Long term adaptation of a microbial population to a permanent metabolic constraint: overcoming thymineless death by experimental evolution of Escherichia coli

Table 1 Carbon source utilization by β7328 and descendents

	Strains and generations
Substrates	β7328	γ₁₇₁₀	γ₃₃₃₀	γ₅₀₁₀	γ₈₀₉₄
-	-	-	-	-	-
Mannose	+	+	+	+	-
D(+) Galactose	+	+	+	-	-
1-0-Methyl-β-Galactopyranoside	+	+	+	-	-
m-Coumarate	+	+	+	-	-
1-0-Methyl-β-glucopyranoside	+	-	-	-	-
α-L-(-) Fucose	+	-	-	-	-
Mucate	+	-	-	-	-
L(+)-Tartrate	+	-	-	-	-
L(-)-malate	+	-	-	-	-
D(+)-Malate	+	-	-	-	-
5-Keto-D-gluconate	+	-	-	-	-
Succinate	+	-	-	-	-
DL-Glycerate	+	-	-	-	-
L-Aspartate	+	-	-	-	-
L-Proline	+	-	-	-	-
L-Alanine	+	-	-	-	-
L-serine	+	-	-	-	-
propionate	+	-	-	-	-
α-Ketoglutarate	+	-	-	-	-
Calculated pathway inactivation probability by genetic drift		0.085–0.85%	0.079–0.79%	0.082–0.82%	1.02%
Observed pathway inactivation probability (under assumption of independence)		15/100 15%	0/85 0%	3/85 3.5%	1/82 1.2%

Growth on 100 different carbon sources was monitored using API100™ kits (Bio-merieux). Observed phenotypes are designated by +(growth) and – (no growth). The mutation probabilities were calculated as follows: an average pathway for carbon source utilization contains from 1 to 10 pathway specific genes (10 to 10⁴ bp). The mutation rate per bp per generation in E. coli is 5.4 10^-10[30] and if the assumption is made that every mutation is inactivating (which is the most conservative hypothesis), the probability of acquiring a mutation in a given pathway after X generations by genetic drift is X 5.4 10^-10 10^{3 or 4}. As the mannose-deficient-phenotype can be due to a mutation in manA, manXYZ or, nagC corresponding to 4128 bp [31], this value was used for the mutation probability between γ₅₀₁₀ and γ₈₀₉₄.

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