Table 2. Open in new tab Effect of Low...

			RPKM	Fold Change
Tetrapyrrole Biosynthesis	FLP	FLU chloroplast precursor	16	30	199	1.9	13
HEM15	Ferrochelatase	23	40	129	1.7	5.6
POR1	Protochlorophyllide reductase	64	47	243	0.7	3.8
CHLI2	Magnesium chelatase subunit I	46	38	154	0.8	3.4
GSA1	Glutamate-1-semialdehyde aminotransferase	36	23	119	0.6	3.3
CPX1	Coproporphyrinogen III oxidase	40	29	128	0.7	3.2
PBGD1	Porphobilinogen deaminase	32	20	101	0.6	3.1
CHLI1	Magnesium chelatase subunit I	66	44	192	0.7	2.9
GUN4	Tetrapyrrole binding protein	20	13	56	0.7	2.8
GTS2	Glutamyl/glutaminyl-tRNA synthetase	32	23	86	0.7	2.7
CHLD	Magnesium chelatase subunit D	32	19	87	0.6	2.7
CLH1	Chlorophyllase I	2.2	2.4	6.0	1.1	2.7
ALAD	Δ-Aminolevulinic acid dehydratase	132	103	342	0.8	2.6
CHLH1	Magnesium chelatase subunit H	63	62	159	1.0	2.5
UROS	Uroporphyrinogen-III synthase	52	43	127	0.8	2.5
UROD1	Uroporphyrinogen-III decarboxylase	49	26	106	0.5	2.2
CHLG	Chlorophyll synthetase	37	26	79	0.7	2.1
Iron Proteins	Cre09.g403550	2OG-Fe(II)-dependent oxidoreductase	1.2	3.0	30	2.5	25
Cre10.g427850	PAS fold	1.0	2.1	19	2.1	19
CDJ3	Chloroplast DnaJ-like protein	19	45	300	2.4	16
CDJ5	Chloroplast DnaJ-like protein	9.9	43	131	4.3	14
FDX6	Ferredoxin 6	41	121	362	3.0	8.8
FDX3	Ferredoxin 3	21	30	144	1.4	6.9
BKT1	β-Carotene ketolase	1.7	1.5	9.3	0.9	5.5
SOUL4	SOUL heme binding protein	4.3	4.6	21	1.1	4.9
SOUL1	SOUL heme binding protein	34	55	133	1.6	3.9
Cre10.g429750	PAS fold	2.8	3.1	10	1.1	3.6
FXL1	FixL-like PAS domain protein	3.4	5.5	12	1.6	3.5
ISC1	Iron-sulfur cluster assembly protein	31	50	91	1.6	2.9
Cre10.g466700	2OG-Fe(II)-dependent oxygenase	6.2	8.4	18	1.4	2.9
Cre13.g586600	Putative cytochrome b ₅₆₁ ferric reductase	4.8	5.5	16	1.1	3.3
ACH1	Aconitate hydratase	1152	1162	566	1.0	0.5
DES6	ω6-Fatty acid desaturase	1815	1807	892	1.0	0.5
CYC	Mitochondrial cytochrome c	730	695	311	1.0	0.4
FDX2	Ferredoxin 2	7.8	9.3	3.1	1.2	0.4
MitoNEET	Iron sulfur domain-containing CDGSH-type subfamily	309	271	112	0.9	0.4
CYP197-1	Cytochrome P450	28	28	9.8	1.0	0.4
GSN1	Glutamate synthase, NADH-dependent	81	88	28	1.1	0.3
Cre02.g093650	Rieske [2Fe-2S] domain-containing protein	421	356	127	0.8	0.3
SIR1	Ferredoxin-sulfite reductase	121	83	20	0.7	0.2
PHX5	Prolyl 4-hydroxylase	37	24	4.9	0.6	0.1

RPKM

Fold Change

Process

Gene^a

Defline

20^b

1^b

0.25^b

1/20

0.25/20

Tetrapyrrole Biosynthesis

FLP

FLU chloroplast precursor

199

1.9

HEM15

Ferrochelatase

129

1.7

5.6

POR1

Protochlorophyllide reductase

243

0.7

3.8

CHLI2

Magnesium chelatase subunit I

154

0.8

3.4

GSA1

Glutamate-1-semialdehyde aminotransferase

119

0.6

3.3

CPX1

Coproporphyrinogen III oxidase

128

0.7

3.2

PBGD1

Porphobilinogen deaminase

101

0.6

3.1

CHLI1

Magnesium chelatase subunit I

192

0.7

2.9

GUN4

Tetrapyrrole binding protein

0.7

2.8

GTS2

Glutamyl/glutaminyl-tRNA synthetase

0.7

2.7

CHLD

Magnesium chelatase subunit D

0.6

2.7

CLH1

Chlorophyllase I

2.2

2.4

6.0

1.1

2.7

ALAD

Δ-Aminolevulinic acid dehydratase

132

103

342

0.8

2.6

CHLH1

Magnesium chelatase subunit H

159

1.0

2.5

UROS

Uroporphyrinogen-III synthase

127

0.8

2.5

UROD1

Uroporphyrinogen-III decarboxylase

106

0.5

2.2

CHLG

Chlorophyll synthetase

0.7

2.1

Iron Proteins

Cre09.g403550

2OG-Fe(II)-dependent oxidoreductase

1.2

3.0

2.5

Cre10.g427850

PAS fold

1.0

2.1

CDJ3

Chloroplast DnaJ-like protein

300

2.4

CDJ5

Chloroplast DnaJ-like protein

9.9

131

4.3

FDX6

Ferredoxin 6

121

362

3.0

8.8

FDX3

Ferredoxin 3

144

1.4

6.9

BKT1

β-Carotene ketolase

1.7

1.5

9.3

0.9

5.5

SOUL4

SOUL heme binding protein

4.3

4.6

1.1

4.9

SOUL1

SOUL heme binding protein

133

1.6

3.9

Cre10.g429750

PAS fold

2.8

3.1

1.1

3.6

FXL1

FixL-like PAS domain protein

3.4

5.5

1.6

3.5

ISC1

Iron-sulfur cluster assembly protein

1.6

2.9

Cre10.g466700

2OG-Fe(II)-dependent oxygenase

6.2

8.4

1.4

2.9

Cre13.g586600

Putative cytochrome b ₅₆₁ ferric reductase

4.8

5.5

1.1

3.3

ACH1

Aconitate hydratase

1152

1162

566

1.0

0.5

DES6

ω6-Fatty acid desaturase

1815

1807

892

1.0

0.5

CYC

Mitochondrial cytochrome c

730

695

311

1.0

0.4

FDX2

Ferredoxin 2

7.8

9.3

3.1

1.2

0.4

MitoNEET

Iron sulfur domain-containing CDGSH-type subfamily

309

271

112

0.9

0.4

CYP197-1

Cytochrome P450

9.8

1.0

0.4

GSN1

Glutamate synthase, NADH-dependent

1.1

0.3

Cre02.g093650

Rieske [2Fe-2S] domain-containing protein

421

356

127

0.8

0.3

SIR1

Ferredoxin-sulfite reductase

121

0.7

0.2

PHX5

Prolyl 4-hydroxylase

4.9

0.6

0.1

			RPKM	Fold Change
Tetrapyrrole Biosynthesis	FLP	FLU chloroplast precursor	16	30	199	1.9	13
HEM15	Ferrochelatase	23	40	129	1.7	5.6
POR1	Protochlorophyllide reductase	64	47	243	0.7	3.8
CHLI2	Magnesium chelatase subunit I	46	38	154	0.8	3.4
GSA1	Glutamate-1-semialdehyde aminotransferase	36	23	119	0.6	3.3
CPX1	Coproporphyrinogen III oxidase	40	29	128	0.7	3.2
PBGD1	Porphobilinogen deaminase	32	20	101	0.6	3.1
CHLI1	Magnesium chelatase subunit I	66	44	192	0.7	2.9
GUN4	Tetrapyrrole binding protein	20	13	56	0.7	2.8
GTS2	Glutamyl/glutaminyl-tRNA synthetase	32	23	86	0.7	2.7
CHLD	Magnesium chelatase subunit D	32	19	87	0.6	2.7
CLH1	Chlorophyllase I	2.2	2.4	6.0	1.1	2.7
ALAD	Δ-Aminolevulinic acid dehydratase	132	103	342	0.8	2.6
CHLH1	Magnesium chelatase subunit H	63	62	159	1.0	2.5
UROS	Uroporphyrinogen-III synthase	52	43	127	0.8	2.5
UROD1	Uroporphyrinogen-III decarboxylase	49	26	106	0.5	2.2
CHLG	Chlorophyll synthetase	37	26	79	0.7	2.1
Iron Proteins	Cre09.g403550	2OG-Fe(II)-dependent oxidoreductase	1.2	3.0	30	2.5	25
Cre10.g427850	PAS fold	1.0	2.1	19	2.1	19
CDJ3	Chloroplast DnaJ-like protein	19	45	300	2.4	16
CDJ5	Chloroplast DnaJ-like protein	9.9	43	131	4.3	14
FDX6	Ferredoxin 6	41	121	362	3.0	8.8
FDX3	Ferredoxin 3	21	30	144	1.4	6.9
BKT1	β-Carotene ketolase	1.7	1.5	9.3	0.9	5.5
SOUL4	SOUL heme binding protein	4.3	4.6	21	1.1	4.9
SOUL1	SOUL heme binding protein	34	55	133	1.6	3.9
Cre10.g429750	PAS fold	2.8	3.1	10	1.1	3.6
FXL1	FixL-like PAS domain protein	3.4	5.5	12	1.6	3.5
ISC1	Iron-sulfur cluster assembly protein	31	50	91	1.6	2.9
Cre10.g466700	2OG-Fe(II)-dependent oxygenase	6.2	8.4	18	1.4	2.9
Cre13.g586600	Putative cytochrome b ₅₆₁ ferric reductase	4.8	5.5	16	1.1	3.3
ACH1	Aconitate hydratase	1152	1162	566	1.0	0.5
DES6	ω6-Fatty acid desaturase	1815	1807	892	1.0	0.5
CYC	Mitochondrial cytochrome c	730	695	311	1.0	0.4
FDX2	Ferredoxin 2	7.8	9.3	3.1	1.2	0.4
MitoNEET	Iron sulfur domain-containing CDGSH-type subfamily	309	271	112	0.9	0.4
CYP197-1	Cytochrome P450	28	28	9.8	1.0	0.4
GSN1	Glutamate synthase, NADH-dependent	81	88	28	1.1	0.3
Cre02.g093650	Rieske [2Fe-2S] domain-containing protein	421	356	127	0.8	0.3
SIR1	Ferredoxin-sulfite reductase	121	83	20	0.7	0.2
PHX5	Prolyl 4-hydroxylase	37	24	4.9	0.6	0.1

Table 2.

Open in new tab

Effect of Low Iron Nutrition on Tetrapyrrole Biosynthesis and Iron-Containing Proteins in Acetate-Grown Cells

Process	Gene^a	Defline	20^b	1^b	0.25^b	1/20	0.25/20
			RPKM			Fold Change
Tetrapyrrole Biosynthesis	FLP	FLU chloroplast precursor	16	30	199	1.9	13
	HEM15	Ferrochelatase	23	40	129	1.7	5.6
	POR1	Protochlorophyllide reductase	64	47	243	0.7	3.8
	CHLI2	Magnesium chelatase subunit I	46	38	154	0.8	3.4
	GSA1	Glutamate-1-semialdehyde aminotransferase	36	23	119	0.6	3.3
	CPX1	Coproporphyrinogen III oxidase	40	29	128	0.7	3.2
	PBGD1	Porphobilinogen deaminase	32	20	101	0.6	3.1
	CHLI1	Magnesium chelatase subunit I	66	44	192	0.7	2.9
	GUN4	Tetrapyrrole binding protein	20	13	56	0.7	2.8
	GTS2	Glutamyl/glutaminyl-tRNA synthetase	32	23	86	0.7	2.7
	CHLD	Magnesium chelatase subunit D	32	19	87	0.6	2.7
	CLH1	Chlorophyllase I	2.2	2.4	6.0	1.1	2.7
	ALAD	Δ-Aminolevulinic acid dehydratase	132	103	342	0.8	2.6
	CHLH1	Magnesium chelatase subunit H	63	62	159	1.0	2.5
	UROS	Uroporphyrinogen-III synthase	52	43	127	0.8	2.5
	UROD1	Uroporphyrinogen-III decarboxylase	49	26	106	0.5	2.2
	CHLG	Chlorophyll synthetase	37	26	79	0.7	2.1
Iron Proteins	Cre09.g403550	2OG-Fe(II)-dependent oxidoreductase	1.2	3.0	30	2.5	25
	Cre10.g427850	PAS fold	1.0	2.1	19	2.1	19
	CDJ3	Chloroplast DnaJ-like protein	19	45	300	2.4	16
	CDJ5	Chloroplast DnaJ-like protein	9.9	43	131	4.3	14
	FDX6	Ferredoxin 6	41	121	362	3.0	8.8
	FDX3	Ferredoxin 3	21	30	144	1.4	6.9
	BKT1	β-Carotene ketolase	1.7	1.5	9.3	0.9	5.5
	SOUL4	SOUL heme binding protein	4.3	4.6	21	1.1	4.9
	SOUL1	SOUL heme binding protein	34	55	133	1.6	3.9
	Cre10.g429750	PAS fold	2.8	3.1	10	1.1	3.6
	FXL1	FixL-like PAS domain protein	3.4	5.5	12	1.6	3.5
	ISC1	Iron-sulfur cluster assembly protein	31	50	91	1.6	2.9
	Cre10.g466700	2OG-Fe(II)-dependent oxygenase	6.2	8.4	18	1.4	2.9
	Cre13.g586600	Putative cytochrome b ₅₆₁ ferric reductase	4.8	5.5	16	1.1	3.3
	ACH1	Aconitate hydratase	1152	1162	566	1.0	0.5
	DES6	ω6-Fatty acid desaturase	1815	1807	892	1.0	0.5
	CYC	Mitochondrial cytochrome c	730	695	311	1.0	0.4
	FDX2	Ferredoxin 2	7.8	9.3	3.1	1.2	0.4
	MitoNEET	Iron sulfur domain-containing CDGSH-type subfamily	309	271	112	0.9	0.4
	CYP197-1	Cytochrome P450	28	28	9.8	1.0	0.4
	GSN1	Glutamate synthase, NADH-dependent	81	88	28	1.1	0.3
	Cre02.g093650	Rieske [2Fe-2S] domain-containing protein	421	356	127	0.8	0.3
	SIR1	Ferredoxin-sulfite reductase	121	83	20	0.7	0.2
	PHX5	Prolyl 4-hydroxylase	37	24	4.9	0.6	0.1

Process	Gene^a	Defline	20^b	1^b	0.25^b	1/20	0.25/20
			RPKM			Fold Change
Tetrapyrrole Biosynthesis	FLP	FLU chloroplast precursor	16	30	199	1.9	13
	HEM15	Ferrochelatase	23	40	129	1.7	5.6
	POR1	Protochlorophyllide reductase	64	47	243	0.7	3.8
	CHLI2	Magnesium chelatase subunit I	46	38	154	0.8	3.4
	GSA1	Glutamate-1-semialdehyde aminotransferase	36	23	119	0.6	3.3
	CPX1	Coproporphyrinogen III oxidase	40	29	128	0.7	3.2
	PBGD1	Porphobilinogen deaminase	32	20	101	0.6	3.1
	CHLI1	Magnesium chelatase subunit I	66	44	192	0.7	2.9
	GUN4	Tetrapyrrole binding protein	20	13	56	0.7	2.8
	GTS2	Glutamyl/glutaminyl-tRNA synthetase	32	23	86	0.7	2.7
	CHLD	Magnesium chelatase subunit D	32	19	87	0.6	2.7
	CLH1	Chlorophyllase I	2.2	2.4	6.0	1.1	2.7
	ALAD	Δ-Aminolevulinic acid dehydratase	132	103	342	0.8	2.6
	CHLH1	Magnesium chelatase subunit H	63	62	159	1.0	2.5
	UROS	Uroporphyrinogen-III synthase	52	43	127	0.8	2.5
	UROD1	Uroporphyrinogen-III decarboxylase	49	26	106	0.5	2.2
	CHLG	Chlorophyll synthetase	37	26	79	0.7	2.1
Iron Proteins	Cre09.g403550	2OG-Fe(II)-dependent oxidoreductase	1.2	3.0	30	2.5	25
	Cre10.g427850	PAS fold	1.0	2.1	19	2.1	19
	CDJ3	Chloroplast DnaJ-like protein	19	45	300	2.4	16
	CDJ5	Chloroplast DnaJ-like protein	9.9	43	131	4.3	14
	FDX6	Ferredoxin 6	41	121	362	3.0	8.8
	FDX3	Ferredoxin 3	21	30	144	1.4	6.9
	BKT1	β-Carotene ketolase	1.7	1.5	9.3	0.9	5.5
	SOUL4	SOUL heme binding protein	4.3	4.6	21	1.1	4.9
	SOUL1	SOUL heme binding protein	34	55	133	1.6	3.9
	Cre10.g429750	PAS fold	2.8	3.1	10	1.1	3.6
	FXL1	FixL-like PAS domain protein	3.4	5.5	12	1.6	3.5
	ISC1	Iron-sulfur cluster assembly protein	31	50	91	1.6	2.9
	Cre10.g466700	2OG-Fe(II)-dependent oxygenase	6.2	8.4	18	1.4	2.9
	Cre13.g586600	Putative cytochrome b ₅₆₁ ferric reductase	4.8	5.5	16	1.1	3.3
	ACH1	Aconitate hydratase	1152	1162	566	1.0	0.5
	DES6	ω6-Fatty acid desaturase	1815	1807	892	1.0	0.5
	CYC	Mitochondrial cytochrome c	730	695	311	1.0	0.4
	FDX2	Ferredoxin 2	7.8	9.3	3.1	1.2	0.4
	MitoNEET	Iron sulfur domain-containing CDGSH-type subfamily	309	271	112	0.9	0.4
	CYP197-1	Cytochrome P450	28	28	9.8	1.0	0.4
	GSN1	Glutamate synthase, NADH-dependent	81	88	28	1.1	0.3
	Cre02.g093650	Rieske [2Fe-2S] domain-containing protein	421	356	127	0.8	0.3
	SIR1	Ferredoxin-sulfite reductase	121	83	20	0.7	0.2
	PHX5	Prolyl 4-hydroxylase	37	24	4.9	0.6	0.1

Genes without functional annotation are indicated with the IDs corresponding to the version 4 assembly (Augustus 10.2).

Genes are sorted with respect to the fold changes in iron-limited conditions (0.25/20).

[Fe] in μM.

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