Identification and expression analysis of OsLPR family revealed the potential roles of OsLPR3 and 5 in maintaining phosphate homeostasis in rice
© The Author(s). 2016
Received: 21 February 2016
Accepted: 14 July 2016
Published: 3 October 2016
Phosphorus (P), an essential macronutrient, is often limiting in soils and affects plant growth and development. In Arabidopsis thaliana, Low Phosphate Root1 (LPR1) and its close paralog LPR2 encode multicopper oxidases (MCOs). They regulate meristem responses of root system to phosphate (Pi) deficiency. However, the roles of LPR gene family in rice (Oryza sativa) in maintaining Pi homeostasis have not been elucidated as yet.
Here, the identification and expression analysis for the homologs of LPR1/2 in rice were carried out. Five homologs, hereafter referred to as OsLPR1-5, were identified in rice, which are distributed on chromosome1 over a range of 65 kb. Phylogenetic analysis grouped OsLPR1/3/4/5 and OsLPR2 into two distinct sub-clades with OsLPR3 and 5 showing close proximity. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed higher expression levels of OsLPR3-5 and OsLPR2 in root and shoot, respectively. Deficiencies of different nutrients ie, P, nitrogen (N), potassium (K), magnesium (Mg) and iron (Fe) exerted differential and partially overlapping effects on the relative expression levels of the members of OsLPR family. Pi deficiency (−P) triggered significant increases in the relative expression levels of OsLPR3 and 5. Strong induction in the relative expression levels of OsLPR3 and 5 in osphr2 suggested their negative transcriptional regulation by OsPHR2. Further, the expression levels of OsLPR3 and 5 were either attenuated in ossiz1 and ospho2 or augmented in rice overexpressing OsSPX1.
The results from this study provided insights into the evolutionary expansion and a likely functional divergence of OsLPR family with potential roles of OsLPR3 and 5 in the maintenance of Pi homeostasis in rice.
KeywordsRice Phosphate deficiency OsLPR family OsLPR3 OsLPR5 Phosphate homeostasis
Phosphorus (P), one of the essential macronutrients, is required for several biochemical and physiological processes and is a component of key macromolecules including nucleic acids, ATP and membrane phospholipids . P is absorbed from rhizosphere as phosphate (Pi), which is often not easily available to plants due to its slow diffusion rates in soils and/or fixation as immobile organic Pi . Limited Pi availability adversely affects growth and development of plants .
In Arabidopsis thaliana, Pi deficiency triggers progressive loss of meristematic activity in primary root tip thereby inhibiting primary root growth (PRG) . LPR1 (At1g23010) and its close paralog LPR2 (At1g71040), encoding multicopper oxidases (MCOs), are major quantitative trait loci (QTLs) associated with Pi deficiency-mediated inhibition of PRG [5, 6]. Loss-of-function mutations in LPR1 and LPR2 affect Pi deficiency-mediated inhibition of PRG . However, unlike Arabidopsis, Pi deficiency either does not exert any significant effect on PRG of taxonomically diverse dicots and monocots [7, 8] or triggeres augmented PRG in rice [9, 10]. These studies suggested that Pi deficiency-mediated inhibition of PRG is not a global response across different plant species. This raised an obvious question about the likely role of homologs of LPR1/2 particularly in species such as rice in which Pi deficiency has a rather contrasting influence on PRG.
Nuclear-localized SIZ1 (At5g60410) encodes a small ubiquitin-like modifier (SUMO) E3 ligase1 and sumoylates transcription factor (TF) PHR1 (At4g28610) in Arabidopsis . PHR1 plays a pivotal role in regulating the expression of Pi 3starvation-responsive (PSR) genes whose promoters are enriched with PHR1-binding sequence (P1BS) motif . PHR1 is a pivotal upstream component of the Pi sensing and signaling cascade comprising miR399s, IPS1 (At3g09922), PHO2 (At2g33770), SPX1 (At5g20150), Pi transporters Pht1;8 (At1g20860),Pht1;9 (At1g76430) and a subset of other PSR genes [13–15]. Interestingly though, promoters of both LPR1 and LPR2 do not have P1BS motif, which suggests a lack of any regulatory influence of PHR1 on the expression of these genes. Therefore, the identification of TFs that regulate LPR1/2 solicits further studies.
Rice, one of the most important cereal crops, feeds over one-third population of the world and sometimes is the only source of calories [16, 17]. Rice is often cultivated in rain-fed system on soils that are poor in Pi availability, which affects its growth and development and consequently the yield potential . Therefore, it is increasingly becoming imperative to decipher the intricacies involved in the maintenance of Pi homeostasis for developing rice with higher Pi use efficiency for the sustainability of agriculture. Pi starvation signal transduction pathway is highly conserved between Arabidopsis and rice . In this context, several homologs of Arabidopsis in rice ie, OsPHR2 [18, 19], OsPHO2 [20, 21], OsSPX1 and OsSPX2  have been functionally characterized and are pivotal components of Pi sensing and signaling cascade . However, the roles of homologs of LPR1/2 in rice during the maintenance of Pi homeostasis have not been elucidated as yet.
In this study, the identification and expression analysis of OsLPR1-5 in rice were carried out. Phylogenetic analysis revealed their grouping into two distinct subclades. Differential expression of these genes under both Pi-replete and Pi-deprived conditions and also under other nutrient deficiencies suggested functional divergence across them. Further, analyses of the relative expression levels of OsLPR3 and OsLPR5 in loss-of-function mutants (ossiz1, osphr2 and ospho2) and transgenic rice overexpressing either OsPHR2 or OsSPX1 provided an insight into their potential roles in Pi sensing and signaling cascade.
Results and discussion
Comparative structure analysis of LPRs in Arabidopsis and rice
Phylogenetic analysis of LPR genes
Cu-oxidase domain analysis of LPR proteins in rice
Tissue-specific expression profiles of OsLPRs
Nutrient deficiencies affect the expression profiles of OsLPRs
Phosphite represses OsLPR3/5 responses to Pi deficiency in rice
Short- and long-term effects of Pi deficiency on the expression profiles of OsLPRs in the roots
Split-root experiment revealed the effect of systemic Pi sensing on the relative expression levels of OsLPR3/5
OsLPR3/5 are negatively regulated by OsPHR2 and are influenced by SIZ1/PHO2/SPX1-mediated Pi sensing
Transcript levels of OsSPX1 induced in –P root and stem and also in OsPHR2-Ox plants suggesting the former to be downstream of the latter . Another study demonstrated the inhibition in the activity of OsPHR2 by OsSPX1 in a Pi-dependent manner . Together these studies suggested a negative feedback loop regulation of OsPHR2 by OsSPX1. Since the relative expression levels of OsLPR3 and OsLPR5 were significantly increased in osphr2 under both + P and –P conditions (Fig. 9a), a similar expression pattern was anticipated in SPX1-Ox. Consistent with this assumption, significant increases in the relative expression levels of OsLPR3 and OsLPR5 were observed in SPX1-Ox under both + P and –P conditions compared with their corresponding wild types (Fig. 9c). On the contrary, relative expression levels of OsLPR4 in SPX1-Ox (+P and –P) were comparable with the wild type. This suggested that OsLPR3 and OsLPR5 are part of OsPHR2-OsSPX1-mediated regulation of Pi homeostasis.
OsPHO2, a signaling component downstream of OsPHR2, plays a key role in regulating the expression of OsPTs and multiple Pi starvation responses thereby influencing Pi utilization in rice [20, 21]. Therefore, the regulatory influence of OsPHO2 on OsLPR3-5 was investigated (Fig. 9d). There were significant increases in the relative expression levels of OsLPR3 in pho2-1 and pho2-2 compared with the wild type. An increased expression of OsSPX1 in the roots of pho2 mutant suggested a negative regulatory influence of OsPHO2 on its downstream OsSPX1 . The accentuated relative expression levels of OsLPR3 in SPX1-Ox (Fig. 9c) and pho2-1 and pho2-2 (Fig. 9d) thus suggested it to be downstream of OsPHR2-OsPHO2-OsSPX1 pathway. On the contrary, significant reductions and no effect on the relative expression levels of OsLPR5 and OsLPR4, respectively in pho2-1 and pho2-2 compared with the wild type (Fig. 9d) highlighted differential roles of the members of OsLPR family in OsPHR2-OsPHO2-OsSPX1-mediated Pi sensing.
Sumoylation is a critical post-translational modification involved in protein-protein interaction, transcriptional activation and localization of proteins . OsSIZ1 and OsSIZ2, homologs of Arabidopsis SIZ1 in rice, partially complemented the morphological phenotype of siz1-2 in Arabidopsis . Further, several genes involved in Pi sensing and signaling were modulated in ossiz1 . Therefore, the effects of OsSIZ1 on the regulation of OsLPR3-5, were assayed (Fig. 9e). Significant reductions were observed in the relative expression levels of OsLPR3 and OsLPR5 in both siz1-1 and siz1-2 compared with the wild-type. Although marginal reductions in the expression levels of OsLPR4 were also detected in these mutants, the values were statistically insignificant. This suggested a post-translational regulatory influence of OsSIZ1 on OsLPR3 and OsLPR5. However, at present it is not known whether OsSIZ1 exerts direct regulatory influence on OsLPR3 and OsLPR5 by sumoylating them or mediated through a target, which is yet to be identified. Functional characterization of OsLPRs could provide an insight into their specific roles in maintaining Pi homeostasis and thus warrants further studies.
This study presented a detailed genome-wide analysis of the gene structure, phylogenetic evolution and tissue-specific expression patterns of LPR family members in rice (OsLPR1- OsLPR5). Phylogenetic analysis revealed their grouping into two distinct subclades. Differential expression of these genes under deficiencies of Pi and other nutrients suggested lack of functional redundancy across them. Further an insight into the likely roles of OsLPR3 and OsLPR5 in the maintenance of Pi homeostasis was gained by assaying their relative expression levels in loss-of-function mutants (ossiz1, osphr2 and ospho2) and transgenic rice overexpressing either OsPHR2 or OsSPX1. The results from this study thus provide a basis for further detailed functional characterization of different members of OsLPR family for elucidation of their specific roles in maintaining homeostasis during deficiency of Pi and/or other nutrients.
Database searches, sequence alignment and phylogenetic analysis
Complete genomic sequence and transcripts of OsLPR1-5 were retrieved from Michigan State University (MSU) Rice Genome Annotation Project assembly (v7) (http://rice.plantbiology.msu.edu/). Identification of LPR homologs was performed using tBLASTn program and PLAZA1.0 database (http://bioinformatics.psb.ugent.be/plaza/). LPR homologs were identified in dicots (Arabidopsis thaliana, Capsella rubella, Carica papaya, Cicer arietinum, Cucumis sativus, Fragaria vesca, Glycine max, Lotus japonicus, Malus domestica, Manihot esculenta, Populus trichocarpa, Prunus persica, Ricinus communis, Solanum lycopersicum, Theobroma cacao and Vitis vinifera), monocots (Aegilop stauschii, Brachypodium distachyon, Hordeum vulgare, Oryza sativa, Setaria italica, Sorghum bicolor, Triticum urartu and Zea mays), gymnosperms (Picea sitchensis and Selaginella moellendorffii), bryophytes (Physcomitrella patens) and chlorophyta (Volvox carteri and Chlamydomonas reinhardtii). The unrooted phylogenetic tree of LPR homologs was made using the neighbor-joining method and displayed using the MEGA4.0 program.
Plant materials and growth conditions
In the present study, wild type rice (Oryza sativa) ssp. japonica varieties (Nipponbare, ZH11 and Dongjin), T-DNA insertion mutants (ospho2-1/2 , ossiz1-1/2 , osphr2  in the backgrounds of Nipponbare, Dongjin and ZH11, respectively) and two homozygous overexpresors (OsSPX1-Ox  and OsPHR2-Ox [Gu unpublished work] in Nipponbare background) were used. For OsPHR2 overexpressors, the ORF of OsPHR2 was amplified using the specific primers from Nipponbare cDNA. The PCR product was ligated into the pTCK303 vector as described . By electroporation, the construct was transferred to Agrobacterium tumefaciens strain EHA105 and then transformed into Nipponbare as described . For hydroponic experiments, rice seeds were surface-sterilized for 1 min with 75 % ethanol (v/v) and for 30 min with diluted (1:3, v/v) NaClO followed by thorough rinsing for 30 min with deionized water. Seeds were germinated in dark at 25 °C for 3 d. The hydroponic experiments were carried out in a growth room with a 16-h-light (30 °C)/8-h-dark (22 °C) photoperiod and the relative humidity was maintained at approximately 70 %. Uniformly grown seedlings (7-d-old) were then transferred to complete nutrient solution containing 1.25 mM NH4NO3, 300 μM KH2PO4, 0.35 mM K2SO4, 1 mM CaCl2 · 2H2O, 1 mM MgSO4 · 7H2O, 0.5 mM Na2SiO3 · 9H2O, 20 μM Fe-EDTA, 20 μM H3BO3, 9 μM MnCl2 · 4H2O, 0.32 μM CuSO4 · 5H2O, 0.77 μM ZnSO4 · 7H2O and 0.39 μM Na2MoO4 · 2H2O. For + P (control) and –P media, KH2PO4 concentrations used were 300 μM and 0 μM, respectively. To maintain equimolar concentration of K in + P and –P media, KH2PO4 in + P medium was replaced with K2SO4 in –P medium. For + K (control) and –K media, 300 μM KH2PO4 and 300 μM NaH2PO4 were used, respectively. For + Mg (control) and –Mg media, 1 mM MgSO4 · 7H2O and 1 mM Na2SO4 · 7H2O were used, respectively. For –Fe medium, 20 μM Fe-EDTA was eliminated from + Fe (control) medium. Deionized water was used throughout the experiments and pH of all the nutrient solutions were adjusted to 5.0. For all the experiments, nutrient solutions in the hydroponic set up were refreshed every 3rd d. For Pi split-root experiment, seedlings were prepared and grown in complete nutrient solution for 14 d, and then transferred to split-root container for 14 d. The roots of individual plants were separated into two equal parts, placed into separate containers such that one half received 300 μM Pi, while the other half did not receive any Pi. The controls included a split-root treatment in which both halves of the roots received + Pi (300 μM Pi) and –P (0 μM Pi). For Phi treatment, seedlings were grown in –Pi (0 μM Pi) for 21 d. Uniformly grown seedlings were then transferred to + Pi (300 μM Pi), −Pi (0 μM Pi) and + Phi/–Pi (300 μM Phi, 0 μM Pi) solutions for 3 d.
Total RNAs from various tissues were isolated using Trizol reagent (Invitrogen) and first-strand cDNA was synthesized with an oligo (dT)-18 primer and reverse transcriptase. OsActin (accession no. AB047313) was used as an internal control for qRT-PCR analysis. qRT-PCR analysis was performed using SYBR green master mix (Vazyme) and ABI StepOnePlus Sequence Detection System (Applied Biosystems), from biological triplicates. Primers used for qRT-PCR are listed in Additional file 8.
Measurements of Pi and total P concentrations in plants
To measure Pi concentration in plants, about 0.5 g Fresh sample was used for the quantification of Pi concentration in plants as described . Total P concentration was quantified by digesting dry sample (0.05 g) with H2SO4-H2O2 at 280 °C followed by assay with molybdenum blue as described .
Data were analyzed by analysis of variance (ANOVA) using the SPSS 13 program. Different letters or asterisks on the histograms between the mutants and the WT and/or different treatments indicate their statistically significant difference using Duncan multiple range test at P < 0.05.
AREB1, ABSCISIC ACID-RESPONSIVE ELEMENT BINDING PROTEIN1; Fe, iron; FFRL, feed-forward regulatory loop; K, Potassium; LTN1, LEAF TIP NECROSIS1; LPR1, low phosphate root1; lpsi, local phosphate sensing impaired; Mg, magnesium; MCOs, multicopper oxidases; MSU, Michigan State University; N, nitrogen; NAC016, NAM/ATAF1/2/CUC2016; NAP, NAC-LIKE, ACTIVATED BY AP3/PI; NCBI, National Center for Biotechnology Information; Ox, overexpressing; P, phosphorus; Pi, phosphate; Phi, phosphite; −P, Pi deficiency; P1BS, PHR1-binding sequence; PSR, Pi starvation-responsive; PRG, primary root growth; PAP, purple acid phosphatase; SUMO, small ubiquitin-like modifier; qRT-PCR, quantitative real-time PCR; QTLs, quantitative trait loci; SI, sequence identity; TF, transcription factor; TNC, trinuclear Cu cluster; UTR, untranslated region
This work was supported by the Chinese National Natural Science Foundation (31172014), the National Program on R&D of Transgenic Plants (2014ZX08 009-003-005, 2014ZX0800931B and 2016ZX08009-003-005), the Jiangsu Provincial Natural Science Foundation (BK20141367), the Innovative Research Team Development Plan of the Ministry of Education (IRT1256) and the 111 Project (number 12009). We also thank the Ministry of Science and Technology, Department of Biotechnology, Government of India for awarding Ramalingaswamy Fellowship to A.J. [BT/HRD/35/02/26/2009]. We also acknowledge Viswanathan Satheesh for his valuable suggestions and correction during the preparation and revision of this manuscript.
Availability of data and materials
All the data supporting the present findings is contained within the manuscript.
YC participated in planning and conducting the experiments, did bioinformatics analysis and helped in writing the manuscript. HA carried out some experiments. AJ participated in analysis of the data, and helped in writing the manuscript. XW, LZ and WP participated in carrying out different experiments. AC helped in bioinformatics analysis. GX participated in planning the study. SS conceived the study, participated in planning and analysis of the data, and helped in writing the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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