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Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology

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Abstract

Key message

Symbiotic nitrogen fixation in root nodules of legumes is a highly important biological process which is only poorly understood. Root nodule metabolism differs from that of roots. Differences in root and nodule metabolism are expressed by altered protein abundances and amenable to quantitative proteome analyses. Differences in the proteomes may either be tissue specific and related to the presence of temporary endosymbionts (the bacteroids) or related to nitrogen fixation activity. An experimental setup including WT bacterial strains and strains not able to conduct symbiotic nitrogen fixation as well as root controls enables identification of tissue and nitrogen fixation specific proteins.

Abstract

Root nodules are specialized plant organs housing and regulating the mutual symbiosis of legumes with nitrogen fixing rhizobia. As such, these organs fulfill unique functions in plant metabolism. Identifying the proteins required for the metabolic reactions of nitrogen fixation and those merely involved in sustaining the rhizobia:plant symbiosis, is a challenging task and requires an experimental setup which allows to differentiate between these two physiological processes. Here, quantitative proteome analyses of nitrogen fixing and non-nitrogen fixing nodules as well as fertilized and non-fertilized roots were performed using Vicia faba and Rhizobium leguminosarum. Pairwise comparisons revealed altered enzyme abundance between active and inactive nodules. Similarly, general differences between nodules and root tissue were observed. Together, these results allow distinguishing the proteins directly involved in nitrogen fixation from those related to nodulation. Further observations relate to the control of nodulation by hormones and provide supportive evidence for the previously reported correlation of nitrogen and sulfur fixation in these plant organs. Additionally, data on altered protein abundance relating to alanine metabolism imply that this amino acid may be exported from the symbiosomes of V. faba root nodules in addition to ammonia. Data are available via ProteomeXchange with identifier PXD008548.

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Acknowledgements

We thank Prof. Dr. Ursula B. Priefer and Prof. Dr. Allan Downie for providing the Rhizobium leguminosarum strains Fix+ and Fix. Our research was supported by the Deutsche Forschungsgemeinschaft (DFG) in the frame of the Graduiertenkolleg Signaling at the plant Soil interface (GRK1798).

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Authors

Contributions

BT conducted all experiments participated in preparation of the manuscript. H-PB participated in the planning of experiments and preparation of the manuscript. HE planned the experiments and participated in the preparation of the manuscript.

Corresponding author

Correspondence to Holger Eubel.

Electronic supplementary material

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Suppl. Table 1: Proteins changing significantly between lines 0 and N (DOCX 25 KB)

Suppl. Table 2: Proteins changing significantly between lines Fix+ and N (DOCX 31 KB)

Suppl. Table 3: Proteins changing significantly between lines Fix+ and Fix- (DOCX 21 KB)

Suppl. Table 4: Proteins changing significantly between lines 0 and Fix- (DOCX 63 KB)

Suppl. Table 5: Top five proteins derived from pairwise comparisons of Fix+/Fix-, Fix+/N, Fix-/0, and N/0 (DOCX 14 KB)

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Suppl. Figure 1: Testing of protein sequence databases for cross species protein identification. Among the three databases, two are species independent and contain a broad spectrum of proteins from all kingdoms of life (NCBInr, SwissProt, both of which were downloaded in Jnuaury 2018) while the third database is a custom made, in house database containing the protein sequences of V. faba, R. leguminosarum, as well as frequent contaminants. One Fix- sample could not be analyzed using our bioinformatics platform, most likely due to memory constraints. In all cases, the in-house M. truncatula and R. leguminosarum database identified more proteins than the two broad species databases, probably due to increased statistical uncertainties inherent to large-scale databases with too many entries. (PDF 168 KB)

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Suppl. Figure 2: Altered cellular processes in Fix+ compared to Fix- and N. Bars indicate the number of altered proteins associated with a given cellular function. Upper panel: Fix+ (red bars) opposed to Fix- (yellow bars). Lower panel compares Fix+ with N (blue bars). AdoMet, S-Adenosyl methionine; OXPHOS, oxidative phosphorylation system; TCA, tricarboxylic acid cycle; PPP, pentose phosphate pathway. (PDF 450 KB)

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Suppl. Figure 3: Pairwise comparisons and meta-comparisons between the four sample groups. The four sample groups differ in two aspects i) nodule formation (true for Fix+ and Fix-, false for N and 0) and ii) nitrogen status (high for Fix+ and N, low for Fix- and 0). Six comparisons are conceivable between the four groups (grey full and dashed arrows) but only the full arrows allow comparison of groups differing only in a single aspect (nodulation or nitrogen status). Pairwise comparisons were thus limited to these combinations. The comparisons of Fix+ with Fix- and of Fix+ with N as these allow the identification of proteins specific for symbiotic nitrogen fixation via a meta comparison (MC) approach (MC1). In a second meta comparison (MC2) the nodule forming groups are compared with N and 0 to pinpoint symbiosis related proteins. (PDF 167 KB)

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Suppl. Figure 4: Mean abundance of core plant and bacteroid SNF enzymes. Significant differences (t-test) between the sample groups are indicated by a star (p<0.05). AS1, asparagine synthase (Medtr3g464580.1, Medtr3g464580.2, Medtr3g464580.3); AS2, glutamine-dependent asparagine synthase 1 (Medtr5g071360.1-2); AspAT1, aspartate aminotransferase (Medtr8g091280.1); AspAT2 (Medtr1g013050.1); AspAT3, aspartate aminotransferase (Medtr3g110065.1-3); GOGAT, ferredoxin-dependent glutamate synthase (Medtr7g089970.1); GDH, NADP-specific glutamate dehydrogenase (Medtr7g085630.1-6); GS1, glutamine synthetase (Medtr2g021255.1-2); GS2, glutamine synthetase domain protein (Medtr6g071070.1); GS3, (Medtr3g065250.1, Medtr5g077950.1); NifD, Nitrogenase (molybdenum-iron) alpha chain (pRL100161); NifH, Nitrogenase iron protein (pRL100162); NifK, Nitrogenase (molybdenum-iron) beta chain (pRL100160); NifN, Nitrogenase FeMo-cofactor scaffold and assembly protein (pRL100158); PEPC1, phosphoenolpyruvate carboxylase (Medtr2g092930.1); PEPC2 (Medtr4g079860.1); PEPC3 (Medtr2g076670.1-3); PEPC4 (Medtr8g463920.1-3). (PDF 526 KB)

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Suppl. Fig. 5: Response of seven proteins commonly found in MC1 and MC2 to SNF activity (Fix+/Fix-) as well as nodulation and SNF activity (Fix+/N). Altered protein abundance are expressed in log2 (fold) change between the groups as derived from pairwise comparisons. (PDF 172 KB)

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Thal, B., Braun, HP. & Eubel, H. Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology. Plant Mol Biol 97, 233–251 (2018). https://doi.org/10.1007/s11103-018-0736-7

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  • DOI: https://doi.org/10.1007/s11103-018-0736-7

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