Iron deficiency responses in rice roots

Kobayashi, Takanori; Nakanishi Itai, Reiko; Nishizawa, Naoko K.

doi:10.1186/s12284-014-0027-0

Rice

Table 1 Rice genes responsible for Fe uptake and translocation, and their expression patterns under Fe deficiency

From: Iron deficiency responses in rice roots

		Fe deficiency response					Effects of regulators
Gene name	Function	Whole root		Microdissected			IDEF1		IDEF2	IRO2	HRZ1/2
		24 h	7d	7d Ep	7d Co	7d VB	1d	2-7d	7d	6d	Cont.	7d
DMA biosynthesis for Fe(III)-DMA uptake/translocation
OsNAS1	Nicotianamine synthase	↑	↑↑	↑	↑↑	↑↑	↑	(↓)^c	→	↑	↓↓	→
OsNAS2	Nicotianamine synthase	↑	↑↑	↑↑	↑↑	↑↑	↑	(↓)^c	→	↑	↓↓	→
OsNAS3	Nicotianamine synthase	→	↑	↑	↑↑	↑	↑	↑	↓	↓	↓	↓
OsNAAT1	Nicotianamine aminotransferase	↑	↑↑	↑↑	↑↑	↑↑	(↓)^c	(↓)^c	→	↑	↓	→
OsDMAS1	Deoxymugineic acid synthase	↑	↑↑	↑↑	↑↑	↑↑	↑	(↓)^c	→	↑	↓	→
Transporters for Fe(III)-DMA uptake/translocation
TOM1	DMA efflux transporter	↑	↑↑	↑↑	↑↑	↑↑	↑?^d	(↓)^c	(↓)	↑^e	↓↓	→
OsYSL15	Fe(III)-DMA transporter	↑	↑↑	↑↑	↑↑	↑↑	↑	→	→	↑	↓↓	→
OsYSL16	Fe(III)-DMA transporter^a	→	↑	(↑)	(↓)	→	→	→	→	→	→	→
Methionine cycle for Fe(III)-DMA uptake/translocation
OsSAMS1	S -adenosyl-L-methionine synthetase	→	(↑)	→	→	→	→	→	→	→	→	→
OsSAMS2	S -adenosyl-L-methionine synthetase	(↑)	↑	↑	↑↑	↑	(↑)	→	→	→	(↓)	→
MTN	Methylthioadenosine/S -adenosyl homocysteine nucleosidase	(↑)	↑	↑	↑↑	↑	(↑)	→	→	↑	↓	→
OsMTK1	Methylthioribose kinase	↑	↑^b	↑↑	↑↑	↑	→	(↓)	→	→	↓	→
OsMTK2	Methylthioribose kinase	↑	↑^b	↑↑	↑↑	↑	→	(↓)	→	→	→	→
OsIDI2	Methylthioribose-1-phosphate isomerase	↑	↑	↑↑	↑↑	↑	→	↓	→	↑	↓	→
DEP	Methylthioribulose-1-phosphate dehydratase-enolase-phosphatase	↑	↑	↑↑	↑↑	↑↑	(↑)	↓_c	(↓)	↑	↓	→
OsIDI1/OsARD2	Acireductone dioxygenase	↑	↑	↑↑	↑↑	↑	↑	→	→	↑	↓	→
OsIDI1L/OsARD1	Acireductone dioxygenase	↑	↓	(↑)	(↓)	↓	(↑)	↑	↓	→	(↓)	(↓)
OsIDI4	Aminotransferase catalyzing the synthesis of methionine?	↑	↑	↑↑	↑↑	↑↑	↑	(↓)	→	↑	↓	→
OsAPT1	Adenine phosphoribosyltransferase	↑	↑	↑↑	↑↑	↑	(↑)	(↓)	→	↑	(↓)	→
PRPPS	Phosphoribosyl pyrophosphate synthetase	↑	↑	↑↑	↑↑	↑	(↑)	↓^c	(↓)	(↑)	(↓)	→
RPI	Ribose 5-phosphate isomerase	↑	↑	↑↑	↑↑	↑	(↑)	→	→	→	→	→
FDH	Formate dehydrogenase	↑	↑	↑↑	↑↑	↑	↑	↓^c	→	↑	↓	→
Transporters for ferrous Fe uptake/translocation
OsIRT1	Ferrous Fe transporter	→	↑↑	↑	↑↑	↑↑	↑	↑	→	→	↓	→
OsIRT2	Ferrous Fe transporter	↑	↑↑	↑↑	↑↑	↑↑	↑	↑	→	n.d.	↓	→
OsNRAMP1	Ferrous Fe transporter	↑	↑↑	↑↑	↑↑	↑↑	↑	↑	→	→	↓	→
OsNRAMP5	Ferrous Fe/manganese/cadmium transporter	(↓)	↑	(↑)	↑	(↑)	(↓)	→	→	→	↓	(↓)
PEZ2	Phenolics efflux transporter	→	→	(↑)	↑	↑	→	(↓)	→	→	→	→
Transporters for Fe translocation
OsYSL2	Fe(II)/manganese(II)-NA transporter	↑	↑↑	↑↑	↑↑	↑↑	↑	(↑)	↑↑	→^e	↓↓	↓↓
ENA1	NA efflux transporter	→	↑	↑	↑↑	↑↑	→	(↑)	(↓)	→	↓	(↓)
ENA2	NA efflux transporter	→	(↑)	→	(↑)	(↑)	→	→	→	n.d.	→	→
OsFRDL1	Citrate efflux transporter	→	→	↓	(↑)	→	→	→	→	→	→	→
PEZ1	Phenolics efflux transporter	→	(↓)	→	(↓)	↑	→	→	↓	n.d.	→	→
Transporters for subcellular Fe sequestration
OsVIT1	Fe transporter into vacuole	→	↓	→	→	→	→	→	→	→	→	→
OsVIT2	Fe transporter into vacuole	↓	↓↓	→	↓	↓↓	→	→	→	→	(↑)	→
MIT	Fe transporter into mitochondria	→	↓	(↑)	→	→	→	→	→	n.d.	→	→
Gene regulation in response to Fe deficiency
IDEF1	Positive transcriptional regulator	→	→	↓	(↓)	↓	-	-	→	→	→	→
IDEF2	Positive transcriptional regulator	→	→	→	→	→	→	(↑)	-	→	→	→
OsIRO2	Positive transcriptional regulator	↑	↑↑	↑↑	↑↑	↑↑	↑	↑	(↓)	-	↓	→
OsIRO3	Transcriptional regulator (negative?)	↑	↑↑	↑	↑↑	↑↑	↑	↑	(↑)	→	↓	(↓)
OsbHLH133	Negative transcriptional regulator	↑	↑↑	n.d.	n.d.	n.d.	n.d.	n.d.	n.d.	n.d.	n.d.	n.d.
OsHRZ1	Negative regulator/ubiquitin ligase	↑	↑	↑↑	↑↑	↑	(↑)	(↑)	→	n.d.	-	-
OsHRZ2	Negative regulator/ubiquitin ligase	↑	↑	↑	↑↑	(↑)	→	→	→	→	-	-
OsHORZ1	Positive regulator?	→	(↑)	→	→	→	→	→	(↓)	→	→	→
IBP1.1	IDEF1 protector/trypsin inhibitor	↑	(↑)	(↓)	↓	↓↓	↑	(↑)	↓	→	→	→
IBP1.2	IDEF1 protector?/trypsin inhibitor	↑	↑	→	↓	↓↓	↑	↑	↓	→	→	→
OsRMC	Positive regulator?/receptor-like protein	↑	↓	→	↑	→	→	(↓)^c	(↑)	→	(↓)	(↓)

Functions indicated with a question mark have not been confirmed. Arrows indicate expressional responses: ↑↑, strongly upregulated; ↑, upregulated; (↑), weakly upregulated; →, no significant change; (↓), weakly downregulated; ↓, downregulated; ↓↓, strongly downregulated; n.d., not determined because of the lack of corresponding probe in the microarray. Arrows in boldface indicate expression confirmed by quantitative RT-PCR and/or Northern blotting experiments. The remaining expression data are based on microarray results as follows: Whole root 24 h, root under 24-h Fe deficiency (Itai et al. [2013]); Whole root 7d, root under 7-d Fe deficiency (Ogo et al. [2008]); Microdissected 7d Ep, 7d Co, and 7d VB, rice root segments (Ep, epidermis plus exodermis; Co, cortex; VB, vascular bundle) under 7-d Fe deficiency (Ogo et al. [2014]); IDEF1 1d and 2-7d, roots from an IDEF1 induction line vs. non-transformant under 1-d and 4-d Fe deficiency, respectively (Kobayashi et al. [2009]); IDEF2 7d, roots from an IDEF2 knockdown line vs. non-transformant under 7-d Fe deficiency (Ogo et al. [2008]); IRO2 6d, roots from an IRO2 knockdown line vs. non-transformant under 6-day Fe deficiency (Ogo et al. [2007]); HRZ1/2 Cont. and 7d, roots from OsHRZ1 and OsHRZ2 knockdown lines vs. non-transformant under Fe-sufficient control condition and 7-day Fe deficiency treatment, respectively (Kobayashi et al. [2013]).
^aOsYSL16 is also proposed as a copper-NA transporter involved in internal copper distribution (Zheng et al. [2012]).
^bThe probe used for Northern blotting analysis (Kobayashi et al. [2005]) may not have differentiated between OsMTK1 and OsMTK2.
^cDownregulation was observed in the IDEF1 induction lines, but upregulation was not observed in the IDEF1 knockdown lines, suggesting that negative regulation by IDEF1 may be a secondary effect (Kobayashi et al. [2009]).
^dDownregulation was observed in both the IDEF1 induction and knockdown lines. Positive regulation by IDEF1 may be more plausible, because downregulation in the knockdown lines was more dominant and may reflect more direct effects than overexpression lines.
^eConfirmation by quantitative RT-PCR has been conducted using plants grown on calcareous soil (Ogo et al. [2011]), but not with hydroponically grown plants.

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