Fig. 1
A)
B)
T
100
Nocardia asteroides DSM 43757 (X80606)
100
T
Rhodococcus equi DSM 20307 (X80614)
Rhodococcus equi 103S (NC_014659, REQ_r01)
100
100
66
100
T
Rhodococcus wratislaviensis NCIMB 13082 (Z37138)
Rhodococcus opacus PD630 (PRJNA30413, OPAG_10053)
100
T
T
Rhodococcus koreensis DNP 505 (type 1) DSM44498 (AF124342)
100
Rhodococcus opacus B4 (NC_012522, ROP_r0100)
100
T
Rhodococcus opacus DSM 43205 (X80630)
100
T
Rhodococcus percolatus HAMBI 1752 (X92114)
100
T
Rhodococcus marinonascens DSM 43752 (X80617)
100
T
Rhodococcus maanshanensis M712T DSM 44675 (AF416566)
100
Rhodococcus jostii RHA1 (CP000431, RHA1_ro03936)
99
100
70
97
100
100
100
91
100
100
67
Rhodococcus fascians F7 (RAST1827.3, rna49)
T
Rhodococcus fascians DSM 20669 (X79186)
100
T
Rhodococcus rhodnii DSM 43336 (X80621)
71
100
T
54
Rhodococcus ruber DSM 43338 (X80625)
100
T
Rhodococcus rhodochrous DSM 43241 (X79288)
51
100
T
Skermania piniformis IFO 15059 (Z35435)
100
T
Tsukamurella paurometabola DSM 20162 (X80628)
100
T
Dietzia maris DSM 43672 (X79290)
T
Corynebacterium diphtheriae NCTC 11397 (X84248)
100
100
Rhodococcus jostii IFO 16295 (AB046357)
T
Rhodococcus globerulus DSM 43954 (X80619)
100
T
Rhodococcus erythropolis DSM 43066 (X79289)
100
Rhodococcus erythropolis PR4 (NC_012490, RER_r0040)
500
100
Fig. 2
Fig. 3
A
B
C
D
E
F
Fig. 4
Fig. 5
Table 1: Genes coding for key enzymes of TAG biosynthesis in Rhodococcus species. Presence of the putative active site HHxxxDG or
acyl_WS_DGAT region and the PAP2-like2 and “PlsC” domains were used as selection criteria of DGAT, PAP and AGPAT, respectively. The gene
redundancy is represented in accordance with the locus name (RHA1_, OPAG_, ROP_, RER_, REQ_ and F7_) obtained from NCBI database or RAST
server in the case of F7strain. Orthologs are shown in the same lines. Abbreviation: EC, enzyme classification.
Key enzymes for TAG biosynthesis
Multifunctional fatty acid synthase type 1a (FASI)
Glycerol-3-phosphate O-acyltransferase (GPAT)
1-acylglycerol-3-phosphate O-acyltransferase
(AGPAT)
Phosphatidic acid phosphatase (PAP)
Diacylglycerol acyltransferases (DGAT)
R. jostii
RHA1
RHA1_ro01426
RHA1_ro05648
RHA1_ro04182
RHA1_ro01115
RHA1_ro04047
RHA1_ro04048
RHA1_ro05647
RHA1_ro02025
RHA1_ro02057
RHA1_ro06465
RHA1_ro00075
RHA1_ro03136
RHA1_ro08553
RHA1_ro04970
RHA1_ro00087
RHA1_ro08645
RHA1_ro06332
RHA1_ro06855
RHA1_ro05649
RHA1_ro05565
RHA1_ro05356
RHA1_ro00583
RHA1_ro08660
RHA1_ro00087
RHA1_ro00039
RHA1_ro00024
RHA1_ro00023
R. opacus PD630
R. opacus
B4
OPAG_09195
OPAG_04306
OPAG_06288
OPAG_05898
OPAG_06418
OPAG_06417
OPAG_04305
OPAG_00578
OPAG_00610
OPAG_03466
ROP_11350
ROP_57110
ROP_41110
ROP_08430
ROP_39250
ROP_39260
ROP_57100
ROP_16990
ROP_17290
ROP_65180
OPAG_07226
OPAG_02574
OPAG_03922
OPAG_03918
OPAG_03334
OPAG_03807
OPAG_04307
OPAG_07837
OPAG_07648
OPAG_05286
OPAG_05208
OPAG_06690
OPAG_07212
OPAG_07257
OPAG_07266
OPAG_07267
R. erythropolis PR4
R. fascians F7
-
RER_38730
RER_16280
RER_13990
RER_35800
RER_02010
RER_02020
RER_16270
RER_16780
RER_16370
RER_23760
pREL1_0275
-
ROP _pB01-01880
RER_10170
ROP_50370
ROP_02100
ROP_63930
ROP_68400
ROP_57120
ROP_56340
ROP_54550
ROP_04650
ROP_02100
-
RER_46290
RER_21760
RER_28450
RER_16290
RER_33950
RER_34070
-
F7_2364
F7_1759
F7_1968
F7_2673
F7_3258
F7_1760
F7_1712
F7_0439
F7_1802
F7_3389
F7_4458
-
R. equi
103S
REQ_30820
REQ_16780
REQ_28080
REQ_01880
REQ_16770
REQ_37300
REQ_37680
REQ_31700
REQ_09750
REQ_33280
REQ_20560
REQ_16790
REQ_01690
-
EC
2.3.1.86
2.3.1.15
2.3.1.51
3.1.3.4
2.3.1.20
RHA1_ro01601
RHA1_ro02966
-
OPAG_06225
OPAG_00138
OPAG_01553
-
ROP_13050
ROP_26950
-
RER_11860
RER_12460
RER_15300
RER_15290
-
F7_3568
-
REQ_40870
REQ_12970
REQ_44660
REQ_29020
R. equi 103 S
PR4
R. fascians F7
R. erythropolis
R. opacus B4
catabolism
R. opacus PD630
Triglycerides
R. jostii RHA1
Table 2. Gene redundancy in triglycerides catabolism for species of Rhodococcus genus.
Reaction
Enzyme
number
classification
Genes/Proteins
6
12
11
3
4
16
1
3.1.1.3/ 3.1.1.23
Triacylglycerol lipases/ Monoacylglycerol lipases
27
18
33
25
16
20
1
3.1.1.3
Esterases
11
7
2
1
1
3.1.1.3
Lipasas/esterases
75
16
63
61
28
45
2
6.2.1.3
Long chain fatty acid CoA ligase
1
1
1
1
1
1
3a
1.3.3.6
Acyl CoA oxidase
92
30
101
58
29
47
3a
1.3.99.3
Acyl CoA dehydrogenase
11
1
1
3a
1.3.99.13
Long chain acyl CoA dehydrogenase
10
2
9
3a
1.3.8.1/1.3.99.2
Butyryl CoA deydrogenase
Glycerolipids
hydrolysis
Β-Oxidation
4
4
3
1
2
1
3b
1.3.1.34
2,4-dienoyl CoA reductase
60
5
68
41
15
24
4
4.2.1.17
Enoyl CoA hydratase
11
3
9
4
5
2
5
1.1.1.35
3-Hydroxyacyl CoA dehydrogenase
3
4
3
1
4
1
4/5
ND
Enoyl CoA hydratase/ 3-Hydroxyacyl CoA
dehydrogenase complexes
38
10
33
28
11
18
6
2.3.1.16/2.3.1.9
Acetyl CoA acyl transferase
1
1
1
1
1
1
7
4.1.3.1
Isocitrate lyase
2
3
2
1
1
1
8
2.3.3.9
Malate synthase
24
6
8
10
15
16
ND
Secreted lipases
Glyoxylate cycle
Exracellular
glycerolipid hydrolysis
Gene redundancy
0
1-5
6-10
11-20
21-30
31-40
>40