Mol. Cells

Cross-talk between Phosphate Starvation and Other Environmental Stress Signaling Pathways in Plants

Dongwon Baek, Hyun Jin Chun, Dae-Jin Yun, and Min Chul Kim

Additional article information

Abstract

The maintenance of inorganic phosphate (Pi) homeostasis is essential for plant growth and yield. Plants have evolved strategies to cope with Pi starvation at the transcriptional, post-transcriptional, and post-translational levels, which maximizes its availability. Many transcription factors, miRNAs, and transporters participate in the Pi starvation signaling pathway where their activities are modulated by sugar and phytohormone signaling. Environmental stresses significantly affect the uptake and utilization of nutrients by plants, but their effects on the Pi starvation response remain unclear. Recently, we reported that Pi starvation signaling is affected by abiotic stresses such as salt, abscisic acid, and drought. In this review, we identified transcription factors, such as MYB, WRKY, and zinc finger transcription factors with functions in Pi starvation and other environmental stress signaling. In silico analysis of the promoter regions of Pi starvation-responsive genes, including phosphate transporters, microRNAs, and phosphate starvation–induced genes, suggest that their expression may be regulated by other environmental stresses, such as hormones, drought, cold, heat, and pathogens as well as by Pi starvation. Thus, we suggest the possibility of cross-talk between Pi starvation signaling and other environmental stress signaling pathways.

Keywords: cis-acting regulatory element, microRNA, phosphate transporter, phosphate starvation, PSI gene, transcription factor

INTRODUCTION

The availability of inorganic phosphate (Pi) in soil is a crucial determinant of plant growth and development as well as crop productivity (Raghothama, 1999). Plants have evolved morphological, physiological, biochemical, and molecular processes to improve the mobilization, acquisition, and efficient utilization of Pi under deficiency conditions (Poirier and Bucher, 2002; Yuan and Liu, 2008). Reports on the mechanisms that regulate sensing and the response to Pi starvation have identified Pi starvation signaling pathway components and the cross-talk between Pi starvation responses and other plant signaling pathways, including sugars, phytohormones, and photosynthesis (Franco-Zorrilla et al., 2005; Lei et al., 2011a; Rouached et al., 2010; Rubio et al., 2009).

Cross-regulation occurs between Pi starvation and other plant signaling pathways, such as sugars and phytohormones (Rouached et al., 2010; Yuan and Liu, 2008). Pi starvation often causes sugar accumulation in plant tissues; high sugar levels in roots induce root system architecture (RSA) changes under Pi deprivation (Ciereszko et al., 2005; Hammond and White, 2008). Moreover, exogenous sucrose treatment increases the expression levels of Pi transporters and phosphate starvation–induced (PSI ) genes (Karthikeyan et al., 2007; Lejay et al., 2008; Müller et al., 2005). Sugar signaling is also connected with various hormone signaling pathways under Pi starvation (Gibson, 2004). Auxin and ethylene levels are increased by sucrose in the roots, where they are related to RSA developmental changes in Pi starvation responses (Jain et al., 2007; Ma et al., 2003). Pi and abscisic acid (ABA) signaling pathways mediate developmental processes during RSA changes, including increases in the root:shoot ratio and root hair density (Ciereszko and Kleczkowski, 2002; Trull et al., 1997). The cytokinin receptor CRE1/WOL/AHK4 is implicated in the cross-talk between Pi and cytokinin signal transduction pathways by controlling the transcriptional levels of PSI genes (Franco-Zorrilla et al., 2005; Wang et al., 2006). Thus, Pi starvation signaling is strongly linked with numerous plant signaling pathways to maintain appropriate Pi homeostasis in response to changing environmental conditions.

The signaling networks involved with plant responses to Pi starvation are well known, but the cross-talk between Pi starvation and other abiotic stress signaling pathways remains unclear. Recently, however, their cross-talk has been suggested in physiological, phenotypical, and molecular levels. In barley, heat stress affects the expression of PSI genes, which leads to maintenance of Pi homeostasis in plant tissues (Pacak et al., 2016). They suggest that retarded growth and accelerated senescence of barley under heat stress conditions is probably due to disturbances of the macronutrient, including Pi, homeostasis. Comparative root transcriptome analysis using rice cultivars exhibiting contrasting RSA suggests that plants recruit common molecular machinery controlling different regulatory pathways, such as root development, nutrient signaling, biotic- or abiotic-stress responses (Singh et al., 2016). In addition, the RSA formation under Pi starvation conditions are also adjusted by metal stresses, such as arsenate, iron, and aluminum (Dong et al., 2017). In Arabidopsis accessions sensitivities to Pi deficiency are extremely enhanced by arsenate stress (Shukla et al., 2015). Recent reports mention that the AtMYB2 transcription factor, which functions in abiotic stress signaling pathways in Arabidopsis (Abe et al., 2003; Yoo et al., 2005), also acts as a direct transcriptional activator of the miR-NA399f (miR399f ) gene, which plays a crucial role in maintaining Pi homeostasis (Baek et al., 2013). The miR399f also plays numerous roles in modulating plant responses to abiotic stresses, such as salt, ABA, and drought (Baek et al., 2016). The results indicate that cross-talk occurs between Pi starvation signaling and other abiotic stress signaling pathways.

The transcription factors and cis-acting elements of molecular components involved in the signaling cascade have been analyzed to understand plant signaling regulatory mechanisms (Jain et al., 2012; Liu et al., 2015; Yamaguchi-Shinozaki and Shinozaki, 2005), where some transcription factors play multiple roles in responses to different stresses (Briat et al., 2015; Jain et al., 2012). Thus, in silico analysis of cis-acting regulatory elements in the promoters of stress-responsive genes have clarified the molecular and regulatory mechanisms of cross-talk among several stress signaling pathways. In this review, we summarize the transcription factors that participate in both Pi starvation responses and other signaling responses to phytohormones and biotic and abiotic stresses. We believe that the expression of several genes involved in Pi starvation responses may be mediated via different stress signaling cascades according to in silico analysis of the links between Pi starvation and other stress signaling pathways.

TRANSCRIPTION FACTORS THAT CO-REGULATE PI STARVATION AND OTHER STRESS SIGNALING PATHWAYS

MYB Transcription Factors

MYB transcription factors are associated with the signaling networks in various stress responses (Dubos et al., 2010; Franco-Zorrilla et al., 2004). Phosphate starvation response 1 (PHR1) is a representative MYB transcription factor in Pi starvation response (Rubio et al., 2001). PHR1 and PHR1-like (PHL) belong to the MYB-CC class and they directly bind to PHR1-binding site (P1BS; GNATATNC) or P1BS-like (AC/AATATT/CC) elements in the promoter regions of target genes during the Pi starvation stress (Table 1). PHR1 and PHLs regulate the transcription of Pi starvation response target genes, including Pht, PSI, Pi starvation-responsive, and Pi starvation–induced acid phosphatase genes (Nilsson et al., 2007; Sun et al., 2016). PHR1 primarily acts as a transcriptional activator of Pht1, and PHO1 is necessary for Pi uptake by roots under Pi-deficient conditions (Bayle et al., 2011). PHR1 also controls the transcription of genes, such as FERRITIN 1 and galactolipid synthesis genes in responses to Pi, metals, and oxygen deficiency (Bournier et al., 2013; Briat et al., 2015; Klecker et al., 2014).

Table 1

MYB2 functions as a transcriptional activator of ABA-dependent or ABA-independent genes under abiotic stress. MYB2 increases the transcriptional level of RD22 by activating its promoter under drought and ABA stress conditions (Abe et al., 1997; Hoeren et al., 1998). Results of microarray analyses using transgenic plants that overexpressed MYC2/MYB2 showed upregulation of RD22, ADH1, COR6.6, and RD20 genes and the presence of MYB-binding sequences in their promoter regions (Abe et al., 2003). MYB2 also activates the transcription of miR399f in the Pi starvation response by directly binding to a MYB-binding site (MBS; TAACTG) motif in the miR399f promoter region (Table 1; Baek et al., 2013). Like MYB2, MYB62 is a member of the MYB-R2R3 family and localizes in the nucleus (Table 1; Devaiah et al., 2009). Under Pi-sufficient and Pi-deficient conditions, the transcript levels of gibberellic acid (GA) biosynthetic genes and PSI genes decrease in MYB62-overexpressing plants, which have a GA-deficient phenotype. MYB2 is a transcriptional activator, whereas MYB62 suppresses target gene transcription during stress (Devaiah et al., 2009).

WRKY transcription factors

WRKY transcription factors are involved in auto-regulation and cross-regulation by modulating plant transcriptional processes in multiple stress signaling pathways (Banerjee and Roychoudhury, 2015; Phukan et al., 2016). WRKY transcription factors with a C2H2 zinc finger domain control target gene transcription by binding to W box (TTGACT/C) elements (Chiou and Lin, 2011; Rushton et al., 2010). The WRKY6 transcription factor is a typical WRKY family member with roles in the responses to different stimuli, where it enhances the PR1 promoter activity in senescence and pathogen-defense signaling (Chen et al., 2009; Huang et al., 2016; Robatzek and Somssich, 2002). WRKY6 expression is also highly induced by bacterial pathogens and it increases the senescence-induced receptor-like kinase promoter’s activity in response to the bacterial elicitor flagellin (Robatzek and Somssich, 2002). WRKY6 directly binds to the W box within the RAV1 promoter and decreases its gene transcript level during ABA stress response (Huang et al., 2016). Thus, WRKY6 modulates the cross-talk among different stress responses by regulating the transcription of various target genes (Table 1).

WRKY6 negatively regulates PHO1 expression (Chen et al., 2009) and a WRKY6 homolog, WRKY42, positively regulates Pht1 and PHO1 transcription in the Pi starvation response (Table 1; Su et al., 2015). WRKY6 and WRKY42 are both degraded via 26S proteasome-mediated proteolysis in the Pi starvation response (Chen et al., 2009; Su et al., 2015). WRKY45 is specifically expressed in roots and binds to two W box elements in the promoter of Pht1 to regulate its transcription (Table 1; Wang et al., 2014). A root hair-specific WRKY75 affects transcriptional cross-talk among Pi starvation, phytohormones, and biotic stress signaling pathways (Table 1). WRKY75 mutation suppresses the transcription of PSI genes, including phosphatases, Mt4/TPS1-like genes, and Pi transporters (Devaiah et al., 2007a). WRKY75 overexpression increases the transcript levels of jasmonic acid (JA) marker genes, such as PDF1.2, VSP1, and LOX2, but it decreases the expression of PR1, a salicylic acid (SA) marker gene (Chen et al., 2013; Schmiesing et al., 2016). Interestingly, WRKY45 and WRKY75 are mutual negative regulators in auto-regulation, where WRKY75 represses WRKY45 gene transcription by binding two W box elements within the WRKY45 promoter (Wang et al., 2014).

Other transcription factors

There are numerous other transcription factors that are important components of the transcriptional regulatory system of stress-responsive genes (Nakashima et al., 2009). C2H2-type zinc finger protein transcription factors function as essential components in Pi starvation and other abiotic stresses (Sakamoto et al., 2000). ZAT6 binds to three different sequences of POS9 (P-INO-specific regions) motifs in target gene promoters during developmental processes and the Pi starvation response (Table 1; Devaiah et al., 2007b; Meister et al., 2004). ZAT6 is strongly induced and closely related to abiotic stress responses, such as salt, cold, osmotic, and drought stresses, by binding to DRE (dehydration-responsive element) in target gene promoter regions (Table 1; Liu et al., 2013; Vogel et al., 2005). ZAT6 is highly expressed under cold stress and it regulates CBF2 transcription by binding to DRE within its promoter (Vogel et al., 2005).

IN SILICO ANALYSIS OF PUTATIVE CIS-ACTING REGULATORY ELEMENTS IN PI-RESPONSIVE GENE PROMOTERS

Phosphate transporters

Plants have diverse biological mechanisms for enhancing the availability of external Pi in the soil via Pi transporters (Chiou and Lin, 2011; Raghothama, 2000). Pi transporters are encoded by members of PHT gene families, including nine Pht1 members, one Pht2 member, three Pht3 members, six Pht4 members, and three Pht5 members in Arabidopsis (Guo et al., 2008; Knappe et al., 2003; Liu et al., 2016; Rausch and Bucher, 2002). Pht1;1 transcription is positively regulated by PHR1 (Rubio et al., 2001), WRKY75 (Devaiah et al., 2007a), WRKY45 (Wang et al., 2014), and WRKY42 (Su et al., 2015) but negatively regulated by MYB62 (Devaiah et al., 2009) under Pi-deficient conditions. Several types of cis-acting regulatory elements exist in the Pht1;1 promoter, such as P1BS, W box, and MBS. To understand the transcriptional regulation of Pi transporters, we conducted in silico analysis based on the DNA sequences of Pi transporter promoter regions and showed that the expression of Pi transporters could be regulated by hormones and various other stresses as well as by Pi starvation (Tables 2 and 3).

In silico analysis suggest that Pht1;4, Pht1;7, Pht1;8, Pht1;9, Pht3;1, Pht3;2, Pht4;1, Pht4;5, Pht5;2 and Pht5;3 gene transcription is possibly regulated by auxin because their promoters contain auxin-related putative cis-acting regulatory elements such as AuxRE, AuxRR-core, TGA-element, and TGA-box (Table 2). The Pht1;3, Pht1;4, Pht1;6, Pht3;1, Pht3;3 and Pht4;2 gene promoters contain ethylene-responsive cis-acting elements, and a GA-responsive element is found in most Pi transporter genes except Pht1;6, Pht2;1, Pht3;3, Pht4;3, and Pht4;4 (Table 2). A previous report shows the induction of Pht1;4 expression by ethylene supporting the reliability of our in silico analysis for understanding the regulation of Pi starvation-responsive gene networks by other stresses (Lei et al., 2011b). Most Pi transporters contain putative cis-acting regulatory elements in their promoters, such as CGTCA-motif, TGACG-motif, SARE, and TCA-element, which are related to SA- and JA-mediated plant defense signaling (Table 2). The ABA or drought stress-responsive elements ABRE, DRE, and MBS also exist in most Pi transporters, except Pht1;6, Pht1;7, Pht3;1, and Pht5;2, and the cold-responsive element LTR is found in the Pht1;5, Pht1;6, Pht1;8, Pht2;1, Pht3;1, Pht3;3, Pht4;2, Pht4;5, Pht4;6, and Pht5;2 gene promoters (Table 3). Many Pi transporters have TC-rich repeats related to defense and stress responses, except the Pht1;8, Pht3;3, Pht4;4, Pht4;6, and Pht5;1 genes, and an HSE element for heat stress response, except the Pht1;2, Pht1;5, Pht3;1, Pht4;3, Pht4;5, Pht4;6, Pht5;2, and Pht5;3 genes (Table 3). Fungal stress–related Box-W1 elements are found in the Pht1;1, Pht1;3, Pht1;6, Pht1;9, Pht3;1, Pht3;3, Pht4;3, Pht4;4, Pht4;6, and Pht5;3 genes, and wounding stress-related WUN-motifs are predicted in the Pht1;4, Pht3;1, Pht4;1, and Pht4;6 gene promoters (Table 3).

Table 2
Table 3

microRNAs

Many microRNAs (miRNAs) such as miR156, miR399, miR778, miR827, and miR2111, are major regulators in Pi starvation signaling (Chiou et al., 2006; Hsieh et al., 2009; Pant et al., 2009). We showed that miR399f expression is regulated by the MYB2 transcription factor, which has roles in salt, ABA, and drought stress signaling (Table 1; Abe et al., 2003; Yoo et al., 2005) by directly binding to the MBS element in the miR399f precursor promoter (Baek et al., 2013). Moreover, salt and ABA stress enhance the activity of the miR399f promoter (Baek et al., 2016). The miR399f precursor promoter contains several cis-acting regulatory elements, such as CGTCA-motif (involved with JA) and LTR (linked with cold stress) (Baek et al., 2013). miR156 is a key player in the Pi starvation response and flowering, and it also plays an important role in salt, drought, and heat stress signaling (Cui et al., 2014; Stief et al., 2014). The transcription of miR156c is rapidly and greatly induced in response to salt and drought stresses via MYC, ERF, and W box motifs in the miR156c precursor promoter (Cui et al., 2014). Our in silico analysis showed that the miR156c precursor promoter contains various cis-acting elements, such as TGA-element, P-box, GARE-motif, CGTCA-motif, TCA-element, ABRE, LTR, TC-element, and Box-W1, thereby suggesting cross-talk between Pi starvation and various types of stress signaling during the regulation of miRNAs (Tables 2 and 3).

Phosphate starvation-inducible genes

The expression of many Pi starvation-responsive genes is cross-regulated by Pi starvation and other stress signaling pathways. Plant phytohormones, such as cytokinin, ethylene, ABA, and auxin are associated with the transcription of genes involved in the Pi starvation response. PHO1 plays a crucial role in Pi starvation signaling and it is significantly down-regulated by auxin, cytokinin, and ABA (Ribot et al., 2008). RNS1 is a secreted ribonuclease and another Pi starvation–related gene that is significantly upregulated by ABA (Hillwig et al., 2008). The RNS1 promoter contains several putative cis-acting elements, including ABRE, MYB/MYC, WUN-motif, W box, HSE, P-box, and TCA elements, which mediate various stress signaling pathways (Tables 2 and 3; Hillwig et al., 2008). SIZ1 is a small ubiquitin-like modifier E3 ligase paying important roles in enhancing the tolerance of environmental stresses such as salt, cold, drought, ABA, auxin, SA, and Pi starvation (Catala et al., 2007; Miura et al., 2005; 2007; 2009; 2010; 2011a; 2011b). Multiple functions of SIZ1 are known in various stress signaling pathways, but the transcriptional regulation of its expression remains unknown. Our in silico analysis indicates that the SIZ1 promoter contains various putative cis-acting regulatory elements, such as ABRE, LTR, TC-rich repeats, WUN-motif, CGTCA-motif, and TCA-element, which function in diverse stress signal transduction cascades (Tables 2 and 3). Our results provide biological insights into the mechanisms that regulate SIZ1 expression as well as its biological functions in plant stress responses. In summary, findings of our in silico analysis of the regulatory regions of Pi starvation–related genes, such as Pi transporters, miRNAs, and PSI genes, suggest that their expression may be related to various environmental stresses to maintain Pi homeostasis in plants.

CONCLUSION

Phosphorus in the form of Pi is an essential nutrient for plant growth, development, and productivity, but Pi is one of the least available essential nutrients because of its insolubility and low available concentrations (Poirier and Bucher, 2002; Raghothama, 1999). To cope with Pi starvation, plants reprogram various cellular processes, including the reduction of internal Pi usage and activation of external Pi acquisition and recycling. Studies on Pi starvation signaling in plants have identified signaling components, such as transcription factors, non-coding RNAs, and protein modifiers, but also cross-talk with other plant signaling pathways including phytohormones, sugars, and other nutrients (e.g., iron) (Rouached et al., 2010; Yuan and Liu, 2008). Biotic and abiotic stresses significantly affect plant growth, but the links between Pi starvation and other environmental stress signaling pathways remain unclear. Understanding the cross-regulation of gene expression by identifying the transcription factors involved in both Pi starvation and diverse environmental stress signaling pathways, as well as in silico analysis of cis-acting elements in the regulatory regions of Pi starvation signaling components, will provide molecular mechanisms of the connections between Pi starvation and other environmental stress signaling pathways.

Article information

Mol. Cells.Oct 31, 2017; 40(10): 697-705.
Published online 2017-10-17. doi:  10.14348/molcells.2017.0192
<a href="http://www.ncbi.nlm.nih.gov/pmc/pubmed?cmd=search&amp;db=PubMed&amp;term=Dongwon+Baek">Dongwon Baek</a>, <a href="http://www.ncbi.nlm.nih.gov/pmc/pubmed?cmd=search&amp;db=PubMed&amp;term=Hyun+Jin+Chun">Hyun Jin Chun</a>, <a href="http://www.ncbi.nlm.nih.gov/pmc/pubmed?cmd=search&amp;db=PubMed&amp;term=Dae-Jin+Yun">Dae-Jin Yun</a>, and <a href="http://www.ncbi.nlm.nih.gov/pmc/pubmed?cmd=search&amp;db=PubMed&amp;term=Min+Chul+Kim">Min Chul Kim</a>
1Division of Applied Life Science (BK21 PLUS), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
2Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
3Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
*Correspondence: mckim@gnu.ac.kr
Received September 15, 2017; Accepted September 30, 2017.
Articles from Mol. Cells are provided here courtesy of Mol. Cells

References

  • Abe, H., Yamaguchi-Shinozaki, K., Urao, T., Iwasaki, T., Hosokawa, D., and Shinozaki, K. (1997). Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell. 9, 1859-1868.
  • Abe, H., Urao, T., Ito, T., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2003). Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell. 15, 63-78.
  • Baek, D., Kim, M.C., Chun, H.J., Kang, S., Park, H.C., Shin, G., Park, J., Shen, M., Hong, H., and Kim, W.Y. (2013). Regulation of miR399f transcription by AtMYB2 affects phosphate starvation responses in Arabidopsis. Plant Physiol. 161, 362-373.
  • Baek, D., Chun, H.J., Kang, S., Shin, G., Park, S.J., Hong, H., Kim, C., Kim, D.H., Lee, S.Y., and Kim, M.C. (2016). A Role for Arabidopsis miR399f in salt, drought, and ABA signaling. Mol Cells. 39, 111-118.
  • Banerjee, A., and Roychoudhury, A. (2015). WRKY proteins: signaling and regulation of expression during abiotic stress responses. Sci World J. 2015, 807560.
  • Bayle, V., Arrighi, J.F., Creff, A., Nespoulous, C., Vialaret, J., Rossignol, M., Gonzalez, E., Paz-Ares, J., and Nussaume, L. (2011). Arabidopsis thaliana high-affinity phosphate transporters exhibit multiple levels of posttranslational regulation. Plant Cell. 23, 1523-1535.
  • Bournier, M., Tissot, N., Mari, S., Boucherez, J., Lacombe, E., Briat, J.F., and Gaymard, F. (2013). Arabidopsis ferritin 1 (AtFer1) gene regulation by the phosphate starvation response 1 (AtPHR1) transcription factor reveals a direct molecular link between iron and phosphate homeostasis. J Biol Chem. 288, 22670-22680.
  • Briat, J.F., Rouached, H., Tissot, N., Gaymard, F., and Dubos, C. (2015). Integration of P, S, Fe, and Zn nutrition signals in Arabidopsis thaliana: potential involvement of PHOSPHATE STARVATION RESPONSE 1 (PHR1). Front Plant Sci. 6, 290.
  • Bustos, R., Castrillo, G., Linhares, F., Puga, M.I., Rubio, V., Pérez-Pérez, J., Solano, R., Leyva, A., and Paz-Ares, J. (2010). A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis. PLoS Genet . 6, e1001102.
  • Catala, R., Ouyang, J., Abreu, I.A., Hu, Y., Seo, H., Zhang, X., and Chua, N.H. (2007). The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell. 19, 2952-2966.
  • Chen, Y.F., Li, L.Q., Xu, Q., Kong, Y.H., Wang, H., and Wu, W.H. (2009). The WRKY6 transcription factor modulates PHOSPHATE1 expression in response to low Pi stress in Arabidopsis. Plant Cell. 21, 3554-3566.
  • Chen, X., Liu, J., Lin, G., Wang, A., Wang, Z., and Lu, G. (2013). Overexpression of AtWRKY28 and AtWRKY75 in Arabidopsis enhances resistance to oxalic acid and Sclerotinia sclerotiorum. Plant Cell Rep. 32, 1589-1599.
  • Chen, J., Yang, L., Yan, X., Liu, Y., Wang, R., Fan, T., Ren, Y., Tang, X., Xiao, F., and Liu, Y. (2016). Zinc-Finger Transcription Factor ZAT6 Positively Regulates Cadmium Tolerance through the Glutathione-Dependent Pathway in Arabidopsis. Plant Physiol. 171, 707-719.
  • Chiou, T.J., Aung, K., Lin, S.I., Wu, C.C., Chiang, S.F., and Su, C.L. (2006). Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. Plant Cell. 18, 412-421.
  • Chiou, T.J., and Lin, S.I. (2011). Signaling network in sensing phosphate availability in plants. Annu Rev Plant Biol. 62, 185-206.
  • Ciereszko, I., and Kleczkowski, L.A. (2002). Effects of phosphate deficiency and sugars on expression of rab18 in Arabidopsis: hexokinase-dependent and okadaic acid-sensitive transduction of the sugar signal. Biochim Biophys Acta. 1579, 43-49.
  • Ciereszko, I., Johansson, H., and Kleczkowski, L.A. (2005). Interactive effects of phosphate deficiency, sucrose and light/dark conditions on gene expression of UDP-glucose pyrophosphorylase in Arabidopsis. J Plant Physiol. 162, 343-353.
  • Cui, L.G., Shan, J.X., Shi, M., Gao, J.P., and Lin, H.X. (2014). The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants. Plant J. 80, 1108-1117.
  • Devaiah, B.N., Karthikeyan, A.S., and Raghothama, K.G. (2007a). WRKY75 transcription factor is a modulator of phosphate acquisition and root development in Arabidopsis. Plant Physiol. 143, 1789-1801.
  • Devaiah, B.N., Nagarajan, V.K., and Raghothama, K.G. (2007b). Phosphate homeostasis and root development in Arabidopsis are synchronized by the zinc finger transcription factor ZAT6. Plant Physiol. 145, 147-159.
  • Devaiah, B.N., Madhuvanthi, R., Karthikeyan, A.S., and Raghothama, K.G. (2009). Phosphate starvation responses and gibberellic acid biosynthesis are regulated by the MYB62 transcription factor in Arabidopsis. Mol Plant. 2, 43-58.
  • Dong, J., Piñeros, M.A., Li, X., Yang, H., Liu, Y., Murphy, A.S., Kochian, L.V., and Liu, D. (2017). An Arabidopsis ABC Transporter Mediates Phosphate Deficiency-Induced Remodeling of Root Architecture by Modulating Iron Homeostasis in Roots. Mol Plant. 10, 244-259.
  • Dubos, C., Stracke, R., Grotewold, E., Weisshaar, B., Martin, C., and Lepiniec, L. (2010). MYB transcription factors in Arabidopsis. Trends Plant Sci. 15, 573-581.
  • Franco-Zorrilla, J.M., González, E., Bustos, R., Linhares, F., Leyva, A., and Paz-Ares, J. (2004). The transcriptional control of plant responses to phosphate limitation. J Exp Bot. 55, 285-293.
  • Franco-Zorrilla, J.M., Martín, A.C., Leyva, A., and Paz-Ares, J. (2005). Interaction between phosphate-starvation, sugar, and cytokinin signaling in Arabidopsis and the roles of cytokinin receptors CRE1/AHK4 and AHK3. Plant Physiol. 138, 847-857.
  • Gibson, S.I. (2004). Sugar and phytohormone response pathways: navigating a signaling network. J Exp Bot. 55, 253-264.
  • Guo, Y., and Gan, S. (2011). AtMYB2 regulates whole plant senescence by inhibiting cytokinin-mediated branching at late stages of development in Arabidopsis. Plant Physiol. 156, 1612-1619.
  • Guo, B., Jin, Y., Wussler, C., Blancaflor, E.B., Motes, C.M., and Versaw, W.K. (2008). Functional analysis of the Arabidopsis PHT4 family of intracellular phosphate transporters. New Phytol. 177, 889-898.
  • Hammond, J.P., and White, P.J. (2008). Sucrose transport in the phloem: integrating root responses to phosphorus starvation. J Exp Bot. 59, 93-109.
  • Hillwig, M.S., Lebrasseur, N.D., Green, P.J., and Macintosh, G.C. (2008). Impact of transcriptional, ABA-dependent, and ABA-independent pathways on wounding regulation of RNS1 expression. Mol Genet Genomics. 280, 249-261.
  • Hoeren, F.U., Dolferus, R., Wu, Y., Peacock, W.J., and Dennis, E.S. (1998). Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygen. Genetics. 149, 479-490.
  • Hsieh, L.C., Lin, S.I., Shih, A.C., Chen, J.W., Lin, W.Y., Tseng, C.Y., Li, W.H., and Chiou, T.J. (2009). Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol. 151, 2120-2132.
  • Huang, Y., Feng, C.Z., Ye, Q., Wu, W.H., and Chen, Y.F. (2016). Arabidopsis WRKY6 Transcription factor acts as a positive regulator of abscisic acid signaling during seed germination and early seedling development. PLoS Genet . 12, e1005833.
  • Jain, A., Poling, M.D., Karthikeyan, A.S., Blakeslee, J.J., Peer, W.A., Titapiwatanakun, B., Murphy, A.S., and Raghothama, K.G. (2007). Differential effects of sucrose and auxin on localized phosphate deficiency-induced modulation of different traits of root system architecture in Arabidopsis. Plant Physiol. 144, 232-247.
  • Jain, A., Nagarajan, V.K., and Raghothama, K.G. (2012). Transcriptional regulation of phosphate acquisition by higher plants. Cell Mol Life Sci. 69, 3207-3224.
  • Karthikeyan, A.S., Varadarajan, D.K., Jain, A., Held, M.A., Carpita, N.C., and Raghothama, K.G. (2007). Phosphate starvation responses are mediated by sugar signaling in Arabidopsis. Planta. 225, 907-918.
  • Khan, G.A., Bouraine, S., Wege, S., Li, Y., de Carbonnel, M., Berthomieu, P., Poirier, Y., and Rouached, H. (2014). Coordination between zinc and phosphate homeostasis involves the transcription factor PHR1, the phosphate exporter PHO1, and its homolog PHO1;H3 in Arabidopsis. J Exp Bot. 65, 871-884.
  • Klecker, M., Gasch, P., Peisker, H., Dörmann, P., Schlicke, H., Grimm, B., and Mustroph, A. (2014). A shoot-specific hypoxic response of arabidopsis sheds light on the role of the phosphate-responsive transcription factor PHOSPHATE STARVATION RESPONSE1. Plant Physiol. 165, 774-790.
  • Knappe, S., Flügge, U.I., and Fischer, K. (2003). Analysis of the plastidic phosphate translocator gene family in Arabidopsis and identification of new phosphate translocator-homologous transporters, classified by their putative substrate-binding site. Plant Physiol. 131, 1178-1190.
  • Lei, M., Liu, Y., Zhang, B., Zhao, Y., Wang, X., Zhou, Y., Raghothama, K.G., and Liu, D. (2011a). Genetic and genomic evidence that sucrose is a global regulator of plant responses to phosphate starvation in Arabidopsis. Plant Physiol. 156, 1116-1130.
  • Lei, M., Zhu, C., Liu, Y., Karthikeyan, A.S., Bressan, R.A., Raghothama, K.G., and Liu, D. (2011b). Ethylene signaling is involved in regulation of phosphate starvation-induced gene expression and production of acid phosphatases and anthocyanin in Arabidopsis. New Phytol. 189, 1084-1095.
  • Lejay, L., Wirth, J., Pervent, M., Cross, J.M., Tillard, P., and Gojon, A. (2008). Oxidative pentose phosphate pathway-dependent sugar sensing as a mechanism for regulation of root ion transporters by photosynthesis. Plant Physiol. 146, 2036-2053.
  • Liu, X.M., Nguyen, X.C., Kim, K.E., Han, H.J., Yoo, J., Lee, K., Kim, M.C., Yun, D.J., and Chung, W.S. (2013). Phosphorylation of the zinc finger transcriptional regulator ZAT6 by MPK6 regulates Arabidopsis seed germination under salt and osmotic stress. Biochem Biophys Res Commun. 430, 1054-1059.
  • Liu, J., Wang, F., Yu, G., Zhang, X., Jia, C., Qin, J., and Pan, H. (2015). Functional analysis of the maize C-Repeat/DRE Motif-Binding transcription factor CBF3 promoter in response to abiotic stress. Int J Mol Sci. 16, 12131-12146.
  • Liu, T.Y., Huang, T.K., Yang, S.Y., Hong, Y.T., Huang, S.M., Wang, F.N., Chiang, S.F., Tsai, S.Y., Lu, W.C., and Chiou, T.J. (2016). Identification of plant vacuolar transporters mediating phosphate storage. Nat Commun . 7, 11095.
  • Ma, Z., Baskin, T.I., Brown, K.M., and Lynch, J.P. (2003). Regulation of root elongation under phosphorus stress involves changes in ethylene responsiveness. Plant Physiol. 131, 1381-1390.
  • Meister, R.J., Williams, L.A., Monfared, M.M., Gallagher, T.L., Kraft, E.A., Nelson, C.G., and Gasser, C.S. (2004). Definition and interactions of a positive regulatory element of the Arabidopsis INNER NO OUTER promoter. Plant J. 37, 426-438.
  • Miura, K., Rus, A., Sharkhuu, A., Yokoi, S., Karthikeyan, A.S., Raghothama, K.G., Baek, D., Koo, Y.D., Jin, J.B., and Bressan, R.A. (2005). The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. Proc Natl Acad Sci USA. 102, 7760-7765.
  • Miura, K., Jin, J.B., Lee, J., Yoo, C.Y., Stirm, V., Miura, T., Ashworth, E.N., Bressan, R.A., Yun, D.J., and Hasegawa, P.M. (2007). SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis. Plant Cell. 19, 1403-1414.
  • Miura, K., Lee, J., Jin, J.B., Yoo, C.Y., Miura, T., and Hasegawa, P.M. (2009). Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates abscisic acid signaling. Proc Natl Acad Sci USA. 106, 5418-5423.
  • Miura, K., Lee, J., Miura, T., and Hasegawa, P.M. (2010). SIZ1 controls cell growth and plant development in Arabidopsis through salicylic acid. Plant Cell Physiol. 51, 103-113.
  • Miura, K., Lee, J., Gong, Q., Ma, S., Jin, J.B., Yoo, C.Y., Miura, T., Sato, A., Bohnert, H.J., and Hasegawa, P.M. (2011a). SIZ1 regulation of phosphate starvation-induced root architecture remodeling involves the control of auxin accumulation. Plant Physiol. 155, 1000-1012.
  • Miura, K., Sato, A., Ohta, M., and Furukawa, J. (2011b). Increased tolerance to salt stress in the phosphate-accumulating Arabidopsis mutants siz1 and pho2. Planta. 234, 1191-1199.
  • Müller, R., Nilsson, L., Nielsen, L.K., and Nielsen, T.H. (2005). Interaction between phosphate starvation signaling and hexokinase-independent sugar sensing in Arabidopsis leaves. Physiol Plant. 124, 81-90.
  • Nakashima, K., and Yamaguchi-Shinozaki, K. (2006). Regulons involved in osmotic stress-responsive and cold stress-responsive gene expression in plants. Physiologia Plantarum. 126, 62-71.
  • Nakashima, K., Ito, Y., and Yamaguchi-Shinozaki, K. (2009). Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol. 149, 88-95.
  • Nilsson, L., Müller, R., and Nielsen, T.H. (2007). Increased expression of the MYB-related transcription factor, PHR1, leads to enhanced phosphate uptake in Arabidopsis thaliana. Plant Cell Environ. 30, 1499-1512.
  • Pacak, A., Barciszewska-Pacak, M., Swida-Barteczka, A., Kruszka, K., Sega, P., Milanowska, K., Jakobsen, I., Jarmolowski, A., and Szweykowska-Kulinska, Z. (2016). Heat Stress Affects Pi-related Genes Expression and Inorganic Phosphate Deposition/Accumulation in Barley. Front Plant Sci . 7, 926.
  • Pant, B.D., Musialak-Lange, M., Nuc, P., May, P., Buhtz, A., Kehr, J., Walther, D., and Scheible, W.R. (2009). Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol. 150, 1541-1555.
  • Phukan, U.J., Jeena, G.S., and Shukla, R.K. (2016). WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants. Front Plant Sci . 7, 760.
  • Poirier, Y., and Bucher, M. (2002). Phosphate transport and homeostasis in Arabidopsis. Arabidopsis Book. 1, e0024.
  • Raghothama, K.G. (1999). Phosphate acquisition. Annu Rev Plant Physiol Plant Mol Biol. 50, 665-693.
  • Raghothama, K.G. (2000). Phosphate transport and signaling. Curr Opin Plant Biol. 3, 182-187.
  • Rausch, C., and Bucher, M. (2002). Molecular mechanisms of phosphate transport in plants. Planta. 216, 23-37.
  • Ribot, C., Wang, Y., and Poirier, Y. (2008). Expression analyzes of three members of the AtPHO1 family reveal differential interactions between signaling pathways involved in phosphate deficiency and the responses to auxin, cytokinin, and abscisic acid. Planta. 227, 1025-1036.
  • Robatzek, S., and Somssich, I.E. (2002). Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev. 16, 1139-1149.
  • Rouached, H., Arpat, A.B., and Poirier, Y. (2010). Regulation of phosphate starvation responses in plants: signaling players and cross-talks. Mol Plant. 3, 288-299.
  • Rubio, V., Linhares, F., Solano, R., Martín, A.C., Iglesias, J., Leyva, A., and Paz-Ares, J. (2001). A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes Dev. 15, 2122-2133.
  • Rubio, V., Bustos, R., Irigoyen, M.L., Cardona-López, X., Rojas-Triana, M., and Paz-Ares, J. (2009). Plant hormones and nutrient signaling. Plant Mol Biol. 69, 361-373.
  • Rushton, P.J., Somssich, I.E., Ringler, P., and Shen, Q.J. (2010). WRKY transcription factors. Trends Plant Sci. 15, 247-258.
  • Sakamoto, H., Araki, T., Meshi, T., and Iwabuchi, M. (2000). Expression of a subset of the Arabidopsis Cys(2)/His(2)-type zinc-finger protein gene family under water stress. Gene. 248, 23-32.
  • Schmiesing, A., Emonet, A., Gouhier-Darimont, C., and Reymond, P. (2016). Arabidopsis MYC transcription factors are the target of hormonal salicylic acid/jasmonic acid cross talk in response to Pieris Brassicae egg extract. Plant Physiol. 170, 2432-2443.
  • Shukla, T., Kumar, S., Khare, R., Tripathi, R.D., and Trivedi, P.K. (2015). Natural variations in expression of regulatory and detoxification related genes under limiting phosphate and arsenate stress in Arabidopsis thaliana. Front Plant Sci. 6, 898.
  • Singh, A., Kumar, P., Gautam, V., Rengasamy, B., Adhikari, B., Udayakumar, M., and Sarkar, A.K. (2016). Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses. Sci Rep. 6, 39266.
  • Stief, A., Altmann, S., Hoffmann, K., Pant, B.D., Scheible, W.R., and Bäurle, I. (2014). Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors. Plant Cell. 26, 1792-1807.
  • Su, T., Xu, Q., Zhang, F.C., Chen, Y., Li, L.Q., Wu, W.H., and Chen, Y.F. (2015). WRKY42 modulates phosphate homeostasis through regulating phosphate translocation and acquisition in Arabidopsis. Plant Physiol. 167, 1579-1591.
  • Sun, L., Song, L., Zhang, Y., Zheng, Z., and Liu, D. (2016). Arabidopsis PHL2 and PHR1 act redundantly as the key components of the central regulatory system controlling transcriptional responses to phosphate starvation. Plant Physiol. 170, 499-514.
  • Trull, M.C., Guiltinan, M.J., Lynch, J.P., and Deikman, J. (1997). The responses of wild-type and ABA mutant Arabidopsis thaiiana plants to phosphorus starvation. Plant Cell Environ. 20, 85-92.
  • Vogel, J.T., Zarka, D.G., Van Buskirk, H.A., Fowler, S.G., and Thomashow, M.F. (2005). Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J. 41, 195-211.
  • Wang, X., Yi, K., Tao, Y., Wang, F., Wu, Z., Jiang, D., Chen, X., Zhu, L., and Wu, P. (2006). Cytokinin represses phosphate-starvation response through increasing of intracellular phosphate level. Plant Cell Environ. 29, 1924-1935.
  • Wang, H., Xu, Q., Kong, Y.H., Chen, Y., Duan, J.Y., Wu, W.H., and Chen, Y.F. (2014). Arabidopsis WRKY45 transcription factor activates PHOSPHATE TRANSPORTER1;1 expression in response to phosphate starvation. Plant Physiol. 16, 2020-2029.
  • Yamaguchi-Shinozaki, K., and Shinozaki, K. (2005). Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters. Trends Plant Sci. 10, 88-94.
  • Yoo, J.H., Park, C.Y., Kim, J.C., Heo, W.D., Cheong, M.S., Park, H.C., Kim, M.C., Moon, B.C., Choi, M.S., and Kang, Y.H. (2005). Direct interaction of a divergent CaM isoform and the transcription factor, MYB2, enhances salt tolerance in Arabidopsis. J Biol Chem. 280, 3697-3706.
  • Yuan, H., and Liu, D. (2008). Signaling components involved in plant responses to phosphate starvation. J Integr Plant Biol. 50, 849-859.

Table 1

Transcription factors interconnecting Pi starvation and other stress-responsive signaling pathways in Arabidopsis

Type of Factor Transcription Name Locus Binding Motif Sequence Responses References
MYB Family MYB-CC (R1-type) PHR1 At4g28610 P1BS element (P1BS-like element) GNATATNC (AC/AATATT/CC) Pi starvation, metals deficiency, oxygen deficiency Briat et al., 2015; Bustos et al., 2010; Khan et al., 2014; Klecker et al. 2014; Nilsson et al., 2007; Rubio et al. 2001
PHL1 At5g29000 Pi starvation Bustos et al., 2010; Sun et al., 2016
PHL2 At3g24120 Pi starvation Sun et al., 2016
PHL3 At4g13640 Pi starvation Sun et al., 2016
MYB-CC (R2R3-type) MYB2 At2g47190 MBS TAACTG Pi starvation, cytokinin response, salt/ABA/drought response Abe et al., 1997; 2003; Baek et al., 2013; Guo and Gan, 2011; Yoo et al., 2005
MYB62 At1g68320 Pi starvation, GA deficiency Devaiah et al., 2009
WRKY Family WRKY6 At1g62300 W box TTGACT/C Pi starvation, pathogen defense, ABA response Robatzek and Somssich, 2002; Chen et al., 2009; Huang et al., 2016
WRKY42 At4g04450 Pi starvation Su et al., 2015
WRKY45 At3g01970 Pi starvation Wang et al., 2014c
WRKY75 At5g13080 Pi starvation, JA/SA response, pathogen defense Chen et al., 2013; Devaiah et al., 2007a; Schmiesing et al., 2016
ZFP family Zinc Finger (C2H2-type) ZAT6 At5g04340 POS9A POS9B and POS9C DRE (GA)9 repeat TGTGAGAGA TGGCCGAC Pi starvation, metals stress, salt/drought/osmotic stress response Chen et al., 2016; Devaiah et al., 2007b; Liu et al., 2013; Nakashima and Yamaguchi-Shinozaki, 2006

Table 2

Analysis of hormone signaling-related putative cis-acting regulatory elements in Pi starvation-responsive gene promoters

Stress Motif Name Sequence Gene Name (Number of sites in the promoter)
AtPTs microRNAs PSI
Auxin AuxRE TGTCTCAATAAG AtPht1;8(1) miR2111a(1) None
AuxRR-core GGTCCAT AtPht1;9(1), AtPht4;1(1) miR156g(2) SPX1(1), LPR1(1)
TGA-element AACGAC AtPht1;4(2), AtPht1;7(2), AtPht3;1(1), AtPht3;2(1), AtPht4;1(1), AtPht4;5(1), AtPht4;6(1), AtPht5;2(1), AtPht5;3(1) miR156c(2), miR156g(1), miR156h(1), miR2111a(1) SPX4(2), PHR1(2), SCR(1), PAP2(1)
TGACGTAA None miR156b(1) None
TGA-box TGACGTGGC None miR2111b(1) None
Ethylene ERE ATTTCAAA AtPht1;3(1), AtPht1;4(2), AtPht1;6(1), AtPht3;1(1), AtPht3;3(1), AtPht4;2(1) miR156a(2), miR156b(1), miR156c(1), miR156e(2), miR2111b(1) At4/IPS2(1), PAP2(1)
GA P-box CCTTTTG AtPht1;4(2), AtPht1;5(1), AtPht1;8(2), AtPht4;6(1) miR156b(1), miR156c(1), miR2111a(2) SPX2(1), PHR1(1), RNS1(1), At4/IPS2(2), PDR2(2), LPR2(1), SCR(1), BAH1(1)
GCCTTTTGAGT None miR399d(1), miR399e(1) IPS1(1)
GARE-motif TCTGTTG AtPht1;2(1), AtPht1;4(1), AtPht1;5(1), AtPht1;7(1), AtPht1;8(1), AtPht1;9(1), AtPht3;2(2), AtPht4;5(1), AtPht4;6(1), AtPht5;2(2) miR156b(1), miR156e(1), miR399b(1), miR399e(2), miR778a(1), miR827a(1) SPX3(1), PHO2(1)
AAACAGA AtPht1;1(1), AtPht1;3(1), AtPht1;4(1), AtPht1;7(3), AtPht1;8(2), AtPht1;9(2), AtPht3;1(1), AtPht4;1(1), AtPht4;2(1), AtPht4;6(1), AtPht5;1(1) miR156c(2), miR156d(2), miR399b(1), miR399c(1), miR778a(2), miR827a(3) PHR1(1), PHF1(2), PHO2(5), LPR2(2), SCR(3), BAH1(4)
TATC-box TATCCCA AtPht4;1(2), AtPht4;5(1), AtPht5;3(1) miR156e(1), miR156h(1), miR778a(1) SPX3(1), BAH1(1)
JA CGTCA-motif CGTCA AtPht1;1(1), AtPht1;4(2), AtPht1;5(2), AtPht1;6(2), AtPht1;7(3), AtPht1;9(2), AtPht3;1(1), AtPht3;2(4), AtPht3;3(3), AtPht4;1(2), AtPht4;2(1), AtPht4;3(1), AtPht4;4(2), AtPht4;5(2), AtPht4;6(1), AtPht5;3(1) miR156b(3), miR156c(2), miR156d(1), miR156g(2), miR156h(4), miR399c(1), miR399d(1), miR399f(1), miR778a(3), miR827a(1), miR2111b(2) SPX1(2), SPX3(1), SPX4(2), PHR1(2), PHF1(1), PHO1(2), PHO2(3),SIZ1(1), PDR2(2), LPR1(2), SCR(2), PAP2(2)
TGACG-motif TGACG AtPht1;1(1), AtPht1;4(2), AtPht1;5(2), AtPht1;6(2), AtPht1;7(3), AtPht1;9(2), AtPht3;1(1), AtPht3;2(4), AtPht3;3(3), AtPht4;1(2), AtPht4;2(1), AtPht4;3(1), AtPht4;4(2), AtPht4;5(2), AtPht4;6(1), AtPht5;3(1) miR156b(3), miR156c(2), miR156d(1), miR156g(2), miR156h(4), miR399c(1), miR399d(1), miR399f(1), miR778a(3), miR827a(1), miR2111b(2) SPX1(2), SPX3(1), SPX4(2), PHR1(2), PHF1(1), PHO1(2), PHO2(3),SIZ1(1), PDR2(2), LPR1(2), SCR(2), PAP2(2)
SA SARE TTCGACCATCTT AtPht3;3(1), AtPht5;3(1) None None
TCA-element CCATCTTTTT AtPht1;4(1), AtPht2;1(1), AtPht3;1(1), AtPht4;6(2), AtPht5;1(1), AtPht5;3(2) miR156c(1), miR156e(1), miR156f(1), miR399b(2), miR399c(1), miR2111b(1) SPX1(1), SPX3(1), SPX4(1), PHO1(1), RNS1(3), IPS1(1), SIZ1(1), PDR2(1), SCR(3)
GAGAAGAATA AtPht1;1(1), AtPht1;2(1), AtPht1;3(1), AtPht1;4(1), AtPht1;6(1), AtPht1;7(2), AtPht1;8(1), AtPht1;9(1), AtPht2;1(1), AtPht4;1(2), AtPht4;4(2), AtPht5;1(1), AtPht5;2(1), AtPht5;3(1) miR156a(1), miR156d(1), miR156e(1), miR399c(1), miR827a(3), miR2111a(1), miR2111b(1) SPX3(1), SCR(1), PAP2(1)
CAGAAAAGGA AtPht2;1(1), AtPht3;1(1), AtPht3;3(1), AtPht4;3(1) miR156d(1) LPR1(1), SCR(1)
TCAGAAGAGG AtPht1;4(1), AtPht2;1(1) miR156e(1), miR2111b(1) None

In silico analysis was conducted using 1.5 kb upstream promoter regions from first exon start site of each gene by the PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/).

Table 3

Analysis of various stresses signaling-related putative cis-acting regulatory elements in Pi starvation-responsive gene promoters

Stress Motif Name Sequence Gene Name (Number of sites in the promoter)
AtPTs microRNAs PSI
ABA ABRE ACGTGGC AtPht4;1(1), AtPht4;4(1) miR2111b(1) LPR1(1)
AGTACGTGGC None miR399e(1) None
CACGTG AtPht4;1(1), AtPht4;2(1), AtPht4;3(1), AtPht4;4(1), AtPht4;5(1) miR156b(2), miR156c(1), miR156e(1), miR156h(1), miR399e(1), miR2111a(1) SIZ1(1)
CGCACGTGTC None miR2111a(1) None
GCAACGTGTC AtPht5;1(1), AtPht5;3(1) miR156d(1) None
GCCACGTACA AtPht3;3(1) None None
GCCGCGTGGC AtPht4;1(1), AtPht4;2(1) None BAH1(1)
TACGTG AtPht1;1(1), AtPht1;2(1), AtPht1;3(1), AtPht3;2(1), AtPht3;3(1), AtPht4;1(1), AtPht4;2(1), AtPht4;4(1), AtPht4;6(1), AtPht5;1(1) miR156a(1), miR156d(1), miR156h(1), miR399c(1) SPX1(1), SPX3(1), PHR1(1), PHF1(1), PHO1(1), RNS1(3), IPS1(2), SIZ1(1), LPR10(1)
TACGGTC None miR778a(1), miR827a(1) SIZ1(1)
CE3 GACGCGTGTC None miR156h(1) None
Drought C-repeat/DRE TGGCCGAC AtPht1;9(1) None None
MBS CAACTG AtPht1;8(1), AtPht3;2(1), AtPht4;2(1), AtPht5;1(1), AtPht5;3(1) miR156e(1), miR399a(1), miR399c(1) SPX2(1), PHO2(3), At4/IPS2(1), SCR(1), PAP2(2)
CGGTCA AtPht1;4(1), AtPht4;5(1) miR156h(1), miR399b(1), miR778a(1), miR827a(2) SPX2(1), SPX3(1), PHO2(1)
TAACTG AtPht1;1(1), AtPht1;3(1), AtPht1;4(2), AtPht1;5(1), AtPht1;8(1), AtPht2;1(1), AtPht4;2(1), AtPht4;3(3) miR399c(1), miR399d(2), miR399f(2) SPX1(1), SPX2(4), PHO1(2), PHO2(2), LPR1(1), LPR2(1)
Cold LTR CCGAAA AtPht1;5(1), AtPht1;6(1), AtPht1;8(2), AtPht2;1(3), AtPht3;1(2), AtPht3;3(1), AtPht4;2(1), AtPht4;5(1), AtPht4;6(1), AtPht5;2(1) miR156c(1), miR156d(1), miR156e(1), miR156f(1), miR156g(2), miR399d(1), miR399f(1), miR827a(1) SPX1(2), SPX4(2), PHR1(1), PHO1(1), PHO2(1), SIZ1(2), PDR2(2), LPR2(1)
Defense and stress TC-rich repeats ATTCTCTAAC AtPht1;9(2), AtPht5;3(1) miR156c(1), miR156e(1), miR156f(1), miR827a(1), miR2111a(1) LPR2(1)
ATTTTCTTCA AtPht1;7(2), AtPht2;1(4), AtPht3;1(1), AtPht3;2(1), AtPht4;1(1), AtPht4;2(1), AtPht4;5(1), AtPht5;2(3), AtPht5;3(3) miR156b(1), miR156f(1), miR156h(1), miR399b(1), miR399c(1), miR399d(1), miR399e(2) SPX1(1), SPX2(2), SPX4(1), PHR1(2), At4/IPS2(1), SIZ1(1), PDR2(1), LPR2(1)
ATTTTCTCCA AtPht1;1(1), AtPht1;5(1), AtPht1;6(1), AtPht3;2(2), AtPht4;1(1), AtPht4;3(3), AtPht5;2(1) miR778a(1) PHR1(1), PHF1(1), LPR2(1)
GTTTTCTTAC AtPht1;2(1), AtPht1;3(1), AtPht1;4(1), AtPht1;6(1), AtPht1;7(1), AtPht4;3(1), AtPht5;2(1) miR156c(1), miR156e(1), miR156h(1), miR399c(1), miR778a(2), miR2111b(1) IPS1(1), At4/IPS2(2), SCR(2)
Fungal Box-W1 TTGACC AtPht1;1(2), AtPht1;3(1), AtPht1;6(1), AtPht1;9(1), AtPht3;1(3), AtPht3;3(1), AtPht4;3(1), AtPht4;4(2), AtPht4;6(1), AtPht5;3(1) miR156c(2), miR156h(1), miR399a(1), miR399e(1), miR827a(1) SPX1(1), SPX2(1), SPX3(1), SPX4(1), SCR(1), BAH1(1)
Heat HSE AGAAAATTCG AtPht1;7(2), AtPht3;2(1), AtPht5;1(1) miR156b(1), miR156g(2), miR399a(1) SPX2(3), SPX3(1), PDR2(1), LPR1(1), SCR(1)
AAAAAATTTC AtPht1;1(3), AtPht1;3(1), AtPht1;4(1), AtPht1;6(2), AtPht1;7(3), AtPht1;8(1), AtPht1;9(1), AtPht2;1(3), AtPht3;2(1), AtPht4;1(1), AtPht4;2(1), AtPht4;4(1) miR156a(3), miR156b(1), miR156f(1), miR156g(1), miR399b(2), miR399c(1), miR778a(2), miR2111a(2) SPX2(1), PHR1(1), PHF1(1), PHO1(2), RNS1(4), At4/IPS2(1), PDR2(2), LPR1(1), SCR(1)
CNNGAANNTTCNNG AtPht1;9(1) None None
Wound WUN-motif TCATTACGAA AtPht1;4(1), AtPht3;1(1), AtPht4;1(1), AtPht4;6(1) miR399c(2) SPX3(1), PHO1(1), BAH1(1), PAP2(1)

In silico analysis was conducted using 1.5 kb upstream promoter regions from first exon start site of each gene by the PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/).