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

BMC Genomics

Table 3 BM28 and BM28 ΔlysU mutations in and around heat shock genes

Gene(s)^a	B number(s)^b	Gene product(s)	Mutation(s)^c	ΔΔG predicted by DDGun [40] (kcal/mol)^d
ycjX	b1321	DUF463 domain-containing protein YcjX	R278C	-0.8
topA*	b1274	DNA topoisomerase 1	Silent codon 666	n/a
< *-hslV-* / < -ftsN-	b3932 / b3933	peptidase component of the HslVU protease / cell division protein FtsN	G₆—> G₄	n/a

^aFor intergenic mutations, arrows surrounding genes indicate their directions, the heat shock 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 there are no BM28 ΔlysU specific mutations
^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 T_max of BM28) [36]
^cFor coding mutations, nonsilent mutations are shown in bold and all changes are at 100% frequency
^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

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