Overlap of Proteome Changes in Medicago ... - Plant Physiology

Overlap of Proteome Changes in Medicago truncatula in Response to Auxin and Sinorhizobium meliloti1[W][OA] Giel E. van Noorden, Tursun Kerim, Nicolas Goffard, Robert Wiblin, Flavia I. Pellerone, Barry G. Rolfe, and Ulrike Mathesius* Australian Research Council Centre of Excellence for Integrative Legume Research (G.E.v.N., N.G., F.I.P., B.G.R., U.M.), Genomic Interactions Group, Research School of Biological Sciences (G.E.v.N., T.K., N.G., B.G.R.), and School of Biochemistry and Molecular Biology (G.E.v.N., T.K., R.W., F.I.P., U.M.), Australian National University, Canberra, Australian Capital Territory 0200, Australia

We used proteome analysis to identify proteins induced during nodule initiation and in response to auxin in Medicago truncatula. From previous experiments, which found a positive correlation between auxin levels and nodule numbers in the M. truncatula supernodulation mutant sunn (supernumerary nodules), we hypothesized (1) that auxin mediates protein changes during nodulation and (2) that auxin responses might differ between the wild type and the supernodulating sunn mutant during nodule initiation. Increased expression of the auxin response gene GH3:b-glucuronidase was found during nodule initiation in M. truncatula, similar to treatment of roots with auxin. We then used difference gel electrophoresis and tandem mass spectrometry to compare proteomes of wild-type and sunn mutant roots after 24 h of treatment with Sinorhizobium meliloti, auxin, or a control. We identified 131 of 270 proteins responding to treatment with S. meliloti and/or auxin, and 39 of 89 proteins differentially displayed between the wild type and sunn. The majority of proteins changed similarly in response to auxin and S. meliloti after 24 h in both genotypes, supporting hypothesis 1. Proteins differentially accumulated between untreated wild-type and sunn roots also showed changes in auxin response, consistent with altered auxin levels in sunn. However, differences between the genotypes after S. meliloti inoculation were largely not due to differential auxin responses. The role of the identified candidate proteins in nodule initiation and the requirement for their induction by auxin could be tested in future functional studies.

Many legume species form symbioses with nitrogenfixing bacteria called rhizobia. The symbiosis starts with the exudation of flavonoids by the legume host, which stimulate the synthesis of so-called Nod factors by the bacterial partners. Nod factors are lipochitin oligosaccharides that are perceived by plant receptors and trigger a series of events leading to bacterial invasion and development of a nodule. Inside the nodule, rhizobia convert atmospheric nitrogen into ammonia, which is exported to the plant in exchange for carbohydrates. The development of a nodule starts with the reinitiation of cortical and pericycle cell divisions in the root in the zone of root hair emergence. In most deter1

This work was supported by funding from the Australian Research Council (ARC) through the ARC Centre of Excellence for Integrative Legume Research (grant no. CE0348212) and a Research Fellowship from the Australian Research Council to U.M. (DP0557692). * Corresponding author; e-mail [email protected]; fax 61–2–6125–0313. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Ulrike Mathesius ([email protected]). [W] The online version of this article contains Web-only data. [OA] Open Access articles can be viewed online without a subscription. www.plantphysiol.org/cgi/doi/10.1104/pp.107.099978

minate legumes, like Lotus japonicus or soybean (Glycine max), cortical cell divisions start in the outer cortex and lead to the formation of a nodule with a determinate meristem. In indeterminate legumes, like Medicago truncatula or pea (Pisum sativum), cortical cell divisions start in the inner cortex and often occur simultaneously to cell divisions in the pericycle located opposite xylem poles (Timmers et al., 1999). A small nodule primordium is formed that later differentiates into a nodule and is invaded by rhizobia (Kinkema et al., 2006). Nod factors have many functions during nodule initiation, one of which is thought to be an indirect effect on plant hormone signaling and transport (Ferguson and Mathesius, 2003; Roudier et al., 2003; Kondorosi et al., 2005). Auxin is likely to be an important regulator of nodulation. Auxin is crucial in plant development for the regulation of cell division and elongation, embryogenesis, and meristem formation in plants. The location of auxin maxima in the plant, regulated in part through polar auxin transport, is essential for the correct placement of meristems and organs (Blilou et al., 2005; Heisler et al., 2005). Auxin is mainly synthesized in the young leaves, and transported to the root tip in an acropetal direction, which reverses at the root tip. Auxin transport is facilitated by auxin importers, including AUX1 and PGPs (P-glycoproteins), and auxin exporters, including PIN (pin-formed) proteins and other PGPs (for a recent review, see Kramer and Bennett, 2006). Polar auxin transport can be inhibited by synthetic

Plant Physiology, June 2007, Vol. 144, pp. 1115–1131, www.plantphysiol.org Ó 2007 American Society of Plant Biologists

1115

van Noorden et al.

auxin transport inhibitors, for example, N-(1-naphthyl) thalamic acid, or internal regulators, for example, flavonoids (Brown et al., 2001). Auxin transport and localization are also important for nodule development, although the exact role of auxin during nodulation is not fully understood. Nodule initiation in indeterminate legumes is preceded by an inhibition of acropetal auxin transport at the site of nodule initiation (Mathesius et al., 1998; Wasson et al., 2006), which can also be triggered by application of purified Nod factors (Boot et al., 1999). Just before and during nodule initiation, auxin-responsive reporter gene expression is localized in the dividing inner or outer cortical cells in indeterminate (white clover [Trifolium repens] and M. truncatula; Mathesius et al., 1998; Huo et al., 2006) and determinate (L. japonicus) legumes (Pacios-Bras et al., 2003), respectively. Moreover, an auxin-inducible A2-type cyclin, is induced by Nod factors and is located in dividing cells of a nodule primordium (Roudier et al., 2003), indicating that one of the main roles of auxin during nodulation is in the regulation of mitosis (Kondorosi et al., 2005). Application of N-(1-naphthyl)thalamic acid or the auxin action inhibitor p-chlorophenoxyisobutyric acid, but also high concentrations of auxin, led to reduced nodule numbers in M. truncatula, whereas treatment with low external auxin concentrations increased nodule numbers (van Noorden et al., 2006), suggesting that optimal auxin levels and auxin action are required for nodule development. In addition, it was shown that silencing of PIN genes in M. truncatula inhibits nodulation (Huo et al., 2006). Both MtPIN (Huo et al., 2006) and MtLAX (a homolog of AUX1) expression was observed in developing nodules, possibly to channel auxin into a developing nodule primordium (de Billy et al., 2001). Nodule numbers are strictly controlled by the plant host via a long distance ‘‘autoregulation’’ mechanism (Caetano-Anolle`s and Gresshoff, 1991). Autoregulation of nodulation (AON) is a mechanism by which a plant inhibits further nodule formation on a root system after the first few nodules have been formed. AON is regulated by a Leu-rich repeat receptor-like kinase acting in the shoot, which has been identified in several legumes (Krusell et al., 2002; Nishimura et al., 2002; Searle et al., 2003; Schnabel et al., 2005). It is thought that inoculation of the root with rhizobia triggers an (unknown) signal that moves to the shoot, activates autoregulation, and then causes transport of another unidentified signal to the root, where it inhibits further nodules from forming (Caetano-Anolle`s and Gresshoff, 1991; Oka-Kira and Kawaguchi, 2006). Studies in supernodulating mutants have suggested that auxin is most likely to be a positive regulator required for nodule development, at least in indeterminate legumes. Two supernodulating mutants of M. truncatula, skl (an ethylene-insensitive mutant with root-controlled increases of nodule numbers; Penmetsa and Cook, 1997; Prayitno et al., 2006b) and sunn (supernumerary nodules, an AON mutant; Schnabel 1116

et al., 2005), show increased expression of the auxin response gene GH3 in inoculated roots compared to the wild type (Penmetsa et al., 2003). Direct measurements of auxin (indole-3-acetic acid [IAA]) content in sunn have demonstrated approximately 3-fold increased levels of auxin in the root segment susceptible to nodulation, compared to the wild type, both before and after inoculation of roots with rhizobia. sunn also shows approximately 3 times increased levels of auxin transport from the shoot to the root (van Noorden et al., 2006). These increased levels of auxin transport and content correlate with increased numbers of nodules in sunn roots. The skl mutant of M. truncatula has increased nodule numbers at the site of the first inoculation, and shows increased local auxin transport and increased PIN gene expression at the inoculation site after 24 h (Prayitno et al., 2006b). In addition, it was shown that the transport of auxin from the shoot to the root is involved in the autoregulation mechanism. Inoculation of wild-type roots with rhizobia caused a decrease of auxin loading from the shoot to the root within 24 h, whereas this long-distance inhibition of auxin transport did not occur in the sunn mutant (van Noorden et al., 2006). This suggests that certain levels of auxin are necessary for nodule development and that a lack of auxin after autoregulation could be limiting nodule numbers. In this study we used proteome analysis to identify proteins involved in nodule initiation that may also be regulated by auxin, to extend our knowledge on the role of auxin during nodule initiation. We hypothesized (1) that auxin has a positive role in nodule initiation and (2) that the difference in auxin content between the wild type and sunn mutant could (partially) explain their nodulation phenotypes. First, we characterized local expression of GH3:GUS preceding nodule initiation to pinpoint the best time point for analysis. We then used proteome analysis as a tool to reveal broad differences or similarities in protein accumulation that could test the previous hypotheses, and to identify proteins involved in auxin responses during nodulation. To test hypothesis 1, we compared the proteomes of wild-type root segments corresponding to the inoculation zone 24 h after treatment with either Sinorhizobium meliloti, the symbiont of M. truncatula, IAA, or a sham control. To test hypothesis 2, we compared proteomes of wild-type and sunn root segments following the same treatments as above. Our results show increased auxin localization and a large overlap in proteins induced by rhizobia and auxin at 24 h after inoculation (ai), and support a positive role for auxin during nodule initiation in M. truncatula. RESULTS Expression of GH3:GUS during Nodule Initiation

Under our growth conditions, cortical cell divisions started between 24 and 48 h ai in seedlings of both genotypes and hairy roots of the wild type. We then Plant Physiol. Vol. 144, 2007

Proteome Changes in Nodule Initiation and Auxin Response

examined GH3:GUS expression in hairy roots of wildtype composite plantlets after inoculation with S. meliloti and auxin. At least 20 roots were examined for each treatment, with similar results. GH3:GUS expression in uninoculated wild-type roots was located mainly in the vascular bundle (Fig. 1, A and B). Root tips (including the meristem and root cap) were also stained in about 30% of roots. Treatment with 1 mM IAA for 24 h caused GH3:GUS expression to spread to the cortical cells as well as the vascular bundle along the whole root (Fig. 1, C and D). After spot-inoculation of the roots with S. meliloti, increased GH3:GUS expression could be seen within 24 h ai in vascular and cortical cells around the

inoculation site (Fig. 1, E and F). This staining was located in a patch of several millimeters in length in approximately 60% of the roots, but in 40% almost the whole roots showed blue staining. After 48 h, cortical and pericycle cells could be seen that had just divided. These cells showed strong GH3:GUS expression in contrast to nondividing cells (Fig. 1, G and H). In general, auxin was located in vascular and dividing cells in the root. At 24 h after treatment, there was a similar strong induction of GH3:GUS expression in most cell types in response to auxin and inoculation, indicating that increased auxin levels inside the root at this time point could be involved in preparation for nodule initiation.

Figure 1. GH3:GUS expression in M. truncatula A17 hairy roots. A, Control root showing staining in the vascular bundle. B, Cross section of a control root with GH3:GUS staining in the vascular bundle, mainly around the phloem poles. C, Root treated with 1 mM IAA for 24 h showing increased GH3:GUS staining in the cortex. D, Cross section of a root treated with 1 mM IAA for 24 h showing increased GH3:GUS staining in cortical cells. E, GH3:GUS staining in a root 24 h ai with S. meliloti. Increased cortical expression is seen at the inoculation site (between arrows). F, Cross section of a root 24 h ai with S. meliloti showing enhanced staining in the cortical cells. G, GH3:GUS staining in a root 48 h ai with S. meliloti (arrows) showing expression in a patch of cortical cells. H, Cross section of a root 48 h ai with S. meliloti showing enhanced staining in dividing pericycle and cortical cells (arrows). Magnification bars represent 300 mm in A, C, E, and G, and 100 mm in B, D, F, and H.

Plant Physiol. Vol. 144, 2007

1117

van Noorden et al.

Thus, the 24-h time point was chosen for subsequent proteome analysis. Proteome Analysis

Proteome analysis was used to compare roots treated with rhizobia (24 h ai), with 1 mM auxin for 24 h, or a control, all at the zone of emerging root hairs. Four biological repeats of 50 root segments each were collected of each treatment. Analysis by difference gel electrophoresis (DIGE) was performed that included a dye swap between Cy3 and Cy5 (Supplemental Table S1). Two-dimensional (2D) gels of proteins labeled with CyDyes showed approximately 3,800 spots across all 12 gels (Fig. 2) in a pI range of 4 to 7. All spots were statistically compared for treatment and genotype effects by two-way ANOVA. Overall, 297 of the 3,800 spots (approximately 7.5%) showed statistically significant changes in response to either treatment or genotype (P , 0.05, two-way ANOVA; Table I; Supplemental Tables S2 and S3). The average fold change of all significant changes was 2.74 (SD 5 1.69, n 5 649), with a range of 1.17 to 13.1. To identify differentially accumulated proteins, all samples were combined for a 2D gel stained with Coomassie Brilliant Blue, resolving approximately 1,000 spots (Fig. 2). We could confidently match 201 of the 297 differentially accumulated proteins between DIGE and Coomassie gels. The remaining 96 proteins were too low in quantity to detect on the Coomassie gels due to the dye’s lower staining sensitivity. Using MALDI-TOF/TOF tandem mass spectrometry (MS/ MS), we could identify 140 of the 201 differentially accumulated protein spots excised from Coomassie gels (Fig. 2; Supplemental Table S4). Of the identified protein spots, 21 were successfully matched to two or more tentative consensus (TC) sequences, suggesting that these spots contained two or more proteins, which could not be resolved on the 2D gel, as observed in other studies (Watson et al., 2003). However, 15 of the 21 proteins matched two TCs with the same annotated function, and only six proteins matched to two or more TCs with different annotated functions. The identified proteins matched to 108 different TCs; 28 were found twice or more, indicating the existence of different protein isoforms. Changes in Protein Profiles during Inoculation with Rhizobia and Auxin Treatment

Our first hypothesis was that auxin mediates some of the protein changes during the early stages of nodule initiation. To test this hypothesis and to identify proteins potentially induced by auxin during nodulation, we compared the proteomes of root segments treated with S. meliloti, 1 mM IAA, and a control after 24 h. Overall, the accumulation level of 270 protein spots was significantly changed (P , 0.05, two-way ANOVA) between the three treatments (Supplemental Table S2); 1118

approximately 50% of the spots could be identified (Table II). In the wild-type roots, the accumulation level of 174 protein spots was significantly changed (P , 0.05, Student’s t test) in response to S. meliloti inoculation and 208 in response to auxin (P , 0.05, Student’s t test), compared to the controls. Interestingly, the majority (154) of proteins that changed after inoculation also changed in abundance after treatment with auxin, whereby both treatments resulted in similar accumulation levels of the same proteins (Table I; Supplemental Table S2). Figure 3 shows the overlaps and differences in protein changes between the different treatments in wild-type roots according to their functional classification in the Kyoto Encyclopedia of Genes and Genomes (KEGG; Kanehisa et al., 2004). In the sunn mutant, rhizobia inoculation caused the accumulation level of 103 protein spots to significantly change (P , 0.05, Student’s t test) compared to the control. Auxin altered the accumulation of 169 protein spots (P , 0.05) compared to the control. Similar to the wild type, the majority of proteins showed similar changes in response to auxin and rhizobia inoculation, with the accumulation levels of 92 protein spots changing in both the inoculated roots and the roots treated with auxin (Fig. 3; Table II; Supplemental Table S2). Protein changes in sunn were in general very similar to changes in the wild type in response to auxin and S. meliloti (Fig. 3). In both genotypes, more proteins were induced by auxin than by S. meliloti. Overall, the results showed that the majority of proteins that were up- or down-regulated in response to S. meliloti at 24 h were also up- or down-regulated by a 24-h auxin treatment, supporting our first hypothesis. Comparison of Protein Changes between the Wild Type and sunn

Our second hypothesis was based on two main differences between wild-type and sunn roots: sunn roots were shown to have higher levels of auxin in the inoculation zone and this was accompanied by twice the number of nodules in that zone (van Noorden et al., 2006), Therefore, we expected that there would be an interaction between the effect of auxin and the effect of S. meliloti inoculation between the wild type and sunn. We broke this hypothesis down into three subquestions. (1) Do the genotypes differ in their response to external auxin? We expected that both genotypes have in general a similar response to auxin. ANOVA for treatment effects (Table I; Supplemental Table S2) showed that there were 223 auxin-inducible proteins, of which 142 (63%) were induced/reduced similarly and significantly in both the wild type and sunn. An additional 58 proteins were only altered in the wild type by auxin, and 23 were only changed in sunn by auxin. However, in all of those cases, the proteins showed a similar, although not statistically significant, trend for changed levels in the other genotype. Overall, these data suggest that both the wild type and sunn respond Plant Physiol. Vol. 144, 2007

Proteome Changes in Nodule Initiation and Auxin Response

Figure 2. Proteome reference map for M. truncatula roots. Alignment of a DIGE (A) with the Coomassie gel (B) and the resulting reference map (C). A is an example of a (false-color) DIGE-labeled gel showing differential expression of two samples and an internal control, labeled with Cy3, Cy5, and C2, respectively. White protein spots indicate proteins not differentially displayed; colored spots are induced in one of the treatments (e.g. spots 308, 405, 141, 226, 178). The labeled proteins were marked as landmarks on both gels to aid in the alignment in DeCyder software. C, DIGE gel (Cy2 channel only) showing the position of the differentially accumulated and identified proteins listed in Supplemental Table S1. Proteins were separated across an isoelectric focusing range of pI 4 to 7.

Plant Physiol. Vol. 144, 2007

1119

van Noorden et al.

Table I. Summary of the number of differentially accumulated proteins in the DIGE analysis Feature

Total

Identified

Control

Rhizobia

Auxin

Overlapa

Detected protein spots Differentially displayed protein spots Treatment Wild type total sunn total Wild type and sunn Wild type only sunn only Genotype

3,800 297 270 – – – – – 89

– 140 131 – – – – – 39

– – – – – – – – 27

– – – 174 103 81 93 22 32

– – – 208 169 142 58 23 29

– – – 154 92 – – – –

a

Differentially displayed protein spots in both rhizobia and auxin treatment.

similarly to auxin in general, but that more proteins are inducible by auxin in the wild type than in sunn, possibly because of already higher endogenous auxin levels in sunn. (2) Are the proteins that differ between wild-type and sunn roots also auxin inducible? To analyze the genotype effects between the wild type and sunn, we calculated ANOVAs for genotype effects only (Table III; Supplemental Table S3). We found 27 significant changes between genotypes in control roots, 32 in rhizobia-inoculated roots and 29 in auxin-treated roots. Of 27 proteins that differed significantly between wild-type control and sunn control roots, 19 were also significantly affected by auxin treatment (Table I; Supplemental Table S3). Of those 19, 15 were inducible by auxin in both genotypes and four only in the wild type. In addition, more than 50% of proteins differing between genotypes in rhizobia-inoculated and auxintreated roots could also be induced by auxin in both genotypes. These data support the idea that the differing auxin levels in sunn and the wild type in the examined root zone could lead to changes in protein accumulation level in control (untreated) roots. (3) Are the proteins that differ between S. melilotiinoculated wild-type and sunn roots also different in their auxin response? Of 196 rhizobia-induced proteins, 81 showed similar accumulation patterns between wildtype and sunn roots after inoculation. However, there were 93 proteins that were only significantly altered in the wild type and 22 that were only changed in sunn after inoculation with S. meliloti (Table II; Supplemental Table S2). To find out if these differences could be due to the altered auxin levels in sunn and the wild type, we examined whether these proteins also showed a different response to auxin in the two genotypes. Of the 93 proteins only induced by rhizobia in the wild type, 36 showed similar responses to auxin in both genotypes, 40 showed significant induction by auxin in the wild type only, and three were significantly induced by auxin in sunn only. Of the 22 proteins only induced by rhizobia in sunn, 14 showed similar responses to auxin in both genotypes, five were induced by auxin only in sunn, and two were induced by auxin only in the wild type. Overall, the majority of proteins that were specifically induced by rhizobia in only one 1120

genotype did not differentially change in response to auxin between genotypes.

DISCUSSION

Our study was based on previous observations of a positive correlation between auxin content and auxin transport with the numbers of nodules formed on the roots of M. truncatula (Prayitno et al., 2006b; van Noorden et al., 2006). The hypotheses tested in this study were that auxin is a positive regulator of nodule initiation and that the difference in auxin content between the wild type and sunn mutant could partially explain their nodulation phenotypes. Our primary tool in detecting responses to rhizobia and auxin was proteome analysis. Proteome Analysis

Three main large-scale tools for the analysis of gene expression changes are commonly used in biological systems, proteomics, transcriptomics, and metabolomics. Using the DIGE technology, proteome analysis can be carried out similarly to a microarray experiment in that two samples are compared on one gel by analyzing the ratio of two fluorescent labels between ¨ nlu¨ et al., 1997). Totwo samples for each protein (U gether with the use of a pooled internal standard that combines all samples, this has been shown to reduce gel-to-gel variation and increase statistical confidence in the results (Alban et al., 2003). Compared to other proteomics studies that have analyzed the effect of S. meliloti inoculation on M. truncatula roots using either silver or Coomassie staining, our analysis, using DIGE, showed approximately 10-fold more significant protein accumulation changes (Bestel-Corre et al., 2002; Prayitno et al., 2006a). Compared to a microarray analysis of M. truncatula that included a 24-h time point and found approximately 500 gene expression changes (Lohar et al., 2006), a change of approximately 200 proteins in our analysis is comparable, especially considering that only approximately 3,800 proteins were analyzed compared to 6,000 cDNAs in that study. The range and average of ratios in abundance were also Plant Physiol. Vol. 144, 2007

Proteome Changes in Nodule Initiation and Auxin Response

Table II. Changes in protein accumulation levels between the treatments The table shows the identified proteins that were differentially accumulated in response to auxin treatment (Au.) or rhizobia inoculation (Rh.). The table shows separate effects between the treatments for each genotype. Positive value indicates up-regulation in the treatment compared to the controls; negative value indicates down-regulation in the treatment compared to the controls; ns, not significant. No.a

Identityb

6 7 9 10 13 14 16 17 18 19 27 29 43

F17H15.1/F17H15.1i F17H15.1/F17H15.1 Aconitate hydratase Aconitate hydratase Elongation factor EF-2 Aconitate hydratase Aconitate hydratase Aconitate hydratase Protein disulfide isomerase Protein disulfide isomerase Heat shock protein hsp70j Transketolase precursor 2,3-Bisphosphoglycerate phosphoglycerate RNA-binding protein Poly(A)-binding protein NADP-dependent malic enzyme RNA-binding proteinj Protein disulfide isomerase precursor Protein disulfide isomerase precursor Protein disulfide isomerase precursor Protein disulfide isomerase precursor Mitochondrial processing peptidase Dihydrolipoyl dehydrogenase Dihydrolipoyl dehydrogenase F1 ATPase F1 ATPase Enolase/26S protease regulatory subunit 6Bj Enolasei,j Enolase ATP sulfurylase F1 ATPase Enolasej/neutral Leu aminopeptidase preprotein UDP-Glc pyrophosphorylase Mitochondrial processing peptidasej Unknown protein Glutathione reductase Mitochondrial processing peptidasei,j 2-Oxoglutarate dehydrogenase F1 ATPase RAD23 protein Citrate synthase Tubulini,j 26S protease regulatory subunit 6A UDP-Glc pyrophosphorylasei Biotin carboxylase

46 49 51 52 54 57 58 60 76 80 81 85 86 88 89 93 94 98 100 105 106 107 108 109 110 113 119 120 121 123 124 125

TC No.c

ANOVA P Valued

Wild-Type Rh.e P Value

Ratio

Wild-Type Au.f P Value

Ratio

sunn Rh.g P Value

Ratio

sunn Au.h P Value

Ratio

TC95861 TC100382 TC94680 TC100640 TC93936 TC94680 TC100640 TC94680 TC100842 TC100842 TC108910 TC106664 TC100321

0.003 0.003 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 0.013 0.016

,0.001 0.003 0.006 0.008 ,0.001 ,0.001 0.004 ,0.001 0.027 ns 0.004 0.005 ns

4.34 3.01 3.77 3.77 4.30 5.28 5.31 7.50 2.46 1.75 1.87 2.20 1.73

ns ns 0.001 0.005 0.003 ,0.001 ,0.001 ,0.001 0.005 0.002 ,0.001 0.036 0.022

3.87 3.49 4.17 4.13 4.28 6.15 6.83 8.39 3.20 3.23 3.01 1.81 1.91

0.032 ns 0.027 0.041 0.036 ns ns 0.04 ns 0.049 ns ns ns

2.83 2.68 2.93 2.84 2.53 2.69 2.50 3.17 1.41 1.70 1.32 1.31 1.43

ns ns 0.02 0.04 0.028 ns ns 0.031 0.043 0.017 0.004 ns ns

2.37 2.63 3.23 2.84 2.77 3.00 2.30 3.29 2.69 2.64 2.41 1.15 1.39

TC94852 TC96556 TC106706

0.043 ,0.001 0.026

ns 0.001 0.021

1.36 2.29 2.12

ns ,0.001 ns

1.84 3.47 2.41

ns 0.042 ns

1.65 1.80 1.44

0.019 0.008 ns

1.83 2.66 1.31

TC94852 TC106707

,0.001 ,0.001

0.009 0.007

2.03 1.56

0.002 0.003

2.52 1.77

ns 0.025

1.55 1.47

0.016 0.001

1.99 2.19

TC106707

,0.001

0.009

1.65

0.003

2.26

ns

1.41

0.002

2.17

TC106707

0.025

1.15

,0.001

1.48

ns

1.09

ns

1.27

TC106708

0.014

1.24

,0.001

1.46

ns

1.31

ns

1.32

TC100542

0.035

1.50

ns

1.49

ns

1.61

ns

1.36

TC107247 TC107247 TC93945 TC93945 TC100309/ TC106924 TC100309 TC100309 TC100144 TC93945 TC100309/ TC94615 TC94328 TC106831

ns 0.033 ns

0.001 ,0.001 ,0.001 ,0.001 ,0.001

0.012 0.026 ns 0.004 0.008

2.21 2.24 1.67 2.82 4.14

0.01 0.014 0.025 ,0.001 ,0.001

2.54 2.56 1.73 3.91 6.07

ns ns ns ns 0.018

1.53 1.58 1.59 1.92 3.44

ns ns 0.013 0.014 0.007

1.17 1.59 2.42 3.07 5.07

,0.001 0.002 ,0.001 ,0.001 ,0.001

0.003 ns 0.007 ns 0.002

3.43 2.07 2.20 1.45 4.55

,0.001 0.041 ,0.001 0.036 ,0.001

5.25 2.20 2.67 1.63 6.71

0.028 ns ns ns 0.023

2.91 2.95 1.67 1.60 2.74

0.013 ns ns 0.023 0.008

4.17 4.32 1.53 2.26 3.63

,0.001 ,0.001

0.01 0.006

1.77 2.17

,0.001 ,0.001

2.19 2.68

ns ns

1.38 1.64

ns 0.016

2.39 2.37

TC102673 TC107373 TC102101

,0.001 0.025 ,0.001

0.018 0.007 0.016

1.77 1.58 1.79

,0.001 0.038 0.003

2.03 1.78 1.71

ns ns ns

1.63 1.20 1.45

0.019 ns 0.013

1.95 1.42 1.87

TC100769 TC93945 TC107109 TC107007 TC106434 TC94498

,0.001 0.021 ,0.001 ,0.001 ,0.001 ,0.001

0.002 0.002 0.007 0.006 0.017 ,0.001

1.80 1.60 2.60 1.83 2.60 2.56

,0.001 ns 0.001 ,0.001 ,0.001 ,0.001

1.98 1.53 3.17 2.83 4.40 3.27

0.03 ns ns 0.017 0.037 0.043

1.94 1.33 1.72 1.6 2.27 2.11

0.04 ns 0.016 0.003 0.005 ns

1.76 1.44 2.59 2.04 4.55 1.94

TC94328 TC94796

0.01 ,0.001

ns 0.002

1.51 1.66

0.046 ,0.001

1.81 1.85

ns ns

1.31 1.44

ns 0.023

1.33 1.63

(Table continues on following page.) Plant Physiol. Vol. 144, 2007

1121

van Noorden et al.

Table II. (Continued from previous page.) No.a

Identityb

TC No.c

126 130 133 139 141 142 147 148 155 160 162 170 172 175 178 182 183 186 193 194 196 198 200 203 204 205 209 210 226 229 230 233 239 240 247 263 267 276 278 282 283 288 294 298 303 308

RNA-binding protein 45 Isocitrate dehydrogenase Quinone oxidoreductase S-adenosyl-Met synthetase Unknown protein Heat shock protein 70j Heat shock protein Hsp70j F1 ATPase Acetoacetyl-CoA thiolase OPR Acetoacetyl-CoA thiolase Fru-bisphosphate aldolasej MDAR Succinyl-CoA ligase TGB12K interacting protein Fru-bisphosphate aldolasej Fru-bisphosphate aldolasej Fru-bisphosphate aldolasej Cytochrome c oxidase Fru-bisphosphate aldolasej Malate dehydrogenasej Glyceraldehyde-3-P dehydrogenasei,j Initiation factor 2B Glyceraldehyde-3-P dehydrogenasej Cytosolic malate dehydrogenase Glyceraldehyde-3-P dehydrogenasej Malate dehydrogenase Malate dehydrogenasej Cytochrome c oxidase subunit 6b-1 Isoflavone reductaseb Malate dehydrogenase Isoflavone reductasej Late-embryogenesis-like protein Peroxidase Glyceraldehyde-3-P dehydrogenasej Unknown protein Glyoxalase II Transcription factor APFI Heat shock protein 70i,j Acid phosphatasej Proteasome subunit alpha type 4i Acid phosphatasej Orcinol O-methyltransferase Albumin 2j Triosephosphate isomerase 2,4-D-inducible glutathione S-transferase ATP synthase delta# chain Copper chaperone homolog Cytochrome c oxidase subunit Trypsin protein inhibitor 3 Acid b-fructofuranosidase precursor Pprg2 protein Hypothetical protein Pprg2 protein Pprg2 proteini PR10 protein PR10 protein PR10 protein

TC106318 TC94329 TC94704 TC106563 TC107118 TC100389 TC101527 TC93945 TC106743 TC94407 TC106743 TC106580 TC100873 TC107346 TC100495 TC106580 TC106580 TC106580 TC95313 TC106580 TC100429 TC106519 TC107967 TC106518 TC100430 TC106518 TC100429 TC106473 TC95313 TC107101 TC100430 TC100786 TC95012 TC100928 TC106518 TC107832 TC94505 TC95345 BQ139103 TC93960 TC100691 TC93960 TC106401 TC101004 TC93925 TC94259

340 341 342 343 346 349 352 353 356 359 361 363

ANOVA Wild-Type P Valued Rh.e P Value

Ratio

Wild-Type Au.f P Value

Ratio

sunn Rh.g P Value

Ratio

sunn Au.h P Value

Ratio

2.05 2.34 1.85 2.45 21.03 27.09 24.46 1.30 1.93 2.72 1.68 1.77 1.90 1.23 1.12 2.10 1.93 2.32 1.07 1.53 2.18 1.65 1.08 1.55 1.63 1.77 2.13 1.66 1.43 1.30 1.31 1.57 1.96 1.13 1.41 2.28 1.03 1.41 24.09 1.14 1.23 1.53 1.71 1.27 2.42 1.61

0.021 0.014 ns 0.003 0.034 0.001 ,0.001 ns 0.01 0.004 0.025 0.031 ns ns 0.006 0.014 0.011 0.008 0.009 0.028 0.039 ns 0.017 ns ns 0.013 0.002 0.009 0.012 ns 0.009 0.004 ,0.001 0.01 0.015 ,0.001 0.02 ns ,0.001 ns 0.047 0.028 ns 0.043 0.003 0.003

3.32 3.33 1.46 4.05 1.62 27.14 25.08 1.28 2.49 4.31 2.15 1.87 1.67 1.75 1.90 2.59 2.35 2.98 1.72 1.94 2.56 1.28 1.84 1.34 2.12 1.63 2.76 2.79 2.06 1.74 1.29 2.34 1.92 1.59 23.57 3.29 1.71 1.11 24.59 1.51 1.92 1.57 1.83 1.56 3.53 5.16

,0.001 ,0.001 ,0.001 0.001 0.038 ,0.001 ,0.001 0.011 ,0.001 ,0.001 ,0.001 ,0.001 0.004 0.043 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 0.002 0.003 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 0.005 ,0.001 0.035 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 0.003 0.009 ,0.001 0.004 0.001 ,0.001 0.007 0.001 ,0.001 0.002

ns 0.001 0.003 0.031 0.038 0.008 0.005 ,0.001 0.028 ,0.001 0.006 0.011 ns ns ns 0.004 0.026 0.01 ns 0.001 0.005 0.017 ns 0.006 0.008 0.001 ns ,0.001 ns 0.004 ns 0.004 0.045 ns ns ns ns 0.036 0.008 0.014 0.03 0.02 0.006 0.016 0.003 ns

1.32 2.80 1.91 2.50 22.11 24.17 23.21 1.42 2.50 4.20 1.81 2.12 1.65 1.59 1.44 2.09 2.30 1.82 1.40 1.86 2.26 1.81 1.52 1.63 2.07 2.06 1.42 2.38 1.30 1.72 1.45 1.75 1.48 1.16 21.33 1.52 21.05 1.52 23.34 2.25 1.33 1.80 2.63 1.59 4.67 21.36

0.013 ,0.001 0.002 ,0.001 ns ,0.001 ,0.001 ns ,0.001 ,0.001 0.002 0.004 0.002 0.023 0.007 ,0.001 0.002 ,0.001 0.001 ,0.001 ,0.001 0.004 ns 0.004 ,0.001 ,0.001 0.007 ,0.001 ns 0.017 ns ,0.001 ,0.001 ,0.001 ns 0.009 ns 0.008 ,0.001 0.032 ns 0.004 ns 0.003 ,0.001 ns

1.97 3.37 2.27 4.76 21.72 28.95 25.11 1.15 4.01 5.68 1.92 3.07 2.07 1.89 1.90 2.87 3.51 2.43 1.64 2.36 3.02 1.92 1.35 2.07 2.53 2.79 1.78 3.50 1.54 1.51 1.52 2.73 2.05 2.34 22.03 2.27 1.38 1.5 24.83 2.58 1.27 2.08 2.44 2.20 7.98 21.89

0.027 0.042 0.036 0.019 ns ,0.001 ,0.001 ns 0.025 0.014 ns 0.038 ns ns ns 0.033 0.027 0.031 ns ns ns ns ns 0.046 ns 0.01 0.01 ns 0.036 0.04 ,0.001 0.018 ,0.001 ns ns 0.003 ns ns ,0.001 ns ns ns ns ns 0.011 ns

TC107637 ,0.001 TC100611 0.002 TC107458 0.038 TC100490 0.004 TC96236 0.003

0.012 ns ns ns ns

1.62 21.12 1.48 1.57 1.02

ns ns ns ns 0.01

2.16 21.20 1.61 2.04 21.35

ns ns ns ns ns

TC106352 ,0.001 TC106862 0.022 TC106352 ,0.001 TC106340 0.005 TC94221 0.049 TC94221 0.008 TC94221 ,0.001

0.027 ns 0.039 ns ns ns 0.04

1.67 1.13 1.84 1.29 1.34 1.47 1.43

0.004 ns 0.005 ns 0.022 0.014 0.006

2.84 21.39 3.24 1.63 1.55 1.97 1.91

0.004 ns 0.009 ns ns ns ns

1.34 1.01 1.26 1.19 1.31

0.009 2.00 0.029 21.61 0.012 1.82 0.011 2.12 ns 21.38

1.42 ,0.001 2.90 1.24 ns 21.92 1.41 ,0.001 3.00 1.32 0.003 1.86 1.08 ns 1.32 1.09 ns 1.45 1.27 0.026 1.96

(Table continues on following page.) 1122

Plant Physiol. Vol. 144, 2007

Proteome Changes in Nodule Initiation and Auxin Response

Table II. (Continued from previous page.) No.a

Identityb

364 PR10 protein 365 Gly-rich RNA-binding protein7 366 Thioredoxin-dependent peroxidase 370 Pprg2 protein 371 Pprg2 protein 374 PR10 proteini 376 Pprg2 protein/cytochrome c oxidase 378 Pprg2 protein 380 PR10 protein 381 PR10 proteini 382 PR10 proteini 384 Pprg2 protein 385 PR10 proteini 387 PR10 protein 389 Pprg2 proteini 391 PR10 proteini 394 PNDKN1 nucleosidediphosphate kinase 396 PR10 proteini 397 PR10 proteini 398 Gly-rich RNA-binding protein 399 Profilin-1 400 Thioredoxin h 401 Pprg2 protein/profilin-1 404 405 408 409 411

PR10 protein Cys proteinase inhibitor PR10 proteini Enolasej Glyceraldehyde-3-P dehydrogenasej

TC No.c

ANOVA Wild-Type P Valued Rh.e P Value

TC94221 TC96436 TC106854

,0.001 ,0.001 ,0.001

TC106314 TC106314 TC106613 TC110438/ TC106352 TC106314 TC94217 TC106613 TC106613 TC106314 TC106613 TC94219 TC106314 TC106613 TC106697

0.003 ,0.001 ,0.001 0.001

TC106613 TC106613 TC107478 TC94454 TC101267 TC106314/ TC94454 TC106613 TC94886 TC106613 TC100309 TC106518

ns ns ns

Ratio

Wild-Type Au.f P Value

Ratio

sunn Rh.g P Value

Ratio

sunn Au.h P Value

ns ns 0.031

1.20 1.33 1.32

0.016 0.001 0.005

1.83 2.75 1.34

1.47 1.42 1.48 1.03

ns 0.002 0.032 0.035

1.44 2.55 1.75 1.85

0.013 0.008 0.022 ns 0.018 0.024 0.003 0.017 ns ns

1.88 1.72 1.62 1.51 1.48 1.63 1.60 2.51 1.54 2.00

0.003 ,0.001 ,0.001 0.041 ,0.001 ,0.001 ,0.001 0.004 ns 0.034

2.58 5.51 3.05 1.64 2.88 2.99 3.34 3.34 1.60 3.00

0.021 2.09 0.048 1.51 ,0.001 29.37 0.007 22.17 ,0.001 21.91 0.023 1.78

1.44 1.21 1.29

0.034 0.009 0.019

1.62 1.70 1.39

0.016 0.028 0.027 ns

1.46 1.75 1.77 1.28

0.006 0.016 0.004 0.034

2.18 2.48 2.56 1.93

,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 ,0.001 0.002 ,0.001

0.005 0.013 0.014 ,0.001 ns 0.011 0.016 ns ns 0.004

1.84 2.09 1.91 1.47 1.54 2.01 2.14 1.74 1.39 3.60

0.017 ,0.001 ,0.001 0.005 0.016 0.001 0.001 0.01 0.009 ,0.001

2.67 7.19 4.52 2.62 2.38 4.14 4.93 3.74 2.63 5.98

,0.001 0.002 ,0.001 ,0.001 ,0.001 ,0.001

0.001 ns 0.014 0.004 ns ns

21.59 1.28 23.14 21.98 21.65 1.24

0.009 0.027 ,0.001 0.045 ,0.001 0.009

21.57 0.046 1.85 ns 23.83 ,0.001 21.60 ,0.001 23.10 0.002 1.82 ns

1.84 1.01 9.78 3.65 1.34 1.09

,0.001 0.003 ,0.001 ,0.001 ,0.001

0.009 ns 0.013 0.008 0.007

23.07 21.21 22.71 25.31 25.15

,0.001 0.026 0.001 ,0.001 ,0.001

22.68 0.008 21.84 ns 22.74 0.025 210.69 0.047 211.81 ,0.001

4.89 1.32 4.45 3.21 7.31

ns ns ns ns

0.008 0.048 0.012 0.023 0.001

Ratio

24.12 21.81 23.79 23.55 26.56

a b Protein ID used during matching and statistical analysis; ID number corresponds to Supplemental Table S4 and Figure 2. Predicted function c d TC number after matching to the M. truncatula EST database. Two-way ANOVA of all treatment effects across both of the TC. e genotypes, P , 0.05. P values (Student’s t test) and ratios for proteins differentially accumulated between wild-type control and wild-type f rhizobia-inoculated roots. P values (Student’s t test) and ratios for proteins differentially accumulated between wild-type control and wild-type g auxin-treated roots. P values (Student’s t test) and ratios for proteins differentially accumulated between sunn control and sunn rhizobiah P values (Student’s t test) and ratios for proteins differentially accumulated between sunn control and sunn auxin-treated inoculated roots. i j roots. Protein spot matched successfully to multiple TCs with the same predicted identity, as shown in Supplemental Table S4. Gene with the same annotated function also induced by rhizobia at 24 h in the transcriptome analysis by Lohar et al. (2006).

similar in the two studies, with an average fold change of 2.7 (range 1.17–13.1) in our study and about 2.0 (range 1.5–11.3) for the 24-h time point in Lohar et al. (2006). While there were some similarities in the proteins induced in the microarray and proteomics studies, most of the changes were found to affect different genes, and this could be due to the different half-lives of the transcripts and proteins in the cell as well as the slightly different growth conditions in the different experiments. Of 89 proteins identified in our study as significantly changed by rhizobia at 24 h (in wild-type roots), 28 matched to genes with the same annotated function that were also found to be affected in a transcriptome study (Lohar et al., 2006; Table II), whereas 61 proteins (matching to 44 TCs) were not found in the transcriptome study. In contrast to transcriptome analyses, proteomics was able to reveal the accumulation Plant Physiol. Vol. 144, 2007

of many protein isoforms from one transcript, thus giving a more accurate picture of the actual gene products. For example, 27 individual PR10 and related Pprg2 protein spots were identified in the roots, which matched to nine different TCs. These were overall the most abundant proteins. However, transcriptome analysis only found one PR10 transcript in M. truncatula roots at 24 h, and this was not affected by rhizobia (Lohar et al., 2006). In addition, our study found multiple isoforms of metabolic enzymes, for example, malate dehydrogenase, Fru-bisphosphate aldolase, and glyceraldehyde-3-P dehydrogenase (Table II), where only one gene appeared to be affected at the transcript level (Lohar et al., 2006). In general, the up- or downregulation of the proteins and genes was similar in both studies. Compared to transcriptome analysis, our study showed a lack of transporters and signaling components. 1123

van Noorden et al.

Figure 3. Overlap of proteins regulated by auxin and S. meliloti treatment. Left, Wild type; right, sunn mutant. The graph shows each class of proteins as classified in KEGG, and the number of proteins from that class that are either changed in both auxin- and S. meliloti-treated roots (black bars), only S. meliloti-inoculated roots (gray bars), or only in auxin-treated roots (white bars).

Comparison of Proteins Affected by Auxin and S. meliloti

We used GH3:GUS expression in hairy roots to compare timing and location of auxin response to auxin and rhizobia. Some variation in GUS staining was observed between individual roots. Similarly, this variation was observed in white clover fully transformed with GH3:GUS (Larkin et al., 1996), and could be due to differences in transgene numbers or expression in individual hairy roots and possible effects of the rol genes on auxin sensitivity (Nilsson and Olsson, 1997). We confirmed that GH3:GUS expression is located in cortical cells preceding cell division, and in the first dividing pericycle and cortical cells of a nodule primordium (24–48 h ai). This was similar to observations in white clover (Mathesius et al., 1998) and L. japonicus (Pacios-Bras et al., 2003) and in M. truncatula hairy roots transformed with the DR5 auxin reporter showing expression in nodule primordia 72 h ai (Huo et al., 2006). Thus, it appears that auxin responses occur at the site of nodule initiation. This conclusion was supported by the proteomics results that showed that 89% of the proteins affected by inoculation with S. meliloti at 24 h also changed in response to auxin. In addition, the trend toward up- or down-regulation of these proteins was very similar after both treatments. At the moment it is impossible to determine the exact internal auxin concentration in the cortical cells undergoing division, and how that correlates to the concentrations of auxin induced by the external application of 1 mM auxin and the time of treatment with auxin. It is also difficult to find out if the responses we measured in 1124

root segments reflect responses in specific cell types that could differ between auxin and S. meliloti treatment. For example, S. meliloti causes cell divisions in pericycle and cortical cells (compare with Fig. 1H; Timmers et al., 1999), which require auxin signaling (Roudier et al., 2003; Kondorosi et al., 2005); external auxin treatment stimulates pericycle division and lateral root initiation (Beeckman et al., 2001; Casimiro et al., 2001). However, in general, the results suggest that increased auxin responses in the root could be responsible for a number of the changes in gene expression following inoculation with rhizobia 24 h ai. In the future this hypothesis could be further tested by comparing auxin responses in inoculated roots of auxin response mutants; however, none has been described yet in M. truncatula. Most of the proteins that were affected by both auxin and S. meliloti at 24 h included metabolic enzymes, proteins involved in energy metabolism and protein processing (Fig. 3). These changes could be due to a general requirement for metabolites used for the preparation for cell division induced by S. meliloti and auxin. It is interesting to note that only one protein that changed in response to auxin treatment (and only in the sunn mutant) was previously identified as an auxin-inducible protein, a 2,4-D-inducible glutathione S-transferase, although this protein was actually down-regulated by auxin. This protein was also found to be downregulated in response to early mycorrhizal infection in M. truncatula in a study that also found other evidence for auxin-induced protein changes during mycorrhization (Amiour et al., 2006). The microarray study by Lohar et al. (2006) showed an increase in expression of Plant Physiol. Vol. 144, 2007

Proteome Changes in Nodule Initiation and Auxin Response

Table III. Changes in protein accumulation levels between the wild type and sunn The table shows the identified proteins that were differentially accumulated in response to genotype effects. The table shows separate effects between the wild type and sunn for proteins differing in their abundance between genotypes in the controls, the rhizobia-inoculated roots, and the auxin-treated roots. Positive value indicates up-regulation in sunn; negative value indicates down-regulation in sunn compared to wild type; ns, not significant. No.a

Identityb

TC No.c

ANOVA P Valued

Controle P Value

Ratio

Rhizobiaf P Value

Ratio

Auxing P Value

Ratio

34 53 57 58 60 133 136 142 144 147 160 170 172 185 188 204 206 229 244 267 298 303 338 346 350 359 361 363 364 365 366 370 371 374 378 380 387 389 394

Luminal binding protein 4 precursor Heat shock cognate protein 70 Protein disulfide isomerase precursor Protein disulfide isomerase precursor Protein disulfide isomerase precursor Quinone oxidoreductase RAD23 protein Heat shock cognate protein 70 Isocitrate dehydrogenase precursor Heat shock protein Hsp70 OPR Fru-bisphosphate aldolase MDAR Adenosine kinase 2 Adenosine kinase 2 Malate dehydrogenase Late-embryogenesis-abundant proteinsh Isoflavone reductase Malate dehydrogenase precursor Glyoxalase II Albumin 2 Triosephosphate isomerase Trypsin inhibitor Acid b-fructofuranosidase precursor Kunitz proteinase inhibitor-1 PR10 protein PR10 protein PR10 protein PR10 protein Gly-rich RNA-binding protein 7 Thioredoxin-dependent peroxidase Pprg2 protein Pprg2 protein PR10 proteinh Pprg2 protein PR10 protein PR10 protein Pprg2 proteinh PNDKN1 nucleoside-diphosphate kinase

TC100382 TC100389 TC106707 TC106707 TC106708 TC94704 TC107109 TC100389 TC94329 TC101527 TC94407 TC106580 TC100873 TC94061 TC94061 TC100430 TC108292 TC107101 TC107189 TC94505 TC101004 TC93925 TC107914 TC96236 TC106781 TC94221 TC94221 TC94221 TC94221 TC96436 TC106854 TC106314 TC106314 TC106613 TC106314 TC94217 TC94219 TC106314 TC106697

0.015 0.004 0.014 0.005 0.01 0.027 0.005 0.011 0.037 0.004 0.018 0.024 0.019 0.045 0.043 0.019 0.027 ,0.001 0.017 0.01 0.006 0.016 ,0.001 ,0.001 0.003 ,0.001 0.001 ,0.001 ,0.001 0.018 ,0.001 0.025 0.001 ,0.001 0.038 ,0.001 ,0.001 0.019 0.022

ns ns ns ns ns ns ns 0.009 ns 0.011 ns ns ns ns ns ns ns ns ns ns ns 0.041 0.023 ns 0.041 ns ns 0.005 0.012 ns 0.039 0.013 0.014 0.008 ns 0.004 0.001 ns ns

21.13 21.47 21.18 21.22 21.22 1.58 21.10 21.69 21.01 21.49 1.90 1.70 1.49 21.09 21.11 1.76 21.05 1.49 21.25 21.48 21.08 2.38 21.82 21.16 1.48 21.38 21.35 21.68 21.77 1.04 1.29 1.51 1.65 21.56 1.31 1.94 2.08 1.40 2.28

0.026 ns 0.031 ns ns 0.018 0.023 ns ns ns 0.028 0.044 ns ns 0.01 ns ns ns ns ns 0.014 ns 0.002 0.006 ns 0.007 0.025 0.003 0.002 ns 0.047 ns ns 0.034 ns 0.048 ns ns ns

21.69 21.61 21.39 21.29 21.17 1.52 21.36 22.87 21.24 22.07 1.23 1.42 1.70 21.32 21.40 1.38 21.40 1.13 21.20 21.36 21.35 1.23 22.52 21.54 1.28 21.99 21.82 21.89 22.13 1.14 1.31 1.53 1.35 21.86 1.34 1.60 1.56 2.02 1.26

ns ns ns 0.004 0.01 ns ns ns ns ns 0.033 ns ns ns ns ns ns 0.047 0.048 ns 0.023 ns ns ns ns ns 0.045 ns ns 0.009 0.024 ns ns 0.018 ns ns ns ns ns

21.76 21.47 21.23 21.41 21.35 1.01 21.59 21.35 21.4 21.48 1.44 1.04 1.20 21.13 1.06 1.47 21.71 1.73 21.27 21.19 21.52 1.05 21.32 21.19 1.86 21.61 21.83 21.64 21.57 1.67 1.25 21.00 1.70 22.28 1.27 1.49 1.41 1.25 1.14

a

b Protein ID used during matching and statistical analysis; ID number corresponds to Supplemental Table S4 and Figure 2. Predicted function c d of the TC. TC number after matching to the M. truncatula EST database. Two-way ANOVA of genotype effects across all treatments, P , e f 0.05. P values (Student’s t test) and ratios for proteins differentially accumulated between wild-type and sunn control roots. P values g P values (Student’s t (Student’s t test) and ratios for proteins differentially accumulated between wild-type and sunn rhizobia-inoculated roots. h test) and ratios for proteins differentially accumulated between wild-type and sunn auxin-treated roots. Protein spot matched successfully to multiple TCs with the same predicted identity as shown in Supplemental Table S4.

two auxin-inducible genes and reduction of two auxin-repressed proteins at 24 h ai. Neither these nor other known auxin response proteins were identified in our study, and this is possibly due to their low accumulation level. Other proteins of interest that could play a role during nodulation in response to auxin are 12-oxophytodienoic acid 10,11-reductase (OPR), isoflavone reductase, a late-embryogenesis-like protein, a number of redox-related proteins, and a large group of PR10 and Pprg2 proteins. Plant Physiol. Vol. 144, 2007

OPR converts 12-oxophytodienoic acid into 3-oxo-2(2#-Z-pentenyl)-cyclopentane-1-octanoic acid, a precursor of jasmonic acid (JA; Schaller and Weiler, 1997). JA inhibits Nod factor signal transduction by modulating the calcium signature of responding root hair cells and prevents early nodulation gene accumulation, resulting in the inhibition of nodule formation (Sun et al., 2006). In addition, the application of a volatile derivative of JA, methyl jasmonate, to the shoot of L. japonicus inhibits nodule formation, suggesting that JA plays a 1125

van Noorden et al.

part in long-distance regulation of nodule numbers (Nakagawa and Kawaguchi, 2006). OPR was strongly induced in response to S. meliloti and auxin, suggesting that JA synthesis is activated during the early stages of nodulation, possibly to limit the numbers of nodules. OPR was more strongly induced in sunn than in the wild type, and this could suggest that JA is locally induced as part of the nodule initiation process. Isoflavone reductase, an enzyme of the isoflavonoid biosynthetic pathway, was induced by auxin and S. meliloti. Various members of the flavonoid pathway are induced during nodulation (El Yahyaoui et al., 2004; Lohar et al., 2006), and this could be due to a requirement for flavonoids as Nod gene inducers or regulators of auxin transport (Subramanian et al., 2006; Wasson et al., 2006). In Arabidopsis (Arabidopsis thaliana), it has been suggested that a feedback mechanism exists among auxin accumulation, flavonoid induction, and subsequent regulation of auxin transport by flavonoids (Peer et al., 2004). The induction of flavonoid biosynthetic enzymes by auxin treatment in our study supports those findings. Our data also showed an effect of auxin and rhizobia on proteins involved in redox control, which has emerged as an important regulator of cell division (Jiang and Feldman, 2005). The most important redox couples include ascorbic acid/dehydroascorbate and reduced/oxidized glutathione. In addition, thioredoxin, glutaredoxin, and peroxidases also play a role in redox control. It is likely that auxin might partially influence cell division through its effects on redox control, as changes in the auxin distribution altered both the patterns of redox state and cell division in maize (Jiang et al., 2003). Our study showed evidence for the induction of redox-related proteins by auxin and a connection of redox control with nodulation: Four enzymes contributing to a more reduced redox state were upregulated in auxin- and in S. meliloti-treated roots, including glutathione reductase, monodehydroascorbate reductase (MDAR), a peroxidase, and a thioredoxindependent peroxidase. MDAR and a peroxidase were also found to be induced at 24 h in a microarray study (Lohar et al., 2006). Ascorbate peroxidase was induced in meristems compared to nonmeristematic tissue in M. truncatula (Holmes et al., 2006). Altogether the results suggest that auxin might play a role in inducing enzymes that form a more reduced redox state, which could be important for nodule initiation. Various biotic and abiotic conditions have been shown to induce members of the JA biosynthesis pathway, including OPR (Sasaki-Sekimoto et al., 2005); the flavonoid pathway (Stafford, 1997); and changes in redox control (Mittler et al., 2004). Additionally, there is evidence for cross talk between these pathways; for example, JA responses mediate induction of antioxidant enzymes (Sasaki-Sekimoto et al., 2005). Different members of these stress response pathways are induced in response to different pathogens and environmental stresses. Their induction during nodulation might reflect the possibility that symbiotic rhizobia are recognized 1126

as pathogens initially, and that selective down-regulation of defense responses allows symbiosis under appropriate conditions (Mitho¨fer, 2002). A comparison of the individual protein isoforms induced by different stimuli will be necessary in an individual plant species to identify specific members that might be responsible for certain responses. The PR10 protein class was the second highest class (18%) of identified proteins that changed accumulation after both rhizobia inoculation and auxin treatment. A microarray study in M. truncatula showed several PR10 proteins to be differentially regulated at later (3–10 d ai) stages of nodulation (El Yahyaoui et al., 2004), and some of these proteins were also differentially accumulated in meristems of M. truncatula (Holmes et al., 2006). The function of the PR10 class of proteins is so far unknown. They were originally described as pathogen-related proteins (van Loon et al., 2006). However, the PR10 class of proteins has key roles in many plant developmental programs as PR10 is also induced by auxin (Poupard et al., 2001), salicylic acid, JA (McGhee et al., 2001), abscisic acid (Colditz et al., 2004), ethylene (Prayitno et al., 2006a), and biotic and abiotic stress (Hashimoto et al., 2004). PR10 proteins are also known to bind fatty acids, flavonoids, steroids, cytokinins, and brassinosteroids (Mogensen et al., 2002; MarkovicHousley et al., 2003), and could thus link different hormone responses. For example, the correct ratio of auxin and cytokinin signaling is likely to be important in nodule initiation (Gonzalez-Rizzo et al., 2006; Murray et al., 2007; Tirichine et al., 2007). In Brassica napus, overexpression of a pea PR10 protein caused elevated cytokinin and decreased ABA levels, suggesting that changes in expression of PR10 could have an effect on hormone-regulated developmental processes (Srivastava et al., 2006). From our analysis it appears that the specific isoforms of PR10 might have distinct roles as they were very specifically altered in response to the different treatments and genotypes. A PR10 protein (MtN13) was previously found to be expressed specifically during nodulation; thus, this class of proteins might have evolved specific functions for different developmental processes (Gamas et al., 1998). Furthermore, six isoforms of PR10 were found to be induced by the oomycete pathogen Aphanomyces euteiches in M. truncatula, in a proteome study (Colditz et al., 2004); only three showed coinduction by either drought or ABA. The three PR10 isoforms specifically induced by the pathogen were also induced in our study by S. meliloti and auxin (represented in our gels by spots 353, 387, and 356). Thus, a particular combination of isoforms of PR10 proteins might be characteristic for responses to certain elicitors. It was surprising to find only a few proteins induced by rhizobia but not by auxin, for example, infectionrelated proteins. A possible explanation could be that only a few cells are involved in infection of the whole root segment harvested, and, thus, changes in protein accumulation in those cells would be diluted. Interestingly, we found three ATPases that were induced in Plant Physiol. Vol. 144, 2007

Proteome Changes in Nodule Initiation and Auxin Response

S. meliloti but not auxin in the wild type. Visualization of extracellular ATP in M. truncatula was shown to be high in growing root hairs (Kim et al., 2006). Redirection of root hair growth is part of the infection process of rhizobia, and the induction of the three ATPases could thus indicate a role in root hair curling and infection of rhizobia. Can Proteome Analysis Determine Whether the Difference in Auxin Content between the Wild Type and sunn Mutant Explains Their Nodulation Phenotypes?

Roots of the sunn mutant were shown to have approximately 2- to 3-fold increased auxin levels at the zone of nodule initiation (van Noorden et al., 2006), which are accompanied by higher long-distance auxin transport in sunn (van Noorden et al., 2006) and increased GH3 expression levels during nodulation (Penmetsa et al., 2003). Roots of the sunn mutant are also shorter than those of the wild type (Penmetsa et al., 2003; van Noorden et al., 2006), and this could also be a result of higher auxin levels, as high levels of auxin inhibit root growth, including in M. truncatula (van Noorden et al., 2006). Overall, there was a high similarity between wildtype and sunn proteomes, and genotype effects were less numerous than treatment effects. Compared to 270 proteins with significant changes in response to one of the treatments (Supplemental Table S2), there were only 89 proteins that showed significant genotype effects (Supplemental Table S3). Contrary to our expectation, sunn did not show a more extensive response to either auxin or rhizobia than the wild type. This is in contrast to a microarray study that showed more extensive gene expression changes in a sunn mutant than in the wild type during nodulation, although this study examined later time points (3–10 d ai) compared to ours (El Yahyaoui et al., 2004). There was also no evidence that the proteins induced by S. meliloti or auxin in the wild type but not in sunn were present at higher background levels in sunn control roots due to their higher internal auxin levels. It is possible that proteome analysis is not sensitive enough to determine differences in accumulation levels of proteins that might exist between the wild type and sunn, especially if those changes only occur in a few cells out of the total root segments analyzed here. Alternatively, there might be feedback mechanisms that are activated in sunn to compensate for high auxin levels. The response to auxin was very similar between the wild type and sunn in the proteome analysis; it was mirrored by very similar root growth responses to auxin in the wild type and sunn (van Noorden et al., 2006). Some notable differences were observed, including the expression of two protein disulfate isomerases, OPR, isoflavone reductase, a Gly-rich RNA-binding protein, albumin 2, two PR10 proteins, and a thioredoxin-dependent peroxidase. The Gly-rich RNA-binding protein (TC93436) was a protein specifically induced by auxin but also significantly higher in sunn than in the wild type. Plant Physiol. Vol. 144, 2007

There were also some interesting differences in protein accumulation between the wild type and sunn in response to inoculation with S. meliloti; these included OPR, albumin 2, a trypsin inhibitor, six PR10 proteins, and the thioredoxin-dependent peroxidase. As discussed above, the differential accumulation level of PR10 proteins and the thioredoxin-dependent peroxidase could indicate altered stress response and/ or redox control during nodulation. Whereas the PR10 proteins were more highly accumulated in the wild type, the thioredoxin-dependent peroxidase was present at higher levels in sunn under all three treatment conditions. It would be interesting in the future to assess redox state in the sunn mutant to find out if this might contribute to its supernodulation phenotype. CONCLUSION

Using DIGE combined with MS/MS, we identified 131 of 270 proteins differentially displayed after treatment of M. truncatula roots with S. meliloti or auxin, and 39 of 89 proteins differentially displayed between the wild type and the sunn mutant, the highest number of proteins identified from M. truncatula roots during nodule initiation. We found evidence for coregulation of a large number of proteins by rhizobia and auxin, suggesting that these proteins could be regulated by auxin changes during the early stages of nodulation. Protein accumulation patterns also indicated that some of the differences between the wild type and sunn could be due to their different internal auxin levels, although in general both genotypes showed very similar responses to rhizobia and to auxin. The differentially accumulated candidate proteins could be used in future studies, for example, using RNA interference or overexpression, to determine their function during nodulation. MATERIALS AND METHODS Plant Growth and Treatments Medicago truncatula ‘Jemalong’ genotype A17, which was used as the wildtype control, and its derivative sunn mutant (Penmetsa et al., 2003; Schnabel et al., 2005) were used in this study. Seeds were scarified with sandpaper and surface sterilized for 10 min with 6.25% (w/v) hypochlorite, followed with six washes with sterile water. Additional sterilization included immersion in a solution of 200 mg L21 augmentin for 6 h at 29°C and washing six times with sterile water. Sterilized seeds were spread on petri dishes containing 0.8% (w/v) agar (Grade J3; Gelita Pty Ltd.) and moistened with a drop of sterile water to prevent the seeds from drying. Seeds were then germinated by incubating the plate upside-down in the dark overnight at 29°C. The germinated seeds were transferred to large petri dishes (diameter 15 cm, 150 mL) containing nitrogen-free Fa˚hraeus agar medium (Fa˚hraeus, 1957), with the seed placed at a distance of 4 cm from the top of the plate. Plates were kept vertical and the bottom half of each plate was sealed with Nescofilm (Bando Chemical Ind. Ltd.), with the sides covered for two-thirds with black paper to reduce light intensity around the root. An aluminum foil spacer was placed between the lid and the petri dish to allow for air exchange. Plates were incubated in a growth chamber at 21°C for a 16-h-day/8-h-night cycle with a photon flux density of 100 mmol m22 s21. The rhizobia strain used for inoculating the roots was Sinorhizobium meliloti strain 1021. S. meliloti were grown on agar plates containing Bergensen’s

1127

van Noorden et al.

modified medium (BMM; Rolfe et al., 1980) for 3 d at 28°C. For plant inoculations, 5 mL of liquid BMM was inoculated from a single bacterial colony and incubated at 28 °C overnight in a shaker. The bacterial culture was diluted with liquid BMM medium to an optical density of 0.1 at the wavelength of 600 nm. Three-day-old seedlings were flood inoculated at the root tip with 10 mL of the rhizobial culture. Control roots were sham inoculated with the same amount of sterile liquid BMM medium. For proteome analysis, the inoculation zone was marked and the root segment comprising the inoculation zone (1 cm length, 5 mm either side of the inoculation) was harvested after 24 h, and the apical 2 mm of the root tip was removed. Auxin treatments of roots was done by placing 3-d-old seedlings of similar length onto plates containing IAA, which was dissolved as a stock solution in ethanol at 1 mM and then diluted to the correct final concentration. All control plates contained equivalent amounts of ethanol. For proteome analysis, the zone of the root corresponding to the inoculation zone of the S. melilotiinoculated roots was marked and harvested 24 h after transfer to the IAAcontaining plates (1 mM final concentration). This concentration was chosen because it showed physiological effects in M. truncatula, including stimulation of pericycle cell divisions (data not shown; van Noorden et al., 2006). Again, the root tip was removed from the analyzed root segments and the root segment was of 1 cm length, comparable to that of the inoculated roots.

Plant Transformation with the GH3:GUS Reporter Gene For promoter:GUS analysis, a 722-bp region upstream of the ATG start codon of the GH3 gene from soybean (Glycine max; Hagen et al., 1991) was PCR amplified from genomic DNA using the following primers: GH3-F ggg gac aag ttt gta caa aaa agc agg ct and GH3-R ggg gac cac ttt gta caa gaa agc tgg gtg. The resulting PCR product was verified by sequencing and subcloned into the pKGWFS7 vector (Karimi et al., 2002) using GATEWAY technology (Invitrogen). The construct was transformed into the Agrobacterium rhizogenes ARqua1 strain (Boisson-Dernier et al., 2001) using electroporation. Transformation of M. truncatula wild-type plants was performed as described by Boisson-Dernier et al. (2001), with identical conditions as described (Wasson et al., 2006). For nodulation experiments, NH4NO3 was omitted from the media and agar was replaced by Phytagel (Sigma). Hairy root plantlets were grown in a growth chamber at 25°C with a 16-h-light period at 150 mmol m22 s21 light intensity. For GUS staining, roots were fixed in 0.5% p-formaldehyde in 100 mM potassium phosphate buffer, pH 7, on ice for 45 min under vacuum and rinsed with phosphate buffer before staining with X-gluc buffer [100 mM potassium phosphate buffer, pH 7, containing 1 mM EDTA, 1% (v/v) Triton X-100, 5 mM ferri- and ferrocyanide, 50 mg/mL 5-bromo-4-chloro-3-indolyl-beta-D-GlcUA (X-Gluc Direct)] at 37°C over night. For sectioning, roots were embedded in 3% DNA grade agarose (Progen Biosciences) and sectioned on a Vibratome (1000 Plus; Vibratome Company) at 100 mm thickness. Sections were mounted on glass slides in water and examined with a Leica DMBL microscope (Leica Microsystems) and photographed with a mounted SPOT RT slider CCD camera (Diagnostic Instruments).

Protein Extraction The root proteins were extracted using a TCA-acetone precipitation method as described before (Mathesius et al., 2001). For each sample, root segments from about 50 to 60 seedlings were harvested and immediately frozen in liquid nitrogen before extraction.

Experimental Design for the DIGE Experiment The experiment included six different treatments (wild type or sunn, each treated with S. meliloti, auxin, or a control), and for each treatment four biological repeat samples were generated. Each ‘‘repeat’’ included approximately 50 to 60 root segments, which were grown on separate occasions. To allow for differences in CyDye intensity, two of each of the biological repeat samples were labeled with Cy3 and the other two with Cy5 labels. Each gel contained one Cy3 and one Cy5 sample, as well as an internal control consisting of a mixture of all 24 samples, which was labeled with Cy2. All possible combinations of pairwise comparisons between the samples were included, as recommended in the Amersham Biosciences Ettan DIGE User Manual. For the exact composition of samples of each of the 12 gels, see Supplemental Table S1.

1128

Protein Quantification and Minimal DIGE Labeling of the Protein Sample The pH of the protein samples was adjusted to pH 8 to 8.5 and the total protein concentrations of the samples were quantified using the Bradford protein assay (Bio-Rad). Bovine serum albumin over a concentration range from 0 to 1 mg mL21 was used as a standard. The protein samples were labeled using the CyDye DIGE Fluors (minimal dyes) for Ettan DIGE kit (Amersham Biosciences), according to the manufacturer’s instructions with minor modifications. Protein samples, 100 mg each, were labeled with 400 pmol amine reactive cyanine freshly dissolved in anhydrous dimethyl formamide. The labeling reaction was incubated on ice in the dark for 30 min. The reaction was terminated by addition of 10 nmol Lys. Equal volumes of 23 sample buffer (7 M urea, 2 M thiourea, 20 mg/mL DTT, and 2% Bio-Lyte 3-10) were added to each of the labeled protein samples, and the two samples plus the internal standard were mixed.

2D Gel Electrophoresis The combined protein samples were separated by isoelectric focusing using linear precast immobilized pH gradient gel strips of 24 cm length with a pH gradient of 4 to 7 (Amersham Biosciences). Immobilized pH gradient strips were rehydrated and focused as described previously (Mathesius et al., 2001). The SDS-PAGE gels were 1-mm-thick, self-cast gels containing 12.5% acrylamide without gradient; the gels were cast using the EttanDaltsix system (Amersham Biosciences). The gel-cast unit was assembled using low fluorescent glass plates (Amersham Biosciences), which are compatible with the DIGE system. First-dimension strips were equilibrated as described (Mathesius et al., 2001) and placed on the second-dimension gels. SDS-PAGE was carried out at 20°C in running buffer (25 mM Tris, pH 8.3, 192 mM Gly, and 0.1% SDS) until the bromphenol blue front had reached the bottom of the gel (600 V, 10 mA, and 2.5 W per gel for the first hour; 600 V, 40 mA, and 13 W per gel for the following 4–5 h).

Gel Imaging Immediately after running the second dimension, the DIGE-labeled proteins were visualized using a Typhoon Trio laser scanner (Amersham Biosciences). The Cy3 images were scanned using a 532-nm laser and a 580-nm band pass (BP) 30 emission filter. Cy5 images were scanned using a 633-nm laser and a 670-nm BP30 emission filter. Cy2 images were scanned using a 488-nm laser and an emission filter of 520-nm BP40. All gels were scanned at 100-mm resolution. The photo multiplier tube was set to ensure maximum pixel intensity between 40,000 and 60,000 pixels. Images were cropped to remove areas extraneous to the gel image using ImageQuant Version 5.2 (Amersham Biosciences) prior to analysis. The Coomassie-stained gel was scanned identically to the Cy5 images for matching to the DIGE gels. For presentation in the figure, it was additionally scanned at 600 dpi as a TIFF file on a flatbed scanner (UMAX Powerlook III; UMAX Technologies).

Gel Analysis Spot detections and analyses were done using DeCyder Version 5 (Amersham Biosciences), a 2D gel analysis software package designed specifically for DIGE. The difference in gel analysis (DIA) module of the DeCyder was used for protein spot detection and quantification. The maximum number of spots was set at 10,000. Protein spots with a slope .1.5 and a volume ,3,000 were excluded to eliminate nonproteinaceous spots (e.g. dust particles with a steep slope) from further analysis. All gels were normalized before analysis using the internal Cy2-labeled standard. For the normalization, the DIA module calculates the log volume ratios of all spots on a gel against the internal standard, and creates a model histogram of spot frequency against log volume ratios with the center at a log volume ratio of zero, assuming that most spots are not differentially accumulated between samples. For the histogram selection, the scatter parameter was set to ‘‘maximum volume’’ and the threshold mode was set to 2 times the SD. The biological variation analysis (BVA) module was used for gel-to-gel matching of spots and quantitative comparisons of protein accumulation across multiple gels. Gel maps were then matched to a master map using the BVA software module; however, most abundant spots were manually checked to see if the matching was correct. Two-way ANOVA

Plant Physiol. Vol. 144, 2007

Proteome Changes in Nodule Initiation and Auxin Response

followed by Student’s t tests was performed using the BVA module. The results were extracted using the XML toolbox module of the DeCyder software. To match the Coomassie-stained image to the DIGE gels, the Coomassie image was imported as a spot map into DeCyder software and matched in the BVA module after applying landmarks across the gel (see Supplemental Fig. S1).

Colloidal Coomassie Staining For protein identification, 2D gel electrophoresis was performed, with 500 mg of (unlabeled) proteins as starting material from A17 or sunn roots of a pooled sample of all treatments used in the DIGE analysis. Coomassie staining was done as described (Mathesius et al., 2001).

Mass Spectrometry Protein spots of interest were excised from the preparative gels stained with Coomassie blue using sterile scalpel blades. The excised gel pieces were destained, digested, and analyzed using MALDI-TOF/TOF MS with an Applied Biosystems 4800 Proteomics Analyser as described by Prayitno et al. (2006a).

Database Searches Mass spectra and ion data generated by MALDI-TOF MS/MS were used to search for protein identification against the M. truncatula EST database (MtGI; http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb5medicago) using the Mascot Daemon Version 2.1.0 software program (Matrix Science), which at the time of analysis (February 2006) contained 226,923 entries. For peptide matching, a maximum of one miscleavage per peptide, and peptide modifications by oxidation of Met and carbamidomethylation of Cys were allowed. The peptide mass tolerance and ion mass (MS/MS) accuracy used for peptide matching were 100 ppm and 0.4 D, respectively. The confidence of peptide matches was based on the significant value of the MOWSE score (.35), the mass accuracy, number of peptide matches, and the percentage of sequence coverage. Because calculations of the expected Mr and pI are unreliable from EST data as EST sequences are often incomplete, we did not compare expected and actual molecular weight and pI of the proteins. The search parameters for the single peptide matches included no miscleavage, no allowance of any modifications, a peptide charge of 11, and a peptide tolerance of 50 ppm unless de novo sequences of at least eight amino acids obtained. The raw MS data of proteins that did not match significantly to the current M. truncatula EST database are available on request.

Protein Classification Identified proteins have been assigned to a hierarchical functional classification modeled on KEGG database (Kanehisa et al., 2004) by homology relationship (Goffard and Weiller, 2006, 2007). To detect if a certain functional category is statistically overrepresented in a group of proteins (as shown in Fig. 3) compared to the rest of the identified proteins, the P value for all functional categories throughout the classification was calculated using the hypergeometric distribution. This P value represents the probability that the intersection of the set of proteins belonging to the given functional classification occurs by chance.

Supplemental Data The following materials are available in the online version of this article. Supplemental Table S1. Labeling scheme for DIGE gels. Supplemental Table S2. Protein accumulation levels following rhizobia and auxin treatment. Supplemental Table S3. Protein accumulation level changes between the wild type and sunn. Supplemental Table S4. Identity of protein spots as determined by MS.

Plant Physiol. Vol. 144, 2007

ACKNOWLEDGMENTS We thank Nijat Imin for help with protein identification; Peter Milburn and the Australian Cancer Research Foundation at the Biomolecular Resource Facility, John Curtin School of Medical Research, Australian National University, for MALDI-TOF/TOF analysis; and Marike van Noorden for editing the figures. Many thanks to Julia Frugoli for kindly supplying the sunn seed and for discussions on the topic. Received March 22, 2007; accepted April 13, 2007; published April 27, 2007.

LITERATURE CITED Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I (2003) A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3: 36–44 Amiour N, Recorbet G, Robert F, Gianinazzi S, Dumas-Gaudot E (2006) Mutations in DMI3 and SUNN modify the appressorium-responsive root proteome in arbuscular mycorrhiza. Mol Plant Microbe Interact 19: 988–997 Beeckman T, Burssens S, Inze´ D (2001) The peri-cell-cycle in Arabidopsis. J Exp Bot 52: 403–411 Bestel-Corre G, Dumas-Gaudot E, Poinsot V, Dieu M, Dierick JF, van Tuinen D, Remacle J, Gianinazzi-Pearson V, Gianinazzi S (2002) Proteome analysis and identification of symbiosis-related proteins from Medicago truncatula Gaertn. by two-dimensional electrophoresis and mass spectrometry. Electrophoresis 23: 122–137 Blilou I, Xu J, Wildwater M, Willemsen V, Paponov I, Friml J, Heidstra R, Aida M, Palme K, Scheres B (2005) The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature 433: 39–44 Boisson-Dernier A, Chabaud M, Garcia F, Becard G, Rosenberg C, Barker DG (2001) Agrobacterium rhizogenes-transformed roots of Medicago truncatula for the study of nitrogen-fixing and endomycorrhizal symbiotic associations. Mol Plant Microbe Interact 14: 695–700 Boot KJM, van Brussel AAN, Tak T, Spaink HP, Kijne JW (1999) Lipochitin oligosaccharides from Rhizobium leguminosarum bv. viciae reduce auxin transport capacity in Vicia sativa subsp nigra roots. Mol Plant Microbe Interact 12: 839–844 Brown DE, Rashotte AM, Murphy AS, Normanly J, Tague BW, Peer WA, Taiz L, Muday GK (2001) Flavonoids act as negative regulators of auxin transport in vivo in Arabidopsis. Plant Physiol 126: 524–535 Caetano-Anolle`s G, Gresshoff PM (1991) Plant genetic control of nodulation. Annu Rev Microbiol 45: 345–382 Casimiro I, Marchant A, Bhalerao RP, Beeckman T, Dhooge S, Swarup R, Graham N, Inze´ D, Sandberg G, Casero PJ, et al (2001) Auxin transport promotes Arabidopsis lateral root initiation. Plant Cell 13: 843–852 Colditz F, Nyamsuren O, Niehaus K, Eubel H, Braun HP, Krajinski F (2004) Proteomic approach: identification of Medicago truncatula proteins induced in roots after infection with the pathogenic oomycete Aphanomyces euteiches. Plant Mol Biol 55: 109–120 de Billy F, Grosjean C, May S, Bennett M, Cullimore JV (2001) Expression studies on AUX1-like genes in Medicago truncatula suggest that auxin is required at two steps in early nodule development. Mol Plant Microbe Interact 14: 267–277 El Yahyaoui F, Kuster H, Ben Amor B, Hohnjec N, Puhler A, Becker A, Gouzy J, Vernie T, Gough C, Niebel A, et al (2004) Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program. Plant Physiol 136: 3159–3176 Fa˚hraeus G (1957) The infection of clover root hairs by nodule bacteria studied by a simple glass slide technique. J Gen Microbiol 16: 374–381 Ferguson BJ, Mathesius U (2003) Signaling interactions during nodule development. J Plant Growth Regul 22: 47–72 Gamas P, de Billy F, Truchet G (1998) Symbiosis specific expression of two Medicago truncatula nodulin genes MtN1 and MtN13, encoding products homologous to plant defense proteins. Mol Plant Microbe Interact 11: 393–403 Goffard N, Weiller G (2006) Extending MapMan: application to legume genome arrays. Bioinformatics 22: 2958–2959 Goffard N, Weiller G (2007) GeneBins: a database for classifying gene expression data, with application to plant genome arrays. BMC Bioinformatics 8: 87

1129

van Noorden et al.

Gonzalez-Rizzo S, Crespi M, Frugier F (2006) The Medicago truncatula CRE1 cytokinin receptor regulates lateral root development and early symbiotic interaction with Sinorhizobium meliloti. Plant Cell 18: 2680–2693 Hagen G, Martin G, Li Y, Guilfoyle TJ (1991) Auxin induced expression of the soybean GH3 promoter in transgenic tobacco plants. Plant Mol Biol 17: 567–579 Hashimoto M, Kisseleva L, Sawa S, Furukawa T, Komatsu S, Koshiba T (2004) A novel rice PR10 protein, RSOsPR10, specifically induced in roots by biotic and abiotic stresses, possibly via the jasmonic acid signaling pathway. Plant Cell Physiol 45: 550–559 Heisler MG, Ohno C, Das P, Sieber P, Reddy GV, Long JA, Meyerowitz EM (2005) Patterns of auxin transport and gene expression during primordium development revealed by live imaging of the Arabidopsis inflorescence meristem. Curr Biol 15: 1899–1911 Holmes P, Farquharson R, Hall PJ, Rolfe BG (2006) Proteomic analysis of root meristems and the effects of acetohydroxyacid synthase-inhibiting herbicides in the root of Medicago truncatula. J Proteome Res 5: 2309–2316 Huo X, Schnabel E, Highes K, Frugoli J (2006) RNAi phenotypes and the localization of a protein:GUS fusion imply a role for Medicago truncatula PIN genes in nodulation. J Plant Growth Regul 25: 156–165 Jiang K, Feldman LJ (2005) Regulation of root apical meristem development. Annu Rev Cell Dev Biol 21: 485–509 Jiang K, Meng YL, Feldman LJ (2003) Quiescent center formation in maize roots is associated with an auxin-regulated oxidizing environment. Development 130: 1429–1438 Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277–D280 Karimi M, Inze´ D, Depicker A (2002) GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7: 193–195 Kim SY, Sivaguru M, Stacey G (2006) Extracellular ATP in plants. Visualization, localization, and analysis of physiological significance in growth and signaling. Plant Physiol 142: 984–992 Kinkema M, Scott PT, Gresshoff PM (2006) Legume nodulation: successful symbiosis through short- and long-distance signalling. Funct Plant Biol 33: 707–721 Kondorosi E, Redondo-Nieto M, Kondorosi A (2005) Ubiquitin-mediated proteolysis. To be in the right place at the right moment during nodule development. Plant Physiol 137: 1197–1204 Kramer EM, Bennett MJ (2006) Auxin transport: a field in flux. Trends Plant Sci 11: 382–386 Krusell L, Madsen LH, Sato S, Aubert G, Genua A, Szczyglowski K, Duc G, Kaneko T, Tabata S, de Bruijn F, et al (2002) Shoot control of root development and nodulation is mediated by a receptor-like kinase. Nature 420: 422–426 Larkin PJ, Gibson JM, Mathesius U, Weinman JJ, Gartner E, Hall E, Tanner GJ, Rolfe BG, Djordjevic MA (1996) Transgenic white clover. Studies with the auxin-responsive promoter, GH3, in root gravitropism and lateral root development. Transgenic Res 5: 325–335 Lohar DP, Sharopova N, Endre G, Penuela S, Samac D, Town C, Silverstein KAT, VandenBosch KA (2006) Transcript analysis of early nodulation events in Medicago truncatula. Plant Physiol 140: 221–234 Markovic-Housley Z, Degano M, Lamba D, von Roepenack-Lahaye E, Clemens S, Susani M, Ferreira F, Scheiner O, Breiteneder H (2003) Crystal structure of a hypoallergenic isoform of the major birch pollen allergen Bet v 1 and its likely biological function as a plant steroid carrier. J Mol Biol 325: 123–133 Mathesius U, Keijzers G, Natera SHA, Weinman JJ, Djordjevic MA, Rolfe BG (2001) Establishment of a root proteome reference map for the model legume Medicago truncatula using the expressed sequence tag database for peptide mass fingerprinting. Proteomics 1: 1424–1440 Mathesius U, Schlaman HRM, Spaink HP, Sautter C, Rolfe BG, Djordjevic MA (1998) Auxin transport inhibition precedes root nodule formation in white clover roots and is regulated by flavonoids and derivatives of chitin oligosaccharides. Plant J 14: 23–34 McGhee JD, Hamer JE, Hodges TK (2001) Characterization of a PR-10 pathogenesis-related gene family induced in rice during infection with Magnaporthe grisea. Mol Plant Microbe Interact 14: 877–886 Mitho¨fer A (2002) Suppression of plant defence in rhizobia-legume symbiosis. Trends Plant Sci 7: 440–444 Mittler R, Vanderauwera S, Golery M, van Breusegem F (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9: 490–498

1130

Mogensen JE, Wimmer R, Larsen JN, Spangfort MD, Otzen DE (2002) The major birch allergen, Bet v 1, shows affinity for a broad spectrum of physiological ligands. J Biol Chem 277: 23684–23692 Murray JD, Karas BJ, Sato S, Tabata S, Amyot L, Szczglowski K (2007) A cytokinin perception mutant colonized by Rhizobium in the absence of nodule organogenesis. Science 315: 101–104 Nakagawa T, Kawaguchi M (2006) Shoot-applied MeJA suppresses root nodulation in Lotus japonicus. Plant Cell Physiol 47: 176–180 Nilsson O, Olsson O (1997) Getting to the root: the role of the Agrobacterium rhizogenes rol genes in the formation of hairy roots. Physiol Plant 100: 463–473 Nishimura R, Ohmori M, Fujita H, Kawaguchi M (2002) A Lotus basic leucine zipper protein with a RING-finger motif negatively regulates the developmental program of nodulation. Proc Natl Acad Sci USA 99: 15206–15210 Oka-Kira E, Kawaguchi M (2006) Long-distance signaling to control root nodule number. Curr Opin Plant Biol 9: 496–502 Pacios-Bras C, Schlaman HRM, Boot K, Admiraal P, Langerak JM, Stougaard J, Spaink HP (2003) Auxin distribution in Lotus japonicus during root nodule development. Plant Mol Biol 52: 1169–1180 Peer WA, Bandyopadhyay A, Blakeslee JJ, Makam SI, Chen RJ, Masson PH, Murphy AS (2004) Variation in expression and protein localization of the PIN family of auxin efflux facilitator proteins in flavonoid mutants with altered auxin transport in Arabidopsis thaliana. Plant Cell 16: 1898–1911 Penmetsa RV, Cook DR (1997) A legume ethylene-insensitive mutant hyperinfected by its rhizobial symbiont. Science 275: 527–530 Penmetsa RV, Frugoli JA, Smith LS, Long SR, Cook DR (2003) Dual genetic pathways controlling nodule number in Medicago truncatula. Plant Physiol 131: 998–1008 Poupard P, Brunel N, Leduc N, Viemont JD, Strullu DG, Simoneau P (2001) Expression of a Bet v 1 homologue gene encoding a PR 10 protein in birch roots: induction by auxin and localization of the transcripts by in situ hybridization. Aust J Plant Physiol 28: 57–63 Prayitno J, Imin N, Rolfe BG, Mathesius U (2006a) Identification of ethylene-mediated protein changes during nodulation in Medicago truncatula using proteome analysis. J Proteome Res 5: 3084–3095 Prayitno J, Rolfe BG, Mathesius U (2006b) The ethylene-insensitive sickle mutant of Medicago truncatula shows altered auxin transport regulation during nodulation. Plant Physiol 142: 168–180 Rolfe BG, Gresshoff PM, Shine J (1980) Rapid screening for symbiotic mutants of Rhizobium and white clover. Plant Sci Lett 19: 277–284 Roudier F, Fedorova E, Lebris M, Lecomte P, Gyorgyey J, Vaubert D, Horvath G, Abad P, Kondorosi A, Kondorosi E (2003) The Medicago species A2-type cyclin is auxin regulated and involved in meristem formation but dispensable for endoreduplication-associated developmental programs. Plant Physiol 131: 1091–1103 Sasaki-Sekimoto Y, Taki N, Obayashi T, Aono M, Matsumoto F, Sakurai N, Suzuki H, Hirai MY, Noji M, Saito K, et al (2005) Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis. Plant J 44: 653–668 Schaller F, Weiler EW (1997) Enzymes of octadecanoid biosynthesis in plants: 12-oxo-phytodienoate 10,11-reductase. Eur J Biochem 245: 294–299 Schnabel E, Journet EP, de Carvalho-Niebel F, Duc G, Frugoli J (2005) The Medicago truncatula SUNN gene encodes a CLV1-like leucine-rich repeat receptor kinase that regulates nodule number and root length. Plant Mol Biol 58: 809–822 Searle IR, Men AE, Laniya TS, Buzas DM, Iturbe-Ormaetxe I, Carroll BJ, Gresshoff PM (2003) Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science 299: 109–112 Srivastava S, Emery RJN, Kurepin LV, Reid DM, Fristensky B, Kav NNV (2006) Pea PR 10.1 is a ribonuclease and its transgenic expression elevates cytokinin levels. Plant Growth Regul 49: 17–25 Stafford HA (1997) Roles of flavonoids in symbiotic and defense functions in legume roots. Bot Rev 63: 27–39 Subramanian S, Stacey G, Yu O (2006) Endogenous isoflavones are essential for the establishment of symbiosis between soybean and Bradyrhizobium japonicum. Plant J 48: 261–273 Sun JH, Cardoza V, Mitchell DM, Bright L, Oldroyd G, Harris JM (2006) Crosstalk between jasmonic acid, ethylene and Nod factor signaling allows integration of diverse inputs for regulation of nodulation. Plant J 46: 961–970

Plant Physiol. Vol. 144, 2007

Proteome Changes in Nodule Initiation and Auxin Response

Timmers ACJ, Auriac MC, Truchet G (1999) Refined analysis of early symbiotic steps of the Rhizobium-Medicago interaction in relationship with microtubular cytoskeleton rearrangements. Development 126: 3617–3628 Tirichine L, Sandal N, Madsen LH, Radutoiu S, Albrektsen AS, Sato S, Asamizu E, Tabata S, Stougaard J (2007) A gain-of-function mutation in a cytokinin receptor triggers spontaneous root nodule organogenesis. Science 315: 104–107 ¨ nlu¨ M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a U single gel method for detecting changes in protein extracts. Electrophoresis 18: 2071–2077

Plant Physiol. Vol. 144, 2007

van Loon LC, Rep M, Pieterse CMJ (2006) Significance of inducible defense-related proteins in infected plants. Annu Rev Phytopathol 44: 135–162 van Noorden GE, Ross JJ, Reid JB, Rolfe BG, Mathesius U (2006) Defective long distance auxin transport regulation in the Medicago truncatula super numerary nodules mutant. Plant Physiol 140: 1494–1506 Wasson AP, Pellerone FI, Mathesius U (2006) Silencing the flavonoid pathway in Medicago truncatula inhibits root nodule formation and prevents auxin transport regulation by rhizobia. Plant Cell 18: 1539–1540 Watson BS, Asirvatham VS, Wang L, Sumner LW (2003) Mapping the proteome of barrel medic (Medicago truncatula). Plant Physiol 131: 1104–1123

1131