catabolic enzyme of the pyrimidine deoxyribonucleosides degradation pathway

GAC

GgC

848

283 D-G

 dhaM

Dihydroxyacetone kinase subunit M, homologous to certain PTS components

TGg

TGa

1038

346 W-stop

 glpT

Major uptake transporter for glycerol-3-phosphate, belongs to the major Facilitator Superfamily (MFS)

CCG

CtG

416

139 P-L

 ispG

IspG, catalyzes the sixth step in the methylerythritol phosphate pathway

GTC

GcC

749

250 V-A

 mepA

Penicillin-insensitive d-alanyl-d-alanine (DD) endopeptidase

CGT

CaT

197

66 R-H

 msbA

ATP-binding lipopolysacchride transport complex

ACG

gCG

367

123 T-A

 xapB

Xanthosine MFS transporter

ACC

gCC

1051

351 T-A

 ydcT

YdcT is an ATP-binding component of a predicted spermidine/putrescine ABC transporter

CCG

CtG

113

38 P-L

Cellular constituents

 fliN

FliN, is one of three components of the flagellar motor’s “switch complex”

GAT

GgT

371

124 D-G

Regulatory genes

 polA

DNA Polymerase I (Pol I)

GCG

GtG

2084

695 A-V

(B) JM101 vs PB13 Deletions (WG)

 ptsP

Member of a second PTS chain involved in nitrogen metabolism

Pres

Abs

–

–

 rppH

RNA pyrophosphohydrolase that initiates mRNA degradation by hydrolysis of the 5′-triphosphate end

Pres

Abs

–

–

 ygdT

Hypothetical protein

Pres

Abs

–

–

 mutH

dGATC endonuclease in the MutHLS complex, the methyl-directed mismatch repair pathway

Pres

Abs

–

–

 ygdQ

Putative transport protein

Pres

Abs

–

–

 ygdR

Predicted protein

Pres

Abs

–

–

 tas

Putative NAD(P)-linked reductase that acts in starvation-associated mutations

Pres

Abs

–

–

 lplT

Lysophospholipid transporter (LplT)

Pres

Abs

–

–

 aas

2-acylglycerophosphoethanolamine acyltransferase/acyl-ACP synthetase

Pres

Abs

–

–

 omrA

Small RNA that is involved in regulating the protein composition of the outer membrane

Pres

Abs

–

–

 omrB

Small RNA that is involved in regulating the protein composition of the outer membrane

Pres

Abs

–

–

 galR

DNA-binding transcription factor; represses transcription of the operons involved in transport and catabolism of D-galactose

Pres

Abs

–

–