The symbiotic interaction between legumes and Rhizobiaceae leads to the formation of new root organs called nodules. Within the nodule, Rhizobiaceae differentiate into nitrogen-fixing bacteroids. However, this symbiotic interaction is time-limited as a result of the initiation of a senescence process, leading to a complete degradation of bacteroids and host plant cells. The increase in proteolytic activity is one of the key features of this process. In this study, we analysed the involvement of two different classes of cysteine proteinases, MtCP6 and MtVPE, in the senescence process of Medicago truncatula nodules.
Spatiotemporal expression of MtCP6 and MtVPE was investigated using promoter– β-glucuronidase fusions. Corresponding gene inductions were observed during both developmental and stress-induced nodule senescence. Both MtCP6 and MtVPE proteolytic activities were increased during stress-induced senescence.
Down-regulation of both proteinases mediated by RNAi in the senescence zone delayed nodule senescence and increased nitrogen fixation, while their early expression promoted nodule senescence.
Using green fluorescent protein fusions, in vivo confocal imaging showed that both proteinases accumulated in the vacuole of uninfected cells or the symbiosomes of infected cells. These data enlighten the crucial role of MtCP6 and MtVPE in the onset of nodule senescence.
For thousands of years, legumes have played a crucial role in sustainable agriculture by establishing a symbiotic interaction with a soil nitrogen (N2)-fixing bacteria of the Rhizobiacea family. N2-fixing symbiosis enables an optimal growth of legumes in nitrogen-limited soils. Moreover, symbiotic N2 fixation enriches soil with c. 50 million tons of nitrogen annually, sustaining subsequent nonlegume crops, avoiding the need for nitrogen fertilizer (Pislariu et al., 2012). Legumes account for 27% of crop production worldwide (Graham & Vance, 2003) and are an important food source for animal and human consumption, grain legumes contributing to 33% of human needs for dietary protein (Vance, 2001).
Nitrogen-fixing symbiosis occurs inside specialized root organs, called nodules. Nodules provide a proper microenvironment wherein the plant partner supplies a carbon source from photosynthesis to differentiated N2-fixing bacteria, called bacteroids. Bacteroids, through nitrogenase, are able to reduce atmospheric N2 into ammonia, which is subsequently assimilated by the plant.
In the Medicago truncatula/Sinorhizobium meliloti symbiotic model, important progress has been achieved towards the characterization of initial recognition between both partners and root nodule development. Signal exchanges between both partners initiate the formation of the characteristic shepherd's crook in root hair tips and elicit cell division in the root inner cortex, promoting the initiation of nodule meristems (Oldroyd & Downie, 2008). Bacteria divide inside infection threads, progress towards cortical root cells and are finally released into plant cell cytoplasm to form a new organelle-like compartment, the symbiosome (Wang & Dong, 2011). The interaction finally leads to the formation of a functional nodule. Medicago truncatula nodules are indeterminate and highly structured organs. At 4 wk postinoculation (wpi) nodules, all development stages are present in nodules, from host cell differentiation and S. meliloti infection to symbiosis disruption (Puppo et al., 2005). The apical meristematic region (zone I) ensures an indeterminate growth of the nodule. Newly formed cells issued from the meristematic zone are infected by S. meliloti (zone II). Host plant cells and microsymbionts (interzone II–III) initiate a differentiation process to form the N2-fixing symbiotic cells (zone III). In zone III, bacteria differentiate in bacteroids, which express nitrogenase and reduce atmospheric N2 into ammonia (NH4+). NH4+ is exported to the plant in exchange for carbohydrates (Crespi & Gàlvez, 2000). This symbiotic interaction is time-limited, and from 4 wpi, proximal nodule cells initiate a senescence process which induces a rapid and complete degradation of bacteroids and host plant cells (Zone IV; van de Velde et al., 2006). During nodule senescence, both bacteroids and host plant cells undergo sequential degradation. First, bacteroids and the peribacteroid membrane (PBM) are degraded with the presence of numerous vesicles in the plant cytoplasm and symbiosomes (van de Velde et al., 2006). Then host plant cells start to decay, leading to the complete degradation of the proximal part of the nodule (van de Velde et al., 2006).
A key feature of the nodule senescence process is the triggering of proteolytic activities, inducing extensive protein degradation (Malik et al., 1981; Pladys & Vance, 1993). Cysteine proteinase (Cys-P) genes are highly induced in soybean (Alesandrini et al., 2003a,b), Chinese milk vetch (Naito et al., 2000) and M. truncatula senescing nodules (Fedorova et al., 2002). In Astragalus nodules, knockdown analysis of AsNodF32 (a Cys-P) led to a delay in nodule senescence (Li et al., 2008), implying a crucial role for this Cys-P in the nodule senescence process. To unravel the onset of developmental nodule senescence, a cDNA-amplified fragment length polyphormism (cDNA-AFLP) transcriptomic analysis was performed in the senescence zone, as opposed to the N2-fixing zone of M. truncatula nodules (van de Velde et al., 2006). The analysis of the 508 differentially expressed gene tags confirmed the induction of Cys-Ps genes during senescence, and highlighted the induction of two of them, a papain-like enzyme, MtCP6, and a vacuolar processing enzyme, MtVPE.
Sequence analysis (van de Velde et al., 2006) showed that MtCP6 is homologous to AtSag12, a hallmark proteinase of Arabidopsis leaf senescence (Lohman et al., 1994). Previous analysis showed that MtCP6 was induced either during developmental, dark-induced nodule senescence (Perez Guerra et al., 2010) or during the interaction with the defective S. meliloti hmp strain (Cam et al., 2012). MtVPE is related to the legumain proteinase family. Legumains are caspase-like proteinases involved in the processing of vacuolar-based proteins during seed germination, leaf senescence (Muntz & Shutov, 2002), and in developmental or pathogen-mediated programmed cell death (Hatsugai et al., 2004; Rojo et al., 2004). MtVPE was shown to be induced during both developmental and stress-induced nodule senescence (van de Velde et al., 2006; Perez Guerra et al., 2010).
To date, the processes controlling the shift from functional infected cells (zone III) to senescent cells (zone IV) are essentially unknown. Considering the key role of proteolytic activities in the nodule senescence process, and the early induction of both MtCP6 and MtVPE genes during nodule senescence, we raised the hypothesis that these two genes could be early markers of the symbiotic breakdown. To test this hypothesis, we first investigated their spatiotemporal expression during developmental and stress-induced senescence, and characterized their proteolytic activities. Using reverse genetic approaches, we analysed the effects of up- and down-regulation of both genes on N2 fixation, nodule development and nodule senescence. The data reported in this study highlight the role of MtCP6 and MtVPE in the nodule senescence process and confirm the hypothesis that MtCP6 may be considered as a specific gene marker for the breakdown of symbiosis at the onset of senescence.
Materials and Methods
Plant materials, growth conditions and root transformation
Medicago truncatula ecotype A17 seeds were surface-sterilized and germinated as previously described (Boisson-Dernier et al., 2001). M. truncatula and composite plants with transgenic roots were grown in a phytotron under a 16 : 8 h, light : dark photoperiod associated with 23/21°C thermoperiod, watered with nitrogen-free nutrient medium (Puppo et al., 1982) and inoculated 5 d after germination with S. meliloti. The induction of hairy root was performed using a modified protocol from Vieweg et al. (2004) with Agrobacterium rhizogenes strain A4S (Alpizar et al., 2006). Nontransgenic roots were discarded from plantlets by screening for green fluorescent protein (GFP) fluorescence of transgenic roots expressed from the T-DNA construct. Composite and wild-type plants were grown for 6 wpi with S. meliloti, and mature nodules were harvested for analysis. Alternatively, for protein extraction, hairy roots were obtained as described by Boisson-Dernier et al. (2001). A. rhizogenes-transformed Medicago roots were excised (1 cm from the tip) and transferred onto SHb10 agar (Ramos & Bisseling, 2003). GFP fluorescence of each root line of transgenic roots was checked before selection. Transgenic roots were grown for 3–4 wk, at 20°C, in darkness.
Bacterial strains were grown on appropriate medium supplemented with selective antibiotics, at 30°C for S. meliloti, 28°C for A. rhizogenes or 37°C for Escherichia coli (Supporting Information, Table S1). Binary vectors were introduced into A. rhizogenes A4S by electrotransformation and colonies were selected by growth on spectinomycin (100 μg ml−1).
Construction of promoter:GUS constructs
Plasmid pENTL4L1-PMtCP6 with a 1.73 kb promoter fragment of the MtCP6 cysteine protease gene was provided by M. Holsters' group (van de Velde et al., 2006). Cloning into the pKM43GWD destination vector was previously described by Cam et al. (2012), resulting in the PMtCP6:GUS construct (Cam et al., 2012). The MtVPE promoter was obtained by PCR from genomic DNA with the following primers: PMtVPE-F/PMtVPE-R. The resulting 2 kb PCR fragment was inserted into the pDON207 donor vector and then, using Gateway Technology (Invitrogen), recombined into the pKGWFS7 vector in order to obtain the PVPE:GUS construct (Table S2).
Precocious expression and depletion of MtCP6 and MtVPE
The full-length MtCP6 and MtVPE coding sequences were amplified by PCR using primers CP6-F/CP6-R and VPE-F/VPE-R, respectively. The resulting amplified fragments were inserted into the pENTR4 donor vector. The corresponding inserts were then inserted in an overexpression plasmid, pKM43GWD (VIB, Ghent, Belgium) using PMtNCR001 (Mergaert et al., 2003) 5′ and T35S 3′ elements, using Gateway Technology (Invitrogen; resulting in PMtNCR001:MtCP6 and PMtNCR001:MtVPE, Table S2).
For the RNAi construct, the CaMV 35S promoter (P35S) in pK7GWIWG2D(II),0 vector (VIB) was replaced by the MtCP6 promoter (van de Velde et al., 2006). SacI and SpeI restriction sites were added to PMtCP6 by a PCR amplification with PMtCP6SacI-F and PMtCP6SpeI-R primers, using pENTL4L1-PMtCP6 as the template. The resulting 1732 bp PCR product was subcloned into pGEM-T vector (Promega). The insertion of this promoter was done in three sequential subcloning steps. First, a 2472 bp SacI-P35S:ccdB:intron-MluI from pK7GWIWG2D(II),0 vector was subcloned into a modified ΔEagIpGEM-T vector without SpeI site. Secondly, P35S was replaced by PMtCP6 in SacI-SpeI sites. Finally, pK7GWIWG6D(II) was obtained by insertion of the SacI-PMtCP6:ccdB:intron-MluI cassette back into the original pK7GWIWG2D(II),0 vector.
The RNAi construct was obtained by amplification of the CP6 5′ untranslated region (UTR) with the RNAi-MtCP6-F and RNAi-MtCP6-R primers, to generate an 80 bp PCR product (Table S2). This PCR product was inserted into a pDONR207 donor vector (Invitrogen). Finally, the CP6 5′ UTR insert was inserted into pK7GWIWG6D(II),0, using Gateway Technology (PMtCP6:RNAi MtCP6 and PMtCP6:RNAi MtVPE; Table S2). Similarly, a 270 bp PCR product of MtVPE was cloned into the pDONR207 donor vector (Invitrogen) and finally inserted into pK7GWIWG6D(II),0, using Gateway Technology. Efficiencies of RNAi and absence of an off-target for both RNAi constructs were checked using the RNAiScan tool (Xu et al., 2006).
GFP fusion protein constructs
The full-length MtCP6 and MtVPE sequences from pDONR207-MtCP6 or -MtVPE were inserted into pK7FWG2 (VIB) using Gateway Technology (Invitrogen; P35S:MtCP6:GFP, P35S:MtVPE:GFP; Table S2).
RNA extraction and real-time quantitative PCR (RT-qPCR) analysis
Total RNA was extracted with Trizol (Invitrogen) and cDNA pools were synthesized from 2 μg for RNA using the Omniscript RT kit (Qiagen) following the manufacturer's instructions. RT-qPCR was performed using a DNA engine Chromo4 (MJ Research; Bio-Rad) with qPCR Master Mix Plus for SYBR green I (Eurogentec, Angers, France). Each reaction was performed with 5 μl of 100-fold diluted cDNA template and 300 nM of each specific primer set (Table S2). Primer design and specificity have been tested with Primer-BLAST tools (Sayers et al., 2011) on a nonredundant (nr) database. The primers used (Table S2) had a calculated melting temperature of between 59 and 62°C and were unique in the MtGI (TIGR) and Medicago EST Navigation System (Journet et al., 2002) databases. After 2 min at 50°C followed by 10 min at 95°C for initial denaturation, 40 thermal cycles of 15 s at 95°C and 1 min at 60°C were performed. The amplification quality was checked by the presence of a single dissociation peak in a melting curve performed in each well and the end of the PCR reaction. Reactions were performed in triplicate and the results were averaged. The expression level was calculated and normalized using the method (Livak & Schmittgen, 2001). The constitutively expressed Mtc27 (Favery et al., 2002) 40S ribosomal protein S8 genes (Fedorova et al., 2002) and A39 (del Giudice et al., 2011) were used as endogenous controls. Data and statistical analysis were performed as described in del Giudice et al. (2011) using the RT qPCR Base.
Nitrogen-fixing capacity of bacteroids
The nitrogen-fixing capacity of bacteroids was determined in vivo by measuring acetylene-reducing activity (ARA; Pierre et al., 2013). Nodulated roots were harvested and incubated at 30°C for 1 h in rubber-capped tubes containing a 10% (v/v) acetylene atmosphere. Ethylene formation was determined using a GC (Agilent GC 6890N; Agilent Technologies, Massy, France) equipped with a GS-Alumina (30 m × 530 μm) separating capillary column.
Histological analysis of transgenic tissues
For light microscopy, nodules were fixed in 1% (v/v) glutaraldehyde, 4% (v/v) formaldehyde in 0.1 M phosphate buffer, at pH 7.2, washed, dehydrated, and embedded in Technovit 7100 (KulzerHisto-Technik, Heraeus France, Villebon, France), according to the manufacturer's instructions and as described by Cam et al. (2012). Sections were cut on a microtome (Jung, Adamas Intrumenten BV, Leersum, the Netherlands) to yield 5 μm slices, which were mounted with DPX mountant (VWR International Ltd). β-Glucuronidase (GUS) activity was localized, in nodule sections, after overnight incubation with the histochemical substrate 5-bromo-4-chloro-3-indolyl-β-d-glucuronide, cyclohexylammonium salt (Sigma), as described by Journet et al. (1994). Bright- and dark-field images were taken using an Axioplan2 microscope (Carl Zeiss, Le Pecq, France). For a general overview of nodule structure, staining with toluidine blue was done (van de Velde et al., 2006).
Mature nodules were harvested and freshly sectioned with a Leica VT1200S vibratome (Leica, Wetzlar, Germany) in 70-μm-thick tissue slices. Nodule slices were stained with 5 μM SYTO83 according to Pierre et al. (2013) or with 100 μM of monochlorobimane (MCB) as described in Fricker & Meyer (2001). In cytoplasm, MCB conjugates with glutathione (GSH), producing a red fluorescent component specifically sequestrated in the vacuole (Fricker & Meyer, 2001). Excess dye was removed by a short wash with 50 mM Tris (pH 7) buffer, and then samples were mounted on slides and observed using a laser scanning confocal microscope LSM780 (Carl Zeiss) equipped with a plan-Apo × 63/1.4 Oil DIC objective. Spectral analysis was performed to verify the GFP signal.
Protein extraction and enzymatic activities
Transgenic roots were collected and total protein was extracted in extraction buffer (50 mM Tris, pH 8, 5 mM EDTA, 20 mM NaCl and 10% (v/v) glycerol) at 4°C. After manual disruption of the tissue, the extracts were clarified by centrifugation at 10 000 g for 10 min at 4°C. Protein concentrations were estimated using the standard Bradford protein assay (Bio-Rad) and 5 μg of total protein was used to measure activities. The cleavage of substrates was followed by the liberation of a fluorescent molecule, coumarin, which has an excitation wavelength of 380 nm and an emission wavelength of 460 nm. DEVD, YVAD, ESEN, GGR, FR and RR activities were tested using N-acetyl-DEVD7-amido-4-methylcoumarin, N-acetyl-YVAD7-amido-4-methylcoumarin, N-acetyl-ESEN7-amido-4-methylcoumarin, (peptide institute), N-acetyl-GGR7-amido-4-methylcoumarin, N-acetyl-FR7-amido-4-methylcoumarin and N-acetyl-RR7-amido-4-methylcoumarin (Sigma) as substrates, respectively. Activities were followed using a Xenius spectrofluorimeter (Safas, Monte-Carlo, Monaco) and a reaction mix at pH 5.5 of 100 mM sodium acetate buffer, 1 mM EDTA, 1 mM dithiothreitol, 10 μg ml−1 total protein and 50 μM of substrate at 28°C for 20 min. Once an activity was established, this was quenched with either inhibitors such as E-64d at 20 μM (Sigma) for the papain family, protease-specific inhibitors at 50 μM (Ac-DEVD-CHO and Ac-YVAD-CHO) for caspase-like activities (caspase-1 and -3) or iodoacetamide at 10 μM for the legumain activity (ESEN). Activities were measured as a cleavage of substrate over time and values are expressed as ∆(fluorescence) min–1.
Protein extracts from cultured roots were subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) on a 12% gel, and then transferred to a polyvinylidene difluoride (PVDF) membrane. The membrane was blocked with 10% (w/v) milk in PBS and then incubated overnight in the same buffer with the addition of a polyclonal antibody raised against GFP (Promega). Alkaline phosphatase-conjugated goat anti-rabbit immunoglobulin G was used as the secondary antibody (Sigma) and revealed by detection of alkalin phosphatase activity with BCIP/NCB (5-bromo-4-chloro-3-indolyl-phosphate/nitro-blue tetrazolium; Sigma).
Papain and legumain sequences were retrieved via BlastP (Altschul et al., 1997) with M. truncatula MtCP6 and MtVPE as query sequences against the NCBI nonredundant database (www.ncbi.nlm.nih.gov) and the MEROPS peptidase database (Rawlings et al., 2011; www.merops.sanger.ac.uk). Analysis was performed using Phylogeny.fr platform (Dereeper et al., 2008).
MtCP6 and MtVPE are members of two different Cys-P families in M. truncatula
To explore the potential role of MtCP6 and MtVPE in the senescence process, proteases with similar sequences were analysed via BlastP (Altschul et al., 1997), and a minimum likelihood phylogenetic tree was generated (Fig. 1). MtCP6 and MtVPE belong to two different classes of proteinase, and clustered in two distinct phylogenetic groups. MtCP6 featured a double cysteine motif (CCWAF) typical of this class of papain proteinase (Richau et al., 2012). The cluster containing MtCP6 includes Cys-Ps, belonging to the papain proteinase family, which is related to multiple senescence processes. In this group, MtCP6 clustered with Cys-P-encoding genes from M. truncatula, named MtCP2–MtCP6 according to the nomenclature of previous works (Perez Guerra et al., 2010). These genes are up-regulated during the early stages of M. truncatula nodule senescence (van de Velde et al., 2006) as well as in dark-induced nodule senescence (Perez Guerra et al., 2010). MtCP6 was also closely related to TrCP5-TrCP12 genes, whose expressions increase during nodule senescence of Trifolium repens (Asp et al., 2004). The papain AtSAG12 is a hallmarked gene of leaf senescence (Otegui et al., 2005). However, despite sequence similarities with other papains involved in various senescence processes, AtSAG12 clustered in a distinct papain group from MtCP6. In the same way, AtXCP1-3, AtCEP1-3 and AtRD21 Cys-Ps, which participate in developmental (AtXCP1-3, AtCEP1-3) or pathogen (AtRD21)-mediated senescence (Avci et al., 2008; Helm et al., 2008; Shindo et al., 2012), clustered in a distinct group, implying that nodule senescence papain may differ from other senescence-related papain proteinase.
MtVPE belongs to the legumain, or VPE (vacuolar processing enzyme), family (Fig. 1). βVPE are involved in protein maturation during seed maturation (Kinoshita et al., 1999; Okamoto & Minamikawa, 1999) and δVPE are involved in programmed cell death of inner seed tegument cells (Nakaune et al., 2005). In the same way, α and γVPE are involved in multiple vacuole-mediated cell death processes, from developmental cell death (such as tracheary differentiation and leaf senescence) to pathogen-induced cell death (Hatsugai et al., 2006; Hara-Nishimura & Hatsugai, 2011).
The expression of MtCP6 and MtVPE in symbiosome-infected cells are promoted by either developmental or induced nodule senescence
To analyse their spatiotemporal expression in the nodule and during the senescence process, both MtCP6 and MtVPE promoters were cloned and fused to GUS. Promoter–GUS fusions were inserted into M. truncatula roots by A. rhizogenes-mediated transformation, and histochemical analysis of GUS activity were performed in transgenic roots and nodules at 3 and 6 wpi with S. meliloti. No GUS staining was detected in MtPCP6:GUS transgenic roots and nodules at 3 wpi (Fig. 2a). By contrast, a strong GUS staining was found in the meristematic (zone I) and the infection zone (zone II), but not in the N2-fixing zone (zone III), of PMtVPE:GUS nodules at 3 wpi (Fig. 2e). GUS staining was also observed in vascular bundles of PMtVPE:GUS transgenic roots and nodules (Fig. 2e,f,i). In mature nodules (6 wpi), PMtCP6:GUS expression was observed only in infected cells at the junction between zones III and IV (Fig. 2b). By contrast, for PMtVPE:GUS expression, a dual staining pattern was observed in 6 wpi nodules (Fig. 2f). Indeed, a strong GUS staining was detected in both meristematic and infection zones (Fig. 2f), and a weaker expression was observed in nodule infected cells in the whole senescence zone (Fig. 2j). The expression of both MtCP6 and MtVPE in the transition between zones III and IV suggests a potential involvement of both Cys-Ps in the nodule senescence process.
Previous works on nodulated M. truncatula plants report that a prolonged exposure to either darkness or nitrogen treatment entails a rapid and global senescence of whole nodules, accompanied by an induction of Cys-P (Puppo et al., 2005; Perez Guerra et al., 2010; de Zelicourt et al., 2012). Hence, using physiological and histological approaches, we assessed the effect of a 3 d period of either darkness or nitrogen treatment in 6 wpi M. truncatula nodules. Measurement of ARA showed 97% and 76% decreases in biological nitrogen fixation (BNF) 3 d after dark and nitrogen treatments, respectively (Fig. S1a). In these conditions, the observation of 5 μm nodule sections stained by toluidine blue revealed an extension of the senescence zone (zone IV; Fig. S1b).
Histochemical detection of GUS activity was performed on 6 wpi transgenic nodules carrying PMtCP6:GUS or PMtVPE:GUS fusions after 3 d of dark or nitrogen treatment (Fig. 2c,d,g,h). As shown in Fig. 2(panels c, d, g and h), the expression of both MtCP6 and MtVPE extended to all the nodule infected cells.
The expression of MtCP6 and MtVPE was also investigated in impaired nodules promoted by either a defective symbiotic M. truncatula line (Mtdnf1) or an S. meliloti mutant strain (nifH; Fig. 3). Mtdnf1 line is mutated for a subunit of a signal peptidase crucial for bacteroid differentiation (Wang et al., 2010). The MtDNF1 gene is highly expressed in nodules and its expression is restricted to the infection and differentiation zone (Wang et al., 2010; Fig. 3b,e,h). The SmnifH gene encodes one of the nitrogenase subunits (Ruvkun et al., 1982). The SmnifH mutant strain, defective for nitrogenase activity, promotes early nodule senescence (Maunoury et al., 2010; Fig. 3c,f,i). As shown by observation of a microsection of toluidine blue-stained nodules (Fig. 3a–c), the M. truncatula line and S. meliloti strain exhibited a defective symbiotic process, with an early nodule senescence (zone IV) at 3 wpi in comparison to the wild-type (Fig. 3a). At 3 wpi, in comparison to control nodules (Fig. 3d,g), MtCP6 and MtVPE were expressed earlier in the infected cells of nodules using the plant mutant Mtdnf1 (Fig. 3e,h) or promoted by SmnifH (Fig. 3f,i) undergoing early senescence as a consequence of failed symbiosis.
Thus, under either abiotic stress or defective symbiotic conditions, both MtCP6 and MtVPE were induced early in comparison to control conditions, indicating that the expression of the two proteinases is correlated to the nodule senescence process.
MtCP6 and MtVPE exhibit cathepsin-L and legumain activities, respectively
MtCP6 and MtVPE have been identified as putative Cys-Ps (van de Velde et al., 2006; Perez Guerra et al., 2010), but they were not proven to possess effective proteolytic activity. MtCP6 and MtVPE coding sequences were cloned into the pET30a expression system in E. coli, and the two proteinases were overexpressed. However, as already reported for other Cys-Ps (Bromme et al., 2004), both recombinant proteinases were retrieved in inclusion bodies, and the purification of functional enzymes failed. To circumvent this obstacle we produced transgenic roots overexpressing either MtCP6 or MtVPE, with A. rhizogenes-mediated transformation. Overexpression of MtCP6 and MtVPE were driven by the ubiquitous and strong cauliflower mosaic virus CaMV35S promoter (P35S) from the pK7FWG2 binary vector fusing GFP in frame with the proteinases. Transgenic roots were screened for a GFP signal by microscopy. Transgenic root lines carrying a P35S:GUS:GFP construct were used as controls. Effective overexpression of intact MtCP6:GFP and MtVPE:GFP in transgenic roots was validated by western blotting (Fig. S2). According to the MEROPS Peptidase Database (Rawlings et al., 2011), MtCP6 is an SPG31-like protease, belonging to a papain-like proteinase family. Therefore, two papain substrates, Z-FR-AMC (cathepsin-L activity) and Z-RR-AMC (cathepsin-B activity), were assayed to characterize MtCP6. The specificity of the proteolytic activity was monitored using the known papain inhibitor E-64d (Tamai et al., 1987; McGowan et al., 1989). Compared with control root lines, the overexpression of MtCP6 entailed a fourfold increase in cathepsin-L activity (Fig. 4a). This activity was 92% inhibited in the presence of E-64d (Fig. 4a). No cathepsin-B activity could be detected in protein extracts from root overexpressing MtCP6 when compared with the GUS control (Fig. 4a). A similar approach was used to investigate MtVPE activity. The MEROPS database (Rawlings et al., 2011) classifies MtVPE as an asparagyl-endopeptidase (legumain activity). Three substrates were tested to characterize the activity: Z-ESEN-AMC, a legumain-specific substrate (Hatsugai et al., 2004; Kuroyanagi et al., 2005); Z-YVAD-AMC, a caspase-1 substrate; and Z-DEVD-AMC, a caspase-3 substrate.
In control lines, legumain activity was strongly inhibited by iodoacetamide (> 95%), and caspase-1 and -3 activities were 85% inhibited by their specific inhibitors Ac-YVAD-CHO and Ac-DEVD-CHO, respectively. In MtVPE overexpressing root lines, ESENase and YVADase activities (calculated as the difference between the activity without and with inhibitor) were found to increase by 71 and 118%, respectively, whereas DEVDase activities were not significantly modified (Fig. 4b). These data showed that MtCP6 and MtVPE may be considered as papain- and legumain-type proteases, respectively, and followed through their cathepsin-L and legumain activities. These two activities were analysed in nodules of plants submitted to 3 d of either dark treatment (3dDT) or nitrogen treatment (3dNT). As shown in Fig. 5(a,c), dark treatment entailed an 80% increase of cathepsin-L and legumain activities. Similarly, nitrogen treatment increased cathepsin-L and legumain activities by 125 and 225%, respectively (Fig. 5b,d). These data strongly argue in favour of the involvement of both MtCP6 and MtVPE in the nodule senescence process.
Deregulation of MtCP6 and MtVPE strongly affect the nodule senescence process
The role of MtCP6 and MtVPE in the nodule senescence process was also assessed using a reverse genetic approach to alter their specific expressions. To this end, specific RNAi target sequences of 80 and 270 bp, from MtCP6 and MtVPE transcripts, respectively, were fused to the promoter of MtCP6 (PMtCP6), which drives a specific expression at the junction between the N2-fixing and senescence zones (Fig. 2). Composite transgenic plants were generated by A. rhizogenes-mediated transformation and nodulated with S. meliloti. In 6 wpi nodules, both genes were found to be significantly down-regulated: 25-fold for MtCP6 and fourfold for MtVPE, in RNAiMtCP6 and RNAi MtVPE nodules, respectively (Fig. 6a). Control plants expressing an RNAi empty construct showed no change in MtCP6 or MtVPE expression levels.
The BNF of MtCP6 and MtVPE-RNAi of 6 wpi nodules was estimated through the measurement of ARA. As compared with control nodules, the depletion of MtCP6 and MtVPE transcripts resulted in 160 and 60% increases in ARA, respectively (Fig. 6b). Moreover, decreased MtCP6 or MtVPE expression was found to promote an increase of c. 20% in nodule size, with an average length of 2.45 and 2.55 mm, respectively, compared with that of control nodules (2.05 mm; Fig. 6c). Interestingly, the depletion in either MtCP6 or MtVPE transcripts resulted in the extension of the N2-fixing zone (zone III) of the RNAi nodules compared with control nodules (Fig. 6d). This increase in N2-fixing zone and total nodule length suggests that the depletion of MtCP6 or MtVPE delays the senescence process in nodules.
To analyse the effects of MtCP6 and MtVPE overexpression in the N2-fixing zone, the zone III-specific promoter PMtNCR001 (Mergaert et al., 2003) was used to drive the expression of both genes. Composite transgenic plants were generated and 6 wpi nodules were collected. Overexpression of both genes was observed in both constructions, with a 207-fold and 139-fold overexpression for MtCP6 and MtVPE, respectively, compared with control nodules (Fig. 7a). Reductions in nodule length of 46 and 33% related to an increase of the senescence zone were associated with earlier expression of MtCP6 and MtVPE, respectively (Fig. 7b,c). Thus, similar to observations in nodules undergoing dark- and nitrogen-induced senescence (Fig. 2c,d,g,h), an earlier ectopic expression of MtCP6 and MtVPE during nodule development led to an acceleration of nodule senescence.
MtCP6 and MtVPE proteins are localized in symbiosomes of infected cells and in the vacuole of uninfected cells
Previous work on M. truncatula reported that symbiosomes are the first targets of the nodule degradation process (van de Velde et al., 2006). To determine a possible role for MtCP6 and MtVPE in this process, we investigated their subcellular localization in infected and uninfected cells. First, the putative localization of both Cys-Ps was determined using various amino-acid sequence-based predictor programs such as TargetP, Epiloc, and Multiloc (Höglund et al., 2006; Emanuelsson et al., 2007; Brady & Shatkay, 2008). In silico analysis predicted a putative localization of MtCP6 and MtVPE in the secretory pathway, that is endoplasmic reticulum, and the vacuole (data not shown). Both Cys-Ps were fused with GFP in the carboxyterminal-end and placed under control of the P35S promoter for a constitutive expression. Constructs were inserted into M. truncatula roots by A. rhizogenes-mediated transformation (Vieweg et al., 2004), and the roots were inoculated with S. meliloti. In vivo localization of MtCP6:GFP and MtVPE:GFP was investigated by confocal laser scanning microscopy (CLSM) in roots, and in 6 wpi nodules. In root cells, the GFP signals from MtCP6 and MtVPE fusions were found to co-localize with the fluorescence signal of MCB, a specific vacuolar probe (Fig. 8a–f; Fricker & Meyer, 2001). In nodule infected cells, MtCP6:GFP and MtVPE:GFP were found to colocalize with SYTO83, a nucleic acid dye used to visualize symbiosomes (Haynes et al., 2004), indicating that MtCP6 and MtVPE are present in symbiosomes (Figs 8g–l, S4). By contrast, in uninfected cells in the nodule, MtCP6 and MtVPE accumulated in the vacuoles, as observed in root cells (Fig. S3).
Considered together, these observations show that in root and in nodule uninfected cells, MtCP6 and MtVPE are delivered to the vacuole, whereas in bacteroid infected cells they are targeted to symbiosomes. This suggests that at the onset of senescence, vacuolar Cys-Ps such as MtCP6 and MtVPE are addressed to symbiosomes where they may ensure its degradation.
A key feature of legume nodule senescence is the triggering of proteolytic activities, inducing protein degradation and remobilization (Alesandrini et al., 2003b; Puppo et al., 2005; Groten et al., 2006; Dupont et al., 2012). Transcriptomic analysis performed to unravel the nodule senescence process in M. truncatula–S. meliloti symbiosis emphasized the induction of Cys-Ps at the onset of nodule senescence (Fedorova et al., 2002; van de Velde et al., 2006). In M. truncatula, two putative Cys-P genes, MtCP6 and MtVPE, have been shown to be strongly induced during both developmental and stress-induced nodule senescence (van de Velde et al., 2006; Perez Guerra et al., 2010). The present study aimed to specify their spatiotemporal expression patterns, characterizing their enzymatic activity and clarifying their functional involvement in the senescence process of M. truncatula root nodules.
Sequence homology analysis (Fig. 1) identified MtCP6 as a putative papain-like Cys proteinase. Proteinases of the papain family have been shown to be involved in various degradation processes, including developmental mediated senescence and cell death, such as abscission, fruit ripening, seeds germination, but also environmental and pathogen-mediated cell death (Otegui et al., 2005; van der Hoorn, 2008; Shindo & Van der Hoorn, 2008; Martinez et al., 2012). The present phylogenetic analysis reveals a close relation of MtCP6 with TrCP8, but a lower one with AsNod32, two Cys-Ps encoding genes shown to be specifically expressed at the junction between N2-fixing and senescence zones in Trifolium repens and Astragalus sinicus mature nodules (Naito et al., 2000; Asp et al., 2004; Li et al., 2008). Similarly, the phylogenetic analysis (Fig. 1) shows that MtVPE clustered with genes of the legumain proteinase family (Hara-Nishimura & Hatsugai, 2011). MtVPE presents significant sequence homology with the VPEs (α and γ VPEs) known to be involved in developmental programmed cell death, such as tracheid differentiation and leaf senescence (Hara-Nishimura & Hatsugai, 2011). During infection of Arabidopsis thaliana with the fungus Piriformospora indica or with the oomycete Hyaloperonospora arabidopsidis, the activation of a VPE leads to programmed cell death (Qiang et al., 2012; Misas-Villamil et al., 2013). VPEs have also been shown to be involved in pathogen-mediated cell death in response to bacteria, virus or mycotoxins (Hatsugai et al., 2004; Kuroyanagi et al., 2005; Hara-Nishimura & Hatsugai, 2011).
In the present study, spatiotemporal analysis of MtCP6 and MtVPE expression showed that both genes are up-regulated during developmental senescence (Fig. 2) and are expressed at the junction between the N2-fixing and senescence zones (Fig. 2). Similar expression patterns were reported for TrPC8 and AsNod32 (Naito et al., 2000; Asp et al., 2004; Li et al., 2008). Our data showed that dark- or nitrogen-induced senescence (Fig. 2), as well as defective symbiotic interactions generated with defective M. truncatula lines or S. meliloti strains (Fig. 3), promoted an extended expression of MtCP6 and MtVPE in the senescent cells. By contrast, the down-regulation of either gene resulted in increased N2-fixation capacities of the nodules and delayed nodule senescence (Fig. 6). Taken together, these results substantiate the involvement of both MtCP6 and MtVPE at the onset of and during the nodule senescence process. It may be noted that MtVPE was also found to be highly and transitorily expressed in zone II (Fig. 2), indicating an additional role of MtVPE in nodules. Sequence similarity analysis (Fig. 1) related MtVPE to VPEs known to play a crucial role in pathogen-mediated cell death (Hatsugai et al., 2004; Kuroyanagi et al., 2005; Hara-Nishimura & Hatsugai, 2011), and it may be suggested that, in the infection zone (zone II), MtVPE could act as a defence response of the host plant to control and contain Rhizobia infection. Similarly, the high expression of MtVPE in root and nodule vascular bundles may be compared with the up-regulation of VPEs during differentiation of tracheary elements (Hara-Nishimura & Hatsugai, 2011), and potentially associated with the formation of vascular elements during nodule growth.
Although MtCP6 and MtVPE were identified as putative Cys-Ps, a definitive enzymatic characterization was a prerequisite to understanding their functional role during nodule senescence. Using various proteinase substrates and inhibitors, we found that MtCP6 and MtVPE possess cathepsin-L and legumain activities, respectively (Fig. 4). The up-regulation of MtCP6 and MtVPE expression in either dark- or nitrogen-treated nodules (Fig. 2), associated with the corresponding relevant increase of their respective cathepsin-L and legumain activities (Fig. 5), strongly argues in favour of their involvement in the triggering of proteolytic activities associated with developmental or stress-induced nodule senescence (Puppo et al., 2005; Groten et al., 2006).
Our data are in agreement with previous work which reported that the silencing of the expression of AsNodf32 papain proteinase in whole nodule tissues (using the ubiquitous P35S promoter) delayed nodule senescence (Li et al., 2008). Indeed, AsNodf32 was also shown to be highly up-regulated during nodule senescence in the infection zone, at the junction between the N2-fixing zone and the senescence zone (zone III–zone IV; Naito et al., 2000). In addition, both MtCP6 and AsNodf32 feature a putative vacuole targeting consensus signal peptide LQDA on their N-terminal extremities, a motif absent from most papain proteinases (Li et al., 2008).
Although vacuole proteinases, such as papains and legumains, were demonstrated to be key components of leaf senescence and vegetal cell death (Otegui et al., 2005; Hara-Nishimura & Hatsugai, 2011), their precise role in nodule senescence, and particularly degradation of symbiosomes and host plant cells, remained largely unknown. Thus, to clarify how MtCP6 and MtVPE participate in nodule senescence, we investigated the distribution of MtCP6:GFP and MtVPE:GFP fusions in M. truncatula hairy roots and defined targeted subcellular compartments. In roots, confocal observations of the distribution of either MtCP6:GFP or MtVPE:GFP fusions showed that both Cys-P are found to be localized in the vacuole (Fig. 8a). Similar localization was observed in uninfected nodule cells (Fig. S3). The vacuolar location of both MtCP6 and MtVPE:GFP fusions is consistent with the in silico sequence-based analysis, predicting an endoplasmic reticulum and/or vacuole location. These data are strengthened by the presence of the putative LQDA vacuole sorting peptide present in the MtCP6 sequence (Perez Guerra et al., 2010), and by previous work demonstrating the vacuolar location of VPE in tobacco (Hatsugai et al., 2004; Lam, 2005). Vacuolar localization of MtCP6 and MtVPE could be related either to cell housekeeping functions, such as amino acid recycling of misfolded proteins and degradation of autophagic bodies that have entered the vacuole, or to more specific functions in vacuole-mediated cell death. In this process, the vacuole serves as a lytic reservoir up to the disruption of the tonoplast once plant cell death is initiated (Beers et al., 2000). Seed maturation or germination, differentiation of tracheary elements, and pathogen or insect attacks were reported to promote vacuole-mediated cell death involving the participation of papain and/or legumain proteinases activities (Hatsugai et al., 2004; van der Hoorn & Jones, 2004; Lam, 2005; Hara-Nishimura & Hatsugai, 2011). Thus, CP6 and VPE are potentially involved in the proteolytic process triggered when vacuole collapses at the onset of nodule cell senescence (van de Velde et al., 2006).
Confocal observations showed that, in infected nodule cells, MtCP6 and MtVPE are exclusively sorted out to symbiosomes (Fig. 8). The symbiosome is considered as a form of lytic compartment because of the presence of typical vacuole phosphatase, and nuclease and proteinase activities in the peribacteroid space (PBS; Mellor, 1989; Brewin, 1991). A recent study showed that the PBM acquires vacuolar receptors (e.g. V-SNARE) during the early steps of senescence, changing it from a plasmic to a vacuolar identity (Limpens et al., 2009). This new identity would allow the docking of vacuolar cargo vesicles to the PBM, ensuring the delivery of vacuole-targeted proteins into the PBS (Limpens et al., 2009). In a recent work, we showed that, at the interface of the N2-fixing and senescence zones, the PBS pH is acidic (Pierre et al., 2013), and may provide an optimal pH for cathepsin-L (MtCP6) and legumain (MtVPE) activation (Li et al., 2008; Martinez et al., 2012) during nodule senescence. Therefore, MtCP6 and MtVPE, once delivered into the PBS, may directly participate in symbiosome degradation, leading to disruption of the symbiotic interaction with S. meliloti.
The coinduction during nodule senescence and colocalization of both proteinases in the symbiosome may imply a joint function of MtCP6 and MtVPE. Interestingly, previous works on animal and plant models report that VPE acts as a transactivator of other proteinases, including cathepsin-L, through post-translational maturation, during seed maturation (Okamoto & Minamikawa, 1995), leaf senescence (Muntz & Shutov, 2002; Rojo et al., 2004) or Schisotoma parasitism of mouse blood cells (Delcroix et al., 2006). MtVPE could play such a regulatory role during nodule senescence by activating a cascade of other proteinases. The precise molecular mechanism whereby MtCP6 or MtVPE potentially interacts and ensures nodule senescence is the next challenging question. To answer this question, future works should first focus on the trafficking pathway controlling the delivery of MtCP6 and MtVPE to the symbiosome. The identification of target partners and substrates of MtCP6 and MtVPE is another objective to specify how MtCP6 and MtVPE participate in the degradation of symbiosomes within host plant cells.
O.P. was the recipient of a doctoral grant from the ‘Ministère de l'Education Nationale, de l'Enseignement Supérieur et de la Recherche’. This work was funded by the French government (National Research Agency, ANR) through the ‘Investments for the Future’ LABEX SIGNALIFE: program reference no. ANR-11-LABX-0028-01.