Skip to main content

Table 2 BM28 and BM28 ΔlysU mutations in and around essential genes

From: Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains

Gene(s)a

B number(s)b

Gene product(s)

Mutation(s)c

ΔΔG predicted by DDGun [40] (kcal/mol)d

tsf

b0170

protein chain elongation factor EF-Ts

Q114R

0.1

 < -proS‡- / < -trmO‡-

b0194 / b0195

proline–tRNA ligase / tRNA m(6)t(6)A37 methyltransferase

A8 —> A7

n/a

dxs

b0420

1-deoxy-D-xylulose-5-phosphate synthase

M159V

-0.1

hemH

b0475

ferrochelatase

Silent codon 195

n/a

sucA

b0726

subunit of E1(0) component of 2-oxoglutarate dehydrogenase

T434A

0

cydC

b0886

glutathione/L-cysteine ABC exporter subunit CydC

R183C

0

rpsA

b0911

30S ribosomal subunit protein S1

Silent codon 73 (70.3%)

n/a

mukB

b0924

chromosome partitioning protein MukB

Silent codon 1374

n/a

 < -asnS- / < -pncB-

b0930 / b0931

asparagine–tRNA ligase / nicotinate phosphoribosyltransferase

A7 —> A8 (74.4%)

n/a

topA*

b1274

DNA topoisomerase 1

Silent codon 666

n/a

 < -glyA- / -hmp- > 

b2551 / b2552

serine hydroxymethyltransferase / nitric oxide dioxygenase

A7 —> A6

n/a

alaS

b2697

alanine-tRNA ligase/DNA-binding transcriptional repressor

Silent codon 196

n/a

cca‡

b3056

fused tRNA nucleotidyltransferase/2',3'-cyclic phosphodiesterase/2' nucleotidase and phosphatase

Silent codon 345

n/a

 < -rbfA- / < -infB-

b3167 / b3168

30S ribosome binding factor / translation initiation factor IF-2

tnpA insertion

n/a

murA*

b3189

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

T10M

0.4

rpsH

b3306

30S ribosomal subunit protein S8

R13C

-0.5

rplC

b3320

50S ribosomal subunit protein L3

V189I

0.1

rho

b3783

transcription termination factor Rho

T96I

0.6

rpoC

b3988

RNA polymerase subunit beta'

A595V, T1135I

0.6

dnaB

b4052

replicative DNA helicase

P264S

0.3

  1. aFor intergenic mutations, arrows surrounding genes indicate their directions, the essential gene in underlined and genes in bold have the insertion upstream of their start codons, meaning the insertions may affect the promoters or ribosome-binding sites of the genes. Mutations only present in BM28 are indicated with an asterisk (*) and mutations only present in BM28 ΔlysU are indicated with a double dagger (‡)
  2. bThe b number is shown in bold if the encoded protein was detected in an E. coli protein melting temperature study and determined to have a melting temperature ≤ 53.5 °C (≤ 5 °C above the Tmax of BM28) [36]
  3. cFor coding mutations, nonsilent mutations are shown in bold and if a change is at < 75% frequency the percent frequency is shown in brackets
  4. dThe change in the Gibbs free energy of unfolding as predicted by DDGun [40] using the amino acid substitution(s) and a PDB structure or Alphafold predicted structure [42] of the protein. Positive values indicate an increase in protein stability and negative values indicate a decrease in protein stability
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us