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. 2021 Jan 13;21:7. doi: 10.1186/s12896-021-00668-9

Table 3.

N. simplex VKM Ac-2033D genes whose products taking part in steroid degradation, predicted

Step Enzyme annotation M. tub R. jostii C. testosteroni References N. simplex Cluster Regulon Phyt
Regulation
TetR transcriptional repressor kstR [2] KR76_12270 B KstR
TetR transcriptional repressor kstR2 [2] KR76_25115 C KstR2
A-ring activation
 I-II cholesterol oxidase cho [56] KR76_09550 KstR +
 I-II 5-∆4–3-ketosteroid isomerase ksi [57] KR76_23530 KstR +
[57] KR76_24125 KstR
Cholesterol side chain degradation
 III-V cytochrome P450 125 cyp125 [10, 58] KR76_14335 A KstR +
 V-VI 3-oxocholest-4-en-26-oate-CoA ligase fadD19 [59] KR76_14210 A KstR +
 VI-VII Acyl-coA dehydrogenases chsE4–5 (fadE26–27) [60] KR76_14175-KR76_14180 А KstR +
 VII-VIII 2-enoyl-CoA hydratase echA19 [6] KR76_14215 A KstR +

 IX-X;

 XI-XII

aldol lyase ltp3 [12] KR76_14285 А KstR +
aldol lyase ltp4 KR76_14280 А KstR +
 XII-XIII steroid-22-oyl-CoA synthetase fadD17 casI [61] KR76_14185 A KstR
 XIII-XIV acyl-CoA dehydrogenase chsE3 (fadE34) [60, 62] KR76_12295 B KstR +
 XIV-XV 3α,7α,12α-trihydroxy-5β-chol-22-en-24-oyl-CoA hydratase

hsd4B,

Rv3538

casD [4, 61, 63] KR76_14505 A KstR +
 XV-XVI dehydrogenase hsd4A [4] KR76_12260 В KstR
 XIV-XVII 3-ketoacyl-CoA thiolase fadA5 casB [64] KR76_14340 А KstR +

 XVII-XVIII;

igr-operon

7α,12α-dihydroxy-23,24-bisnorchola-1,4-dien-22-oyl-CoA dehydrogenase chsE2 (fadE29) casL [65] KR76_12325 B KstR +
acetyl-CoA acetyltransferase chsH2 casM [66, 67] KR76_12330 B KstR +
acyl dehydratase casN [66] KR76_12335 B KstR
beta-hydroxyacyl-ACP dehydratase chsH1 casO [66, 67] KR76_12340 B KstR +
3-ketoacyl-CoA thiolase ltp2 casP [66] KR76_12345 B KstR +
Opening of B-ring
 XVIII-XIX; XX-XXI

Δ-3-ketosteroid dehydrogenase

with preference for 9-OH-AD and testosterone

kstD kstD1 [54, 68] KR76_02655 KstR +
KR76_27115 +

Δ-3-ketosteroid dehydrogenase

with preference for progesterone

kstD kstD2 [69] KR76_27125 D Acin1,3 +

Δ-3-ketosteroid dehydrogenase

with preference for saturated steroid substrates

kstD kstD3 tesH [54, 70] KR76_14500 A KstR +
 XVIII-XX; XIX-XXI 3-ketosteroid 9α-hydroxylase, oxygenase subunit kshA [71] KR76_14170 A KstR +
KR76_27070 +
3-ketosteroid 9α-hydroxylase, reductase subunit kshB KR76_14160 A KstR
KR76_27080
eCleavage of A-ring
 XXII-XXIII flavin-dependent monooxygenase hsaA tesA1A2 [18, 72] KR76_14480 A KstR +
hsaB KR76_14465 A KstR
KR76_27090 D
 XXIII-XXIV extradiol dioxygenase hsaC tesB [72, 73] KR76_14470 A KstR +
KR76_27095 D +
 XXIV-XXV carbon–carbon hydrolase hsaD tesD [19, 72] KR76_14475 A KstR +
KR76_27085 D
 XXV-XXVI hydratase hsaE tesE [17, 74] KR76_14495 A KstR
KR76_24180 +
 XXVI-Propanal 4-hydroxy-2-oxovalerate aldolase hsaF tesG KR76_14485 A KstR +
KR76_24170 +
 Propanal-Propionate acetaldehyde dehydrogenase, acetylating hsaG tesF KR76_14490 A KstR +
KR76_24175 +
Ring D degradation
 XVII-XVIII HIP-CoA synthetase fadD3 scdA [75, 76] KR76_25120 С KstR2 +
 XVII-XIX 5-Oxo HIC-CoA oxidase ipdF scdG [20, 76] KR76_14435 A KstR2 +
 XXIX-XXX COCHEA-CoA hydrolase, α-subunit ipdA scdL1L2 [20, 76] KR76_14365 A KstR2 +
KR76_25105 С KstR2 +
COCHEA-CoA hydrolase, β-subunit ipdB KR76_14370 A KstR2 +
KR76_25110 С KstR2 +
 XXX-XXXI acyl-CoA dehydrogenase fadE30 scdC1C2 [76, 77] KR76_14440 A KstR2 +
 XXXI-XXXII acyl-CoA hydrolase scdD [76]
 XXXII-XXXIII

dehydrogenase,

oxidized a hydroxyl in propionate chain

hsd4A scdE [76] KR76_14350 A KstR2 +
 XXXIII-XXXIV acetyl-CoA acetyltransferase fadA6 scdF [20, 76] KR76_14430 A KstR2 +

 XXXIV-XXXV;

XXXVI-XXXVII

5-Oxo HIC-CoA oxidase ipdF scdG [20, 76] KR76_14435 A KstR2 +

 XXXIV-XXXVI;

XXXV-XXXVII

5-OH HIC-CoA reductase ipdC scdK [20, 76] KR76_14375 A KstR2 +
Ring C degradation
 XXXVII-XXXVIII HIEC-CoA hydrolase echA20 scdY [20, 76] KR76_14360 A KstR2 +
 XXXVIII-XXXIX CoA transferase ipdA scdL1L2 [20, 76] KR76_14365 A KstR2 +
KR76_25105 С KstR2 +
CoA transferase ipdB KR76_14370 A KstR2 +
KR76_25110 С KstR2 +
 XL-XLI acyl-CoA dehydrogenases fadE31, fadE32 ro04591-ro04593 [61, 78]

KR76_14445

KR76_14450

A KstR2 +
acyl-CoA dehydrogenases fadE33 KR76_14455 A KstR2 +
 XLI-XLII enoyl-CoA hydratase echA13 scdN [20, 76] KR76_25020 С KstR2 +

Step – degradation step from Fig. 7

Enzyme annotation – function of enzyme

M. tub. – name of gene in M. tuberculosis investigations

R. jostii - name of gene (or locus_tag) in R. jostii investigations

C. testosteroni - name of gene in C. testosteroni investigations

N. simplex - locus_tag of ortholog that is candidate gene for this function. Functions are predicted by the annotation, location, predicted regulon that ortholog belongs to and gene expression changes

Cluster – cluster where gene is located in genome [27]

Regulon – repressor whose binding site is predicted in the promoter of operon that ortholog belongs to

Phyt – gene in N. simplex VKM Ac-2033D that is induced by phytolesterol (+)