https://orcid.org/0000-0002-2435-4343
Figures
Abstract
Apyrase (APY) is a nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) which is a member of the superfamily of guanosine diphosphatase 1 (GDA1)—cluster of differentiation 39 (CD39) nucleoside phosphatase. Under various circumstances like stress, cell growth, the extracellular adenosine triphosphate (eATP) level increases, causing a detrimental influence on cells such as cell growth retardation, ROS production, NO burst, and apoptosis. Apyrase hydrolyses eATP accumulated in the extracellular membrane during stress, wounds, into adenosine diphosphate (ADP) and adenosine monophosphate (AMP) and regulates the stress-responsive pathway in plants. This study was designed for the identification, characterization, and for analysis of APY gene expression in Oryza sativa. This investigation discovered nine APYs in rice, including both endo- and ecto-apyrase. According to duplication event analysis, in the evolution of OsAPYs, a significant role is performed by segmental duplication. Their role in stress control, hormonal responsiveness, and the development of cells is supported by the corresponding cis-elements present in their promoter regions. According to expression profiling by RNA-seq data, the genes were expressed in various tissues. Upon exposure to a variety of biotic as well as abiotic stimuli, including anoxia, drought, submergence, alkali, heat, dehydration, salt, and cold, they showed a differential expression pattern. The expression analysis from the RT-qPCR data also showed expression under various abiotic stress conditions, comprising cold, salinity, cadmium, drought, submergence, and especially heat stress. This finding will pave the way for future in-vivo analysis, unveil the molecular mechanisms of APY genes in stress response, and contribute to the development of stress-tolerant rice varieties.
Citation: Chowdhury AT, Hasan MN, Bhuiyan FH, Islam MQ, Nayon MRW, Rahaman MM, et al. (2023) Identification, characterization of Apyrase (APY) gene family in rice (Oryza sativa) and analysis of the expression pattern under various stress conditions. PLoS ONE 18(5): e0273592. https://doi.org/10.1371/journal.pone.0273592
Editor: Chien Van Ha, Texas Tech University, UNITED STATES
Received: August 10, 2022; Accepted: February 27, 2023; Published: May 10, 2023
Copyright: © 2023 Chowdhury et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the manuscript and its Supporting Information files.
Funding: The author(s) received no specific funding for this work.
Competing interests: The authors have declared that no competing interests exist.
Introduction
Apyrase (APY), which is a class of nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) and a member of the superfamily of GDA1-CD39 (guanosine diphosphatase 1- cluster of differentiation 39) nucleoside phosphatase [1], mediates the concentrations of NTP (nucleoside triphosphate) and NDP (nucleoside diphosphate) [2], especially of ATP (adenosine triphosphate) and ADP (adenosine diphosphate) and catalyzes their breakdown and converts them into ADP and AMP (adenosine monophosphate) [3, 4]. ATP, the general source of energy in every cell, functions in a stress-dependent fashion since it promotes cell growth and development when present in lower concentrations. When the plant cells encounter wound [5], pathogen elicitors ([6, 7], cell growth [8], abiotic stress ([9, 10], touch [9, 11], they discharge ATP into the extracellular matrix (ECM) where it becomes known as eATP (extracellular ATP). These stimuli typically occur simultaneously and involve hormonal and signaling pathway cross-talk [12, 13]. Survival of plants [8], development [4, 6, 14] gravitropism [15], plant defense strategy [16], cellular apoptosis [17], stress responsiveness [3, 5, 9, 18], are controlled by eATP. When this happens, the level of eATP rises, which has a number of detrimental effects on cells, such as slowing cell proliferation [19], ROS (reactive oxygen species) production, NO (nitric oxide) burst, as well as triggering apoptosis [20]. At this point, APY comes into action by breaking down eATP, which helps plants in cell survival, growth, development, and face off several stresses [21].
The presence of five apyrase conserved regions (ACRs) is a defining trait of NTPDase family proteins [22], and APYs can be separated as ecto-and endo-APY, as per the subcellular localization [23]. Ecto-APYs are situated on the cell’s surface, and the ones located on cytoplasmic organelles are generally called endo-apyrases. Many apyrase genes include transmembrane domains at their N- and C- terminals [24] and generally feature amino acid glycosylation, which is necessary to ensure proper folding of proteins, targeting at the membrane, cellular distribution, and enzymatic function [1]. However, APYs are not similar to ATPases such as APYs can employ several divalent cofactors like Mn2+, Zn2+, Ca2+, and Mg2+, in contrast to ATPases, which employ Mg2+ as a cofactor [25]. It also demonstrates insensitivity towards alkaline phosphatase as well as to certain types of ATPase inhibitors [26].
There are several plant species in which APYs were discovered, including potato [27, 28], Arabidopsis [2], soybean [29], cotton [30], wheat [23], peanut [31]. Especially in Arabidopsis, wheat and peanut, the gene family has been intensively studied. Seven APY members in Arabidopsis have been identified and described [2]. AtAPY1 and AtAPY2 are endo-APYs as they are found in the Golgi body. They control various cellular phases [2, 32], and their mutation can dramatically increase extracellular ATP (eATP), which confirms that APYs located intracellularly might also be able to control eATP homeostasis [4, 19]. Others are ecto-APYs, and there have been many pieces of evidence about the involvement of ecto-APYs in the hydrolyzing of eATP [17]. Two other AtAPYs, AtAPY6 and AtAPY7, are also essential to pollen production by controlling the synthesis of polysaccharides [33]. Nine APY members are identified in wheat with different expression patterns when subjected to various stresses and even in different tissues [23]. In many species, APYs have been found to have involvement in different stress tolerance, such as tolerance towards salinity and drought conditions in Arabidopsis after overexpression of PeAPY1 and PeAPY2 [34], tolerance to waterlogging in soybean [35]. PsAPY, when expressed ectopically, has been reported to exhibit resistance in tobacco to pathogen attack [36]. However, the total signaling pathway working behind the activity of APY is still not explained.
Rice is among the world’s most widely grown as well as consumed cereals. The majority of the world relies on rice as a main meal [37]. Agricultural production is at risk due to climate change. Likewise, rice production is being hampered due to climate anomalies, including submergence, less rainfall, cold weather, increasing salinity levels, and many more. Fungal and bacterial blight are two of the most severe and prevalent rice diseases that reduce annual rice production [38]. Developing stress-resistant rice may increase yield tremendously as genome-editing and genetic transfer technologies are improving rapidly; these methods have made it possible to grow crops that can withstand stress. A thorough genome-wide investigation on stress-associated gene families using bioinformatics approaches has been accomplished thanks to the recent availability of information on the genomes of various crop species. Rice is the first food grain of which the entire genome sequence is available [38]. It provides a chance to locate the genes and systematically categorize the genes and biochemical pathways essential for expanding rice production, conferring tolerance towards several stresses, as well as enhancing the product’s quality.
Different families of genes such as PYL [39], NAC [40], GRAS [41], MYB [42], WRKY [43], DREB [44] are reported in rice as gene families associated with responsiveness towards stress. When exposed to various stress environments, many genes have been observed to exhibit particular responses. For example, cold, high salinity, and drought are associated with the induction of OsNAC6/SNAC2 [45]. During dehydration, the HKT-1 protein is required for cell osmoregulation and the maintenance of turgor [46]; the HSP20 family provides tolerance to prolonged heat stress and resistance to different environmental stresses [45]. The CRT/DREBP protein family is mainly regulated by cold stress; on the other hand, DREBP (DRE-binding protein) family induction is caused by drought and high salt stress [47]. Overexpression of different genes responsive to stress in rice could increase the tolerance level when subjected to such stress. Such genes include OsNHX1 in salt stress [48], OsDREB under drought conditions [49], Sub1A when subjected to submergence stress [50]. Identifying and characterizing such genes responsive to stresses and applying molecular methods could pave the way toward developing rice varieties tolerant of several stresses.
Since there is ample evidence about the role of APYs during the stress response, their identification and characterizing in plants might help find new development sites for strengthening tolerance towards several stresses through different gene modification methods. There is an absence of studies about APYs in rice. The purpose of this research is to characterize APY genes in O. sativa and provide insight into their function throughout development and in response to stress by doing a genome-wide identification and analyzing their expression profiles. Rice APY family members are identified using bioinformatics techniques throughout this study. We have further studied the functional characterization, including phylogenetic relationship analysis with the APYs from Arabidopsis, peanut and wheat. Both RT-qPCR and RNA-seq data are utilized in profiling the pattern of gene expression of the OsAPYs and suggest their importance in the process of development as well as response to stress. Conclusively, this result will provide a foothold in further analyzing the roles of OsAPY in different stress conditions and in identifying targets to enhance rice’s tolerance level under various stresses.
Materials and methods
Identification of APY family members in Oryza sativa
The TAIR database (https://www.arabidopsis.org/) [51] was employed to get the sequences of the proteins for the seven genes (At3g04080, At5g18280, At1g14240, At1g14230, At1g14250, At2g02970, and At4g19180) of Arabidopsis thaliana that belong to the apyrase gene family [2]. On Phytozome v12.1 (https://phytozome.jgi.doe.ov) [52], these sequences were used to run a BLASTp search against the Oryza sativa v7 jGI (Rice) dataset. They were also used for the BLASTp search against the NCBI protein database (https://www.ncbi.nlm.nih.gov/protein) and the Rice genome annotation project (http://rice.plantbiology.msu.edu/) [53] separately so that no putative member was missed out. The best hits from these databases were subjected to domain analysis via InterPro (http://www.ebi.ac.uk/interpro/) [54] to ensure the presence of the GDA1-CD39 domain, which is a characteristic feature of APYs. Entries having this domain were chosen for multiple sequence alignment, which was conducted via MEGA X (Molecular Evolutionary Genetics Analysis) software [55]. Their multiple sequence alignment was visualized via GeneDoc version 2.7 [56] to search for the presence of 5 ACRs [22]. Sequences that contained these 5 ACRs were chosen as members of the apyrase family. To confirm that all members of the apyrase family were included, those sequences were submitted as input sequences for a BLAST analysis in Phytozome [52]. The coding sequence (CDS), genomic, and peptide sequence of the OsAPYs were obtained from Phytozome [52].
Analysis of the physicochemical properties
For assessment of the physicochemical characteristics of the genes, the theoretical isoelectric point (pI), index of instability, grand average of hydropathy (GRAVY), as well as molecular weight of the proteins were determined. It was done via ProtParam hosted by ExPASy (https://web.expasy.org/protparam/) [57] by uploading the protein sequence. By uploading the protein sequences to WoLF PSORT (https://wolfpsort.hgc.jp/) [58] and CELLO v.2.5 (http://cello.life.nctu.edu.tw/) [59], the subcellular distribution of the proteins was determined.
Analysis of conserved motifs and gene structure
MEME version 5.3.0 (Multiple Em for Motif Elicitation; http://meme-suite.org) [60] was employed to investigate the conserved motifs on proteins in classic mode, and the motif number was determined to be 10. The minimum width was kept to 6, and the maximum one was 50; each motif’s highest and lowest sites were set to 600 and 2 accordingly. Depending on the appearance frequency of the motifs in MEME [60], they were numbered sequentially and positioned beside their corresponding OsAPYs according to their phylogenetic groups. In order to determine their role, each of the ten detected motifs was evaluated via Pfam (http://pfam.xfam.org/) [61].
OsAPY CDS sequences were compared against their respective genomic sequences lacking the UTR (untranslated region) to assess gene structure. Gene structure was determined using the GSDS 2.0 (Gene Structure Display Server) tool (http://gsds.gao-lab.org/) [62], and this web server graphically depicted the gene structure of OsAPY genes.
Analysis of phylogenetic relationship
TAIR [50] along with EnsemblPlants (https://plants.ensembl.org) [63] database and Peanut Genome Recourse (PGR) database (http://peanutgr.fafu.edu.cn) [64] was employed to get the peptide sequences of APYs from Arabidopsis thaliana, Triticum aestivum and Arachis hypogaea correspondingly. An unrooted phylogenetic tree was created utilizing MEGA X [55]. It was generated using protein sequences from Oryza sativa, Arabidopsis thaliana, Triticum aestivum and Arachis hypogaea [65] to keep the rates uniform across sites. It was visualized using the web tool iTOL (https://itol.embl.de/) [66].
Prediction of gene duplication
PGDD (Plant genome duplication database) (http://chibba.agtec.uga.edu/duplication/) [67] was employed to examine the gene duplication events and to find out the orthologous and paralogous gene pairs. PGDD [67] provided the Ka (synonymous substitution rate) and Ks (non-synonymous substitution rate) values for the duplicated gene pairs. Using the Ks values and a clockwise rate of synonymous substitution (λ) of 1.5 x 10−8, the approximate timing of duplication was computed following the formula T = Ks/2λ [68]. A circle plot of the paralogous genes was created using TBTools (https://github.com/CJ-Chen/TBtools/releases) [69].
Study of the cis-regulatory elements
The sequence located 1000 bp upstream of OsAPYs was retrieved from the genomic sequence of rice using Phytozome [52] for investigating the cis-elements and their function. PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/htmL/) [70] was utilized for predicting the cis-elements. Cis elements were categorized into different groups, and their functions were identified from the literature review. TBTools [69] was utilized to create a visual description of the cis-regulatory elements.
Analysis of chromosomal distribution
Information from rice genome sequences was used to build a chromosomal organization of OsAPY genes based on their location. Phytozome [52] provided details on the number of chromosomes, gene loci, as well as length for the physical map. MapChart (http://www.joinmap.nl) [71] software was used to create a rudimentary physical map of the OsAPY gene family, illustrating its location and distribution.
Specification of OsAPY targeting miRNAs
For the identification of miRNAs which target APY genes in rice, psRNATarget (http://plantgrn.noble.org/psRNATarget/) [72] was used, and it was tested against every mature rice miRNAs present in the database of miRbase [73]. Using Cytoscape (https://cytoscape.org/) [74], the predicted miRNAs were deployed to build a network. To perform the analysis of pre-computed expression of the detected miRNAs, miRid was employed to search against the rice datasets of the PmiRExAt (http://pmirexat.nabi.res.in/) [75] and a heatmap was generated via GraphPad Prism 9.0.0 (https://www.graphpad.com/company/) [76].
Identification of SNPs in APY genes
The sequences of APY genes from 11 rice varieties with different genotypes based on responses towards abiotic stress [39, 77] were compared to the reference Nipponbare sequence using the Rice SNP-Seek database (https://snp-seek.irri.org/index.zul) [78]. SNPs that could be predominantly attributed to variations in the peptide sequence were recognized throughout the genotypes and were termed single amino acid polymorphisms (SAPs). Employing the Rice Stress-Resistant SNP Database, the detected SNPs were studied to determine which ones contributed to the development of specific stress resistance in the rice varieties [79].
Analysis of secondary and tertiary structure of proteins
The secondary structures were generated utilizing the STRIDE program (http://webclu.bio.wzw.tum.de/stride/) [80]. The number and percentage of α helices, extended beta-sheet, turns, coils, and 310-helix were displayed in various colors as part of the structural study. The membrane-spanning motif was investigated by using default parameters of the online tool TMHMM server v.2.0 (http://www.cbs.dtu.dk/services/TMHMM/) [81].
The tertiary structure was generated using the RoseTTAFold method of the Robetta server (https://robetta.bakerlab.org/) [82]. Refinement of the created structures was done via the GalaxyRefine web server (http://galaxy.seoklab.org/refine) [83], and then the energy minimization was done using Swiss-PdbViewer v4.1 (http://www.expasy.org/spdbv/) [84]. PROCHECK (https://servicesn.mbi.ucla.edu/PROCHECK/) [85] and ERRAT (https://servicesn.mbi.ucla.edu/ERRAT/) [86] servers were further used for the validation of the structure. For the assessment of Z-scores and energy plots, ProSA-web (https://prosa.services.came.sbg.ac.at/prosa.php) [87] was utilized. Discovery Studio software was finally used to visualize the tertiary protein structures [88].
Analysis of protein-ligand docking
Molecular docking is an in-silico strategy for assessing the binding affinity of a ligand to a receptor molecule. Since ATP is a vital ligand of APY proteins, it was chosen as the ligand for the study. HDOCK server (http://hdock.phys.hust.edu.cn/) [89] was used as the docking tool to conduct the docking analysis between the OsAPY proteins and ATP. It was done using the default parameters. The 3D structure of ATP was downloaded from the PubChem database (PubChem CID: 5957). After docking, the top 10 solution complex generated via HDOCK [89] were downloaded, and their structures were further analyzed and validated using PDBsum (http://www.biochem.ucl.ac.uk/bsm/pdbsum) [90], PROCHECK [85] and ERRAT [86] servers. The best structure was selected, and it was aligned and visualized. Then finally, the protein and ligand residue interaction was studied using Discovery Studio [88].
Study of expression profiling of OsAPYs in rice using RNA-seq data
Rice Genome Annotation Project [54] was utilized to collect the data for the expression of APY genes under several tissues. Accordingly, the RNA-seq expression values were listed. GraphPad Prism 9.0.0 [76] software was used to create a heat map from the data. GENEVESTIGATOR (https://genevestigator.com/gv/) [91] provided the pattern of OsAPY expression in various stresses, and the log2 values of relative expression were used to generate the heat map via GraphPad Prism 9.0.0 [76].
Plant germination, treatment, and total RNA isolation
The healthy, high-quality and mature seeds of BRRI dhan28 were obtained from the Bangladesh Rice Research Institute (BRRI) and used in this experiment. They were properly cleaned before being placed in a petri dish with tissue paper that had been soaked in water. The seedlings that had sprouted were relocated to the hydroponic culture system after three to four days. In the culture room, a controlled environment was managed, including a temperature of 25±2°C with a photoperiod consisting of 16 hours of light followed by 8 hours of darkness and 1500–2000 lux light intensity. After 20 days, the seedlings were subjected to different stresses for 18–20 hours which included cadmium stress (100mM CdCl2 dissolved in distilled water), cold (4°C), salinity (100mM NaCl dissolved in distilled water), submergence, drought (3 mg/L polyethylene glycol dissolved in distilled water), heat stress (42°C). As control, seedlings that had been untreated were utilized. After the treatment, fresh young leaves were collected and washed several times with 70% alcohol and distilled water in order to extract the RNA. Using InvitrogenTM TriZOLTM reagent (Thermo Fisher Scientific Corporation, USA), total RNA was isolated from leaves. The extracted RNA was subsequently processed with DNase I of InvitrogenTM DNA-freeTM DNA Removal Kit (Thermo Fisher Scientific Corporation, USA) to remove the genomic DNA contamination. Finally, the GoScriptTM Reverse Transcription System (Promega Corporation, USA) was utilized to synthesize the complementary DNA (cDNA). These procedures were carried out per the protocol of the manufacturers.
Analysis of gene expression under abiotic stress conditions using RT-qPCR data
Primer3 v.0.4.0 (https://bioinfo.ut.ee/primer3-0.4.0/) [92] was used to generate primers for the RT-qPCR, keeping the product length between 208 and 220 bp. The real-time PCR was done using GoTaq® qPCR Master Mix (2X) (Promega Corporation, USA) on CFX96TM Real-Time PCR Detection System (BioRad). For the reference gene, eukaryotic elongation factor 1 alpha (eEF-1α) was chosen [93]. Each set of gene-specific primers took up 1 μL of the 15 μL reaction mixture. It also comprised 7.5 μL of GoTaq® qPCR Master Mix (2X), 2 μL of cDNA (10 times diluted), and 3.5 μL of nuclease-free water. In order to carry out each of the reactions, the following conditions were applied: at 95°C initial denaturation for 10 min preceding 40 cycles of denaturation at 95°C for 15s, annealing for 30s, and extension at 72° C for 40s. The annealing temperature was 55.4°C for OsAPY2 and OsAPY4; 56.4°C for OsAPY1 and OsAPY5; 57.4°C for OsAPY3, OsAPY6, and OsAPY8; 58.4°C for OsAPY7 and OsAPY9; 55.7°C for eEF-1α. Each sample was subjected to three separate experiments and melting curve analysis was performed following PCR amplification. The delta-delta Ct value approach [94] was utilized in calculating the ratio of relative expression. Technical replication was used to find the mean value of expression at different treatments. MS Office 365 and GraphPad Prism 9.0.0 [76] were used to analyze the data. A one-way ANOVA, followed by a Bonferroni post hoc test, was used to assess the significant differences (P ≤ 0.05). To represent the significant differences, different means were labeled with different number of stars (*).
Results
Identification of APY family members in rice and study of their physicochemical properties
Rice was found to contain nine members of the APY gene family. To BLAST against the rice genome, the Arabidopsis APYs were utilized as reference sequences. Upon performing BLASTp searches against the Oryza sativa, a total of 19 hits were found containing the GDA1-CD39 domain. All the domain annotations were confirmed by sequence analysis in InterPro [54].
These 19 transcripts belonged to a total of 12 genes. The primary transcripts annotated by Phytozome [52] were selected as the representative transcripts of the genes with alternative splice forms. Nine of the 12 genes were found to possess all five Apyrase Conserved Regions (ACRs) (S1 Fig); hence they were designated Apyrase genes. For the naming of the genes (OsAPY1-OsAPY9), the prefix ’Os’ for Oryza sativa was used, followed by ’APY’ for Apyrase, and then the sequential number that corresponded to their chromosome number and location was used. Table 1 lists the physicochemical properties of all representatives of the OsAPY Family.
The theoretical pI of proteins belonging to the apyrase gene family ranged between 5.44 and 9.34, with an average of 7.73. OsAPY4 had the highest and OsAPY7 had the lowest pI value. The proteins had molecular weights ranging from 48900.8 Da to 77242.54 Da belonging to OsAPY9 and OsAPY5, respectively. The average molecular weight of the proteins was 55978.8 Da. The GRAVY value for all the proteins was negative, and as per the data, all protein molecules were hydrophilic [95]. Six genes had an instability index lower than 40, meaning they were stable. It revealed that 67% of the genes were stable, and 33% of them were unstable.
For the prediction of subcellular location, two different tools were used, and per the subcellular localization, both ecto- and endo-APYs were present in this gene family [23]. Their results varied in OsAPY3, OsAPY4, and OsAPY9. According to CELLO [59], they were located on mitochondria, plasma membrane, and chloroplast. On the other hand, according to WoLF PSORT [58], their subcellular localization was on chloroplast for OsAPY3 and endoplasmic reticulum for OsAPY4 and OsAPY9. The predicted subcellular localization of the proteins according to two different tools is given in Table 1.
Analysis of conserved motifs and gene structure
Ten conserved motifs in total were discovered, which were numbered 1–10 (Fig 1B). 4 motifs among them (motif 1, 5, 8, and 10) were conserved and existed in all the OsAPYs. Members of each phylogenetic group had similar motif distribution, which affirms the classification of groups. All the members of group I in the phylogenetic tree (Fig 1A) had the same motif distribution, containing all the ten motifs. On the other hand, the members of group II in the phylogenetic tree, OsAPY2, and OsAPY4, contained almost similar numbers of motifs except motif 2, which was present in OsAPY4 only. Though only OsAPY5 belonged to group III, its motif distribution was the same as OsAPY4 despite being in different phylogenetic groups. Functions of these motifs were also analyzed, but there was no information on the function of motif 9 and 10. Their analysis revealed that the remaining eight motifs belonged to the GDA1/CD39 (nucleoside phosphatase) family (S1 Table).
a- Phylogenetic relationship among OsAPYs generated via maximum likelihood approach. The green, pink and blue boxes represent groups I, II, and III, respectively. b- OsAPY conserved motif distribution. Ten varying-colored boxes represent the motifs. The legend below shows the corresponding motif’s protein sequence. c- Gene structure of APYs. Yellow color boxes specify exons, and introns are depicted by lines. The exon-intron lengths can be calculated following the scale shown below.
The exon and intron arrangement of OsAPYs was studied in order to better comprehend their structure. The total number of coding sequences (CDS) or exons and introns of the OsAPY genes were 2–12 and 1–11, respectively (Fig 1C), and there was no intronless gene. OsAPY5 contained the lowest number of exons and introns, which were two exons and one intron, and on the other hand, OsAPY6 contained the highest number of exons and introns, which was 12 exons and 11 introns.
Analysis of phylogenetic relationship in OsAPY family
The maximum likelihood method was utilized to create an unrooted phylogenetic tree to study the evolutionary relationship between the APY genes. It was done using the peptide sequences of seven apyrase homologs from Arabidopsis thaliana (AtAPY) [2], nine apyrase homologs from Triticum aestivum (TaAPY) [23], seventeen homologs from Arachis hypogaea (AhAPY) [31] and the nine identified apyrase homologs from Oryza sativa (OsAPY). This phylogenetic tree (Fig 2) demonstrated that the nine OsAPY genes could be split into three distinct groups referred to as I, II, and III. There were already three distinct groups for the AtAPY, TaAPY and AhAPY genes [23]. No OsAPY gene was classified into the new group. Among the 9 OsAPY genes, OsAPY1, OsAPY3, OsAPY6-OsAPY9 belonged to group I. TaAPY1-TaAPY3.4, AhAPY1-1-AhAPY1-5, AhAPY2-1-AhAPY2-4 and AtAPY1, AtAPY2 also were in group I. OsAPY2, and OsAPY4 fell in group II. Group II also contained TaAPY5, TaAPY6, AtAPY3-AtAPY6, AhAPY6-1-AhAPY6-2. Group III consisted of OsAPY5, AtAPY7, and TaAPY7, AhAPY7-1-AhAPY7-6.
The MEGA X software was employed to generate a phylogenetic tree by utilizing the maximum likelihood approach along with 1000 bootstrap replications. Genes were divided into three different groups, each marked with a different color.
Analysis of gene duplication
Duplication events are crucial for broadening the gene family and for the emergence of novel gene functions. The rice genome had a total of six duplications, three of which were in the APY family (Fig 3 and S2 Table). There was no tandem duplication since no genes on the same chromosome had been duplicated. In this study, the duplication type was segmental. The three groups of segmentally duplicated genes within the rice apyrase gene family were OsAPY1/9, located on chromosomes 3 and 12, respectively; OsAPY1/3, found on chromosomes 3 and 7, respectively; OsAPY3/9, situated on chromosomes 7 and 12 respectively.
Duplication of the OsAPYs was specified by the red lines, and the one among the whole rice genome was denoted by the gray lines. TBTools was used to create the circle plot.
The non-synonymous (Ka) and synonymous (Ks) substitution rate of genes was used to measure the selection pressure of duplication occurrences. Ka/Ks = 1 implies neutral selection, whereas Ka/Ks<1 represents purifying selection, and Ka/Ks>1 denotes positive selection [96]. Between 0.1476 to 0.5560, Ka/Ks of segmental duplication had a mean of 0.28021. As demonstrated by Ka/Ks ratios lower than 1, all the genes originated under the influence of purifying selection (S2 Table). The duplication time of each event was counted in million years ago (MYA) unit (S2 Table), and it occurred between 66.6 MYA and 1.54 MYA.
Eight orthologous pairs were found between rice OsAPYs and other species (Table 2). It was duplicated with sorghum, western poplar, cotton, grapevine, maize, and soybean. The range of Ka/Ks was between 0.143 and 0.357, and the mean was 0.2471. These data suggested that duplication events had a significant impact on the expansion and functional diversity, and an important role was served by segmental duplication in the evolution of the APY family of genes.
Cis-acting regulatory elements (CAREs) analysis
Rice APY genes might be regulated by promoter sequences, which are known to be associated with the regulation of transcription of the genes in plants. Analysis of 1 kbp upstream promoter sequences in O. sativa indicated the presence of 69 CAREs. These cis-elements were grouped into eight different functional categories (Fig 4): i) Light responsive cis-elements, ii) Abiotic challenge responsive elements, iii) Hormonal regulation responsive elements, iv) Elements responsible for cellular development, v) Promoter associated elements, vi) Biotic challenge responsive elements, vii) Elements with miscellaneous functions and viii) Elements with unknown functions. Hormonal regulation responsive elements were further divided into a) MeJA responsive, b) Salicylic acid-responsive, c) Auxin responsive, d) Gibberellin responsive, e) Ethylene responsive, and f) Abscisic acid-responsive elements (Fig 4).
Upstream nucleotides of the translation initiation point are shown by the scale at the end. Different colored boxes depict different cis-regulatory elements.
Different abiotic stress-associated elements (anaerobic, anoxic, low temperature, drought, salt, and cold) were observed in the OsAPY promoter region (Table 3). STRE, TC-rich repeats, MBS, ARE, GC-motif, LTR, CCAAT-box, AP-1, DRE core, MYB, MYC¸ were the abiotic challenge responsive cis-elements. Among all these elements, STRE was present in the highest frequency, and DRE1 was present in the lowest frequency. W box, WRE3, and WUN-motif (Table 3), the biotic challenge responsive elements, mainly were found to act as fungal elicitors and wound-responsive elements. WRE3 occurred in the highest frequency, and WUN-motif occurred in the lowest frequency.
TGACG motif, CGTCA motif, TGA element, TCA element, GARE-motif, ABRE, P-box, ERE, as-1, and box S constituted the hormonal regulation responsive cis-elements (Table 3). Cellular development-responsive cis-elements played a major role in meristem expression, palisade mesophyll tissue differentiation, circadian control, seed-specific regulation, zein metabolism regulation, and xylem-specific expression (Table 3). These cis-elements included CAT-box, HD-Zip 1, circadian, RY-element, O2-site, CCGTCC motif, CCGTCC box, AAGAA-motif, and AC-II.
Light responsive cis-elements included 3-AF1 binding site, TCT-motif, TCCC-motif, MRE, Gap-box, I-box, GT1-motif, ATCT-motif, Box 4, GATA-motif, GA-motif, G-box, G-Box, AE-box, L-box, Sp1, (Table 3). They mainly functioned as a light-responsive element or a module or a component of such an element. TATA-box and CAAT-box were the two elements, related to the promoter, found in OsAPY genes, and they were core promoter elements that mainly functioned in promoter and enhancer regions. Cis-elements with miscellaneous functions included 3-AF3 binding site, MYB-like sequence Myb-binding site, Box III, and AT-rich sequence (Table 3). OsAPY5 contained a 3-AF3 binding site that was a DNA module array component. The AT-rich DNA binding protein (ATBP-1) utilized a binding site situated on OsAPY7, which was located on the AT-rich sequence. On the other hand, Box III was located on OsAPY7 as a binding site for proteins.
Analysis of chromosomal distribution
The distribution of APY genes on all 12 of rice’s chromosomes was investigated, and the findings showed that there was an uneven distribution of APY genes (Fig 5). No OsAPY member was mapped onto chromosome 1, 2, 4, 5, 6, and 9. It was observed that both OsAPY1 and OsAPY2 were on chromosome 3. The chromosomal positions of OsAPY3, 4, 5, and 9 were 7, 8, 10, and 12, respectively. OsAPY6-OsAPY8 was located on chromosome 11. Near the centromere, OsAPY1, 2, 5, and 8 were clustered. OsAPY6, 7, and 9 were situated on the p arm of the chromosome, and on the other hand, OsAPY3 and 4 were placed on the q arm of the chromosome. The location of all the OsAPYs in different chromosomes, their position, and orientation are mentioned in the S3 Table.
The figure was generated using MapChart. Chromosome number is presented on top. C depicts the centromere position. The position of every gene can be easily compared following the reference chromosome at the left.
Identification of miRNAs targeting OsAPY genes
In this investigation, 103 putative and distinct rice OsAPY family member-targeting miRNAs with lengths of 19–24 nucleotides were discovered. The highest number of miRNAs targeted OsAPY9, whereas OsAPY3 was targeted by the lowest number. Fig 6 illustrates the regulatory relationships involving potential miRNAs as well as their targeted APYs. The majority of the miRNAs expected to target OsAPYs had a strong inhibitory effect through cleavage. The inhibitory action for only a few numbers of miRNAs was translation. The list of miRNAs targeting different OsAPYs and their mode of inhibition is given in the S4 Table.
Visual depiction of miRNA-OsAPY interaction is generated via Cytoscape. Arrows depict the regulatory relationship, elliptical shapes of different colors represent the OsAPYs, and the miRNAs are shown in ash-colored boxes.
Twenty-three miRNAs out of all the miRNAs targeted multiple OsAPYs, whereas the remaining miRNAs were specific to each gene. Most miRNAs were found to have lower expression patterns. A heat map was generated (Fig 7) by comparing miRNA expression levels from PmiRExAt [75] across tissues and under a number of different abiotic stress conditions. Among all the miRNAs, osa-miR159a.1 targeting OsAPY4 was expressed highly in all stresses and tissues except anther and leaves during the flowering stage. The target of osa-miR5532 was OsAPY2 and OsAPY5, which was abundantly expressed in anther. osa-miR3979-3p, which targeted OsAPY4, was strongly expressed in roots. osa-miR408-3p targeting OsAPY5, 9, was highly expressed in leaves during the flowering stage and in seedlings exposed to H2O2. These expressions of most of the miRNAs were downregulated during different stresses suggesting the increased expression of the OsAPYs in such stress conditions. Therefore, sequence-specific miRNA-mediated interaction may have a vital function in regulating OsAPY genes, which in turn may help plants act on environmental as well as growth signals.
The expression profile of each miRNA can be analyzed following the scale at the right. A heat map was generated using GraphPad Prism 9.0.0.
Study of SNPs in OsAPYs
Rice SNP-Seek database [76] was used to better understand the variations in alleles of OsAPY members throughout 11 rice varieties and were selected based on their stress responses. It allowed identifying the Single Amino acid Polymorphisms (SAPs) (Table 4). SAPs were identified in 6 OsAPYs, but not in OsAPY1, 5, and 8. It indicated that the genes of OsAPY1, 5, and 8 are substantially conserved among rice genotypes. The indica varieties included NERICA-L-27, Pokkali, Rasi, Vandana, Swarna, and IR-64, while Azucena and NERICA-1 were tropical japonica varieties. GIZA 159, Nagina 22, and Pusa (Basmati 1) were the members of the temperate japonica, aus, and unassigned variety, respectively. The study revealed that indica rice varieties had a higher rate of SAPs than other rice varieties. 5 SAPs were identified in OsAPY2; OsAPY3, 7, and 9 showed 3 SAPs, while OsAPY4 had only one SAP, but OsAPY6 contained 4 SAPs.
Analysis showed that SNPs located at each position were specific for different stresses in particular rice varieties (Table 4). The presence of such stress-resistant SNPs was involved in providing resistance to various stresses in rice varieties. Azucena, a moderately salt, and cold-resistant variety and at the same time susceptible to heat stress [79], contained SNPs that were involved in salt and cold resistance. Similarly, Pokkali was resistant to heat and brown planthopper pest and susceptible to cold and salt stress [79]. The SNPs present in Pokkali were heat and brown planthopper pest resistant and so they can act as markers for these two stress conditions in Pokkali. IR-64 had the SNPs that were blast fungus resistant; Nipponbare had the ones against bacteria leaf blight; Vandana was resistant to heat and blast fungus. As a result, those SNPs can act as markers for screening the putative rice genotypes for that specific stress conditions.
Analysis of secondary and tertiary structure
The secondary structure analysis revealed the position of alpha-helix, beta-sheet, isolated beta bridge, turn, coil, 310-helix, and transmembrane helix (Fig 8). Their percentage and the position of the transmembrane helix are given in the S5 Table. It showed that alpha-helix was dominant over all the other secondary structures, followed by the turn, beta-sheet, coil, and 310-helix. There were some exceptions in OsAPY2, 4, 5, and 8. In OsAPY5, the coil percentage was higher than the beta-sheet, and in OsAPY2, it was higher than the turn and beta-sheet. In OsAPY4 and OsAPY8, the beta-sheet percentage was higher than that of turn. The higher percentage of helix and beta-sheet indicate the stability of the OsAPYs [135], and the structures like random coils are critical for the signaling cascades [136]. The analysis of the motifs spanning the membrane (MSM) indicated that 4 OsAPYs contained one membrane-spanning motif (MSM), 4 OsAPYs contained 2 MSMs, and 1 OsAPY contained no MSM. OsAPY1, 3, 7, 8 contained only one membrane-spanning motif at N-terminal. OsAPY2, 4, 5, and 6 had two MSMs positioned at the N- and C-terminals separately except OsAPY6, where both the MSMs were located on N-terminal. On the other hand, OsAPY9 contained no MSM.
Secondary structures were generated using the STRIDE program, and the corresponding positions of membrane-spanning motifs were identified via the TMHMM server. The cross-membrane domains were marked with a black colored box. Legend at the bottom-right side shows the icon for each secondary structure.
RoseTTAFold, a deep learning-based modeling approach, was applied to construct 3D models of proteins using the Robetta web server [82]. The generated models were further refined by GalaxyRefine [83], and then the energy minimization was done via Swiss-PdbViewer [84]. Fig 9 illustrates the modeled tertiary structures of all the OsAPY proteins, visualized via Discovery Studio. These generated structures were then subjected to validation analysis utilizing PROCHECK [85], ERRAT [86], and ProSA-web server [87] (S6 Table). Ramachandran plot analysis in PROCHECK was used to evaluate protein quality [85]. In the favored and additional allowed regions, over 90% of the residues were located, with only <1.5% in the disallowed regions, which confirmed that the projected models were of good quality (S2 Fig). The proteins exhibited an overall quality factor of >87, according to ERRAT [86] analysis (S3 Fig). ProSA-web [87] revealed the Z-score, the level of nativeness of the designed models (S6 Table), and the energy plot, which showed the local quality of the models. The Z-score was found to be in the spectrum of values generally reported for native proteins, implying higher quality of the structures generated, and the models were well within the range of X-ray crystal structure (S4 Fig). As per the energy plot (S5 Fig), all the residues in the simulated structure had a lower value of energy. These findings indicated the excellent quality of the tertiary structures of modeled proteins.
The online tool Robetta was used to construct the tertiary structure, and these structures were visualized via Biovia Discovery Studio Visualizer.
Analysis of molecular docking
ATP, a vital ligand of APY proteins, was chosen for the analysis of docked protein-ligand complex. The docking analysis was done using the HDOCK server, and it revealed that the docking score of the protein and ATP was between -199.05 and -152.53 (S7 Table). This optimal docking indicated an excellent binding affinity. According to PDBSum [90] analysis, the protein and ATP complex contained 3 to 11 hydrogen bonds (S8 Table). The interaction between the protein and ATP visualized via Discovery Studio [88] revealed the presence of different types of H-bond, electrostatic bonds, and hydrophobic bonds (Fig 10 and S9 Table). Validation of the protein-ligand complex via PROCHECK and ERRAT suggested the high quality of the complexes (S6 and S7 Figs).
Illustration of bonds: carbon-hydrogen bonds- snowy mint lines, conventional hydrogen bonds- green lines, pi-cation bonds- black lines, unfavorable bumps- red lines, unfavorable negative-negative interactions- yellow lines, attractive charge interactions- orange lines, pi-donor hydrogen bonds- deep brown lines, pi-sigma bonds- light purple lines, unfavorable acceptor- acceptor interactions- navy blue lines, pi-alkyl bonds- magenta lines, unfavorable donor-donor interactions- pink lines, pi-anion bonds- deep-sea blue lines, pi-lone pair interactions- lemon green lines, salt bridge- purple lines.
OsAPY1 formed seven conventional hydrogen bonds, 2 Pi-cation interactions, and seven unfavorable interactions (Fig 10). Among all the protein residues, THR168 formed 2 of the seven hydrogen bonds, and ARG99 formed both the Pi-cation interactions (S9 Table). OsAPY2 had one attractive charge interaction, 1 Pi-donor hydrogen bond, six conventional hydrogen bonds, five unfavorable interactions, six carbon-hydrogen bonds, and 1 Pi-sigma interaction with ATP. OsAPY3 made one attractive charge interaction, three Pi-alkyl bonds, carbon-hydrogen bonds, two unfavorable interactions, and nine conventional hydrogen bonds. OsAPY4 created four conventional hydrogen bonds, 2 Pi-donor hydrogen bonds, and two carbon-hydrogen bonds. OsAPY5 formed ten carbon-hydrogen bonds, six conventional hydrogen bonds, 1 Pi-lone pair interaction, 2 Pi-anion interactions, and seven unfavorable interactions. OsAPY6 made 2 Pi-cation interactions, Pi-donor hydrogen bonds, carbon-hydrogen bonds, Pi-anion interactions, four conventional hydrogen bonds, four attractive charge interactions, and 1 Pi-alkyl interaction. OsAPY7 and OsAPY8 formed 9 and 12 interactions with ATP, respectively. OsAPY9 had one salt bridge interaction, two attractive charge interactions, seven conventional hydrogen bonds, 2 Pi-cation interactions, 1 Pi-anion interaction, 1 Pi-alkyl interaction, and eight unfavorable interactions. These bonds between the OsAPYs and ATP pointed to a robust docking interaction.
Investigation of the expression profiles of OsAPY genes using RNA-seq data
Using RNA transcript profiling to analyze gene expression is an efficient technique. To better comprehend the expression profile of OsAPYs, the RNA-seq data was utilized under several tissue types and stresses (Fig 11). The Rice Genome Annotation Project [52] provided RNA-seq data for OsAPY expression profiling in several tissues which was used to produce a heatmap (Fig 11).
The RNA-seq data collected from the Rice Genome Annotation Project was used to conduct expression analysis. The heat map was generated using GraphPad Prism 9.0.0. Expression profile can be analyzed following the bottom located scale. The red boxes represent high expression rates, greens depict low expression rates, and black boxes signify moderate expression levels.
The analysis revealed that the expression was higher in the inflorescence, seed, pistil, embryo, and endosperm. OsAPY1 and 3 were upregulated in most of these tissues, whereas in the pre-emergence inflorescence and anther, OsAPY2 and 4 were upregulated. OsAPY4 was expressed highly in the pistil. For OsAPY5, it was higher in pistil, seed, embryo, and endosperm among all these tissues. Some of these showed an expression pattern that was tissue-specific, including OsAPY2, upregulated in anther, inflorescence, and downregulated in the other types of tissues. In the same manner, the expression of OsAPY8 was high in shoots. All the OsAPYs were downregulated in leaves, post-emergence inflorescence, and seedlings except OsAPY9, which was upregulated in these tissues. In shoot tissue, OsAPY3 and 8 were highly expressed; on the other hand, OsAPY3 and 5 were upregulated in callus, and it was OsAPY1 and 9 in panicles.
The profile of expression from RNA-seq data of OsAPYs was investigated to reveal their role in response to different stresses. Their expression profile revealed expression in abiotic and biotic stresses. Figs 12 and 13 show a heat map of their expression profile in biotic and abiotic stress. There was no pre-analyzed RNA-seq data of OsAPY9, so the gene expression data of only eight genes were analyzed.
Expression analysis was done utilizing the RNA-seq values of relative expression from GENEVESTIGATOR and using GraphPad Prism 9.0.0, the heat map was generated. The expression profile could be analyzed according to the scale just at the base. The red boxes represent upregulated expression; greens depict downregulated expression, and black boxes signify no change in expression levels.
Expression analysis was done using the RNA-seq values of relative expression from GENEVESTIGATOR. The heat map was generated using GraphPad Prism 9.0.0. The expression profile could be analyzed according to the scale just at the base. The red boxes represent upregulated expression; greens depict downregulated expression, and black boxes signify no change in expression levels.
In response to infection by two strains of rice bacterial leaf streak pathogen (Xanthomonas oryzae pv. oryzicola), OsAPY1-5 were upregulated, but OsAPY8 was downregulated (Fig 12). This finding addressed the role of OsAPYs in managing rice stress responses against bacterial leaf streak pathogens. It was observed that the infection with Rhizoctonia solani upregulated the expression of OsAPY2, 4, and 8. Rice blast fungus (Magnaporthe oryzae) inoculation induced the expression of OsAPY2, 5, and 8 indicating their possible role in rice blast disease. Infection with rice dwarf virus (RDV) upregulated the expression of OsAPY1-5; on the other hand, OsAPY6, 8 were downregulated. OsAPY2, 3, 5, and 8 got upregulated in response to rice stripe virus (RSV) infection, but at the same time, OsAPY1 and 6 got downregulated.
During anoxic conditions, the expression of OsAPY1-3 and 8 was upregulated, but OsAPY4 and 5 were downregulated (Fig 13). OsAPY4 showed a slight increase in expression only in 3 hours-long anoxic conditions. In OsAPY8, the level of expression was proportional to the duration of the anoxic condition. Rice subjected to drought for 2 and 3 days showed upregulation of OsAPY4 and 5, but all the other OsAPYs, especially OsAPY7, were downregulated except OsAPY6, which showed no change in expression. The extended period of drought condition downregulated the expression level. The gene expression level increased with time duration in heat stress, but after a specific time, it started to decrease. In the case of heat treatment for 120 minutes, the expression of OsAPY1-6 was upregulated, but gene expression levels were reduced during an extended period of heat treatment (165 minutes). This result indicated that OsAPYs displayed late-term responses to heat stress, but extended stress interrupted their expression. When subjected to dehydration, similar late-term expression was observed. 135 minutes long dehydration stress induced the expression of all the OsAPYs except OsAPY4 and 7. Under salt stress, the expression was relatively higher in leaves than in roots. All the genes except OsAPY1, 5, and 6 were upregulated in leaves, whereas in root tissues, only OsAPY5, 7, and 8 were upregulated. Under submergence stress, the expression level increased with the increase in time. As the heatmap depicted (Fig 13), after 22 days of submergence for 24 hours, there was an increase in the expression of OsAPY1, 3, 5, and 8. OsAPY5 and 8 had an increased expression after prolonged exposure to submerged conditions as there was no significant expression in the case of short-term exposure to submerged conditions. Alkali treatment upregulated the expression of OsAPY5, 6, and especially of 8, whereas, for OsAPY2 and 8, the expression was induced in cold.
Investigation of expression profile using RT-qPCR data in response to several abiotic stresses
The relative expression ratio of OsAPY genes in the rice seedling leaves was assessed under cold, cadmium, salinity, submergence, drought, and heat stress. A bar chart of their real-time expression data in these different stress conditions after 18–20 hours is depicted in Fig 14.
The Y-axis depicts the relative expression of each gene analyzed via RT-qPCR in the rice plant leaves. The X-axis indicates the various abiotic stress conditions under which the relative expression analysis was done. Technical replication was used to find the mean value of expression at different treatments. MS Office 365 and GraphPad Prism 9.0.0 were used to analyze the data. A one-way ANOVA, followed by a Bonferroni post hoc test, was used to assess the significant differences (P ≤ 0.05). To represent the significant differences, different means were labeled with the different number of asterisks (*). *, **, and *** represent the various level of significance (P ≤ 0.05, P ≤ 0.01, P ≤ 0.001 respectively).
As shown in Fig 14, all the OsAPY genes except OsAPY8 and 9 showed significantly higher expression under heat stress. Among all the stress environments, OsAPY5 had considerably higher expression levels (more than five-fold) in all the stress conditions. The RNA-seq data (Fig 13) also demonstrated its enhanced expression during drought, submergence, dehydration, alkali, salt, and heat stress.
Cold, submergence, drought, and heat stress, all resulted in considerably more significant levels of OsAPY1 expression. The expression level during submzergence stress (more than ten-fold) was significantly higher, and the result obtained from RNA-seq data (Fig 13) corroborated this observation. Under cadmium, cold, salinity, submergence, and heat stress, OsAPY2 demonstrated significant expression, and RNA-seq data revealed consistent outcomes (Fig 13), especially in cold conditions, its expression was very high. However, the real-time expression level was much more significant in response to cadmium and salinity stress. OsAPY3 expression was substantially increased in heat and cold stress. Compared to the control condition, it was much greater during cold stress and demonstrated an 8-fold upregulation. Only heat stress raised the expression of OsAPY4 (approximately eight-fold) and 7 (more than four-fold), whereas salinity and heat stress significantly downregulated the expression of OsAPY9. Under heat stress, RNA-seq data also revealed a higher level of OsAPY4 expression. During cadmium, cold, salinity, and heat stress, OsAPY6 expression was significantly enhanced, and RNA-seq data also exhibited upregulated expression under salinity and heat stress (Fig 13). Under cadmium, salinity, submergence, drought, and heat stress, OsAPY8 demonstrated significant downregulation. Though the expression under cold conditions was higher, it was not significant. Its downregulated expression level during drought, heat, and submergence stress and the increased one in cold was also supported by RNA-seq data. According to RNA-seq data, prolonged exposure to submerged situations increased its expression. This result indicates a potential function for OsAPYs in regulating abiotic stress.
Discussion
A noteworthy role is played by apyrase (APY) in regulating the growth of plants, developmental changes, and different stresses [18, 24]. The extracellular ATP (eATP) level rises when the plants are under any kind of stress which in turn increases ROS expression, triggers several other stress-induced genes, and can also cause apoptosis [5, 17]. Apyrase can hydrolyze eATP [137], and thus it has a major function in regulating eATP-mediated ROS production, and cellular apoptosis and in providing tolerance towards various stress conditions. Rice is the primary food consumed by the majority of people worldwide, and Asia alone contributes 90% to global rice production [138]. Different stresses are blamed for yield losses in commercially essential crops in many parts of the world. So, manipulating APYs can be a great step towards developing genetically modified multiple stress-tolerant rice and improving its annual production as APYs are associated with various developmental stages as well as stress responses of the plants. For this, the APY gene family should be studied intensively. Wheat, peanut and Arabidopsis have been extensively investigated for this gene family [2, 23, 31], but an investigation in rice is still not conducted. This study was designed to identify, characterize, and for analyzing the patterns of APY expression in rice.
Rice was found to have nine apyrase genes, as per this study, and all of these genes contained all the 5 ACRs [22]. An expanded insight into the significance of apyrase under abiotic and biotic stress was gained by the identification, characterization, and profiling of the expression of APY genes. These genes are different in their sequence length, molecular weight, pI value, and GRAVY value which means that this gene family is diverse. The GRAVY value of the proteins is negative, confirming the hydrophilic nature of the proteins [95].
Ecto-APYs are usually present on the plasma membrane and other cell surfaces, and endo-APYs are localized on ER, Golgi body, etc. [23, 139], and extracellular ATP is regulated by both endo- and ecto-APYs [19, 140]. In this investigation, the proteins were present on the plasma membrane, mitochondria, endoplasmic reticulum, and chloroplast, suggesting that both endo-APYs and ecto-APYs are present in rice [2, 23]. Nevertheless, the localization of OsAPY3, 4, and 9 varies according to the two different tools. Findings of CELLO [59] indicated there are three ecto-APYs (OsAPY2, 4, 5), but WoLF PSORT [58] suggested there are two ecto-APYs (OsAPY2, 5). It will take further research to find their precise position.
During evolution, gene duplication has a significant contribution to the process of gene expansion, and during plant development and growth, gene duplication can assist plants in adapting to various conditions [141]. The study of duplication events identified six duplication occurrences within the genome. The evolution of these genes occurred under the influence of purifying selection, which was suggested by the value of Ka/Ks and it was less than 1 [96]. These duplications occurred in genes situated on different chromosomes, indicating the segmental type of duplication being the main force of diversification [96]. Although segmental duplication preserves the primary functional group, it leads to differentiation in the manner of duplicated genes [142].
OsAPYs were related to APYs from Arabidopsis, peanut and wheat by constructing a phylogenetic tree in order to better understand their structure and functions. It was found that the phylogenetic tree was composed of three distinct groupings. According to earlier research on Arabidopsis, peanut and wheat APYs, this conclusion is in accordance [2, 23, 31]. None of the OsAPYs was categorized as members of any new group. OsAPY was found to be a very archaic family of genes, originating before even the splitting of monocotyledon (rice and wheat) and dicotyledon (Arabidopsis, peanut) plants because the OsAPY genes shared an equal number of groups with the AtAPY and AhAPY genes and with the TaAPY genes [143].
The number and orientation of exon-introns in plant genes play an essential role in evolution [144]. Gene structure analysis predicted that there was no intronless gene which indicates their high expression, and this gene family is an ancient one and not recently evolved [145, 146]. OsAPY5 contained the lowest exon and intron, whereas OsAPY6 contained the maximum exons and introns. Although OsAPY1, 3, and 6 belonged to group I of the phylogenetic tree, their exon-intron structure was different from the other members of group I. OsAPY2 and OsAPY4 belonged to group II, but their gene structure was consistent with the other members of group I. OsAPY5 which belonged to group III had a completely different exon-intron structure.
For proteins to function and to be particular, conserved motifs are necessary. Finding the structural patterns that are common to many proteins will help us better understand how proteins interact [147]. Conserved motif analysis revealed that motif 1, 5, 8, and 10 were conserved across all OsAPYs; motif 2 was present in all the OsAPYs except OsAPY2. Motif 3, 4, 6, 7, and 9 were the least distributed. These were only found in phylogenetic group I, and each group’s members had a remarkably comparable structure. Their function analysis revealed that 8 of the identified motifs are members of the GDA1-CD39 family, which confirms that the identified genes are members of this GDA1-CD39 nucleosidephosphatase superfamily.
The percentage of alpha-helix, beta-sheet, isolated beta bridge, turn, coil, and 310-helix was similar in all the proteins. The secondary structure analysis showed the dominance of alpha-helix over other structures, which implied the stability of the protein structure [135]. The membrane-spanning motif numbers varied from 0 to 2, which are similar to the previous findings [2, 23]. Proteins containing one motif had only N- terminal MSM. The proteins with two motifs had both N- and C- terminal MSMs except OsAPY6, which had only 2 N-terminal MSMs. N- as well as C- terminal MSMs are found in OsAPY2, 4, and 5. These proteins with both the N- and C- terminal MSMs were considered as ecto-APYs according to CELLO [59]. In the earlier studies on human APYs, proteins containing both the MSMs were also predicted to be ecto-APYs [2]. This finding is in accordance with the result obtained from CELLO [59] and TMHMM web servers [81].
The tertiary structure analysis showed that all the proteins’ projected structures were of high quality, which was validated by a number of tools. These structures could be utilized in analyzing the proteins more precisely in future research. Their docking analysis showed that there existed four categories of bonds between the proteins and their ligand ATP. The protein-ligand complex’s stability is supported by its high number of hydrogen bonds because these bonds normally aid in the stability of such complexes [148].
In the promoter region of a gene, cis-elements and transcription factors (TFs) interact, where they initiate gene transcription by assembling into the transcription initiation complex and then activating the RNA polymerase [104]. Sixty-nine cis-elements were identified in OsAPYs and categorized into eight groups. They played a crucial role in controlling different stresses and developmental phases, demonstrating the involvement of OsAPYs in these circumstances. A trait’s development and expression in plants are influenced by the gene’s chromosomal location [110]. Genes were unequally distributed throughout the genome in this study, and all of the OsAPY genes were found on chromosomes 3, 7, 8, 10, 11, and 12, with chromosome 11 having the most OsAPY genes.
We identified six distinct hormone-sensitive cis-elements in the promoter region, including those that are responsive to auxin, gibberellin, salicylic acid, ethylene, abscisic acid and methyl-jasmonate. The involvement of APY in maintaining the level of auxin and ethylene [149] and in controlling the closure of stomata in drought conditions induced by abscisic acid [150] was well documented. Additionally, there is ample evidence regarding the crosstalk between ethylene, gibberellin, and auxin [151–153]. These earlier results and the current investigation show that OsAPYs are probably important in the associated hormonal pathways.
The responsiveness of plants to external stimuli is tightly regulated by miRNA-mediated regulation of genes [39]. The OsAPY family members of rice were the targets of 103 miRNAs found in this investigation. Only 23 miRNAs specifically targeted more than one gene; the rest were gene-specific. osa-miR5819 targeted four different genes. It implies that osa-miR5819 could have an important function in the expression of OsAPYs. Maximum of the miRNAs were found to be downregulated in many stresses and tissues, with exceptions of osa-miR159a.1, osa-miR5532, osa-miR408-3p and osa-miR3979-3p. Comparatively, the miRNAs displayed decreased expression in response to a variety of stresses; this suggests that the miRNA-mediated regulation of the OsAPY genes may play a decisive role in how plants adapt to changing stress factors and growth conditions.
As per the 3K SNP search database, the prevalence of nonsynonymous SAPs in OsAPYs is significantly greater for indica rice cultivars than other rice cultivars. OsAPY1, 5, and 8 showed no SAPs in the studied varieties. Results indicate that the OsAPY1, 5, and 8 are substantially conserved among the studied genotypes. OsAPY2 contained the maximum number of SAPs which was 5 SAPs. The studied varieties are stress-responsive [39, 77] the presence of SAPs indicates their stress responsiveness might be related to these SAPs [154].
OsAPY2 was found to have elevated expression levels under cold, heat, salt, and submergence stress, and the SNP analysis revealed that it contained 6 different SNPs that resulted in SAPs and 5 of them were cold, heat, salt, blight, pest, and blast fungus-resistant ones (Table 4). This finding strengthened the possibility of its involvement in those stresses. They were found to be involved in different types of stress resistance depending on the variety of rice. The varieties in which these SNPs appeared were resistant to the respective stresses indicating their possible role in those varieties for the specific stress. Though the expression profiling of OsAPY3 and 4 revealed their upregulated expression under heat stress, their SNPs did not show any involvement in heat stress. OsAPY9 did not exhibit any significant expression under salt and heat stress in RT-qPCR analysis, but the SNPs located in the gene were confirmed to be salt, heat, and cold-resistant ones for the specific rice varieties. This finding implies that these SNPs might play a role in creating resistance against those stress conditions. SNPs in OsAPY6 and 7 were mainly involved in creating resistance against the biotic stress conditions suggesting their involvement in providing resistance against these biotic stresses. The SNPs for OsAPY2 at 14938900, 14940235, 14940827, 14941519, and 14941823bp; for OsAPY3 at 28963907bp; for OsAPY6 at 1204513bp; for OsAPY7 at 1226429bp; for OsAPY9 at 1107655, 1109364, and 1109753bp were unique for a particular rice variety under a specific stress condition (Table 4). Due to this specificity, they can act as markers for screening the related rice genotype under specific stress conditions.
The involvement of OsAPYs in various tissues during the development and growth of rice was determined by an analysis of their expression patterns (Fig 11) using RNA-seq data. OsAPY1-4, 9 showed higher levels of gene expression in inflorescence, implying their possible function in flower development. Previous studies have demonstrated the function of APY in flowers [25, 155]. OsAPY2 and 4 had an abundant expression in anther, whereas OsAPY1, 3–5 showed elevated expression in the pistil, suggesting their potential roles in the germination of pollen, fertilization, and reproduction, respectively. The activity of APYs in pollen and pistils was reported in Arabidopsis [25, 33]. OsAPY9 expression was found to be higher in the leaves and seedling stage, indicating that it plays a potential function in leaf development and early phases of plant growth. The involvement of APYs in leaves has previously been documented in Medicago truncatula [155] and Arabidopsis [25]. Another research on pea seedlings found that APYs were involved in early growth and development [156].
To further consider the dynamics of the OsAPYs in various biotic and abiotic stresses, their expression profiles via RNA-seq data were studied. The activity of OsAPYs was investigated in response to bacteria, fungus, and viruses, and OsAPY1-5, and 8 exhibited higher activation. APYs have been discovered to function in defensive and symbiotic relationships between plants and microorganisms [157]. OsAPY1-5 demonstrated higher activity under blight-causing bacteria Xanthomonas oryzae pv. oryzicola. Both types of viral infections elevated the expression of OsAPY2, 3 and 5; under fungal infection, the expression of OsAPY2, 5, and 8 increased. This discovery is in line with an earlier study that found the pea APY gene (PsAPY1) to be engaged in delivering protection against fungal infections [158]. The analysis of cis-elements showed that in the promoter region of OsAPYs, WRE3, WUN motifs, and W-box, which regulate biotic stresses in plants were present. The presence of such motifs corroborates our findings regarding the involvement of these genes in providing a defense under such stress conditions.
To identify the role of OsAPYs in abiotic stresses, the data retrieved from the RNA-seq database and the RT-qPCR analysis result were correlated. OsAPY2 and 8 were essential genes concerning cold stress in both cases, suggesting their potential role under cold condition. In cold condition, APY involvement has been reported in Populus euphratica (PeAPY2) [137]. OsAPY1, 2, and 5 showed increased activity under submergence stress suggesting their probable involvement in this condition. OsAPY1-6 had upregulated expression under heat stress, suggesting these genes’ involvement in heat stress. Under salt stress, OsAPY2 and 6 demonstrated elevated expression in both cases, indicating their role in helping the plant survive under salt stress. Similar results were found in wheat, where majority of the APY genes had higher expression after being exposed to salt for 12 hours in both roots and leaves [23]. OsAPY5 showed higher expression under drought conditions indicating its role in helping plants cope with this condition, as the role of APY was previously reported in a study where the pea ectoapyrase was expressed in soybean and Arabidopsis and it resulted in better growth and tolerance towards drought conditions [159]. Presence of many abiotic stress-responsive cis-elements supports the notion concerning the role of APYs in abiotic stress conditions. Gene expression is one of the complicated biological processes, and it requires further research for elucidating the mechanisms of the OsAPYs behind the regulation of several stresses. These findings indicate the function of OsAPYs under diverse biotic and abiotic stresses, and so this gene family could prove to be an important candidate for genetic engineering that can provide protection against various stress conditions.
Conclusion
In this study, the rice APY gene family has been identified, characterized, and its expression profiling has been done extensively. Nine genes were identified, and they were found to be located on chromosomes 3, 7, 8, 10, 11, and 12. Phylogenetic analysis grouped the nine identified OsAPY genes into three groups, and the identified cis-elements revealed their involvement in different stress conditions, hormonal regulation, and developmental stages. This ancient gene family evolved via segmental duplication and some SAPs were present in the stress-responsive varieties, some of which might act as markers for screening a certain rice genotype under specific stresses. Four different categories of bonds were identified between the OsAPYs and ATP, suggesting strong docking interactions between them. miRNA analysis helped in understanding the function of miRNA in modulating OsAPY activity, while expression profiling via RNA-seq data unveiled the role of OsAPYs under various growth phases as well as stresses. The expression analysis using RT-qPCR data also confirmed the response of OsAPYs in various abiotic stress conditions, especially in heat stress. OsAPY2 and 5 demonstrated increased expression when RNA-seq and RT-qPCR data were compared, suggesting they could be potential candidates for further study. These findings would give the insight to broaden the understanding and knowledge regarding APYs in rice as well as provide a foundation in future research regarding OsAPYs and also in the genomic alterations towards the improvement of rice and eventually developing stress-tolerant varieties.
Supporting information
S1 Fig. Apyrase conserved region (ACR) analysis of the OsAPYs.
The alignment was done using MEGA X and visualized via GeneDoc. The navy blue, pink, and aqua colors indicate the amino acids that are conserved 100%, 80%, and 60%, respectively, and the red-colored boxes depict the apyrase conserved region (ACR).
https://doi.org/10.1371/journal.pone.0273592.s001
(TIF)
S2 Fig. Ramachandran plot of the tertiary structures of OsAPYs.
The Ramachandran plot was generated via PROCHECK. Residues in the most favored, additional allowed, generously allowed, and disallowed regions are specified via red, yellow, pale yellow, and white colors, respectively.
https://doi.org/10.1371/journal.pone.0273592.s002
(TIF)
S3 Fig. ERRAT plot of the tertiary structures of OsAPYs.
ERRAT plot was generated via ERRAT. Yellow bars indicate the segment of the proteins which could be excluded at a 95% confidence level, and the red bars denote the ones at a 99% confidence level. The section with a lower error rate is marked by white bars.
https://doi.org/10.1371/journal.pone.0273592.s003
(TIF)
S4 Fig. Z-score plot of the tertiary structures of OsAPYs.
The Z-score plot was generated via ProSA-web. The light blue color indicates the Z-score of the proteins measured by X-ray crystallography, and the dark blue color indicates the Z-score of the proteins measured by nuclear magnetic resonance (NMR) spectroscopy. Black dots indicate the Z-score of each protein.
https://doi.org/10.1371/journal.pone.0273592.s004
(TIF)
S5 Fig. Energy plot of the tertiary structures of OsAPYs.
The energy plot was generated via ProSA-web. The dark green line represents the energy averaged across each fragment of 40 residues, and the light green line depicts the one across each fragment of 10 residues.
https://doi.org/10.1371/journal.pone.0273592.s005
(TIF)
S6 Fig. Ramachandran plot of the protein (OsAPYs)- ligand (ATP) complex structure.
The Ramachandran plot was generated via PROCHECK. Residues in the most favored, additional allowed, generously allowed, and disallowed regions are specified via red, yellow, pale yellow, and white colors, respectively.
https://doi.org/10.1371/journal.pone.0273592.s006
(TIF)
S7 Fig. ERRAT plot of the protein (OsAPYs)- ligand (ATP) complex structure.
ERRAT plot was generated via ERRAT. Yellow bars indicate the segment of the proteins which could be excluded at a 95% confidence level, and the red bars denote the ones at a 99% confidence level. The section with a lower error rate is marked by white bars.
https://doi.org/10.1371/journal.pone.0273592.s007
(TIF)
S1 Table. Description of the conserved motifs in OsAPYs.
https://doi.org/10.1371/journal.pone.0273592.s008
(DOCX)
S2 Table. Duplicated APY genes and the probable dates of duplication blocks in rice.
https://doi.org/10.1371/journal.pone.0273592.s009
(DOCX)
S3 Table. The location of all the OsAPYs in different chromosome, their position, and orientation.
https://doi.org/10.1371/journal.pone.0273592.s010
(DOCX)
S4 Table. List of miRNAs targeting different OsAPYs and their mode of inhibition.
https://doi.org/10.1371/journal.pone.0273592.s011
(DOCX)
S5 Table. The percentage of alpha-helix, beta-sheet, beta bridge, turn, coil, 310 helix, and the position of the transmembrane motif in the OsAPY members.
https://doi.org/10.1371/journal.pone.0273592.s012
(DOCX)
S6 Table. Validation score of OsAPY tertiary structure via different tools.
https://doi.org/10.1371/journal.pone.0273592.s013
(DOCX)
S7 Table. Docking score of the docked complexes generated via HDOCK server.
https://doi.org/10.1371/journal.pone.0273592.s014
(DOCX)
S8 Table. Number of bonds formed between OsAPYs and ATP according to PDBSum analysis.
https://doi.org/10.1371/journal.pone.0273592.s015
(DOCX)
S9 Table. Analysis of the interaction of OsAPY proteins with their ligand (ATP).
https://doi.org/10.1371/journal.pone.0273592.s016
(DOCX)
S10 Table. List of primers used in RT-qPCR analysis.
https://doi.org/10.1371/journal.pone.0273592.s017
(DOCX)
Acknowledgments
The authors are thankful to the Plant Genetic Engineering Lab, Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet for supporting to conduct of this research.
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