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Table 2 Gene fitness values of selected genes in Rhodospirillum rubrum S1H

From: New perspectives on butyrate assimilation in Rhodospirillum rubrum S1H under photoheterotrophic conditions

Locus Tag

Description

Succinate

gene

fitnessc

Butyrate

gene

fitnessc

P-value2

Rru_A1471

Butyryl-CoA:acetate CoA transferase

n.a.

n.a.

n.a.

Rru_A1927

Acetyl-CoA hydrolase

− 0.01

0.1

3e-01

Rru_A3801b

Short chain enoyl-CoA hydratase

n.a.

n.a.

n.a.

Rru_A3079

3-hydroxyacyl-CoA dehydrogenase

−0.45

− 1.16

2e-02

Rru_A1946

Acetoacetyl-CoA thiolase

0.06

−0.03

7e-01

Rru_A0273b

Acetoacetyl-CoA reductase

n.a.

n.a.

n.a.

Rru_A2964

(R)-specific enoyl-CoA hydratase

−0.04

0.79

9e-05

Rru_A2413

Poly(R)-hydroxyalkanoic acid synthase

−0.48

0.11

3e-02

Rru_A2817b

Phasin

n.a.

n.a.

n.a.

Rru_A3283a

Activator of polymer mobilization

n.a.

n.a.

n.a.

Rru_A1585

Polyhydroxyalkanoate depolymerase PhaZ1

−0.04

− 0.05

7e-01

Rru_A3356

Polyhydroxyalkanoate depolymerase PhaZ2

0.03

−0.42

5e-03

Rru_A1057

3-hydroxybutyrate dehydrogenase

−0.11

−0.48

9e-02

Rru_A3695

Acetoacetyl-CoA synthase

−0.17

−0.41

2e-02

Rru_A3063

Crotonyl-CoA carboxylase/reductase

−0.15

−0.18

7e-01

Rru_A1572a

Ethylmalonyl-CoA/Methylmalonyl-CoA epimerase

n.a.

n.a.

n.a.

Rru_A3062

Methylmalonyl-CoA mutase (EC 5.4.99.2)

0.02

−1.77

5e-04

Rru_A3064

Methylsuccinyl-CoA dehydrogenase

−0.01

−2.3

1e-03

Rru_A1201

Mesaconyl-CoA hydratase

0.06

−3.42

2e-07

Rru_A0217

L-Malyl-CoA/b-methylmalyl-CoA lyase

−0.05

−3.11

1e-05

Rru_A1200b

Malyl-CoA thioesterase

n.a.

n.a.

n.a.

Rru_A0052

Biotin carboxylase

−0.03

−1.83

2e-05

Rru_A0053

Carboxyl transferase

−0.09

−1.77

2e-04

Rru_A2479

Methylmalonyl-CoA mutase

−0.12

−0.53

1e-02

Rru_A1927

Acetyl-CoA hydrolase

−0.01

0.1

3e-01

Rru_A2129

Fumarate hydratase class II

0.15

−0.03

1e-01

Rru_A2206

Fumarate hydratase class I

n.a.

n.a.

n.a.

Rru_A2398

Pyruvate-flavodoxin oxidoreductase

−0.15

−0.17

6e-01

Rru_A0695

2-isopropylmalate synthase

−0.08

−0.06

8e-01

Rru_A1189

3-isopropylmalate dehydratase large subunit

−3.87

−3.24

1e-02

Rru_A1190

3-isopropylmalate dehydratase small subunit

n.a.

n.a.

n.a.

Rru_A1191

3-isopropylmalate dehydrogenase

−3.32

− 3.17

8e-01

Rru_A0467

Acetolactate synthase, large subunit

−1.95

−3.46

1e-02

Rru_A0468b

Acetolactate synthase, small subunit

n.a.

n.a.

n.a.

Rru_A0469

Ketol-acid reductoisomerase (NADP(+))

−2.21

−3.31

3e-02

Rru_A1786

Dihydroxy-acid dehydratase

−2.35

−3.49

5e-02

Rru_A2223

Branched chain amino acid aminotransferase

−0.11

0.01

3e-01

Rru_A0508

Aminotransferase, class IV

0.02

0.1

5e-01

Rru_A1040

Leucine dehydrogenase

0.05

0.03

8e-01

Rru_A1977

Pyruvate/ketoisovalerate oxidoreductase subunit beta

n.a.

n.a.

n.a.

Rru_A1978

Pyruvate/ketoisovalerate oxidoreductase subunit alpha

−0.01

−0.07

5e-01

Rru_A1835

2-methylbutanoyl-CoA dehydrogenase

−0.02

0.08

6e-01

Rru_A1948

Isovaleryl-CoA dehydrogenase

−0.01

0

9e-01

Rru_A1834

3-hydroxyisobutyryl-CoA hydrolase

−0.15

0.04

5e-01

Rru_A1945

Short-chain dehydrogenase/reductase SDR

0.09

−0.04

2e-01

Rru_A1946

3-ketoacyl-CoA thiolase

0.06

−0.03

7e-01

  1. aCentral sequence too short to be included in data set based on acceptance criteria used in this study
  2. bNot included in the dataset because fitness could only be accurately measured in 2 out of 3 of the replicates
  3. cThe strain fitness is defined as the log2 of the ratio between the strain abundance reached after 5 generations to the abundance at T0 in the relevant condition. The gene fitness values are calculated by averaging the strain fitness values for each gene. The presented gene fitness values are the average values resulting of three independent fitness assays for each condition. The statistical significance (P-value) between the acetate and succinate condition was determined with an unpaired t-test. The complete data set is available in supplemental material