. 2011 May 26;156(3):1067–1077. doi: 10.1104/pp.111.174987

Table I. Pi starvation-related genes in Arabidopsis and their orthologs from rice, maize, sorghum, and Brachypodium distachyon.

Gene models from Arabidopsis (The Arabidopsis Information Resource version 10), rice (release 6.1), maize (release 4a.53, filtered set), Brachypodium (release 1.0), and sorghum (release 1.4) were considered for identification of the putative orthologs by using the OrthoMCL pipeline (Li et al., 2003) with default parameters except for miR399, At4, and IPS1. Adapted from Lin et al. (2009). ND, No data; NPOI, no putative ortholog identified.

Gene	Arabidopsis	Rice	Maize	Sorghum	Brachypodium	Description of Function	References
PHR1	At4g28610	LOC_Os03g21240	GRMZM2G006477	Sb01g036440	Bradi1g63530	A MYB transcription factor; it activates a subset of Pi starvation-induced genes by binding to the P1BS element; phr1 shows reduced Pi concentration	Rubio et al. (2001); Nilsson et al. (2007); Zhou et al. (2008)
		LOC_Os07g25710	GRMZM2G162409	Sb02g010520	Bradi1g28920
SIZ1	At5g60410	LOC_Os05g03430	GRMZM2G155123	Sb09g002225	Bradi2g38030	SUMO E3 ligase; it facilitates the sumoylation of PHR1 and regulates the expression of several Pi starvation-responsive genes; siz1 shows higher shoot Pi concentration	Miura et al. (2005)
		LOC_Os03g50980	GRMZM2G002999	Sb08g000380	Bradi4g45080
PHF1	At3g52190	LOC_Os07g09000	GRMZM2G158489	Sb02g005080	Bradi1g55000	An endoplasmic reticulum-located SEC12-related protein; it facilitates the trafficking of PHT1 proteins to plasma membrane regulated by PHR1; phf1 shows reduced Pi content	González et al. (2005)
PHO1	At3g23430	LOC_Os02g56510	GRMZM2G466545	Sb04g036730	Bradi3g54920	A protein with SPX and EXS domains; it is involved in Pi loading into the xylem; pho1 displays Pi starvation symptoms with reduced shoot Pi	Poirier et al. (1991); Hamburger et al. (2002); Stefanovic et al. (2007)
PHO2 (UBC24, LTN1)	At2g33770	LOC_Os05g48390	GRMZM2G381709	Sb09g028110	Bradi2g16960	Ubiquitin E2 conjugase; it regulates Pi uptake, allocation, and remobilization; a target gene of miR399s; pho2 displays Pi toxicity with excessive shoot Pi	Delhaize and Randall (1995); Dong et al. (1998); Aung et al. (2006); Bari et al. (2006); Hu et al. (2011)
			GRMZM2G464572
miR399	At1g29265, At1g63005, At5g62162, At2g34202, At2g34204, At2g34208	osa-MIR399a osa-MIR399b osa-MIR399c osa-MIR399d osa-MIR399e osa-MIR399f osa-MIR399g osa-MIR399h osa-MIR399i osa-MIR399j osa-MIR399k	zma-MIR399a zma-MIR399b zma-MIR399c zma-MIR399d zma-MIR399e zma-MIR399f zma-MIR399g zma-MIR399h zma-MIR399i zma-MIR399j	sbi-MIR399a sbi-MIR399b sbi-MIR399c sbi-MIR399d sbi-MIR399e sbi-MIR399f sbi-MIR399g sbi-MIR399h sbi-MIR399i sbi-MIR399j sbi-MIR399k	ND	A microRNA; it negatively regulates PHO2 and serves as a shoot-derived long-distance signal; regulated by PHR1 overexpression of miR399; mimics the Pi toxic phenotype of pho2	Jones-Rhoades and Bartel (2004); Fujii et al. (2005); Bari et al. (2006); Chiou et al. (2006); Lin et al. (2008); Pant et al. (2008);Zhang et al. (2009)
PHO3 (SUC2)	At1g22710	NPOI	A Suc/H⁺ symporter; it regulates Pi starvation responses; pho3 shows reduced total P concentration	Lloyd and Zakhleniuk (2004); Zakhleniuk et al. (2001)
PHT1;1 (PT1)	At5g43350	LOC_Os04g10800	GRMZM2G170208	Sb06g002560	Bradi5g02750	High-affinity Pi transporters involved in Pi acquisition; pht1;1 mutant shows reduced Pi uptake and shoot Pi content; increased Pi uptake by overexpression of PHT1;1 in tobacco cells; pht1;1/pht1;4 double mutant shows significant decrease in Pi uptake, shoot Pi content, and fresh weight	Mitsukawa et al. (1997); Misson et al. (2004); Shin et al. (2004)
PHT1;4 (PT2)	At2g38940	LOC_Os04g10750	GRMZM2G045473	Sb06g002800	Bradi5g02730
		LOC_Os04g10690	GRMZM2G154090	Sb01g046900	Bradi3g27680
		LOC_Os03g05610		Sb01g020570
		LOC_Os10g30790
PHT2;1	At3g26570	LOC_Os02g38020	GRMZM2G092780	Sb04g024630	Bradi3g47550	A low-affinity Pi transporter in chloroplast; it is involved in Pi allocation between roots and shoots and Pi remobilization between old and young leaves	Daram et al. (1999); Versaw and Harrison (2002)
At4, IPS1	At5g03545 At3g09922	LOC_Os03g05334 LOC_Os01g0838350	GRMZM2G086179 GRMZM5G843352 GRMZM2G436295	ND	ND	Noncoding RNAs; they regulate Pi allocation between roots and shoots; inhibit the cleavage of miR399 to PHO2 mRNA by mimicking the target sequence of miR399	Hou et al. (2005); Shin et al. (2006); Franco-Zorrilla et al. (2007)
PTF1	NPOI	LOC_Os06g09370	GRMZM2G024530	Sb10g006250	Bradi1g46700	A bHLH transcription factor; it regulates the expression of several Pi starvation-responsive genes; overexpression of OsPTF1 increases Pi content, root growth, and tiller number; overexpression in maize leads to improved tolerance of low-P stress	Yi et al. (2005); Li et al. (2011)
WRKY75	At5g13080	LOC_Os05g45230	NPOI			A WRKY transcription factor; it positively regulates Pi starvation responses but negatively regulates lateral root and root hair growth	Devaiah et al. (2007a)
ZAT6	At5g04340	LOC_Os03g32230	GRMZM2G106026	Sb01g031900	NPOI	A C2H2 zinc finger transcription factor; it regulates several Pi starvation-responsive genes; controls root architecture, Pi uptake, and Pi accumulation	Devaiah et al. (2007b)
BHLH32	At3g25710	LOC_Os03g15440	GRMZM2G043854	Sb01g040450	Bradi1g67500	A bHLH transcription factor; it is a negative regulator of Pi starvation responses; bhlh32 has hypersensitive Pi starvation responses and increased Pi concentration	Chen et al. (2007)
		LOC_Os01g06640	GRMZM2G088443	Sb03g005250	Bradi2g03830
SQD2	At5g01220	LOC_Os07g01030	GRMZM2G100652	Sb02g000240	Bradi1g59860	Involved in sulfolipid biosynthesis; sqd2 mutant shows reduced growth under Pi-deficient conditions	Yu et al. (2002)
		LOC_Os01g04920	NPOI	Sb03g006480	Bradi2g02800
		LOC_Os03g15840	GRMZM2G049190	Sb01g040150	Bradi1g67200
PLDζ1	At3g16785	LOC_Os05g29050	GRMZM2G066485	Sb09g017850	Bradi2g27950	Involved in phospholipid degradation and synthesis of galactolipid in roots; regulates root architecture in response to Pi starvation	Cruz-Ramírez et al. (2006); Li et al. (2006a, 2006b)
		LOC_Os01g20860	Sb03g012720	Bradi2g11810			Cruz-Ramírez et al. (2006); Li et al. (2006a, 2006b)
CAX1	At1g08960	LOC_Os11g05070	GRMZM2G004414	Sb08g002860	Bradi4g42870	Tonoplast Ca²⁺/H⁺ antiporters; cax1/cax3 double mutant has increased shoot Pi content	Cheng et al. (2003, 2005)
					Bradi4g42880		Cheng et al. (2003, 2005)
CAX3	At3g51860	LOC_Os01g37690	GRMZM2G011592	Sb03g024820	Bradi2g41090
		LOC_Os02g21009	NPOI	Sb04g010130	NPOI
IPK1	At5g42810	LOC_Os04g56580	GRMZM2G150496	Sb06g031650	Bradi5g24890	An inositol polyphosphate kinase; reduced phytate but increased Pi concentration in ipk1 mutant seeds; ipk1 mutant has high leaf Pi concentration	Stevenson-Paulik et al. (2005)
SPX1	At5g20150	LOC_Os06g40120	GRMZM2G171423	Sb04g006990	Bradi1g36610	SPX domain-containing proteins; regulates the expression of several Pi starvation-responsive genes involved in Pi uptake, allocation, and remobilization	Duan et al. (2008); Wang et al. (2009); Liu et al. (2010)
				Sb10g023590	Bradi3g07470
SPX3	At2g45130	LOC_Os10g25310	GRMZM2G370780	Sb01g032880	Bradi1g60250
		LOC_Os03g29250	NPOI	Sb01g023270	NPOI
PDR2	At5g23630	LOC_Os05g33390	GRMZM2G060824	Sb09g019760	Bradi2g25860	P5-type ATPase; mediates developmental responses of root meristems to Pi availability	Ticconi et al. (2004, 2009)
MYB62	At1g68320	LOC_Os01g03720	GRMZM2G096358	Sb03g007360	Bradi2g01960	Transcription factor; overexpression represses the expression of GA biosynthetic and PSR genes; controls root architecture and Pi uptake	Devaiah et al. (2009)
			GRMZM2G162709
ARP6	At3g33520	LOC_Os01g16414	GRMZM2G088487	Sb08g021780	Bradi2g10130	Component in the SWR1 (SWI/SNF related) chromatin-remodeling complex; suppresses PSR gene expression if Pi concentration is optimal	Smith et al. (2010)
LPR1	At1g23010	LOC_Os01g03530	GRMZM2G086727	Sb03g007480	NPOI	A multicopper oxidase; mediates the arrest in primary root growth when the root tip is in contact with low-Pi medium	Svistoonoff et al. (2007)
		LOC_Os01g03549	GRMZM2G054050	Sb03g007470	Bradi2g01850
		LOC_Os01g03620	NPOI	Sb03g007440	NPOI