Table 1 Targets of adaptation differ in E. coli evolving in WT and Rag2−/− animals.

From: Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

Gene

Function

Frequency of mice

  

WT

Rag2 −/−

gat Operon

Metabolism of galactitol

100% (±7%)

100% (±7%)

srlR

Metabolism of sorbitol

50% (±13%)

60% (±13%)

focA/ycaO

Anaerobic respiration (formate transporter)

29% (±12%)

40% (±13%)

yjjP/yjjQ

Inner membrane protein

57% (±13%)

13% (±9%)***

kdgR

Metabolism of sugar acids

14% (±9%)

13% (±9%)

dcuB/dcuR

Anaeobic respiration (fumarate, succinate transporter)

50% (±13%)

0%***

yeaR

Metabolism of nitric compounds

14% (±9%)

0%

arcB

Regulation of respiration

0%

13% (±9%)

frlR

Metabolism of fructosamines

0%

13% (±9%)

rimJ

Modification of ribosomal proteins

0%

13% (±9%)

  1. WGS, whole-genome sequencing; WT, wild type.
  2. Frequency (±2 s.e.m.) of WT (n=14) or Rag2−/− (n=15) populations in which parallel mutations at a given locus were found segregating at high frequency (>10%). These loci, identified through WGS of population samples, were observed in at least two populations and thus correspond to bona fide targets of beneficial mutations. Mutations whose emergence differs significantly between the two host genetic backgrounds are highlighted in bold, with the level of significance displayed (binomial test ***P<0.001).
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