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Insights into PPR Gene Family in Cajanus Cajan and Other Legume Species

Parampreet Kaur, Mohit Verma, Pavan K Chaduvula, Swati Saxena, Nikita Baliyan, Alim Junaid, Ajay K Mahato, Nagendra Kumar Singh and Kishor Gaikwad*

National Research Centre on Plant Biotechnology, Pusa, New Delhi, India

*Corresponding Author:
Kishor Gaikwad
National Research Centre on Plant Biotechnology
Indian Agricultural Research Institute, New Delhi, India
Tel: 011-25841787/25842789
Fax: +911125843984
E-mail: [email protected]

Received date: June 30, 2016; Accepted date: July 11, 2016; Published date: July 18, 2016

Citation: Kaur P, Verma M, Chaduvula PK, Saxena S, Baliyan N, et al. (2016) Insights into PPR Gene Family in Cajanus cajan and Other Legume Species. J Data Mining Genomics Proteomics 7:203. doi: 10.4172/2153-0602.1000203

Copyright: ©2016 Kaur P, 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.

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Abstract

PPR proteins comprises of several hundred members among land plants and govern a fascinating array of functions in organeller genomes that ranges from participation in stabilization of organeller transcripts, RNA editing to fertility restoration of CMS lines. Despite the availability of genome sequences of several legume species, comprehensive cataloguing of members of PPR gene family has not been carried out. In the current study, we identified 523, 830, 534, 816, 441 and 677 PPR proteins in Cajanus, Glycine, Phaseolus, Medicago, Vigna and Cicer genomes, respectively and their complete in silico categorization was undertaken to classify them into various sub-classes and their localization prediction. Chromosomal coordinates of 271 Cajanus PPR genes were predicted and their homologues were identified in 5 other legumes revealing extensive genome conservation. PPR genes of all 6 legume species were further probed to identify restorer of fertility-like PPRs (RFLs) on the basis of protein clustering and followed by homology searches to already known Rf-PPR genes. Seventy RFL PPR genes (P sub-class) were identified and were scrutinized by phylogenetic analysis which revealed extended similarity and common features shared by these RFLs across the species. Some of these RFL PPRs were present as small clusters in Glycine, Phaseolus, Vigna and Cicer genomes. This study has generated a knowledge base about PPR gene family in legumes and opens several avenues for future investigations into their molecular functions, evolutionary relationships and their potential in identifying markers to enable cloning of Rf genes.

Keywords

PPR protein; Legumes; Restorer of fertility like-PPR (RFL); Synteny; P sub-class; Mitochondrion

Introduction

PPR motifs containing proteins were first discovered from the genome of Arabidopsis thaliana [1,2] and later reported in other sequenced eukaryotes. PPR proteins have gained importance in context of their role in various RNA processing events such as RNA stabilization, splicing, editing, cleavage and transcriptional activation [3]. Though PPRs are encoded by nuclear genome, they are mostly targeted to either mitochondria or plastids for their functions [4] and thus play an important role in organeller gene regulation. By using classical genetic screens, number of PPR mutants have been characterized with varied phenotypes ranging from those showing photosynthetic defect [5] to restricted growth [6], defective seed and embryo development [7], aberrant leaf growth [8] and restoration of pollen fertility [9]; implying the role of PPRs as sequence specific RNA binding proteins in organelles. Other reports also suggest important role of PPR and these includes, abnormal splicing of chloroplast targeted PPR encoding Rpl2 gene in rice resulted in mutant with white stripe leaf (WSL mutant) characterized by enhanced sensitivity to abiotic stresses and chlorotic striations during its early development [10], Rf1A in rice functions in atp6 mRNA editing [11], RPF2 affects mitochondrial nad9 and cox3 mRNAs in Arabidopsis [12] and so on. Non plant organisms have very few PPRs whereas great expansion of this gene family via retrotransposition has been observed in plants [13]. Their number in a particular species could range from less than 30 in eukaryotes (Chlamydomonas reinhardtii) [14] to 1882 members in T. aestivum [15].

PPR proteins are categorized into different sub-classes and subgroups on the basis of the sequence content and arrangement of peptide repeat motifs that constitutes their structural and functional divergence [16]. It is the sequence variability within repeats that provides specificity to the action of different members of this protein family. The two major sub-classes are denoted as P and PLS. Classical PPRs or P class PPRs are defined as those containing degenerate 35 amino acid peptide motif present in multiple tandem repeats and this sub-class constitutes half of the PPR family in any plant species. PPR motif is known to form two anti-parallel α-helices that interact to produce a helix-turn-helix motif, series of which forms a superhelix with central groove for interaction with RNA [17]. Many P class proteins have special appendages present at C-terminal domain (PRORP, SMR, LAGLIDADG etc.) that confers functional specificity to proteins due to presence of variable motifs. Proteins with LAGLIDADG motif are involved in catalytic processes due to its similarity with group-1 intron maturases [18] and those with SMR domain are related to MutS2 family which participate in transcription or repair of chloroplast DNA [19]. PRORP (proteinaceous RNaseP) sub-class possess metallonuclease domain which are involved in processing of mitochondrial tRNA, for example Arabidopsis PRORP3 protein [20]. The classical P motif when interspersed by L motifs (36 amino acids) and S motifs (31 amino acids) in triplets constitute PLS sub-class, wherein this ordered association could have variable number of S motif repeats [21]. PLS-PPRs also possess additional C terminal domains designated as E (extended), E+ (slightly longer than E domain) and DYW (characterised by Asp-Tyr-Trp triplet at terminating end). Thus, a PLS protein will terminate with either a PPR motif or a non- PPR motif i.e., E motif, EE+ motif or EE+DYW motif sequence. The members of these three sub-groups are mainly involved in RNA editing in chloroplast and mitochondria [22].

Due to certain limitations of delmarking PPR motifs by classical system of categorization, PPR motifs has been redefined by Cheng et al. [15] whereby 10 PPR motif variants have been described and used to annotate PPR sequences in 109 genomes. Newly identified motif variants in PLS sub-class includes P1 and P2 motifs that differ from classical P motif in first helix; S2 (32 amino acid), SS (31 amino acid), E1 (34 amino acid) and E2 (34 amino acid) motif. This revision of PPR classification has provided a clearer picture of PPR structure and thus will provide new insights into their role in molecular and structural evolution.

Most of these nuclear encoded PPRs carry N-terminal mitochondrial or chloroplast targeting sequence and are important contributors of various organellar post-transcriptional processes by virtue of their sequence specific RNA binding activity. Considering the array of functions governed by PPR proteins, identification and characterization of homologous and species specific PPR proteins in other plant species is critical for understanding the dynamics of nuclear cytoplasmic interactions.

Cytoplasmic male sterility system is widely exploited/ phenomenon for hybrid seed production and has been extensively studied at molecular and biochemical level in various crops. Fertility restorers are an important component of hybrid breeding that suppresses the male sterility in plants bearing defective mitochondrial transcripts. These Rf genes belong to several protein families, out of which majority have been found to encode for PPR proteins [23]. Few examples of PPR containing genes include Rf1 gene in Petunia [24], Rf1 in rice [25, 26] and Rfk and rfo in radish [27-29]. On the basis of their homology within PPR family and also with known CMS restorers PPRs from related plant species, restorers of fertility-like PPRs (RFL) can be identified. RFLs generally constitutes around 10-30 members/plant genome. In silico based approaches to identify RFLs on the basis of phylogenetic analysis and orthologous clustering has been used to identify candidate genes for fertility restoration in perennial ryegrass by Sykes et al. [30].

With approximately 20000 species, legumes are placed second to grasses in term of their economic contribution to world agricultural system. Approximately 33% of human nitrogen requirement is fulfilled by grain legumes as they contain twice the amount of proteins in comparison to cereals [31] and legumes are the single chief dietary source of proteins in many developing countries. They are unique in their capacity for symbiotic nitrogen fixation and thus enhance soil fertility along with serving as an important source of fodder, forage, secondary metabolites and industrial and edible oils. Legumes are divided in three sub-families and the important species fall under two papilionoid clades i.e., phaseoloid clade and galegoid clade [32]. Considering the importance of legumes, in depth analysis of their genome structure is important to improve their yield and quality using various genetics and genomics approaches.

Though recently, a documentation of PPR proteins in 109 genomes has been done [15] and includes few legume species, the goal of the current study is to expand the knowledge base on these proteins in legumes. The members of Phaseoleae, Cicereae and trifolieae tribe i.e., Cajanus cajan, Glycine max, Vigna radiata, Phaseolus vulgaris, Cicer arietinum and Medicago truncatula were selected to provide an understanding of the PPR gene family in legumes. As the draft genome sequence is available for all these species, insights onto PPR family in legumes will be provided by i) identifying PPR encoding genes, ii) classifying and categorizing them on the basis of the domain structure, iii) mapping them onto genome, iv) studying their evolutionary relationship among legumes and v) isolation of potential RFLs that could serve as candidate Rf genes.

Materials and Methods

PPR gene identification and classification in Cajanus cajan and other legumes

Genome sequencing data of 80.4 Gb from Illumina sequencing platform of cultivar Asha (unpublished data) was used as a seed sequences to search against nr database for PPR hits followed by gene prediction using FGENESH [33] and domain identification using Interproscan (version 5) [34]. Further, the predicted protein sequences were used as query against Uniprot (http://www.uniprot.org/) PPR database of Glycine max. The search was based on BLASTx with an e value of 1e-3 to identify putative PPR proteins. Simultaneously, already available draft genome sequence data of Asha (ICPL87119) was also used for PPR identification. Annotated data of 454-FLX sequencing chemistry of Asha [35] was searched to identify PPR genes directly whereas protein sequence data submitted by [36] was used as query in BLASTp search against Arabidopsis and rice PPR dataset from Uniprot database (http://www.uniprot.org/) followed by confirmation by domain prediction using Interproscan. To remove redundancy between three datasets, reciprocal BLAST was done among the putative PPRs to identify unique PPRs. Among PPRs found in common between either datasets, the longest ones were retained to compute the actual number of putative PPRs in Cajanus and subsequent downstream analysis.

PPR proteins present in other legume species viz. Glycine max, Phaseolus vulgaris and Medicago truncatula were downloaded from Uniprot database (http://www.uniprot.org/). PPR proteins in Vigna radiata and Cicer arietinum were identified from Legume Information System (www.legumeinfo.org). Unique PPRs for each legume were sorted out to eliminate alternative splicing products.

Domain architecture of PPR proteins was described as per new classification system [15] using PPR browser website (http://plantppr. genomics.cn:8080/plantppr/nav.do?flag=group).

Subcellular localization prediction

TargetP v. 1.01 (http://www.cbs.dtu.dk/services/TargetP/) and Predotar v. 1.03 (https://urgi.versailles.inra.fr/predotar/predotar.html) were used to predict the organelle targeting domains of PPR proteins. In case of ambiguity between the results of two predicting software, the prediction with the better confidence was retained.

Genome organization and chromosome distribution of PPRs in Cajanus cajan and Glycine max

The chromosomal location for Cajanus and Glycine PPRs was obtained through BLASTp searches against whole genome sequence information using LIS database (http://legumeinfo.org/) and soybase (http://soybase.org/, Wm82.a2.v1), respectively. Their physical distribution on chromosomes was drawn using ArkMAP (http://www. bioinformatics.roslin.ed.ac.uk/arkmap/help/) on the basis of their coordinates in their respective genomes and the position of each gene on the chromosome was represented in base pairs.

Comparative genome analysis

Homologues of Cajanus cajan PPRs were identified from Glycine max, Phaseolus vulgaris, Medicago truncatula, Vigna radiata and Cicer arietinum by BLASTp search using LIS database. Chromosomal coordinates i.e., chromosome number and position were used to depict the homologues using Circos program (circos.ca/).

Prediction of restorers of fertility like (RFLs) PPR genes

All predicted PPR protein sequences from six legume species were analyzed for putative RFL genes. CD-hit [37,38] was used to cluster all proteins at different identity percents. PPRs clustered with ≥3PPRs/cluster and at 60% identity were selected for alignment with already well characterised restorer of fertility (Rf) genes that encodes for PPR proteins. Rf protein sequence of 5 species i.e., Brassica napus (ACJ70132.1), Zea mays (ACN24620.1), Oryza sativa (AB110016.2), Petunia hybrida (AY1027.1) and Raphanus sativus (DQ445625.1) were downloaded from NCBI. Using Mega7, these Rf protein sequences were then aligned individually with the PPR proteins clusters of individual species followed by construction of phylogenetic tree using iTOL (http://itol.embl.de/), PPRs showing homology with atleast two of these 5 known Rfs were designated as putative RFL genes. To provide authenticity to this approach, PPRs of all legumes were simultaneously subjected to online version of OrthoMCL (http://www.orthomcl.org/orthomcl/) to cluster the proteins into orthologous clusters.

Results

PPR genes in Cajanus cajan and other legumes

PPR genes in Cajanus were identified using three different data sets as described in Figure 1 and in totality 523 putative PPRs were identified (Supplementary file 1). The predicted numbers of PPRs in current study are based on homology searches and use of annotated data sets, thus explaining the less number of predicted PPRs to those already reported by Cheng et al. [15]. Similarly, a total of 677, 830, 534, 816 and 441 PPR proteins were identified in other legumes i.e., Cicer arietinum, Glycine max, Phaseolus vulgaris, Medicago truncatula and Vigna radiata, respectively. It was observed that though the genome size of Medicago (257 Mb) is considerably smaller than that of Cicer (738 Mb) but higher frequency of PPRs were predicted in Medicago. Interestingly, despite large variation in genome sizes between Glycine (1115 Mb) and Medicago (257 Mb), there was little variation in the number of PPR genes predicted.

data-mining-in-genomics-proteomics-mining-PPR-genes

Figure 1: Outline of strategy used for mining PPR genes in Cajanus cajan. PPR mining was done using three data sets of cultivar Asha, in which Illumina + Sanger data (237.2Gb) and 454GS-FLX data (10.1Gb) were already publically available while 80.4Gb Illumina data is yet unpublished. BLAST against nr dB (non redundant database) was performed at 1e-3 while BLASTp, BLASTx and reciprocal BLAST searches were conducted at an e value of 1e-5.

Domain architecture, classification and organelle targeting of PPR protein

PPR proteins in legumes were classified into two sub-classes (Figure 2) i.e., P and PLS, based on the presence and arrangement of different motifs. For 1 and 5 of predicted PPR protein sequences in Cajanus and Medicago, respectively no PPR domains were predicted and hence these could not be classified and were not included in further analysis. For rest of the legume species, all the predicted proteins were classified. In Cajanus, Glycine and Medicago 51.1%, 50.2% and 62.5% of the predicted PPRs, respectively were classified in P sub-class while for other 3 legumes less than half of the PPRs were categorized as P sub-class i.e., Cicer (45.05%), Phaseolus (49.8%), Vigna (48.5%). In all 6 species, small proportion of PPRs within P sub-class (2-6% of P subclass) was observed to possess C-terminal motifs i.e., SMR, PRORP and LAGLIDADG. PLS sub-class was further sub categorized into PLS, E1, E2 and DYW and majority of the proteins were found to posess DYW editing motif (Figure 2b) except in Cicer. None of the PPR was categorized into E+ sub-group that is known to constitute proteins with a degenerate or truncated DYW domain [15]. A small proportion of sequences were identified with E1 motif present as a C terminal domain in all legumes (Figure 2b).

data-mining-in-genomics-proteomics-C-terminal-motifs

Figure 2: Classification of PPRs in P sub-class (a) and PLS sub-class (b) in different legume species using PPR browser website. X axis represents number of proteins of a particular sub-class in different legume species represented on y axis. Numbers indicated on top of each bar in Figure 2 (a) represents number of P sub-class proteins in a particular species. PLS sub-class was further classified on the basis of C-terminal motifs i.e., DYW, E1, E2 and PLS as shown in Figure 2 (b) where, total height of each bar corresponds to total number of proteins in PLS sub-class of each species while different colours in each bar reflects proteins with different C-terminal motifs, their numbers represented in the table below y axis.

N-terminal PPR protein sequences of all 6 species were characterized to predict their sub cellular localization. Majority of the PPRs (Figure 3) were classified and were found to be targeted to mitochondria in all legumes. For Cajanus, Glycine, Medicago and Vigna, <30% of total PPRs were not predicted with any targeting signal whereas for Cicer and Phaseolus, 42% of the PPRs lack to possess localization signal. Out of the PPRs with predicted localization in all legumes, more than 80% of proteins were found to be targeted to mitochondria and chloroplast except in Cicer, where only 65% of the sequences with predicted sub cellular localization were targeted to mitochondria and chloroplasts.

data-mining-in-genomics-proteomics-sub-cellular-localization

Figure 3: Classification of PPRs on the basis of their sub cellular localization in different legumes using TargetP v 1.01 and Predotar v 1.03. Total height of each bar corresponds to total number of predicted PPR proteins (X axis) in each legume species (Y axis). Different colors in each bar reflects number of proteins with different sub cellular targeting peptides i.e., mitochondrial, chloroplast and endoplasmic reticulum (ER) or secretory pathway (SP). Number of proteins in which no organelle targeting peptides were predicted are represented as no predictions.

Despite the differences between number of PPRs predicted in each legume, approximately same percent of PPRs were found to be targeted to chloroplast and mitochondria, except for Cicer, in which mitochondrial targeting PPRs were less as compared to other legumes (Table 1).

Species Cp genome (Kb) Mt genome (Kb) PPRs with sub cellular localization % PPR targeted to Mt % PPR
 targeted to Cp
Cajanus cajan 152.2 545.7 365 60.0 28.7
Glycine max 152.2 392.0 601 59.9 28.1
Phaseolus vulgaris 150.2 - 307 59.9 29.6
Vignaradiata 151.2 401.2 309 59.5 26.8
Cicerarietinum 125.3 - 388 42.2 23.4
Medicagotruncatula 124.0 271.6 578 54.8 28.0

Table 1: Characteristics of hollow fibre module.

Genome organization and chromosome distribution of PPRs in Cajanus cajan and Glycine max

Chromosomal location i.e., chromosome number and position of the predicted PPRs of Cajanus cajan and Glycine max, is shown in Figure 4 and Figure 5, respectively and depicts their random distribution across the genome. No correlation was observed between the PPR sub-class and subcellular localization with respect to mapping in either Cajanus or Glycine and some chromosomes possessed dense distribution of PPR genes whereas on other chromosomes, genes were sparsely distributed.

data-mining-in-genomics-proteomics-Each-chromosome-designated

Figure 4: Distribution of 271 Cajanus cajan (Cc) PPRs on its 11chromosomes drawn using ArkMAP.

data-mining-in-genomics-proteomics-protein-designated

Figure 5: Distribution of 827 Glycine max (Gm) PPRs across its genome (5a-chromosome 1-10, 5b-chromosome 11-20) drawn using ArkMAP. Each chromosome is designated as Gm followed by chromosome number. Scale drawn on the left is in base pairs. PPRs are designated on the right side of chromosomes using only its unique identifier number (Uniprot database number). For instance, PPR protein designated as ‘K7K128’ instead of ‘tr_K7K128_K7K128_SOYBN’ (Uniprot database).

In Cajanus, 271 out of 523 were mapped onto its eleven chromosomes. Maximum number of PPRs i.e., 41 were mapped onto chromosome 3. Highest number of PPRs mapped/Mb of chromosome i.e., gene density was found for chromosome 6 where 37 PPRs mapped onto 23.79 Mb of chromosome giving gene density of 1.55 PPRs mapped/Mb while lowest gene density i.e., 0.57 PPRs mapped/ Mb was observed for chromosome 10. PPRs were designated using the following convention: Name of the species ‘Cc’ (Cajanus cajan) followed by chromosome number, PPR number on chromosome and lastly the sub-class of particular PPR.

Similarly for Glycine max, 827 PPRs were found to be mapped on its 20 chromosomes while only 2 PPRs mapped to the scaffolds. Gene density ranging from 1-1.2 PPRs mapped/Mb was observed for 5 chromosomes i.e., 8, 9, 11, 13 and 16 while for rest of the chromosomes it was less than 1PPR mapped/Mb. For ease in handling, the naming of the Glycine PPR was changed and limited to only its unique identifier number as obtained from Uniprot database. For instance, name of the PPR protein ‘tr_K7K128_K7K128_SOYBN’ (as given in Uniprot database) was changed to ‘K7K128’.

Conserved genome synteny among legumes

The level of synteny between Cajanus and other 5 legumes was assessed and shown in Figure 6 by comparison of physical map positions of 271 Cajanus PPRs with corresponding map positions in other legume genomes i.e., Glycine, Phaseolus, Medicago, Vigna and Cicer. It was observed that maximum homologues of Cajanus PPRs were obtained with Glycine and Phaseolus genomes where except for 1, hits were identified for all Cajanus PPRs. In Cajanus versus Medicago, Cicer and Vigna synteny, BLAST hits were obtained for 264 (97.41%), 251 (92.61%) and 220 (81.18%) sequences, respectively. This high level of homology shared across legumes supports their close evolutionary relationship. Majority of the Cajanus PPRs were found to map on chromosome 7 (41 PPRs), chromosome 17 (21 PPRs), chromosome 6 (46 PPRs), chromosome 9 (29 PPRs) and chromosome 8 (33 PPRs) of Medicago, Glycine, Cicer, Phaseolus and Vigna, respectively.

data-mining-in-genomics-proteomics-correspond-chromosome-number

Figure 6: Circos diagram illustrating syntenic relationship of 271 mapped Cajanus cajan (Cc) PPRs with Medicago truncatula (Mt), Vigna radiata (Vr), Cicer arietinum (Ca), Glycine max (Gm) and Phaseolus vulgaris (Pv).

PPRs that mapped onto a particular chromosome of Cajanus, identified their homologues scattered onto different Glycine chromosomes. For instance, 40 PPRs mapped onto Cajanus chromosome 11, identified their homologues that were distributed across the entire Glycine genome except for chromosome 4 and 19. Similar trend was observed between Cajanus and other legume species. Further it was observed that 14% of the Cajanus PPRs were found to map to the same genomic regions in one or the other target legumes while other 86% of the genes were getting mapped uniquely. Some of the Cajanus PPRs showed homology with small clusters of genes across all the five legumes, for e.g., a group of 5 genes mapped on Cajanus chromosome 1 showed homology with chromosome 7, 8, 3, 18 and 4 of Medicago, Phaseolus, Cicer, Glycine and Vigna, respectively. Maximum number of PPRs i.e., 41 were mapped onto Cajanus chromosome 3. Out of which, 15 PPRs found their homologues both onto chromosome 1 and chromosome 7 of Phaseolus and Medicago, respectively. While 10, 13 and 11 PPRs of Cajanus chromosome 3 were mapped onto chromosome 3 of Glycine, Cicer and Vigna, respectively. This is a representative of conserved synteny that exists across legumes. Certain other small groups of genes also displayed homology in small clusters in one or more than one legume species. No large syntenic blocks were observed between Cajanus and Glycine or with other target legumes though a high level of shared synteny was observed to cover all linkage groups of 5 legume species.

Prediction of restorers of fertility like (RFLs) PPR genes

RFL PPRs could be predicted by cross species comparison of PPR proteins with Rf-PPR genes on the basis of extended sequence similarity shared between them. Our analysis revealed that same set of PPR genes of Glycine, Cajanus, Medicago and Vigna, respectively showed homology with Rf genes of Brassica, Zea, Oryza, Petunia and Raphanus. Similarly, common set of PPRs from Cicer was identified to be homologous to Rf gene of Brassica, Petunia and Raphanus while different set of PPRs displayed homology with rice and maize Rf gene. Those PPR genes that were found to be in common in terms of similarity with atleast two of the Rf genes, were selected. In totality, 70 PPR genes (8-Cajanus, 8-Glycine, 6-Vigna, 16-Medicago, 13-Phaseolus and 19-Cicer) were found to be candidate RFLs, on the basis of their homology with known Rf genes from 5 different species. All 70 genes were found to belong to P sub-class, which encode for fertility restorer genes reported so far.

Phylogenetic analysis (Figure 7) among the 70 P sub-class RFL PPR genes, revealed that with exception of 1 RFL from Cicer and Medicago each, all Cicer proteins were present in two sub-clusters while Medicago RFLs were either present as outliers or in few small sub-clusters. Six RFLs from Phaseolus were found to be present in one clade along with Vigna RFLs while 7 other Phaseolus RFLs were present as a cluster along with Cajanus RFLs. Eight Glycine RFLs formed separate clade with 4 Cajanus RFLs. Three seperate clusters constituted all candidate RFLs of Glycine, Cajanus, Vigna and Phaseolus.

data-mining-in-genomics-proteomics-Amino-sequences-Clustal

Figure 7: Phylogenetic tree of 70 RFLs predicted from 6 legume species. Amino acid sequences were aligned using Clustal W (Mega7), NJ tree was constructed and designed using iTOL. PPRs from different species are represented in different colors and legume species are represented as Cajanus cajan (Cc), Medicago truncatula (Mt), Vigna radiata (Vr), Cicer arietinum (Ca), Glycine max (Gm) and Phaseolus vulgaris (Pv).

Out of 3821 proteins subjected for orthologous clustering using OrthoMCL, 89.66% were assigned to 397 orthologous clusters whereas no orthologous cluster was assigned to 396 proteins. Thirty four clusters represented single protein sequences, representing species specific clusters whereas the largest cluster identified consisted of 268 proteins from all 6 legume species. A total of 249 clusters represents proteins comprising all legumes and this indicated high level of similarity between PPR proteins from different species. Cajanus PPRs (469 proteins) were represented in 330 clusters and a plot of number of proteins with respect to number of species represented in these clusters showed a linear relationship with presence of few outliers (Figure 8). Largest cluster that comprised of 268 PPRs formed an outlier and represented 56 of the candidate RFL genes identified. Fourteen other RFLs (6-Vigna, 7-Phaseolus, 1-Medicago) were present in six other minor clusters.

data-mining-in-genomics-proteomics-plot-displaying-orthologous-clustering

Figure 8: Scatter plot displaying orthologous clustering of proteins using OrthoMCL. Number of species (x-axis) and number of proteins (y-axis) present in 330 clusters that contained at least one PPR from Cajanus cajan are represented. The outlined cluster represented 268 proteins, out of which 56 were predicted RFL PPRs from 6 legumes.

Further, the genomic coordinates i.e., chromosome number and position of these 70 RFLs on their respective genomes and other 5 legumes were identified. The mapping of these RFLs in legumes proved to be advantageous in identifying regions that correspond to high RFL density. Four such genomic regions i.e., one each on genomes of Glycine, Vigna, Cicer and Phaseolus were identified (Table 2). Except 1 RFL of Cicer, all other RFLs identified in these clusters were also found to be present in the same groups in their phylogenetic analysis.

Species RFL Gene Chromosome Start (bp) End (bp) Putative region of high RFL density Number of RFLs
Glycine max Gm_K7K229 Gm01 7774549 7777396 226Kb 4RFLS
Gm_I1J603 Gm01 7790857 7792847
Gm_I1JDJ0 Gm01 7995614 8000555
Gm_I1J608 Gm01 7995614 8000555
Phaseolus vulgaris Pv_V7C5P3 Pv04 42980045 42981604 148Kb 3RFLs
Pv_V7C3H4 Pv04 43033197 43034818
Pv_V7C3F3 Pv04 43128239 43128922
Vignaradiata Vr_08g17090.1 Vr08 38093705 38095304 41.6Kb 2RFls
Vr_08g17130.1 Vr08 38133690 38135303
Cicerarietinum Ca_16837 Ca8 11204750 11206138 142.7Kb 7RFLs
Ca_16831 Ca8 11268414 11269907
Ca_16829 Ca8 11289683 11291083
Ca_16827 Ca8 11308003 11309391
Ca_16825 Ca8 11319550 11320938
Ca_16824 Ca8 11335760 11336293
Ca_16823 Ca8 11346389 11347480

Table 2: Species specific genomic regionsin legumes predicted with high density of RFL genes.

Discussion

Nuclear genome encoded PPR protein family is widely associated with processing of mitochondrial and chloroplast transcripts. Considering the wealth of genome sequence information available for various legume species, Cajanus cajan along with 5 other species i.e., Glycine max, Cicer arietinum, Phaseolus vulgaris, Medicago truncatula and Vigna radiata were selected for genome wide analysis of PPR gene family using various bioinformatics tools. Owing to the important role governed by this gene family, the RFLs i.e., restorers of fertility like genes were narrowed down from PPR genes which could potentially serve as candidate Rf genes in legumes.

PPR gene family in legumes

The number of proteins identified in all 6 legumes were well in range and as already described for other land plants. More than 80% of the documented Arabidopsis and rice PPRs are known to form orthologous pairs, indicating a remarkable conservation in terms of sequence and functioning [13,39]. The number of PPRs identified for Arabidopsis, rice and Glycine from Uniprot database were used to scan the Cajanus genome sequence for presence of PPR genes. No direct correlation was observed between the genome size and number of members of PPR gene family in legumes and is in agreement with a similar study undertaken for members of AP2/ERF transcription factor superfamily where number of genes predicted in Cicer, Cajanus, Phaseolus, Medicago and Lotus did not show any relation with the genome size of the legume [40]. Categorization of <50% of PPRs as P sub-class members in Cicer, Phaseolus and Vigna could be attributed to the lack of availability of complete sequence data, presence of gaps and sequencing errors. The numbers representing PPRs for any representative species may change in future with the availability of their completely finished genome sequence data.

As all the proteins required for organeller functioning cannot be encoded by their own genomes, the rest are encoded by nuclear genomes. These include genes for respiratory pathway, photosynthesis, mRNA maturation etc. To possess an organelle localization feature, N terminal of PPR protein is either merged with 40-50 amino acid long mitochondrial targeting peptide or a chloroplast targeting peptide of upto 60 amino acid long [4]. Except for Cicer and Phaseolus, number of PPRs predicted as untargeted proteins, is equivalent to the false negative results (~20-30%) obtained by Predotar and TargetP [41,42].

Presence of more number of PPRs with mitochondrial targeting signal could be related to the larger mitochondrial genome of land plants (200-2000 Kbp) harboring low gene densities. Remarkable increase of mitochondrial genome size in plants is reported to occur in union with proportional expansion of PPR gene family and range of post transcriptional activities, for eg., RNA editing required in higher plants necessitating the diversification of PPR protein functioning [43]. Expansion of PPR gene family in land plants is hypothesised to be in proportion with the editing of organelle transcripts [44]. Mitochondrial and chloroplast genome of Arabidopsis contain 525 and 34 editing sites, respectively and possess 225 PLS proteins [45] whereas >800 PLS proteins are identified in Selaginella with 2150 and 1041 editing sites in mitochondria [46] and chloroplast [44], respectively. This further implies the importance of PPRs in organelle communication. In the current study, no relation was observed between organelle genome size and number of members of PLS sub-class, but in future with decoding of all editing sites in organelle genomes of different legumes, number of PPRs in PLS sub-class could be related to number of editing sites in a genome.

Further the sub cellular targeting of PPR proteins was found to be independent of their sub-class or of C-terminal domains they possess, as reported in other studies [47], though a high proportion of members of both sub-class in all 6 legume species were predicted to be targeted to chloroplast or mitochondria, which reflects their basic necessary feature in organelle functioning.

In chromosomal mapping of members of homeobox genes, more genes were located onto scaffolds of Cajanus, Cicer and Lotus as compared to that in Medicago and Glycine, wherein except few all genes are mapped onto distinct chromosomes and was attributed to the availability of incomplete genome sequence data of these 3 legume species [48]. Similarly, current study revealed that chromosomal localization of PPR genes across the Cajanus and Glycine genome is characterized by their uneven distribution where approximately half of the Cajanus genes were located on unanchored scaffolds while only 2 genes were located onto Glycine scaffolds and rest were assigned to 20 differernt chromosomes. Comparison of a collinear region between arabidopsis and Brassica rapa with respect to PPR genes also demonstrated their random distribution [47].

Synteny studies

Comaparitive information from the well characterized species has often been used to accelerate genetic and genomic studies in less charcaterized orphan species for varied purposes viz. candidate gene identifications for important traits. Similarly, identification of conserved regions across legumes will assist in the detailed analysis of legume genome evolution. Most of the genes in papilionoid legume species are likely to be found within syntenic regions (ranging from 100s of Kb to Mb) to any other given papilionoid species, so that an orthologue of a gene with known phenotype is most likely to be found in a similar genomic region in closely related species [49]. A similar trend is visible from the fact that except 1, homologues were obtained for all Cajanus PPRs in Glycine and Phaseolus genome and majority of Cajanus PPRs were mapped across other 3 legume species as well, this reflects high level of synteny conservation across species that could also be utilized as a resource to identify syntenic regions in other species. Individual Cajanus chromosomes are known to be syntenic to two or more than two Glycine chromosome [36] and was also in accordance with the current study where clusters of homologous PPRs were observed between various Glycine and Cajanus chromosomes. Similarly, chromosome 1 of Phaseolus is known to exhibit synteny with chromosome 3 of Cajanus with respect to genes such as those governing determinacy in Cajanus [50]. It was observed that homologues of 12 out of 41 PPRs mapped onto chromosome 3 of Cajanus (7.3 Mb), were identified as a cluster on chromosome 1 of Phaseolus in a region spanning 12.93 Mb.

Studies between Arabidopsis and rice PPR proteins also observed exceptionally high degree of interspecies individual protein conservation [39]. Legume Tentative Orthologous Genes (TOG) markers have been used to study evolution across pigeon pea [51], common bean [52] and other legumes [32,53]. In a study, 128 out of 377 TOGs that mapped onto L. ervoides genome found their orthologue both in Medicago and Cicer genome, thus reflecting a high level of conservation of synteny among the species and serves as a resource to identify syntenic regions in other species [54]. Remarkably high levels of collinearity were observed in 0.5 Mb region surrounding Rhg1 and Rhg4 SCN resistance loci of Glycine and its corresponding region in Medicago in terms of perfect conservation of gene order and orientation [55]. Key TF orthologs for nodulation and floral meristem development were identified between Medicago and Lotus, which allow direct genome comparison to predict orthologs, for eg., LjNIN and PsSym35 [56]. Further, a clear existence of one-to-two relationship between the Phaseolus and Glycine genomes has already been demonstrated [57].

Conserved synteny among legume species is often disrupted by chromosomal rearrangements defined in terms of translocations or inversions [53] as targeted search for synteny between Glycine and Medicago with respect to Rpg1 displayed limited synteny [58]. Lack of synteny for PPR genes even in otherwise collinear segments of arabidopsis and Brassica rapa genome has also been reported [47].

RFLs prediction in legumes

Rf protein superfamily is known to constitute atleast 51 different families [23] and the number is more likely to expand with the availability of finished genome sequence data of other plant species in future. Till date, only few Rf genes have been cloned, majority of which are known to encode for PPR proteins. Almost all plant genomes contain 10-30 Rf like proteins [59,60] that share significant sequence similarity with the Rf-PPRs from other plant species and thus cross species comparison of PPR proteins with known Rf genes can be used to identify a subset of Rf proteins known as RFL PPRs [39,47,61,62]. A microsynteny analysis was conducted between Arabidopsis and radish and was used to clone the PPR encoding Rfo locus in radish [28]. Utilizing this facet of RFL PPR proteins, RFLs could be identified in any plant. These genes generally belong to the P sub-class of PPR gene family with the exception of Rf1 gene in Sorghum bicolor that belongs to PLS sub class and possess domain for RNA editing [63].

Though RFL PPR represents a small group of PPR proteins, they possess certain features that are distinct. The first distinctive feature is reflected by the observation that upon mapping of RFL PPRs of a particular legume on the genome of other legumes, RFL PPRs formed species specific paralogous groups and displayed limited but significant inter species orthology which is in contrast to non RFL PPR proteins [39]. Their second distinctive feature is clustering in non-conserved genomic locations in comparison to random distribution behaviour of PPRs on the genome [47,61]. These regions where RFL genes are clustered together could be considered as candidate regions to identify Rf genes in these species. For eg., 26 Rf like PPRs were identified in Arabidopsis in two clusters on chromosome 1 [28,60], chromosome 10 of rice possess 9 PPRs, out of which 3 were Rf PPRs [62]. Small cluster of RFL PPRs were identified on genome of Glycine, Vigna, Cicer and Phaseolus and allowed us to narrow down the list to 15 potential Rf genes in 4 legumes (Table 2). Twenty five candidate genes for fertility restoration in CMS perennial reyegrass has been predicted based on homology with known Rf genes and DNA sequence clustering; efficacy of both approaches depending upon the type and quality of input data [30]. Similarly, prediction of RFL PPRs and identification of genomic regions where these are present as clusters on the respective legume genomes is based up on the in silico analysis of draft sequence assemblies. Therefore a complete repertoire of PPR genes and subsequently RFLs could not be predicted efficiently as incomplete genome assemblies do not reveal all clusters that would have otherwise formed, also observed in case of barley [63,64]. However the 70 RFls deduced in this study provides an handle for investigating the typical conserved features and subsequent functioning across legumes.

The organelle genomes of flowering plants are now thoroughly evolved and yet they retain their basic functions. These circular genomes are also very dynamic and are frequently involved in structural changes, leading to disturbances in terms of altered transcripts and generation of new orfs. It is probable that these conserved PPR proteins help in minimizing the abnormal manifestations and hence the high degree of conservation seen across genomes. Utilizing the genome sequence information from 6 legume species, an in silico study was conducted to provide a catalogue of PPR genes and to identify potential candidate Rf genes. Analysis of synteny between Cajanus PPRs and 5 other species revealed a high level of similarity that exists between legumes indicating its evolutionary lineage and conservedness of functionality. To date, PPR genes have been documented in other plant species but this forms the first comprehensive study on the PPR gene family in legumes revealing a repertoire of knowledge that can be further investigated to reveal details about their structure, evolutionary relationships and functional analysis.

Acknowledgement

This work was supported by Indian Council of Agricultural Research- Network Projects on Transgenics in Crops (ICAR- NPTC), New Delhi, India.

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