Itaconic acid degradation in Aspergillus niger: the role of unexpected bioconversion pathways

Hossain, Abeer H.; Ter Beek, Alexander; Punt, Peter J.

doi:10.1186/s40694-018-0062-5

Fungal Biology and Biotechnology

Table 2 Differential expressed genes in high IA producing strains

From: Itaconic acid degradation in Aspergillus niger: the role of unexpected bioconversion pathways

A				2logR values				RPKM values
Locus tag	Old locus tag	Annotation	TargetP	AB1.13	AB1.13 CAD	AB1.13 #49B	CitB#99	AB1.13	AB1.13 CAD	AB1.13 #49B	CitB#99
ANI_1_1474074	An08g10920	Citrate synthase (CitB)	Cytosol	0.02	0.04	− 0.05	11.40	3.05	3.10	2.87	10,838.65
cadA (A. terreus)		Cis-aconitate decarboxylase	Cytosol	0.05	10.62	9.47	10.72	3.54	6887.96	3116.06	7417.64
ANI_1_1906104	An12g05750	MFS phosphate transporter	PM	0.13	1.02	10.28	10.55	1.09	2.87	2375.80	2852.93
hph (S. hindustanus)		Hygromycin B 4-O-kinase	Cytosol	0.23	0.17	8.84	10.04	0.94	0.86	759.61	1743.36
mttA (A. terreus)		Putative mitochondrial tricarboxylite transporter	Mito	− 0.18	0.18	8.46	9.86	0.19	0.54	477.02	1257.78
mfsA (A. terreus)		Putative major facilitator superfamily transporter A	PM	0.07	1.44	7.49	9.19	0.30	2.36	222.56	721.88
amdS (A. nidulans)		Acetamidase A	Cytosol	0.00	8.57	7.57	7.90	0.37	517.76	259.47	325.00
ANI_1_2022014	An01g14940	Phospholipase C PLC-C	Secreted	0.06	0.08	4.99	7.18	8.40	8.53	286.39	1310.11
ANI_1_1486074	An08g11030	3-Phytase B	Secreted	− 0.03	0.21	5.94	6.99	27.36	32.28	1771.34	3663.34
ANI_1_2368024	An02g02840	Sialidase	Secreted	− 0.05	0.06	7.22	6.81	0.21	0.30	184.78	139.52
ANI_1_236084	An09g02180	Lipase	Secreted/Mito	− 0.34	− 0.30	3.96	6.78	2.43	2.55	67.01	479.51
ANI_1_1848144	An16g06190	Metabolite transport protein GIT1	PM	0.04	0.73	6.80	6.46	6.81	11.62	846.83	669.87
ANI_1_166144	An16g01340	Glyoxalase domain-containing protein 5	Mito/Cytosol	0.24	4.70	5.70	6.20	16.28	379.47	761.69	1080.98
ANI_1_248124	An14g01550	Acid phosphatase	Secreted	− 0.16	− 0.27	4.91	5.89	4.20	3.82	174.16	345.29
ANI_1_1500104	An12g02320	Short-chain dehydrogenase/reductase	Cytosol	0.01	3.07	4.70	5.65	2.33	26.63	84.56	164.88
ANI_1_1330084	An09g03700	Hypothetical protein	Secreted	− 0.14	0.10	4.05	5.64	0.46	0.72	25.72	79.39
ANI_1_460094	An11g03340	Alpha-amylase A type-1/2	Secreted	− 0.12	0.33	1.56	5.52	12.80	17.81	43.27	683.63
ANI_1_542164	An18g04140	Acid phosphatase	Secreted	0.04	0.07	4.04	5.50	1.42	1.45	37.62	104.94
ANI_1_1576144	An16g02440	Phytase-like	Secreted	− 0.03	0.04	4.27	5.48	3.98	4.23	97.10	226.06
ANI_1_260144	An16g01850	BYS1 domain protein	Secreted	− 0.64	− 0.16	2.35	5.30	9.22	13.19	79.91	623.78
ANI_1_1250124	An14g02660	NPP1 domain protein	Secreted	0.12	0.24	4.08	5.29	3.11	3.48	63.27	147.19
ANI_1_2836024	An02g08830	Histone transcription regulator 3	Nucleus	0.00	0.09	− 0.03	5.15	9.48	10.11	9.28	371.63
ANI_1_652114	An13g01750	Acid phosphatase	Secreted	0.06	0.10	4.67	5.13	70.73	72.83	1754.06	2422.06
ANI_1_1440124	An14g04660	Aromatic ring-opening dioxygenase, catalytic LigB subunit	Cytosol/Mito/Per	0.13	0.32	0.32	5.13	2.59	3.10	3.09	113.67
ANI_1_1432064	An07g00760	Putative itaconyl-CoA transferase (ictA)	Mito	0.32	3.27	3.92	5.06	13.07	108.35	170.34	375.89
ANI_1_1812184	An04g04240	Phosphate transporter	PM	0.27	1.05	4.83	4.99	2.94	5.74	91.74	102.55
ANI_1_126034	An03g01120	Aromatic-amino-acid aminotransferase	Nucleus	− 0.34	3.62	4.24	4.98	29.79	478.24	735.44	1226.92
ANI_1_246114	An13g01760	Oligopeptide transporter	PM	0.33	0.46	2.43	4.97	1.30	1.51	8.88	56.23
ANI_1_1908104	An12g05810	Multicopper oxidase	Secreted	0.04	0.20	4.33	4.76	0.18	0.31	21.98	30.01
ANI_1_2118064	An07g09220	Putative itaconyl-CoA hydratase (ichA)	Mito	− 0.11	2.78	4.04	4.71	7.32	60.28	146.61	232.65
ANI_1_1324074	An08g09850	Acid phosphatase	Secreted	− 0.18	− 0.36	3.70	4.58	128.06	112.96	1896.57	3490.63
ANI_1_1520134	An15g04760	Glycosyl hydrolase family 71 protein	Secreted	− 0.29	− 0.82	2.21	4.57	1.58	0.79	13.68	74.04
ANI_1_2122184	An04g08320	MFS monocarboxylate transporter	PM	0.17	0.49	1.25	4.46	7.11	9.16	16.14	158.52
ANI_1_3198024	An02g13080	Phenylacetate-coenzyme A ligase	Cytosol	− 0.28	− 0.51	0.35	4.28	0.27	0.08	0.96	28.87
ANI_1_1430064	An07g00750	Fungal transcription factor	Nucleus/Mito	0.02	3.04	3.73	4.28	0.52	11.37	19.01	28.19
ANI_1_820034	An03g06550	Glucoamylase	Secreted	0.13	− 0.02	1.76	4.18	243.81	218.86	756.84	4054.75
ANI_1_1020134	An15g07520	Phosphoglycerate mutase family protein	Cytosol	− 0.20	− 0.60	4.75	4.18	12.67	9.31	420.93	282.80
ANI_1_1810184	An04g04230	Phosphate transporter (reannotated)	Nucleus/Cytosol	− 0.18	0.33	4.60	4.17	4.67	7.06	154.52	114.01
ANI_1_294044	An05g02340	Extracellular dihydrogeodin oxidase/laccase	Secreted	− 0.08	− 0.07	4.48	4.11	0.44	0.44	32.96	25.14
ANI_1_864144	An16g06510	Trans-aconitate 2-methyltransferase (tmtA)	Cytosol	0.08	0.73	2.40	4.08	12.71	20.51	67.34	218.46
ANI_1_342114	An13g02590	Sugar transporter	PM	− 0.01	0.28	2.16	4.06	3.21	4.16	18.01	69.60
ANI_1_1098184	An04g06920	Alpha-glucosidase	Secreted	0.00	− 0.33	0.57	4.04	174.34	138.54	258.87	2884.10
ANI_1_1820094	An11g03450	Small secreted protein	Secreted	0.33	1.68	2.25	4.02	58.07	149.69	222.30	763.49
ANI_1_330024	An02g02480	MFS phosphate transporter	PM	− 0.20	1.65	3.18	4.02	3.12	13.82	41.86	75.60
ANI_1_762014	An01g05900	Cytochrome P450	Secreted	− 0.13	− 0.10	3.86	4.00	0.63	0.66	24.97	27.63
ANI_1_1778074	An08g02590	GPI anchored protein	Secreted	− 0.06	0.21	3.26	4.00	10.62	13.07	115.12	192.81

B				2logR values				RPKM values
Locus tag	Old locus tag	Annotation	TargetP	AB1.13	AB1.13 CAD	AB1.13 #49B	CitB99	AB1.13	AB1.13 CAD	AB1.13 #49B	CitB99
ANI_1_542134	An15g03800	Hydrophobin	Secreted	0.06	− 0.55	− 2.13	− 8.78	981.57	641.93	213.11	1.14
ANI_1_1416134	An15g04010	Hypothetical protein	Nucleus	0.27	− 0.20	− 5.87	− 7.79	288.73	208.03	3.11	0.09
ANI_1_92174	An10g00820	Oxaloacetate acetylhydrolase	Cytosol	− 0.13	− 0.81	− 2.61	− 7.51	1803.48	1122.69	323.44	9.81
ANI_1_220174	An10g00800	Purine nucleoside permease	Secreted	− 0.13	− 0.33	− 2.72	− 6.47	375.32	326.25	61.40	3.64
ANI_1_1046034	An03g01450	Major Facilitator Superfamily	PM	− 0.20	− 0.83	− 2.49	− 6.29	73.83	47.18	14.31	0.10
ANI_1_1062034	An03g01590	Arginine permease	PM	0.13	0.41	− 2.09	− 6.08	243.24	295.39	51.56	2.30
ANI_1_964034	An03g00580	Cytochrome P450 monooxygenase	Mito	− 0.29	− 1.86	− 3.52	− 6.00	228.74	76.05	23.45	3.39
ANI_1_966034	An03g00590	Trichodiene synthase Tri5	Cytosol	− 0.31	− 2.27	− 4.02	− 5.87	94.11	23.35	6.27	1.01
ANI_1_170034	An03g01460	1-Aminocyclopropane-1-carboxylate oxidase	Cytosol	− 0.10	− 0.86	− 2.52	− 5.43	114.81	67.35	20.61	1.88
ANI_1_1914064	An07g06460	C-7 hydroxycephem methyltransferase	Cytosol	− 0.26	− 0.32	− 4.38	− 5.28	36.47	35.03	1.16	0.16
ANI_1_182034	An03g01540	FAD dependent oxidoreductase	Secreted/Cytosol	0.05	− 0.42	− 1.58	− 5.26	78.94	56.69	24.80	1.02
ANI_1_1770144	An16g05290	Purine-cytosine permease	PM	− 0.05	0.00	− 1.13	− 5.22	838.03	867.97	395.45	22.38
ANI_1_990084	An09g00660	OPT oligopeptide transporter protein	PM	0.01	0.10	− 0.27	− 5.09	279.04	298.75	230.29	7.20
ANI_1_2008094	An11g05190	Type 1 glutamine amidotransferase	Cytosol	− 0.02	0.24	− 1.25	− 5.06	70.06	84.12	29.32	1.16
ANI_1_1366064	An07g00170	Hypothetical protein	Secreted	0.37	0.34	− 1.87	− 5.04	56.14	54.96	11.10	0.35
ANI_1_1572014	An01g11640	Ammonium transporter	PM	0.22	0.03	− 1.36	− 5.02	222.82	195.30	74.16	4.91
ANI_1_1862104	An12g05440	Urea active transporter 1	PM	− 0.15	− 0.26	− 2.63	− 5.01	68.04	63.09	11.38	1.38
ANI_1_2238104	An12g09660	Phosphoribosyl transferase	Cytosol	0.64	0.85	− 1.49	− 4.94	126.25	145.43	27.94	1.66
ANI_1_1456124	An14g04760	Male sterility domain containing protein	Cytosol	0.26	− 0.49	− 2.51	− 4.91	258.07	152.77	36.93	6.18
ANI_1_708024	An02g05060	Hypothetical protein	Secreted	− 0.03	− 1.15	− 1.98	− 4.81	810.00	371.87	208.67	28.41
ANI_1_2764024	An02g08200	Short-chain dehydrogenase/reductase	Cytosol	1.05	2.54	− 0.64	− 4.80	308.27	867.28	94.68	4.34
ANI_1_2236104	An12g09640	Uracil-regulated protein 1	Cytosol	0.44	0.67	− 0.72	− 4.80	107.20	125.82	47.45	1.86
ANI_1_46014	An01g00370	Aspartic endopeptidase (AP1)	Nucleus	0.10	− 0.18	− 1.58	− 4.79	1351.68	1115.18	422.54	44.77
ANI_1_1054034	An03g01520	12-oxophytodienoate reductase	Mito	− 0.03	− 1.01	− 1.20	− 4.71	42.16	20.82	18.17	0.68
ANI_1_1850094	An11g03640	OPT oligopeptide transporter family	PM	− 0.11	− 0.52	− 0.49	− 4.71	104.23	78.34	79.93	3.35
ANI_1_1990074	An08g05320	Short-chain dehydrogenase/reductase	Cytosol	− 1.43	− 1.61	− 3.15	− 4.70	16.50	14.51	4.33	0.82
ANI_1_474154	An17g01540	GABA permease	PM	0.07	0.26	− 2.34	− 4.67	85.82	98.28	15.40	2.26
ANI_1_1748104	An12g04260	NAD dependent epimerase/dehydratase	Mito	1.23	2.79	− 2.00	− 4.66	69.28	206.65	6.50	0.19
ANI_1_726064	An07g05830	Formamidase	Cytosol	− 0.03	0.02	− 0.57	− 4.58	267.27	276.94	184.40	10.45
ANI_1_3344014	An01g14400	Cercosporin toxin resistance protein CRG1	Cytosol	0.04	0.02	− 2.87	− 4.56	63.05	62.21	7.56	1.65
ANI_1_176044	An05g01410	Acyl-CoA oxidase	Mito	− 0.30	− 0.96	− 2.25	− 4.55	178.03	111.60	45.07	8.38
ANI_1_568054	An06g02150	DUF3328 protein	Secreted	0.11	0.34	− 4.28	− 4.55	48.49	57.10	1.36	0.96
ANI_1_1554124	An14g05980	MFS transporter	PM	0.01	0.48	− 3.43	− 4.54	29.12	40.79	1.78	0.29
ANI_1_1048034	An03g01470	d-galactonate transporter	PM	− 0.07	− 1.24	− 2.35	− 4.52	37.53	16.20	6.96	0.76
ANI_1_806074	An08g05670	Nitrate transporter	PM	0.13	1.08	− 1.66	− 4.44	44.15	86.17	12.00	0.90
ANI_1_3376014		Fe(II)/2-oxoglutarate (2OG) oxygenase	Cytosol	− 0.17	− 0.07	− 1.01	− 4.38	97.28	104.78	54.14	4.31
ANI_1_1340084	An09g03750	MAC/Perforin domain	Cytosol	0.10	0.11	− 2.61	− 4.37	22.58	22.73	2.58	0.06
ANI_1_1514034	An03g06020	4-Carboxymuconolactone decarboxylase	Cytosol	0.19	− 0.43	− 1.29	− 4.31	5568.62	3603.74	1987.79	245.12
ANI_1_2954014	An01g09970	Surface layer protein	Cytosol	0.37	− 0.03	− 1.62	− 4.29	66.37	50.05	16.01	1.67
ANI_1_2450014	An01g03790	Urea active transporter 1	PM	− 0.05	− 0.17	− 0.10	− 4.29	116.82	107.59	113.28	5.27
ANI_1_616114	An13g01470	Laminin gamma 3	Secreted	− 0.15	− 1.01	− 2.79	− 4.27	110.93	60.59	16.95	5.42
ANI_1_1456104	An12g01910	Phytase	Secreted	− 0.04	− 0.95	− 4.39	− 4.26	30.69	15.78	0.55	0.70
ANI_1_142174	An10g00180	Cupin_like	Cytosol/Mito	0.34	− 0.10	− 1.24	− 4.24	424.35	310.92	140.90	16.72
ANI_1_1362014	An01g09980	Asp-hemolysin	Secreted	0.32	− 0.14	− 1.07	− 4.21	347.94	252.51	132.21	14.06
ANI_1_878114	An13g03990	Nucleobase-cation-symport-1 (NCS1) transporter	PM	− 0.08	0.15	− 2.27	− 4.21	30.66	36.14	5.91	0.81
ANI_1_2456094		S-adenosylmethionine-dependent methyltransferase		0.08	− 0.27	− 3.01	− 4.20	69.27	54.39	7.29	2.63
ANI_1_2086074	An08g07010	DUF3445 protein	Mito	0.00	− 0.25	− 2.44	− 4.17	37.07	31.01	6.01	1.11
ANI_1_212174		Nitrilase		− 0.38	− 0.59	− 2.64	− 4.12	18.92	16.23	3.15	0.49
ANI_1_1828184	An04g04370	Phenylalanine ammonia-lyase	PM	0.17	− 0.10	− 2.11	− 4.11	277.24	229.84	56.44	13.37
ANI_1_76154	An17g00640	Zinc-binding alcohol dehydrogenase domain-containing protein cipB	Cytosol	1.04	2.86	− 2.13	− 4.11	119.10	425.44	12.36	2.40
ANI_1_1094134	An15g00280	Polysaccharide deacetylase	Cytosol	0.00	− 0.07	− 0.98	− 4.08	204.72	194.38	102.72	11.10
ANI_1_1144084	An09g01920	FAD binding domain protein	Secreted	0.75	2.11	− 1.49	− 4.04	39.96	103.97	7.67	0.48
ANI_1_294064	An07g02310	Glutathione S-transferase Ure2-like protein	Cytosol	0.01	− 0.86	− 2.83	− 4.02	187.81	102.94	25.42	10.62

(A) Genes upregulated in high IA producing conditions. Cutoff of 2logR values of 4.00 or higher was held. (B) Genes downregulated in high IA producing conditions. Cutoff of 2logR values of − 4.00 was held

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