TABLE 1.

Gene fitness values and differential protein expression in Rhodospirillum rubrum S1H

Locus	Description	Phaeobacter inhibens BS107						Phaeobacter inhibens BS107
		Protein fold changec	P valuec	Succinate gene fitnessd	Acetate gene fitnessd	P valued	No. of strainse	Acetate gene fitnessf
Ethylmalonyl-CoA pathway
Rru_A1927	Acetyl-CoA hydrolase	1.83	4.2e−3	0.0	2.1	8.7e−5	19	n.a.g
Rru_A2964	MaoC-like dehydratase	0.81	4.9e−1	0.0	−0.8	1.3e−2	7	−1.4
Rru_A3063	Crotonyl-CoA carboxylase/reductase	3.20	2.5e−3	−0.2	−1	1.4e−3	14	−2.7
Rru_A1572a	Ethylmalonyl-CoA/methylmalonyl-CoA epimerase	1.58	8.1e−3	n.a.	n.a.	n.a.	5	n.a.
Rru_A3062	Ethylmalonyl-CoA mutase	8.80	7.9e−5	0.0	−1.0	1.9e−2	35	−2.8
Rru_A3064	Methylsuccinyl-CoA dehydrogenase	2.79	7.0e−3	0.0	−1.2	1.5e−2	26	−3.0
Rru_A1201	Mesaconyl-CoA hydratase	4.46	3.4e−4	0.1	−1.3	6.3e−3	17	−2.7
Rru_A0217	l-Malyl-CoA/b-methylmalyl-CoA lyase	2.08	2.6e−3	0.0	−1.5	1.9e−2	17	−2.5
Rru_A1200b	Malyl-CoA thioesterase	2.31	1.3e−3	n.a.	n.a.	n.a.	6	−1.9
Rru_A0052	Biotin carboxylase	4.75	3.1e−6	0.0	−2.7	2.9e−4	34	n.a.
Rru_A0053	Carboxyltransferase	5.14	4.5e−5	−0.1	−2.6	2.3e−3	21	n.a.
Rru_A2479	Methylmalonyl-CoA mutase	1.98	5.6e−3	−0.1	−3.4	2.4e−3	29	n.a.
Branched-chain amino acid biosynthesis pathway
Rru_A0467	Acetolactate synthase, large subunit	3.12	3.2e−3	−2	−4.0	3.4e−4	33	−2.1
Rru_A0468	Acetolactate synthase, small subunit	3.07	3.5e−3	n.a.	n.a.	n.a.	5	−0.3
Rru_A0469	Ketol-acid reductoisomerase	4.07	5.0e−4	−2.2	−3.5	2.8e−2	20	n.a.
Rru_A1786	Dihydroxy-acid dehydratase	1.62	4.1e−2	−2.4	−3.5	7.0e−2	28	−3.3
Rru_A1040	Leucine dehydrogenase	0.03	1.1e−3	0.0	0.0	9.0e−1	18	1.0
Citramalate cycle
Rru_A06 95	2-Isopropylmalate synthase	1.59	1.2e−2	−0.1	−0.2	4.6e−1	23	1.1

^aCentral sequence too short to be included in the data set based on acceptance criteria used in a previous study (17).

^bNot included in the data set because fitness could be accurately measured in only 2 of 3 of the replicates.

^cProtein fold change is defined as the ratio of the abundance of a protein under acetate conditions to the abundance under succinate conditions. The statistical significance of the results of comparisons of the acetate and succinate conditions was determined with an unpaired t test. Data are from Leroy et al. (13).

^dThe strain fitness is defined as the log₂ value of the ratio between the strain abundance reached after 5 generations and the abundance at time zero (T₀) under the relevant condition. The gene fitness values were calculated by averaging the strain fitness values for each gene. The presented gene fitness values are the average values resulting from three independent fitness assays for each condition. The statistical significance of the results of comparisons of the acetate and succinate conditions was determined with an unpaired t test. Italicized loci are plotted in Fig. 1B. The complete data set is available in the supplemental material.

^eNo. of strains, the number of strains with one independent central transposon insertion per gene in the mutant library.

^fThe gene fitness values for Phaeobacter inhibens BS107 were obtained from the 3H35 experiment set available on the Fitness Browser webtool (http://fit.genomics.lbl.gov) and were determined under dark aerobic conditions with acetate as the carbon source.

^gn.a., not assayed.