articleGenomic survey , characterization and expression profile analysis of the peptide transporter family in rice ( Oryza sativa L . )

Background: Peptide transporter (PTR) family whose member can transport di-/tripeptides and nitrate is important for plant growth and development. Although the rice (Oryza sativa L.) genome has been sequenced for a few years, a genomic survey, characterization and expression profile analysis of the PTR family in this species has not been reported. Results: In this study, we report a comprehensive identification, characterization, phylogenetic and evolutionary analysis of 84 PTR family members in rice (OsPTR) as well as their whole-life expression patterns. Chromosomal distribution and sequence analysis indicate that nearly 70% of OsPTR members are involved in the tandem and segmental duplication events. It suggests that genome duplication might be a major mechanism for expansion of this family. Highly conserved motifs were identified in most of the OsPTR members. Meanwhile, expression profile of OsPTR genes has been analyzed by using Affymetrix rice microarray and real-time PCR in two elite hybrid rice parents, Minghui 63 and Zhenshan 97. Seven genes are found to exhibit either preferential or tissue-specific expression during different development stages of rice. Under phytohormone (NAA, GA3 and KT) and light/dark treatments, 14 and 17 OsPTR genes are differentially expressed respectively. Ka/Ks analysis of the paralogous OsPTR genes indicates that purifying selection plays an important role in function maintenance of this family. Conclusion: These investigations add to our understanding of the importance of OsPTR family members and provide useful reference for selecting candidate genes for functional validation studies of this family in rice. Background Nutrient transport is essential to life and occurs in both prokaryotes and eukaryotes. It is well established that peptide transporters play an important role in the nutrition of bacteria, yeasts and animals [1]. However, the role of transporters of small peptides (2-6 amino acids) in plants is less well defined [2]. Peptide transporter (PTR) family (TC 2.A.17), also called the proton-dependent oligopeptide transport (POT) family [3,4] is a family consists of di-/tripeptides transporters [5]. Besides, some plant PTRs acted as nitrate transporters are termed as the members of Nitrate Transporter 1 family (NRT1, [6]). PTR proteins in plants show significant sequence homology and contain several transmembrane (TM) regions, with a large hydrophilic loop among TMs. Generally, the identified PTR members in plants fall into three types based on the nature of their substrates: di-/tripeptides transporter, nitrate transporter and other substrates transporter [6]. AtPTR2 (At2g02040) was the first identified di-/tripeptides transporter in Arabidopsis [7-10] and had high mRNA expression levels in 3-d-germinating seed, root and young leaf [8]. The antisense plants of AtPTR2 exhibited delayed flowering time and arrested seed development [9,11]. AtPTR1 (At3g54140) transported di-/ tripeptides with low selectivity as well as substrates lacking a peptide bond. AtPTR1 was expressed in the vascular tissue throughout the plant, indicative of a role in longdistance transport [10]. AtPTR3 (At5g46050) was a salt stress and mechanical wounding inducible gene, JA and SA were both involved in regulation of it [12,13]. AtPTR5 (At5g01180) which mediated high-affinity transport of dipeptides was most likely supplying peptides to maturat* Correspondence: zxb018@webmail.hzau. edu.cn 1 National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China Full list of author information is available at the end of the article BioMed Central © 2010 Zhao et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Zhao et al. BMC Plant Biology 2010, 10:92 http://www.biomedcentral. com/1471-2229/10/92 Page 2 of 20 ing pollen, developing ovules and seeds. Overexpression of it resulted in enhanced shoot growth and increased N content [14]. The barley peptide transporter gene, HvPTR1, had seed-specific expression. Transport activity of HvPTR1 was regulated by phosphorylation in response to rising levels of amino acids in the germinating grain [15-17]. Functional di-/tripeptides transporters also have been reported in Nepenthes (NaNTR1, [18]), faba bean (VfPTR1, [19]) and Hakea actites (HaPTR4, [20]). Although PTR is the abbreviation of peptide transporter, many cloned PTR members in plants are nitrate transporters, especially in Arabidopsis. AtNRT1.1 (At1g12110, CHL1), a dual-affinity nitrate transporter, was regulated by phosphorylation and involved in nascent organ development [21-26]. AtNRT1.2 (At1g69850, NTL1) encoded a low-affinity nitrate transporter. RNAi plants of it exhibited reduced nitrateinduced membrane depolarization and nitrate uptake activities [27]. The characterization of AtNRT1.4 (At2g26690) revealed the special role of petiole in nitrate homeostasis [28]. AtNRT1.5 (At1g32450) and AtNRT1.6 (At1g27080) were both plasma membrane proteins. AtNRT1.5 was expressed in root pericycle cells close to the xylem and participated in root xylem loading of nitrate [29] while AtNRT1.6 was only expressed in reproductive tissue and involved in delivering nitrate from maternal tissue to the developing embryo [30]. CsNitr1, a nitrite transporter in Cucumis sativus, had two isoforms: CsNitr1-S and CsNitr1-L. In contrast to that CsNitr1-S enhanced the efflux of nitrite from the cell, CsNitr1-L might load cytosolic nitrite into chloroplast stroma [31]. Amino acids and other substrates can also be transported by some PTRs. BnNRT1.2, isolated from Brassica napus could transport both nitrate and histidine [32]. AgDCAT1 localized at the symbiotic interface was a dicarboxylates transporter in Alnus glutinosa and the mRNA of AgDCAT1 was only detected in the nodules [33]. In rice, only two PTR genes have been functionally verified. OsNRT1 (LOC_Os03g13274), which displayed lowaffinity nitrate transport activity was constitutively expressed in the most external layer of the root, epidermis and root hair [34]. SP1 (LOC_Os11g12740) which determined the panicle size had high expression level in the phloem of the branches of young panicles. Phylogenetic analysis implied that SP1 might be a nitrate transporter, however, neither nitrate nor other compounds transport activity could be obtained from it [35]. As the main staple food for a large segment of the world population, rice also serves as a model plant for monocotyledon species [36,37]. Nutrient transport is critical for plant growth and development, in which PTR family members may play important roles. This work focused on a comprehensive identification, characterization, phylogenetic and evolutionary analysis of all the PTR family members in rice (OsPTR) as well as their whole-life expression profiling. Moreover, it has been demonstrated that the expression of some OsPTR genes is regulated phytohormone (NAA, KT and GA3) and light/dark treatments. Results Collection and identification of PTR genes in rice Domain search (PF00854) of MSU Rice Genome Annotation Project (MSU RGAP) database released 125 sequences, out of which 91 were unique.