Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate

Shtratnikova, Victoria Yu; Sсhelkunov, Mikhail I.; Fokina, Victoria V.; Bragin, Eugeny Y.; Shutov, Andrey A.; Donova, Marina V.

doi:10.1186/s12896-021-00668-9

Table 3 N. simplex VKM Ac-2033D genes whose products taking part in steroid degradation, predicted

From: Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate

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	+
I-II	∆⁵-∆⁴–3-ketosteroid isomerase	ksi			[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	+
IX-X; XI-XII	aldol lyase	ltp4			[12]	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	+
		kstD	kstD1		[54, 68]	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	+
	3-ketosteroid 9α-hydroxylase, oxygenase subunit	kshA				KR76_27070			+
	3-ketosteroid 9α-hydroxylase, reductase subunit	kshB				KR76_14160	A	KstR
	3-ketosteroid 9α-hydroxylase, reductase subunit	kshB				KR76_27080
eCleavage of A-ring
XXII-XXIII	flavin-dependent monooxygenase	hsaA		tesA1A2	[18, 72]	KR76_14480	A	KstR	+
		hsaB				KR76_14465	A	KstR
		hsaB				KR76_27090	D
XXIII-XXIV	extradiol dioxygenase	hsaC		tesB	[72, 73]	KR76_14470	A	KstR	+
XXIII-XXIV	extradiol dioxygenase	hsaC		tesB	[72, 73]	KR76_27095	D		+
XXIV-XXV	carbon–carbon hydrolase	hsaD		tesD	[19, 72]	KR76_14475	A	KstR	+
XXIV-XXV	carbon–carbon hydrolase	hsaD		tesD	[19, 72]	KR76_27085	D
XXV-XXVI	hydratase	hsaE		tesE	[17, 74]	KR76_14495	A	KstR
XXV-XXVI	hydratase	hsaE		tesE		KR76_24180			+
XXVI-Propanal	4-hydroxy-2-oxovalerate aldolase	hsaF		tesG		KR76_14485	A	KstR	+
XXVI-Propanal	4-hydroxy-2-oxovalerate aldolase	hsaF		tesG		KR76_24170			+
Propanal-Propionate	acetaldehyde dehydrogenase, acetylating	hsaG		tesF		KR76_14490	A	KstR	+
Propanal-Propionate	acetaldehyde dehydrogenase, acetylating	hsaG		tesF		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	+
	COCHEA-CoA hydrolase, α-subunit	ipdA				KR76_25105	С	KstR2	+
	COCHEA-CoA hydrolase, β-subunit	ipdB				KR76_14370	A	KstR2	+
	COCHEA-CoA hydrolase, β-subunit	ipdB				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	+
	CoA transferase	ipdA				KR76_25105	С	KstR2	+
	CoA transferase	ipdB				KR76_14370	A	KstR2	+
	CoA transferase	ipdB				KR76_25110	С	KstR2	+
XL-XLI	acyl-CoA dehydrogenases	fadE31, fadE32	ro04591-ro04593		[61, 78]	KR76_14445 KR76_14450	A	KstR2	+
XL-XLI	acyl-CoA dehydrogenases	fadE33	ro04591-ro04593		[61, 78]	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 (+)

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