Introduction

Generation of reactive carbonyl species (RCS) is a common metabolic phenomenon of all living systems including bacteria, fungi, animals, and plants1. Among various RCS, α-oxoaldehyde compounds such as methylglyoxal (MG), glyoxal, phenylglyoxal and hydroxy-pyruvaldehyde are known to be highly reactive2. α-Oxoaldehydes are mainly produced by oxidation of glucose, lipid peroxidation, catabolism of fatty acid and amino acid, and DNA oxidation2,3. Due to their highly electrophilic potential4, α-oxoaldehydes are very reactive in nature and form adducts with the nucleophilic centers of DNA, RNA, and proteins. They can react non-enzymatically with arginine, lysine, cysteine residues of the protein4, and form advanced glycation end-products (AGEs). Formation of AGEs is responsible for aging and various neurodegenerative diseases of human, including diabetes, Parkinson disease, and Alzheimer disease5. Accumulation of excess AGEs or their precursor α-oxoaldehydes cause carbonyl stress in animals6 and plants7.

Reactive α-oxoaldehydes are detoxified by either the glutathione-dependent glyoxalase pathway7 or NAD[P]H-dependent aldo-keto reductase (AKR) system8. The major detoxification system is glyoxalase pathway that includes two enzymes- glyoxalase I (GLY I, EC 4.4.1.5) and glyoxalase II (GLY II, EC 3.1.2.6). GLY I converts hemithioacetal, a highly cytotoxic non-enzymatic adduct of MG and reduced glutathione (GSH), into S-lactoylglutathione (SLG). This SLG is further hydrolyzed into D-lactate by the action of glyoxalase II (GLY II), and one molecule of GSH is recycled back in the system (Fig. S1). The pathway was first discovered simultaneously in rabbit and dog tissues at 19139,10. It has been established to be one of the most ubiquitous and evolutionary highly conserved pathways in both prokaryotic and higher eukaryotic species2. Expression of glyoxalase genes, as well as enzyme activity, have been reported to be altered in response to various abiotic, biotic, hormonal and chemical treatment11. Moreover, overexpression of MG detoxifying glyoxalase pathway provides significant abiotic stress tolerance by resisting the excess accumulation of MG in transgenic tobacco12 and tomato13 plant. Therefore, both glyoxalase enzymes and methylglyoxal level are considered as biomarkers for plant stress tolerance11.

Apart from this well-conserved pathway, the presence of a novel glyoxalase III (GLY III) enzyme activity has been known for a long time in Escherichia coli (E. coli) total cell lysates14. GLY III could convert MG into D-lactate in a single step without the help of any cofactor (Fig. S1). Recently, one of the E. coli gene (hchA) product, Hsp31was reported having in vitro GLY III activity15. Although GLY III activity of Hsp31 is very low as compared to the conventional GLY I/II16, it has been consistent and significant enough to study further in other species. Apart from E. coli, GSH independent GLY III activity has been reported in Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster5, Saccharomyces cerevisiae17, Schizosaccharomyces pombe1, Candida albicans18, Arabidopsis thaliana19, and Oryza sativa L.20 till date. Moreover, GLY III proteins were reported to be metal independent15, while conventional GLY I enzyme requires either Ni2+ or Zn2+ for its optimal activity21.

Structural analysis of E. coli GLY III protein indicates that it is a member of DJ-1/PfpI superfamily15. As GLY III activity was found to reside in the DJ-1 domain containing proteins, they were named as “DJ-1” protein in various species. However, they were named as Hsp protein in E. coli, yeast, and several fungi species. In human, DJ-1 protein has been found to be associated with cancer22 and Parkinson’s disease23. Apart from dicarbonyl detoxification, DJ-1 has been reported to be involved in regulation of transcription and mitochondrial function and having a molecular chaperone and protease activity1. DJ-1 proteins possess a conserved catalytic triad Glu-Cys-His in the active site. Among them, the cysteine residue was found to be highly conserved and oxidation of this residue is critically required for DJ-1 catalytic activity5. The catalytic activity of DJ-1/Hsp31 (GLY III) protein has been reported from various organisms including A. thaliana, O. sativa, H. Sapiens, E, coli, D. melanogaster, C. albicans, S. pombe, S. cerevisiae etc1,5,15,17,18,19,20. Due to the lower catalytic efficiency as compared to conventional GLY enzymes15, concerns were raised about the GLY III activity of DJ-124. Recently, the deglycation activity of DJ-1 protein has been reported as an artifact of TRIS buffer using knockdown DJ-1β Drosophila flies25. But, GLY III activity for AtDJ-1D and OsDJ-1C has been reported using sodium phosphate buffer without such influence19,20. Moreover, E. coli Hsp31 (EcHsp31) serves as a heat-inducible molecular chaperone and provides protection against heat starvation and oxidative stresses, too26. Thus, the exact mechanism of how DJ-1 executes multiple cellular functions is somewhat unclear.

Previously, genome-wide analysis of DJ-1 gene has been carried out in Arabidopsis thaliana (L.) Heynh., Oryza sativa L. and Medicago truncatula L.; and identified six, six and five DJ-1 genes in respective genomes that code for eleven, twelve and six proteins, respectively7,20,27. Among Arabidopsis members, AtDJ-1d showed highest GLY III activity19, while the GLY III activity of OsDJ-1C has been shown experimentally20. Different AtDJ-1, OsDJ-1, MtDJ-1 members showed a different pattern of sub-cellular localization indicating their important role in various organelles. All OsDJ-1 genes showed substrate (MG) and oxidative stress induced transcript up-regulation20. It has been reported that loss-of-function of AtDJ-1a induces cell death28 and knockout of AtDJ-1c lead to non-viable albino seedling generation in Arabidopsis29. Expression of MtDJ-1A and MtDJ-1D found to be highly up-regulated in response to drought stress27. All these studies prompted us to do further research on this novel pathway to unravel their role in plants. In the present study, a database based search was performed to identify DJ-1 proteins in soybean (Glycine max). A sequence homology-based phylogenetic analysis was performed among different GLY III proteins of both prokaryotic and eukaryotic lineages. Further, expression of newly identified members was analyzed in various tissues, and developmental stages as well as in response to adverse environmental conditions using publicly available microarray data and RT-PCR study. These analyses will provide the initial clues to understand the role of DJ-1 protein family in the field of stress physiology and cell biology.

Results

In silico analysis identified eleven putative DJ-1 proteins in soybean

A total of eleven DJ-1 proteins were identified in soybean genome (Table 1) which is almost similar to the previously reported Arabidopsis (11) and rice (12) DJ-1 protein number20. The newly identified members were nomenclature based on their Arabidopsis orthologs as proposed previously30 (Table 1). These eleven proteins were found to be coded by seven unique DJ-1 genes and located on six different chromosomes of soybean namely 2, 7, 11, 12, 13, and 18 (Fig. 1). Two genes resided on chromosome no 18, and rest of the chromosome has only one gene each (Fig. 1). Chromosomes without any DJ-1 genes were not present in Fig. 1. Gene duplication analysis demonstrated three duplication events- GmDJ-1C1/C2, GmDJ-1D1/D2, and GmDJ-1B/A (Fig. 1, Table S1). Based on nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) of each gene pair, the evolutionary history of selection acting on different genes could be measured31,32. The Ka/Ks of three GmDJ-1 duplicated gene pairs (Table S1) was found to be less than 0.55; indicates the influence of purifying selection in the evolution of the gene pairs. Considering the divergence rate of 6.161029 synonymous mutations per synonymous site per year for soybean33, the duplicated pairs showed a divergence time frame between 9.03 to 11.17 Mya (Table S1). Apart from paralogous gene duplications, GmDJ−1 genes were analyzed further to identify the orthologous gene duplication events in three plants (Arabidopsis, Rice, and Medicago) using plant genome duplication database (http://chibba.agtec.uga.edu/duplication/index/downloads)34. This analysis revealed the presence of three AtDJ−1, one OsDJ−1 and three MtDJ-1 duplicated genes with GmDJ-1 family (Table 2). All these orthologous gene pairs showed the Ka/Ks ratio of less than 1; indicating the effect of purifying selection in the evolution of DJ-1 genes among Arabidopsis, rice, Medicago, and soybean.

Table 1 List of putative DJ-1 genes in Soybean (Glycine max) along with their chromosomal locations, alternatively spliced forms, coding DNA sequence (CDS), polypeptide (PP) length, molecular weight (MW), isoelectric point (pI) and localization (bp base pair, aa amino acid, kDa kilodalton).
Full size table
Figure 1
figure 1

Chromosomal distribution and orientation of Soybean Glyoxalase III (GmDJ-1) genes. The position of the newly identified Glyoxalase III genes (DJ-1, A-D) has been identified and marked in different chromosomes of soybean. Only six soybean chromosomes (2, 7, 11, 12, 13, and 18) shown in the Fig. that has DJ-1 genes out of twenty in total. Chromosome numbers are indicated at the top of each bar, centromeres are pointed by a black circle and relative size of the chromosomes are indicated by the scale at the left. Duplicated genes are joined by a green dashed line.

Full size image
Table 2 List of orthologous GmDJ-1 genes present in Arabidopsis thaliana, Oryza sativa, and Medicago truncatula.
Full size table

Identified GmDJ-1 members showed great variation in their structure

As eleven GmDJ-1 proteins are coded by seven genes, indicate the presence of alternative splicing event. Only three out of seven GmDJ-1 genes (GmDJ-1C1, GmDJ-1C2, and GmDJ-1D2) showed alternative splicing (Fig. S2). GmDJ-1C1 generates three transcripts, while GmDJ-1C2 and GmDJ-1D2 generate two each (Fig. S2, Table 1). All these transcripts have minimum 4 (GmDJ-1D2.2) to maximum 8 (GmDJ-1D1) exons, with 7 exons in maximum four transcripts (GmDJ-1C2.1, GmDJ-1C2.2, GmDJ-1B, GmDJ-1A) (Table S2). All these transcripts vary in their size from lowest 801 bp (GmDJ-1C1.3) to highest 1353 bp (GmDJ-1C2.1) with an average of 1100 bp. Similarly, polypeptide length of all these eleven proteins varies from 266 amino acids (GmDJ-1C1.3) to 450 amino acids (GmDJ-1C2.1) with an average of 365 amino acids. Consequently, eleven GmDJ-1 proteins have an average molecular weight of ~40 kDa (39.3 kDa precisely) (Table 1). In terms of isoelectric point (pI) value, proteins showed equal distribution between acidic and basic nature. Five out of eleven (GmDJ-1C1.1, GmDJ-1C1.2, GmDJ-1C1.3, GmDJ-1C2.1 and GmDJ-1C2.2) showed basic isoelectric point (pI) value (more than 7), whereas rest six (GmDJ-1D1, GmDJ-1B, GmDJ-1A, GmDJ-1D2.1, GmDJ-1D2.2 and GmDJ-1D3) showed acidic pI value (Table 1). This ensures the coexistence of both positively and negatively charged GmDJ-1 proteins at neutral physiological pH (~7.2). In terms of protein architecture, all GmDJ-1 proteins were found to have two DJ-1/PfpI domains except for GmDJ-1C1.2 and GmDJ-1C1.3 with a single domain (Fig. S2). Chloroplast localization of GmDJ-1B and GmDJ-1A proteins were predicted by three independent analysis tools (Table 1), followed by GmDJ-1C2.1 and GmDJ-1C2.2 were confirmed by pSORT and ChloroP, while GmDJ-1C1.1, GmDJ-1D2.1, and GmDJ-1D2.2 were predicted by only pSORT (Table 1). Similarly, cytosolic localization of GmDJ-1C1.2, GmDJ-1D2.1, GmDJ-1D2.2, and GmDJ-1D3; and mitochondrial localization of GmDJ-1C1.1, GmDJ-1C1.2, and GmDJ-1C1.3 were confirmed by both CELLO and pSORT (Table 1). Only one protein, GmDJ-1D1 was predicted to be localized in the plasma membrane according to both CELLO and pSORT (Table 1).

Evolutionary GLY III proteins are found to be highly diverged

To evaluate the evolutionary relationship of GLY III proteins among various species, two different types of GLY III activity providing protein such as DJ-1 and Hsp31 sequences were considered. In addition to the newly identified GmDJ-1 proteins; DJ-1 proteins from Arabidopsis, rice, Medicago, Homo sapiens, Drosophila melanogaster and Schizosaccharomyces pombe; and Hsp31 proteins from E. coli, S. cerevisiae, Candida albicans and S. pombe were used for the analysis. The analysis considered a total 38 protein sequences from different species. These protein sequences were initially analyzed using Prottest 2.4 server to identify the best fitted phylogenetic tree model (Text S1). The analysis indicates that Whelan and Goldman (+freq.) model with invariant sites (G + I) rates is the best model for these sequences. An unrooted phylogenetic tree was built based on this model with partial deletion of 90% site coverage and 500 bootstraps (Fig. 2). Two distinct clades were identified; all Hsp proteins of bacteria, yeast, and fungi form a single cluster; while DJ-1 proteins were found to be clustered in a separate clade (Fig. 2). The presence of close relationship among all individual protein class indicates a diverse evolutionary pattern of Hsp31 and DJ-1 proteins. Clade 1 (DJ-1) could be further subdivided into three groups, namely Group I, Group II and Group III. Among them, the group I and III contain only four plant DJ-1 proteins (rice, Arabidopsis, Medicago, and soybean), while group II contains proteins from both plant and non-plant sources (Fig. 2). Plant DJ-1 proteins might have some distinct characteristics that make them separated from non-plant counterparts. Experimentally characterized active GLY III member of rice, OsDJ-1C, and enzymatically most active Arabidopsis GLY III, AtDJ-1D are found to be present in the same group I along with another one rice, two Arabidopsis, three Medicago members, and three soybean members (GmDJ-1D1, GmDJ-1D2, and GmDJ-1D3). However, comparatively less active GLY III members of Arabidopsis such as AtDJ-1A and AtDJ-1B were found to form a separate group (III) with three rice, one Medicago, and two soybean DJ-1 members (GmDJ-1A and GmDJ-1B). However, one member of each plant species formed another group (II) with enzymatically highly active non-plant DJ-1 members. Thus, there is a possibility of fluctuation in GLY III enzyme activity for all plant DJ-1 proteins.

Figure 2
figure 2

Phylogenetic analysis of GmDJ-1 with other characterized GLY III proteins. The phylogenetic tree was constructed based on multiple sequence alignments of GmDJ-1 family, AtDJ-1 family, MtDJ-1 family, OsDJ-1 family, H. sapiens DJ-1 (HsDJ-1), D. melanogaster DJ-1 (DmDJ-1), C. elegans DJ-1 (CeDJ-1.1 and CeDJ-1.2), S. pombe (SpDJ-1), E. coli Hsp31 (EcHsp31), S. cerevisiae Hsp (ScHsp31, ScHsp32, ScHsp33, ScHsp34), C. albicans Hsp31 (CaHsp31), S. pombe Hsp (SpHsp3101 and SpHsp3102) proteins. The sequences were aligned using clustalW and best tree model was predicted using Prottest 2.4 server analysis (http://darwin.uvigo.es/software/prottest2_server.html). The tree was constructed using Mega 7.0 based on Whelan and Goldman ( + freq.) model with five distinct Gamma distributed invariant sites (G + I) with 90% partial deletion and 500 bootstraps. Two major clades were denoted as Clade-I (DJ-1 proteins) and Clade-II (Hsp31 proteins). The bootstrap values are indicated by the exact number in each branch point.

Full size image

GmDJ-1 proteins possess all the conserved residues of active GLY III enzyme

All GmDJ-1 proteins were found to have two DJ-1/PfpI domains (Fig. S2) like previously reported plant DJ-1 proteins from rice and Arabidopsis20. However, DJ-1 proteins from human, Drosophila and Hsp31 proteins from E. coli, yeast, and C. albicans were found to have only one DJ-1/PfpI domain. Thus, the N- and C- terminal DJ-1/PfpI domain of all GmDJ-1 proteins were aligned separately with that of other reported GLY III proteins (Figs 3, S3). DJ-1 proteins have a unique catalytic triad, consists of glutamate, cysteine and histidine residues1. Among these, glutamate and cysteine residues are found to be highly consistent in the N-terminal domains of GmDJ-1 proteins (Fig. 3). But, the position of the third catalytic residue (His) of this triad was found to be variable. GLY III protein of Hsp31 classes has His residue besides the conserved Cys (marked with a star), whereas DJ-1 proteins have His at a distal site from Cys (marked with a triangle). Among seven GmDJ-1 proteins, N-terminal of GmDJ-1C1 showed the absence of catalytically indispensable conserved Cys residue and thus, might lack GLY III activity. Among others, the N-terminal domain of GmDJ-1D1, GmDJ-1D2, and GmDJ-1D3 showed the catalytic triad similar to Hsp31 proteins; whereas GmDJ-1C2, GmDJ-1B and GmDJ-1A showed similarity with DJ-1 proteins. Moreover, the third conserved His residue of the catalytic triad could be replaced by either Tyr or Phe that has been found in different fungal and Bombyx mori DJ-1 proteins1. The almost similar pattern of sequence conservance was observed in the C-terminal domain of six GmDJ-1 proteins (except GmDJ-1C1) with that of other reported GLY III proteins (Fig. S3). GmDJ-1D3 showed the absence of evolutionarily conserved cysteine residue in the C-terminal domain, whereas other members showed similar preference towards Hsp31 or DJ-1 proteins like N-terminal domain.

Figure 3
figure 3

Multiple sequence alignment of GmDJ-1 proteins with other characterized GLY III proteins from various species. Putative N-terminal DJ-1/PfpI domain of all seven GmDJ-1 proteins were aligned with that of AtDJ-1D (AT3G02720) and OsDJ-1C (LOC_Os04g57590.1) and only DJ-1/PfpI domain of H. Sapiens DJ-1 (1PDV:A), D. Melanogaster DJ-1α (4E08:A), S. cerevisiae Hsp31 (4QYX:A) C. albicans Hsp31 (4LRU:A), E. coli Hsp31 (1PV2:A). The sequences were alignment by Clustal omega and alignment Fig. was generated by jalveiw. The conserved catalytic triad residues of for both DJ-1 and Hsp31 proteins are marked by filled triangle and star, respectively.

Full size image

GmDJ-1 transcripts showed diverse level of expression at various developmental stages

Plant development is a highly complex process that altered the expression of several genes drastically to meet the physiological and metabolic demand. To analyze the developmental regulation of GmDJ-1 transcripts, expression of GmDJ-1 genes was checked at different developmental stages. Soybean has seven distinct developmental stages- germination, main shoot growth, inflorescence formation, flowering, fruit formation, bean development and final ripening. Expression of all these GmDJ-I genes was investigated using genevestigator (https://genevestigator.com/gv/doc/intro_plant.jsp) based mRNA-seq data. Among the total of 7 GmDJ-I genes; GmDJ-1D2 showed the highest level of expression at all the developmental stages of soybean, except bean formation stage where GmDJ-1A showed the maximum expression (Fig. 4a). Overall, the analysis revealed that GmDJ-1B, GmDJ-1A and GmDJ-1D2 maintained high transcript abundance at all the developmental stages, followed by a medium level of expression of GmDJ-1C2, and the rest three members such as GmDJ-1C1, GmDJ-1D1, and GmDJ-1D3 maintained the low level of expression (Fig. 4a). Although no specific developmental regulation was observed for GmDJ-1 genes, a contrasting level of expression was observed among seven GmDJ-1 family members.

Figure 4
figure 4

Expression profiling of GmDJ-1 genes at different tissues and developmental stages. (a) Transcriptome data of GmDJ-1 genes at different developmental stages including germination, main shoot growth, inflorescence development, flowering, fruiting, bean formation and final ripening were obtained from genevestigator (https://genevestigator.com/gv/doc/intro_plant.jsp). (b) RNA-Seq expression data of fourteen soybean tissues, such as Root, Nodule, Young Leave, Flower, Pod one cm, Pode Shell (10 day after flowering, DAF and 14 DAF), Seed (10 DAF,14 DAF, 21 DAF, 25 DAF, 28 DAF, 35 DAF, and 42 DAF) was retrieved from soybase database (http://soybase.org/soyseq/) and analyzed. Heat map with hierarchical clustering was performed using MeV software package. The color scale below the heat map indicates expression values; cyan color indicates low transcript abundance while purple indicates a high level of transcript abundance.

Full size image

Tissue-specific alteration of GmDJ-1 transcripts

Previous studies observed a variable pattern of expression among different members of a gene family in different tissues35,36,37. Expression of GmDJ-1 transcripts were analysed on fourteen different Glycine max tissues such as root, nodule, young leaf, flower, pod (One cm), pod-shell (PS; 10 day after fertilization (DAF) and 14 DAF), seed (S; 10 DAF, 14 DAF, 21 DAF, 25 DAF, 28 DAF and 35 DAF) that could be broadly divided into three part; underground, aerial and seed (Table S3). Two distinctive patterns of expression were observed among various GmDJ-1 members (Fig. 4b). Expression of two members GmDJ-1D1 and GmDJ-1D3 were found to be lowest in all tissues, whereas GmDJ-1B, GmDJ-1A, and GmDJ-1D2 showed a high level of expression in all tissues (Fig. 4b) similar to developmental data. Expression of GmDJ-1C1 was found to be confined only to the underground tissue (root, nodule). However, in addition to a medium to high level of underground tissue-specific expression, GmDJ-1C2 showed significant expression at early stages of aerial tissues and mature seeds (Fig. 4b).

Expression of GmDJ-1 transcripts altered in response to environmental stimuli

To check the effect of environmental clues on the expression of GmDJ-1 genes, a qRT-PCR based transcript analysis was performed in response to two abiotic stresses (salinity and dehydration), oxidative stress (H2O2), hormonal treatment (abscisic acid, ABA), and dicarbonyl stress (exogenous MG). Relative fold change in expression of GmDJ-1 genes was analyzed using Tubulin as house-keeping gene; and GmGLYI−6 and GmGLYII−5 as positive control from the previous study38. Expression of GmGLYI−6 and GmGLYII−5 was found to be upregulated in response to salinity and dehydration, and downregulated under ABA treatment; that is quite similar to the previous report38. All members of the GmDJ-1 family showed an interesting pattern of up-regulation in response to exogenous MG stress (Fig. 5e). As MG is the direct substrate for GLY III enzymes and very toxic in nature, plants might try to neutralize them by upregulating the detoxifying genes. Expression of GmDJ-1D1 and GmDJ-1D2 genes have been found to be up-regulated in response other stresses (Fig. 5a–d). Transcript of GmDJ-1D1 showed two to seven folds up-regulation under all conditions; while GmDJ-1D2 showed one to eight folds upregulation, except ABA treatment with slide downregulation (Fig. 5). Moreover, GmDJ-1D3 was found to be the most down-regulated member of GmDJ-1 family, followed by GmDJ-1A and GmDJ-1C1 (Fig. 5). However, other two members (GmDJ-1B and GmDJ-1C2) showed minor alteration in their transcript level to a very narrow range. This indicates the critical role of these members in the stress adaptation and modulation mechanisms of soybean.

Figure 5
figure 5

Expression analyses of GmDJ-1 genes under different stress conditions. Expression of seven GmDJ-1 genes along with two members from conventional GLY pathway (GmGLYI6 and GmGLYII5) was analyzed in response to various unfavorable conditions by qRT-PCR. Bar graphs showed the fold change in expression of GmDJ-1 transcripts against salinity (a), dehydration (b), oxidative stress, H2O2 (c), ABA treatment (d) and dicarbonyl stress, exogenous MG (e). Expression analysis was performed in 15 days old soybean seedlings subjected to 8 hrs stress treatment by qRT-PCR. Error bars showed the standard deviation of three replicates.

Full size image

GLY III enzyme activity for GmDJ-1D2

To check the GLY III activity of GmDJ-1 proteins, developmentally constitutively expressive (Fig. 4) and one of the highly MG-responsive members (Fig. 5e), GmDJ-1D2 was cloned in a bacterial expression vector pET201 (Fig. 6a). The recombinant Thioredoxin-GmDJ-1D2-His-tag protein was purified using Ni-NTA based affinity chromatography and the purified protein showed a prominent band of ~50 kDa (Fig. 6b). GLY III activity has been assayed in three different conditions; (1) Only MG was added (as buffer control), (2) MG was mixed with Ni-NTA purified Thioredoxin-His-tag protein from empty vector transformed cells (as empty vector control), and finally (3) MG and Ni-NTA purified recombinant GmDJ-1D2 protein was mixed (as main GmDJ-1D2 reaction). Both buffer and empty vector controls showed very insignificant change to the level of total MG in a reaction time of 60 min, while GmDJ-1D2 protein showed a significant and static reduction of MG over time (Fig. 6c). That indicates the ability of the GmDJ-1D2 protein to utilize MG as the substrate and acts as functional GLY III enzyme. This observation validates the functional role of GmDJ-1D2 protein as GLY III enzyme. The rate of MG utilization for GmDJ-1D2 was 26,234 µmole/min/mg protein in the present experimental condition, while that was only 0,502 µmole/min/mg protein for empty vector considering the linear range of MG depletion for GmDJ-1D2 (0 to 30 min) (Fig. 6d). The catalytic rate of GmDJ-1D2 is significantly higher as compared to AtDJ-1D (8,60 μmol/min/mg)19, lower than OsDJ-1C (58 μmol/min/mg)20.

Figure 6
figure 6

GLY III activity of the recombinant GmDJ-1D2 protein. Recombinant GmDJ-1D2 protein was tested for the functional GLY III enzyme activity. For that, GmDJ-1D2 was cloned into the SalI and NotI site of the pET201 vector to make the construct (a) used for protein expression. The recombinant protein was purified from E. coli BL21 (DE3) Rosetta cells and run into 12% SDS-PAGE gel, where FT: flow through, WT: wash through (40 mM imidazole), E1–5: (elution fractions using 200 mM imidazole). (c) MG depletion assay has been carried out in three different conditions for 60 min; (i) Only MG + buffer (blue circle), (ii) MG + buffer + empty vector extract (green circle) and (iii) MG + buffer + recombinant GmDJ-1D2 protein (red circle). This experiment clearly indicates the presence of functional GLY III enzyme activity for GmDJ-1D2 protein. (d) Specific GLY III activity of GmDJ-1D2 protein along with empty vector purified (Thioredoxin) was determined and presented as a bar diagram. Experiments were performed in triplicate and presented as mean ± standard deviation.

Full size image

Various stress-responsive cis-acting regulatory elements are present in the promoters of GmDJ−1 genes

To investigate the cellular mechanism behind the altered expression of GmDJ−1 genes in response to various developmental stages and stresses, the 1 kb upstream region of the genes from transcription start site was analyzed in silico to identify the presence of cis-regulatory elements. This analysis identified the presence of several stress-related and hormone inducible motifs such as Homeo Box/ leucine Zipper, Heat Shock factors, CRC domain containing tesmin/TSO1-like CXC (TCX) factors, AT-hook containing transcription factors, Circadian control factors, DNA binding with one finger (DOF), Dehydration responsive element binding factors (DREB), GAP-Box (light response elements), Plant G-box/C-box bZIP proteins, GT-box elements, Jasmonate response element, Transcription repressor KANADI, L1 box (motif for L1 layer-specific expression), Light responsive element motif, MADS box proteins, MYB IIG-type binding sites, MYB-like proteins, MYB proteins with single DNA binding repeat, Plant specific NAC transcription factor binding site, Nodulin consensus sequence 1, NAC factors with transmembrane motif binding, Factors involved in programmed cell death response, Stomatal Carpenter, Sweet potato DNA-binding factor with two WRKY-domains, Storekeeper like transcriptional regulators, Telo box (plant interstitial telomere motifs), Time-of-day-specific cis regulatory elements, target of early activation tagged factors, W Box family found to be present in the promoter of at least 4 genes out of seven (Fig. 7). All these cis-acting regulatory elements play an important role to modulate the molecular switches of dynamic transcriptional regulation in response to developmental processes, stress responses, and hormonal signalling39. These motifs were found to be distributed randomly in both positive (top of the line) and negative strand (down to the line) of the promoters of GmDJ−1 genes (Table S5). The minimum number of 152 conserved motif binding sites were present on the promoter of GmDJ−1D3, while maximum 222 binding sites were found to be present on the OsDJ−1B promoter (Fig. 7). Among others, promoter of GmDJ-1C1, GmDJ-1A, GmDJ-1D1, GmDJ-1D2, and GmDJ-1C2 has 220, 204, 193, 191 and 170 conserved binding sites; respectively. Among the total 29 elements, homeobox-protein binding site matched 285 times, while time-of-day-specific cis-regulatory elements found to be matched 5 times; for all seven promoters.

Figure 7
figure 7

Analysis of GmDJ-1 promoter sequences. The 1 kb upstream promoter sequence of transcription start site was retrieved and analyzed for the presence of various cis-regulatory elements. Different elements were identified and represented with different artworks. Both strands of DNA was presented in the figure, where the artworks up to the black line indicate positive strand and motifs down to the line indicates negative strand.

Full size image

Discussion

Soybean (Glycine max) is one of the major vegetable protein and oil-producing legume plant, under serious threat due to various environmental stresses including drought, salinity, and osmotic stress40,41. Water deficit or impurity could shorten the flowering and seed-filling periods of soybean, and thus accelerate senescence and reduce productivity42,43. Available soybean genome database prompts us to identify novel stress modulating genes44. The current study focuses on the identification and expression analysis of unique DJ-1/PfpI domain-containing glyoxalase III (GLY III) proteins in Glycine max. Genome-wide analysis of soybean reveals the presence of eleven DJ-1 proteins encoded by seven genes (Table 1). Although most of the soybean genes expanded in a species-specific manner due to two gene duplication events of soybean occurred after the monocot/dicot split31, the number of DJ-1 genes are found to be almost similar with that of monocot rice (six DJ-1 genes code for eleven proteins), and dicot Arabidopsis (six DJ-1 genes code for twelve proteins) and Medicago (five DJ-1 genes code for six proteins). However, the number of conventional glyoxalase genes is 2.2 to 4 times more in soybean as compared to Arabidopsis and rice38. Different GmDJ-1 proteins were found to be localized in various organelles, such as mitochondria, cytosol, and chloroplasts (Table 1). Subcellular localization of three AtDJ-1 family members; AtDJ-1a, AtDJ-1b, and AtDJ-1c were analyzed experimentally in transgenic Arabidopsis plants28. Among them, AtDJ-1b and AtDJ-1c were found to be targeted in plastids, while AtDJ-1a shown cytosolic localization. Recently, stress-responsive translocation potential of Hsp31 protein from cytosol to mitochondria has been reported in yeast17.

Like other plant DJ-1 proteins, all GmDJ-1 proteins have two repeated DJ-1/PfpI domain (except GmDJ-1C1.2 and GmDJ-1C1.3) connected by a linker sequence (Fig. S2). The average size of the DJ-1/PfpI domain of soybean has been found to be ~165 amino acids (Fig. S2). However, the average size of rice and Arabidopsis DJ-1/PfpI domain were reported to be around 140 to 150 amino acids, while E. coli has a domain size of 170 amino acids20. Moreover, the size of DJ-1 domain of Hsp31 proteins from E. coli, yeast, and C. albicans was observed more than 200 amino acids (Fig. 3). The precise correlation between domain size and GLY III enzyme activity could not observe. Currently, it is clear that Hsp31 proteins of prokaryotes and lower eukaryotes have a relatively longer length of DJ-1/PfpI domain as compared to that of higher organism DJ-1 proteins. To investigate the difference between domain size and evolutionary history of DJ-1 and Hsp31 proteins, a comprehensive phylogenetic analysis was performed among enzymatically active GLY III proteins from a wide range of taxonomically diverse species (Fig. 2). This study revealed significant information regarding the evolution of GLY III proteins. All Hsp31 proteins of E. coli, yeast, C. albicans and S. pombe are completely distinct from the evolutionary clade of DJ-1 proteins. Interestingly, one of the fungal species, S. pombe is the only organism till date has been reported with both DJ-1 and Hsp31 class of proteins with active GLY III enzyme1. S. pombe DJ-1 protein forms cluster with DJ-1 proteins of other organisms, while Hsp members form a cluster with Hsp counterparts (Fig. 2). Hsp31 proteins were also found to be distributed widely among different other fungal species1, indicating the retention of Hsp31 proteins during fungal evolution. The presence of both DJ-1 and Hsp31 proteins in fungus appears to be an important junction of evolution. In terms of the metazoans divergence from fungal lineages, DJ-1 proteins appeared before this and Hsp31 proteins lost after that1. This phenomenon needs to be investigated further to confirm the evolutionary appearance DJ-1 proteins with simultaneous diminishing Hsp31 proteins.

It has been reported earlier that DJ-1/PfpI domain-containing proteins played important role in the scavenging of reactive species produced under oxidative stress in the animal system5. Expression of DJ-1 transcripts has been found to be altered in response to various external factors in rice20. A significant up-regulation of all OsDJ-1 transcripts were observed in response to external dicarbonyl stress (MG stress). Apart from that, expression of OsDJ-1 transcript was up-regulated in response to various other stresses including salinity, drought, cold, heat and oxidative stress20. Similarly, expression of AtDJ-1A transcript was found to be up-regulated in response to various external factors including strong light, CuSO4, H2O2 and Methyl viologen28. Recently, overexpression of a DJ-1 homolog, yeast Hsp31, in model plant Nicotiana tabacum plants showed dual biotic and abiotic stress tolerance45. In the present study, expression of the GmDJ-1D1 transcript was found to be the most upregulated member in response to various abiotic stresses- salinity and dehydration, oxidative stress, ABA treatment and dicarbonyl stress (Fig. 5). Significantly, all GmDJ-1 members showed up-regulation in response to exogenous MG stress (Fig. 5e), along with conventional GLY pathway (GmGLYI6 and GmGLYII5). The significant increase in the level of MG in response to stress46, might induce the expression of MG metabolizing enzymes as substrate inducible mechanism. A similar level of substrate (MG) induced upregulation was overserved for OsGLYI11.247 and some other metabolic enzymes48. Thus, a differential pattern was observed with two different sets of genes for two different roles. One set of DJ-1 genes might involve in the developmental/tissue-specific signals; while another set is assigned for the stress-specific modulation. This would be interesting to analyze the expression and role of these genes in different physiological needs.

Materials and Methods

Identification and in silico characterization of homologous DJ-1 genes in soybean

All putative DJ-1 proteins in soybean genome were identified by using previously characterized Arabidopsis DJ-1 member with maximum GLY III activity, AtDJ-1D protein sequence (AT3G02720/ Q9M8R4) as a query in the BLASTP search of soybean genome database (Wm82.a2.v1) (http://www.soybase.org/) with an e-value of 1.049 and identified eleven members. Each of these newly identified members was subsequently used as a secondary query, but no new members appear. All these output protein sequences were analyzed individually for the presence of DJ-1/PfpI domain (PF01965.19) using Pfam (http://www.sanger.ac.uk/Software/Pfam) with an e-value of 1.0. All the identified putative DJ-1 proteins of soybean were nomenclature as prefix “Gm” for Glycine max, followed by DJ-1 and English letter (A-D) depending on their orthologous member at Arabidopsis as mentioned previously30. Multiple genes matching having same orthologous member were named by adding a hyphen ‘-’ followed by Arabic numbers after them and alternate splice forms were represented by adding Arabic numbers after “.” sign sequentially. The chromosomal location of all the putative GmDJ-1 genes was identified from the soybase browser (http://soybase.org/gb2/gbrowse/gmax1.01/)49 to draw the chromosomal map. Gene duplication was analyzed using plant genome duplication database (http://chibba.agtec.uga.edu/duplication/index/downloads)50 for soybean. Divergence time (in millions of years) was calculated for each gene pair considering a rate of 6.1 × 10−9 substitutions per site per year31. Thus, divergence time (T) = Ks/(2 × 6.1 × 10−9)X10−6 Mya.

Different physio-chemical properties of the identified proteins including molecular weight and isoelectric point were calculated using Prot-Param software tool (http://web.expasy.org/protparam/) with default parameters. Localization of each GmDJ-1 proteins was predicted using default parameters of CELLO v.2.5: sub-cellular localization predictor (http://cello.life.nctu.edu.tw/)51, pSORT prediction software (http://wolfpsort.org/)52 and ChloroP (http://www.cbs.dtu.dk/services/ChloroP/)53.

Multiple sequence alignment and phylogenetic analysis

To investigate the phylogenetic relationships among DJ-1 proteins from various species, DJ-1 sequence were retrieved from different databases such as NCBI (http://www.ncbi.nlm.nih.gov/), PDB (http://www.rcsb.org/pdb/home/home.do), RGAP7 (http://rice.plantbiology.msu.edu/), TAIR (https://www.arabidopsis.org/) and soybase (http://www.soybase.org/) (Text S2). Multiple sequence alignment was performed using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) with default parameters54 and the best tree model was selected using ProtTest 2.4 server with akaike information criterion (AIC) (http://darwin.uvigo.es/software/prottest2_server.html)55. To identify the conserved active site residues the alignment was edited by Jalview56. The phylogenetic tree was constructed using the Maximum Likelihood method based on the Whelan And Goldman (+) Freq. model with gamma-distributed invariant sites (G + I) distribution57 of MEGA 7.058 with 500 bootstrap replicates. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log-likelihood value.

Expression analysis of GmDJ-1 genes at different developmental stages

Expression patterns of GmDJ-1 genes at different developmental stages were determined using the publically available transcriptomes data from genevestigator database (https://genevestigator.com/gv/doc/intro_plant.jsp). Seven different developmental stages of soybean are Germination, Main Shoot Growth, Inflorescence formation, Flowering, Fruiting Bean development, and final ripening. Corresponding mean expression data was downloaded with standard deviation and scatter diagram was generated.

Expression analysis using RNA-Seq Atlas of Glycine max

To analyze the tissue-specific expression data of seven GmDJ-1 genes, their corresponding probe sets were identified using the soybase tool (http://www.soybase.org/correspondence/index.php). Normalized transcript data was downloaded from soybase (http://soybase.org/soyseq/) for fourteen different soybean tissues including root, nodule (underground tissues); leaf, flower, pod-shell 10 day after flowering (DAF), pod-shell 14 DAF, one cm pod (aerial tissues); and different stages of seed development (seed of 10 DAF, 14 DAF, 21 DAF, 25 DAF, 28 DAF, 35 DAF and 42 DAF). This normalized expression (log10 transformed) was used to generate heatmap and hierarchical clustering using the Institute for Genomic Research MeV software package59.

Plant material, stress treatments, and qRT-PCR

To analyze the expression of GmDJ-1 genes using RT-PCR, fifteen days old soybean (Glycine max L. variety Sohag) seedlings were treated with either normal water or 200 mM NaCl or 0.1 mM H O or 0.01 mM MG or 10 mM ABA solution for depicting experimental control, or salinity, or oxidative, or dicarbonyl or hormonal stress, respectively. To mimic dehydration stress, seedlings were placed on filter paper. After 8 h, shoot tissues were collected from all these seedlings (with triplicates) and total RNA was extracted using TRIzol® Reagent (Thermo Fisher Scientific, USA). First-strand cDNA was synthesized using RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, USA). Gene-specific primer for seven GmDJ-1 genes was designed using Primer-Blast (http://www.ncbi.nlm.nih.gov/tools/primer-blast/), and primer for house-keeping soybean Tubulin gene was taken from literature60. All these primers were synthesized from Macrogen (http://dna.macrogen.com/eng/) and listed in Table S4. The qRT-PCR was conducted in triplicate according to the previously described protocol61 and the fold change in expression was calculated using the 2^(-Delta Delta Ct) method62.

Expression and purification of recombinant GmDJ-1D2 protein, and GLY III enzyme activity

Complementary DNA sequence of GmDJ-1D2 was synthesized from GenScript (https://www.genscript.com/) and subsequently cloned into the SalI and NotI sites of the pET201 vector using gene-specific primers (DJ-1D2_Sal1_FOR: 5′ gggagagtcgagATGGCTCCGAAGAAGGTTC 3′ and DJ-1D2_NotI_REV: 5′ gggagatgcggccgcAGATACTTGAATACCAAG3′) specific amplification. The positive plasmids were confirmed by sequencing, transformed in E. coli BL21 (DE3) Rosetta cells. The expression was induced at 18 °C with 0.1 mM of IPTG for overnight and purified using Ni-NTA based affinity chromatography as mentioned previously46. The purified protein was quantified using the Bradford method63, and the purity was checked in SDS/PAGE. GLY III enzyme activity was performed using 1 mM MG as substrate (M0252, Merck, Germany) and recombinant protein (2–10 µg) in 20 mM potassium phosphate buffer (pH 7.0) for 60 min; and the remain MG at various steps was determined using the colorimetric 2,4-dinitrophenylhydrazine method as described previously19.

Analysis of cis-regulatory elements on promoter

To identify the presence and number of transcription factor binding sites (TFBS), 1 kb 5′ upstream of all seven GmDJ-1 genes was retrieved from the soybase database. The sequences were analyzed using MatInspector tool from the Genomatix software suite (http://www.genomatix.de/cgi-bin/matinspector_prof/mat_fam.pl?)64.

Conclusions

Taken together, a detailed in silico genome-wide analysis of soybean unique glyoxalase III gene family (GmDJ-1) has been carried out. This is the first insight study of DJ-1 family from any legume plant. Soybean genome contains seven GmDJ-1 genes that code for total eleven GmDJ-1 proteins. A detailed analysis of these members was carried out in terms of their structure, chromosomal location, sub-cellular localization and evolutionary relationship. Phylogenetic analyses of different characterized GLY III enzymes revealed the evolutionary divergence of Hsp31 and DJ-1proteins. Moreover, stress-specific expression data narrow down few promising stress-responsive members- GmDJ-1D1 and GmDJ-1D2 that could be used to generate stress tolerant soybean plant. The data presented here will serve as a mine for further functional characterization and validation of GLY III enzymes in soybean.