Proteomic and Carbonylation Profile Analysis at the Critical Node of Seed Ageing in Oryza sativa

The critical node (CN), which is the transition from the plateau phase to the rapid decreasing phase of seed ageing, is extremely important for seed conservation. Although numerous studies have investigated the oxidative stress during seed ageing, information on the changes in protein abundance at the CN is limited. In this study, we aimed to investigate the abundance and carbonylation patterns of proteins at the CN of seed ageing in rice. The results showed that the germination rate of seeds decreased by less than 20% at the CN; however, the abundance of 112 proteins and the carbonylation levels of 68 proteins markedly changed, indicating oxidative damage. The abundance and activity of mitochondrial, glycolytic, and pentose phosphate pathway proteins were reduced; consequently, this negatively affected energy production and germination. Proteins related to defense, including antioxidant system and heat shock proteins, also reduced in abundance. Overall, energy metabolism was reduced at the CN, leading to a decrease in the antioxidant capacity, whereas seed storage proteins were up-regulated and carbonylated, indicating that the seed had a lower ability to utilize seed storage proteins for germination. Thus, the significant decrease in metabolic activities at the CN might accelerate the loss of seed viability.

A notable characteristic of seed viability is the reverse S-shaped survival curve during ageing, which includes a plateau phase (Phase I; P-I), followed by a rapid decreasing phase (Phase II; P-II) and a slow decreasing phase (Phase III; P-III). The transformation from P-I to P-II is defined as the critical node (CN), which is highly important for seed conservation 1 . The average germination of approximately 42,000 diverse accessions stored for 16 to 81 years at the National Center for Genetic Resources Preservation, USA has been decreased by 42% 2 . The average germination rate of peanut (stored for 34 years), soybean (stored for 36 years), wheat (stored for 43.6 years), and barley (stored for 44.4 years) is 6%, 21%, 73%, and 86%, respectively 3 . Similar results have been also reported by the Genebank of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany 4 . Rice is extremely important food crop. One of main aims in genebanks is maintaining the rice seed safe conservation. At the T.T. Chang Genetic Resources Center in International Rice Research Institute, 183 rice accessions stored up to 30 years showed more than 70% germination 5 , and more than 93% of seed lots produced in 1980 still maintained 85% germination after 33 years in storage 6 . Owing to the reduction in seed viability, the regeneration of genetic resources is considered crucial for maintaining genetic integrity. Previous studies have shown that seed regeneration needs to be carried out prior to the CN in order to prevent a large decrease in viability, which can lead to changes in genetic composition 7,8 . Previously, we showed that the mitochondrial ultrastructure of seed at the CN is abnormal owing to the decreased oxygen consumption as well as the decreased activity of cytochrome c oxidase and malate dehydrogenase (MDH) 1 .
The role of reactive oxygen species (ROS) in the loss of seed viability has been well investigated. During natural or accelerated ageing, the levels of seed antioxidative enzymes (e.g., superoxide dismutase, SOD; catalase, CAT; ascorbate peroxidase, APX; and glutathione reductase, GR) and antioxidants (ascorbic acid and glutathione) decrease, leading to the accumulation of ROS and consequently oxidative damage 9,10 . The proteomic analysis of aged maize seeds indicated that the loss of seed viability loss is related to ROS damage 11 . The reduction in antioxidant capacity, i.e., decrease in the expression of CAT1, APX1, and MDHAR1 may be responsible for the loss of rice seed viability during storage 12 . The mitochondrial structure and function alter in aged seeds. For instance, in aged soybean seeds, the mitochondrial ascorbic acid and glutathione cycle activity decreased, leading to elevated ROS accumulation 13 . The aged seed induces dynamic changes in mitochondrial physiology via the increased ROS production, resulting in an irreversible loss of seed viability 14 . Seed possess many repair enzymes, such as PROTEIN l-ISOASPARTYL O-METHYLTRANSFERASE, for proventing age-induced ROS accumulation to improve seed vigor and longevity 15 .
ROS accumulation can induce the formation of protein carbonyls that affect enzyme activity and lead to ageing or death 16,17 . Numerous studies have reported that protein carbonylation contributes to leaf and fruit senescence as well as the decreased rate of seed germination [18][19][20] . In Arabidopsis, HSP70 and LEA were carbonylated after ageing treatment 21 , whereas seed storage proteins (SSPs) were carbonylated during storage 22 . In this study, we aimed to determine the changes in protein abundance and protein carbonylation at the CN of seed ageing in rice. The carbonylated protein patterns were analyzed by two-dimensional (2D) gel electrophoresis followed by western blotting with antidinitrophenyl hydrazone (DNP) antibodies. The carbonylation level and pattern of several proteins might be indicators of seed ageing, and could help to improve seed storage management.

Results
Proteomic and carbonylation profile analysis at the CN. In our previous study, rice seed vigor loss displayed a P-I, and then experienced a rapid decreasing phase after 84% germination (P-II). Therefore, we chose the seed germination percentage at 84% as the critical node 1 . Seed vigor was analyzed from maximum to the CN, as it is this stage that is extremely important for safe conservation of seeds in genebank. This differed to previous studies in Arabidopsis 21 , maize 11 , and Brassica napus seeds 23 where comparison was made at the end of Phase II.
Proteomic and carbonylation profile analysis was carried out to determine the impact of oxidative stress at the CN. Protein profiles of rice embryos was extracted from 97% (control), 92% and 84% germination percentage after 0 d, 3 d, and 4 d aged treatment, respectively, and separated by gel electrophoresis using immobilized pH gradient (IPG) strips in isoelectric focusing (IEF). Three biological repeats were used for either gels or blots of each sample. More than 700 protein spots were detected on 12% (v/v) sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gels by PDQuest 8.0 (Fig. 1). The abundance of 112 protein spots showed a change higher than 1.5-fold at the CN which MOWSE score were higher than 65 (Table 1). Of them, 78 downregulated proteins (D1-D78) and 17 upregulated proteins (U1-U17) were identified in all treated seeds; 11 upregulated proteins (U18-U28) were uniquely detected in 3-d aged seeds; and six upregulated proteins (U29-U34) were uniquely detected in 4-d aged seeds (Tables 1 and 2). Figure 2 shows the change pattern of different proteins related to energy, defense, metabolism, growth or division, transcription, and other unknown functions 24 .
Proteins related to energy metabolism. A total of 16 downregulated proteins were related to energy metabolism ( Table 1). The β -ATP synthase subunit (β ATP), MDH, and succinate dehydrogenase (SDH) showed decrease in abundance (D14, D19, and D48) and significant carbonylation (C12, C16, and C27) ( Table 1). To better understand protein expression at the CN, the activity of MDH was measured in aged seeds after imbibition for 48 h. As compared to the control, the activity of MDH showed a decrease by 11% and 20% in 3-d and 4-d aged seeds, respectively (Fig. 4A), which was consistent with the decrease in abundance. MDH1 also displayed a steady downregulation with ageing (Fig. 5A). Compared with the control, SDH1 showed a decrease by 16% and 40% in 3-d and 4-d aged seeds, respectively (Fig. 5B). The immunodetection of the β ATP subunit showed a significant decrease at the CN (Fig. 5G). Compared with the control, β ATP showed a decrease by 25% and 45% in 3-d and 4-d aged seeds, respectively (Fig. 5C). These results indicated that mitochondrial metabolism significantly decreased at the CN.
Proteins related to defense. In this study, 12 downregulated proteins were related to defense, indicating the decreased ability of aged seeds to combat oxidative stress. Compared with the control, the activity of ascorbate peroxidase 1 (APX, D57) decreased by 47% and 33% in 3-d and 4-d aged seeds, respectively (Fig. 4D). APX1 showed a steady decrease with ageing ( Fig. 5F). Additionally, the reduced abundance in cytosolic APX proteins at the CN was confirmed by immunodetection using the cytosolic APX antibody (Fig. 5G) and indicated ROS accumulation at the CN of seed ageing. Compared with the control, the activity of glutathione S-transferase (GST, D46) decreased by 87% and 70% in 3-d and 4-d aged seeds, respectively (Fig. 4E), negatively affecting the ability of the antioxidant defense system. GST showed a decrease in abundance and significant carbonylation (C26). Five heat shock proteins (HSPs), including HSP70 (D2, D54, and D55), 17.9-kDa class I HSP (D13), 18.0-kDa class II HSP (D44), and two chaperonins (D13 and D60) significantly downregulated at the CN, whereas the HSP D2 and D44 and the chaperonin D13 showed significant carbonylation (C2, C25 and C11). Total 500 μ g protein were separated by immobilized pH gradient (IPG) strips and 12% (w/v) SDS-PAGE gels. Protein codes correspond to those in Tables 1, 2 and 3. Number on the left represents the apparent molecular mass. Number above the gels represents the pI of separated protein spot. U, upregulation; D, downregulation. Upregulated proteins at the CN. Compared with the control, 31 upregulated proteins were related to storage, energy, disease and defense, metabolism, protein synthesis, growth and division, and other unknown functions (Fig. 2B). SSPs formed the largest group of upregulated proteins that included globuline, glutelin, and cupin (Table 2), which showed various experimental molecular weights, indicating that SSPs were post-translationally modified or broken down (Fig. 3). In this study, we also identified 17 SSPs that displayed significant carbonylation, of which 10 were upregulated, whereas the rest showed no change in abundance (Tables 2 and 3).

Discussion
The viability of aged seeds is an important aspect for maintaining genetic diversity during seed storage. In this study, we demonstrated the occurrence of oxidative damage that primarily affects the abundance of proteins related to energy generation, metabolism, and defense. These findings were in agreement with previous studies in Arabidopsis, which showed that proteins related to energy, metabolism, and defense play key roles in seed maintenance and are downregulated at the CN 21,22 . The changes occurring in protein abundance appeared to be related to oxidative stress 25,26 , resulting in an inability to utilize seed storage proteins, as the latter increased in abundance at the CN. Proteins related to energy metabolism formed the largest group of downregulated proteins ( Fig. 2A). The capacity of energy supply is highly important for seed germination and seedling growth, since large amounts of energy are needed prior to the establishment of photosynthesis in the plant 27 . Previous studies in Arabidopsis reported that one of the earliest events during germination is the upregulation of approximately 600 genes that encode proteins related to mitochondrial functions and are critical for germination 28,29 . A variety of mitochondrial mutants involved in electron transport showed slow germination rates or high seedling lethality 28 . The downregulated proteins of mitochondria were observed by carbonylated modification, including β ATP, MDH   and SDH, respectively (Table 1). Mitochondria plays key roles for energy supplying during seed imbibitions. β ATP is the F 0 sector of ATPase 30 . The state and function of ATP synthase machinery may determine the energy supplying. β ATP protein and βATP expression level was significant downregualted at the CN (Fig. 5C,G). Our results were consistent with our previous reported in purified mitochondria from the CN of rice seed ageing 1 that ATP synthase machinery was inactive which leads the ATP supplying was inhibited at the CN. The seed of MDH1 and MDH2 double knockout Arabidopsis mutants had a lower content of 2-oxoglutarate during imbibition 31 . In the present study, the activity of MDH and the levels of MDH1 were significantly decreased and carbonylated in aged seeds compared with the control (Figs 4A and 5A), indicating that the TCA cycle was inhibited at the CN after seed imbibition. In addition, SDH is a key member of the electron transport chain complex II, which catalyzes the oxidation of succinate to fumarate with the reduction of ubiquinone to ubiquinol and participates in succinate dependent O 2 consumption in the electron transport chain 32 . SDH1 knockout Arabidopsis mutants had a decreased activity of the electron transport chain, but an increased amount of ROS under environmental stress 33 . We showed that the level of SDH1 was significantly decreased and carbonylated at the CN (Fig. 5B); these results were in agreement with our previous findings that succinate dependent O 2 consumption is reduced at the CN 1 . The decreased activity of SDH might cause ROS accumulation and oxidative damage. Overall, these results demonstrated that the mitochondrial metabolism was inhibited at the CN, decreasing the production of ATP and its intermediates, which are needed for seed germination and ROS accumulation. Several proteins whose showed a decrease in proteins abundance and exhibited different carbonylation levels were observed which involved in the glycolytic pathway, including phospoglycerate mutase which catalyzes the conversion of 3-phosphoglycerate to 2-phosphoglycerate 34 , pyruvate decarboxylase (PDC) which catalyses the decarboxylation of pyruvic acid to acetaldehyde and carbon dioxide 35 , triosephosphate isomerase which catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate D-glyceraldehyde 3-phosphate 36 , enolase which catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate 37 , and pyrophosphate-dependent phosphofructokinase which catalyzes the reversible phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate 38 . Interestingly, PDC gene family was induced in response to environmental stress in plants 39,40 . By comparison, PDC1 level showed no significant change in the aged seed (Fig. 5D). We propose that the decrease of the PDC activity (Fig. 4B) caused by carbonylation may result in deleterious downstream pathway of glycolytic metabolism, leading to a reduction of energy supplying. These results indicated that glycolytic metabolism was also reduced at the CN. 6PGD was carbonylated modification and showed downregulation in aged seed, which converts 6-phosphogluconate to ribose-5-phosphate and produces NADPH in oxidative pentose phosphate pathway (PPP) 41 . The decrease in the activity and transcript level of 6PGD resulted in reduction of NADPH production, indicating that PPP metabolism was inhibited at the CN. Taken together, the key members of energy supplying were downregulated and carbonylated modification at the CN, which might cause impairment of mitochondrial, glycolysis and PPP metabolism and then lead to decrease in energy supplying during imbibition, in turn, trigger a cascade of deleterious metabolism which could contribute to the process of ageing disorders.
Proteins related to defense were downregulated at the CN ( Fig. 2A). APX1 plays an important role in the antioxidative metabolism, since it catalyzes the conversion of H 2 O 2 to H 2 O in the ascorbate-glutathione cycle 42 . Compared with the activity of APX, the protein and gene level showed a significant decrease at the CN (Fig. 5F,G), indicating that the antioxidative system was inhibited at the CN. These results were consistent with previous findings in the aged seed of soybean, maize, and other species [11][12][13] . The decreased capacity of the antioxidative system could lead to ROS accumulation, reflecting the oxidative damage and increased protein carbonylation.
GST catalyzes the conjugation of the reduced form of glutathione to xenobiotic substrates for the purpose of detoxification 43 and protects against oxidative damage by ROS 44 . In the present study, the activity of GST showed significant decrease at the CN (Fig. 4E), indicating that rice seed was affected by ROS. Additionally, we observed the specific carbonylation of proteins related to oxidative stress such as HSPs and chaperonins. HSPs are encoded by multigene families 45 ; small HSP class I (17.9 kDa) belongs to the small HSP family, which is expressed in rice seed 45,46 . HSPs and chaperonins play an important role in protein folding and protect cells against stress 47 . Carbonylated HSPs and chaperonins were described in aged Arabidopsis seeds 22 . The downregulation of HSPs and chaperonins disrupted the defense system and might cause oxidative damage at the CN.
Our study revealed the carbonylation of upregulated proteins, such as SSP, at the CN. Previous studies reported that the degradation of storage proteins is associated with seed viability 48 and that the seed of SSP mutants is sensitive to ageing 22 . In the present study, SSP displayed a significant upregulation and various experimental molecular weights at the CN (Figs 2B and 3). Our results suggest that the seed had a decreased ability to utilize SSPs at the CN, which might cause SSP accumulation and carbonylation. Previous studies reported that SSP might be a primary target for oxidative stress and protect other proteins for oxidative damage during seed ageing 22,49 . Our results suggest that the increased carbonylation level of SSP indicates the relatively high ROS levels at the CN. Our results were consistent with the decreased capacity of the antioxidant system at the CN.

Conclusion
This study revealed that oxidative stress was related to the loss of seed viability. Our findings indicated the effects of oxidative stress at the CN, since the proteins related to energy and defense metabolism were downregulated and/ or inactivated. The ability to utilize SSPs was also reduced, leading to a rapid decline in seed viability at the P-II.

Materials and Methods
Plant material and treatments. Rice seed (Oryza sativa L. japonica nipponbare) was obtained from the Jiangxi Agricultural Academy of Sciences, Nanchang, China. Rice seeds were treated at 40 °C and 75% relative humidity for 0 d, 3 d, and 4 d to decrease the germination rate by 3%, 8%, and 16%, respectively 1 . The embryos were extracted after seed imbibition at 28 °C for 48 h in the dark, and then stored at − 80 °C until analysis.
Proteomic and carbonylation analysis. The frozen embryos were ground with a mortar and pestle using a buffer, containing 0.1 M Tris-HCl (pH 7.5), 0.1% dithiothreitol (DTT), 2% polyvinylpolypyrrolidone (PVPP), and 0.5% ethylenediaminetetraacetic acid (EDTA). Protein was extracted using the Tris-phenol protocol 50 , and then, 500 μ g of protein was applied to rehydrated gel strips with an immobilized linear pH gradient of 5-8 (BioRad, Hercules, CA, USA). The first-dimensional IEF was performed at 20 °C on a flat-bed electrophoresis unit (BioRad) as follows: rehydration for 12 h, 0 V to 150 V in 15 min, 150 V to 1,000 V in 1 h, 1,000 V to 8,000 V in 5 h, and 8,000 V until a total of 60 kVh. After IEF, the strips were: 1) equilibrated for 15 min in Solution A, containing 6 M urea, 20% (v/v) glycerol, 2% (w/v) SDS, 375 mM Tris-HCl (pH 8.8), and 2% (w/v) DTT, and then, in Solution B, containing 6 M urea, 20% (v/v) glycerol, 2% (w/v) SDS, 375 mM Tris-HCl (pH 8.8), and 2.5% iodoacetamide for analyzing the proteomic profile and 2) derivatized by incubating in 10 mM DNPH for 20 min with gentle agitation, and then, equilibrated as described above for analyzing the profile of carbonylated proteins. The equilibrated strips were placed on SDS-PAGE using homogenous 12% (v/v) polyacrylamide gels with 4% (v/v) stacking gels (BioRad). Gel electrophoresis was performed at 250 V with circulating cooling using a running buffer, containing 25 mM Tris (pH 8.3), 195 mM glycine, and 0.1% (w/v) SDS. The gels were stained with CBB G250 or transferred to PVDF membrane and detected with anti-DNP antibodies. Gel images were obtained using a flatbed scanner and analyzed by PDQuest 5.0 (BioRad). Spot intensity was calculated according to the relative expression volume. Spots with a fold change higher than 1.5 were excised for mass spectrometry.
In-gel digestion, mass spectrometry, and database searching. The protein and carbonylated protein that were corresponded the protein spot on 2D gels, were excised into 1-mm 3 pieces from 2D gels and de-stained with 25 mM NH 4 CO 3 in 50% acetonitrile. The gels were dehydrated by adding acetonitrile and then, digested with 25 μ l of 0.1 mM trypsin in 25 mM NH 4 CO 3 for 15 min 51 . The excess trypsin solution was removed, and gel pieces were incubated at 37 °C overnight in 20 μ l of 25 mM NH 4 CO 3 . A mixture of 1 μ l peptide solution and 1 μ l matrix solution with 1 mg ml −1 , a-cyano-4-hydroxycinnamic acid in 70% acetonitrile, and 0.1% trifluoroacetic acid was loaded onto the AnchorChip MALDI target plate (Bruker Daltonics, Manning Park Billerica, MA, USA) and analyzed by a matrix assisted laser desorption-ionization time of flight (MALDI-TOF)/TOF mass spectrometer (Bruker Daltonics), according to the manufacturer's instructions. MS data were uploaded to the Mascot server using Biotools (Bruker Daltonics) and searched against the National Center for Biotechnology Information (NCBI) protein database (25,010,123 sequences; 8,625,376,125 residues; search parameters, rice; proteolytic enzyme, trypsin; maximum missed cleavages, 1; fix modifications, carbamidomethyl; variable modifications, oxidation; peptide mass tolerance, 100 ppm; fragment mass tolerance, 0.5 Da). Spots with a Mowse score higher than 65 were considered as proteins.
Assay of enzyme activities. The activity of MDH was determined at 340 nm as described by Glatthaar et al. 52 .
The activity of PDC was measured in a reaction medium, containing 200 mM Tris-HCl (pH 6.0), 100 mM pyruvate, 0.1 mM thiamine pyrophosphate, 1.0 mM MgCl 2 , 9.0 units of alcohol dehydrogenase, and 225 μ M NADH as described 53 with minor modifications. The activity of APX was determined at 290 nm as described by Nakano and Asada 54 . The activity of GST was determined at 340 nm as described by Habig et al. 55 . The activity of 6PGD was determined in 50 mM Tris-HCl (pH 7.5) and 0.25 mM NADP, started with 2 mM 6-phosphogluconate as described by Bailey-Serres and Nguyen 56 .
Immunoblot analysis. Equal amounts of rice embryo proteins (10 μ g per lane) were loaded onto SDS-PAGE gels, transferred to PVDF, and incubated with β ATP and APX antibodies. Anti-rabbit IgG was used as a secondary antibody (Agrisera, Vannas, Sweden). Immunodetection was performed using the Chemiluminescent Substrate Kit (KPL, Hemet, CA, USA).
Quantitative real-time polymerase chain reaction (qRT-PCR). Total RNA was isolated from rice embryos after seed imbibition for 48 h using the RNAprep pure plant kit (Tiangen, Beijing, China). Specific primer pairs (Supplemental Table 1) were designed using Primer 5 (Premier Biosoft, Palo Alto, CA, USA). qRT-PCR was Figure 5. Relative levels of malate dehydrogenase 1 (MDH1, (A)) succinate dehydrogenase 1 (SDH1, (B)) β ATP synthase (C)) pyruvate decarboxylase 1 (PDC1, (D)) 6-phosphogluconate dehydrogenase 1 (6PGD1, (E)) and ascorbate peroxidase 1 (APX1, (F)) and abundance of beta subunit of ATP synthase (β ATP) and ascorbate peroxidase (APX) (G) in 0-d, 3-d, and 4-d aged rice seeds after imbibition for 48 h. Transcript levels in 3-d and 4-d aged seeds were calculated in relation to a value of 1.0 that assigned to 0-d aged seeds after imbibition for 48 h. Data represent the mean ± standard deviation of three independent experiments. All treatments significantly differed from the control at p < 0.05 (n = 3). Statistical analysis. Data were pooled across repeated experiments. Analysis of variance in conjunction with the least significant difference test was performed by SPSS (IBM, Chicago, IL, USA). Differences were considered significant at p < 0.05.