[en] Cassava (Manihot esculenta) is the most important root crop in the tropics, but rapid postharvest physiological deterioration (PPD) of the root is a major constraint to commercial cassava production. We established a reliable method for image-based PPD symptom quantification and used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2600 unique proteins were identified in the cassava root, and nearly 300 proteins showed significant abundance regulation during PPD. We identified protein abundance modulation in pathways associated with oxidative stress, phenylpropanoid biosynthesis (including scopoletin), the glutathione cycle, fatty acid alpha-oxidation, folate transformation, and the sulfate reduction II pathway. Increasing protein abundances and enzymatic activities of glutathione-associated enzymes, including glutathione reductases, glutaredoxins, and glutathione S-transferases, indicated a key role for ascorbate/glutathione cycles. Based on combined proteomics data, enzymatic activities, and lipid peroxidation assays, we identified glutathione peroxidase as a candidate for reducing PPD. Transgenic cassava overexpressing a cytosolic glutathione peroxidase in storage roots showed delayed PPD and reduced lipid peroxidation as well as decreased H2O2 accumulation. Quantitative proteomics data from ethene and phenylpropanoid pathways indicate additional gene candidates to further delay PPD. Cassava root proteomics data are available at www.pep2pro.ethz.ch for easy access and comparison with other proteomics data.
Achidi, A.U., Ajayi, O.A., Bokanga, M., and Maziya-Dixon, B. (2005). The use of cassava leaves as food in Africa. Ecol. Food Nutr. 44: 423-435.
Alexa, A., Rahnenführer, J., and Lengauer, T. (2006). Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607.
Amako, K., Chen, G.X., and Asada, K. (1994). Separate assays specific for ascorbate peroxidase and guaiacol peroxidase and for the chloroplastic and cytosolic isozymes of ascorbate peroxidase in plants. Plant Cell Physiol. 35: 497-504.
Baba, A.I., Nogueira, F.C.S., Pinheiro, C.B., Brasil, J.N., Jereissati, E.S., Juca, T.L., Soares, A.A., Santos, M.F., Domont, G.B., and Campos, F.A.P. (2008). Proteome analysis of secondary somatic embryogenesis in cassava (Manihot esculenta). Plant Sci. 175: 717-723.
Baerenfaller, K., Hirsch-Hoffmann, M., Svozil, J., Hull, R., Russenberger, D., Bischof, S., Lu, Q., Gruissem, W., and Baginsky, S. (2011). pep2pro: A new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana. Integr. Biol. (Camb.) 3: 225-237.
Bayoumi, S.A., Rowan, M.G., Beeching, J.R., and Blagbrough, I.S. (2010). Constituents and secondary metabolite natural products in fresh and deteriorated cassava roots. Phytochemistry 71: 598-604.
Beeching, J.R., Han, Y.H., Gomez-Vasquez, R., Day, R.C., and Cooper, R.M. (1998). Wound and defense responses in cassava as related to postharvest physiological deterioration. Recent Adv. Phytochem. 32: 231-248.
Booth, R.H. (1976). Storage of fresh cassava (Manihot esculenta). 1. Post-harvest deterioration and its control. Exp. Agric. 12: 103.
Bull, S.E., Owiti, J.A., Niklaus, M., Beeching, J.R., Gruissem, W., and Vanderschuren, H. (2009). Agrobacterium-mediated transformation of friable embryogenic calli and regeneration of transgenic cassava. Nat. Protoc. 4: 1845-1854.
Buschmann, H., Reilly, K., Rodriguez, M.X., Tohme, J., and Beeching, J.R. (2000a). Hydrogen peroxide and flavan-3-ols in storage roots of cassava (Manihot esculenta Crantz) during postharvest deterioration. J. Agric. Food Chem. 48: 5522-5529.
Buschmann, H., Rodriguez, M.X., Tohme, J., and Beeching, J.R. (2000b). Accumulation of hydroxycoumarins during post-harvest deterioration of tuberous roots of cassava (Manihot esculenta Crantz). Ann. Bot. (Lond.) 86: 1153-1160.
Chen, Z., and Gallie, D.R. (2006). Dehydroascorbate reductase affects leaf growth, development, and function. Plant Physiol. 142: 775-787.
Chong, J., Baltz, R., Fritig, B., and Saindrenan, P. (1999). An early salicylic acid-, pathogen-and elicitor-inducible tobacco glucosyltransferase: Role in compartmentalization of phenolics and H2O2 metabolism. FEBS Lett. 458: 204-208.
De León, I.P., Sanz, A., Hamberg, M., and Castresana, C. (2002). Involvement of the Arabidopsis alpha-DOX1 fatty acid dioxygenase in protection against oxidative stress and cell death. Plant J. 29: 61-62.
Dixon, R.A., Chen, F., Guo, D., and Parvathi, K. (2001). The biosynthesis of monolignols: A "metabolic grid", or independent pathways to guaiacyl and syringyl units? Phytochemistry 57: 1069-1084.
El-Sharkawy, M.A. (2006). International research on cassava photosynthesis, productivity, eco-physiology, and responses to environmental stresses in the tropics. Photosynthetica 44: 481-512.
Fermont, A.M., van Asten, P.J.A., Tittonell, P., van Wijk, M.T., and Giller, K.E. (2009). Closing the cassava yield gap: An analysis from smallholder farms in East Africa. Field Crops Res. 112: 24-36.
Foyer, C.H., and Halliwell, B. (1976). The presence of glutathione and glutathione reductase in chloroplasts: A proposed role in ascorbic acid metabolism. Planta 133: 21-25.
Fujiwara, T., Nambara, E., Yamagishi, K., Goto, D.B., and Naito, S. (2002). Storage proteins. The Arabidopsis Book 1: e0020, doi/ 10.1199/tab.0020.
Grossmann, J., Roschitzki, B., Panse, C., Fortes, C., Barkow-Oesterreicher, S., Rutishauser, D., and Schlapbach, R. (2010). Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods. J. Proteomics 73: 1740-1746.
Han, Y.H., Gomez-Vasquez, R., Reilly, K., Li, H.Y., Tohme, J., Cooper, R.M., and Beeching, J.R. (2001). Hydroxyproline-rich glycoproteins expressed during stress responses in cassava. Euphytica 120: 59-70.
Hanson, A.D., and Roje, S. (2001). One-carbon metabolism in higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52: 119-137.
Hirose, S., Data, E.S., Tanaka, Y., and Uritani, I. (1984). Physiological deterioration and ethylene production in cassava roots after harvest, in relation with pruning treatment. Jpn. J. Crop Sci. 53: 282-289.
Hirsch-Hoffmann, M., Gruissem, W., and Baerenfaller, K. (2012). pep2pro: The high-throughput proteomics data processing, analysis, and visualization tool. Front. Plant Sci. 3: 123.
Hodges, D.M., DeLong, J.M., Forney, C.F., and Prange, R.K. (1999). Improving the thiobarbituric acid-reactive-substances assay for estimating lipid peroxidation in plant tissues containing anthocyanin and other interfering compounds. Planta 207: 604-611.
Huang, J., Bachem, C., Jacobsen, E., and Visser, R.G.F. (2001). Molecular analysis of differentially expressed genes during postharvest deterioration in cassava (Manihot esculenta Crantz) tuberous roots. Euphytica 120: 85-93.
Iqbal, A., Yabuta, Y., Takeda, T., Nakano, Y., and Shigeoka, S. (2006). Hydroperoxide reduction by thioredoxin-specific glutathione peroxidase isoenzymes of Arabidopsis thaliana. FEBS J. 273: 5589-5597.
Kai, K., Mizutani, M., Kawamura, N., Yamamoto, R., Tamai, M., Yamaguchi, H., Sakata, K., and Shimizu, B. (2008). Scopoletin is biosynthesized via ortho-hydroxylation of feruloyl CoA by a 2-oxoglutarate-dependent dioxygenase in Arabidopsis thaliana. Plant J. 55: 989-999.
King, R.R., and Calhoun, L.A. (2005). Characterization of crosslinked hydroxycinnamic acid amides isolated from potato common scab lesions. Phytochemistry 66: 2468-2473.
Kunttu, L., Lepisto, L., Rauhamaa, J., and Visa, A. (2003). Binary histogram in image classification for retrieval purposes. In Journal of WSCG, No. 1, WSCG'2003, February 3-7, 2003 (Plzen, Czech Republic: Copyright UNION Agency, Science Press), pp. 269-273.
Kwon, S.Y., Choi, S.M., Ahn, Y.O., Lee, H.S., Lee, H.B., Park, Y.M., and Kwak, S.S. (2003). Enhanced stress-tolerance of transgenic tobacco plants expressing a human dehydroascorbate reductase gene. J. Plant Physiol. 160: 347-353.
Lobell, D.B., Burke, M.B., Tebaldi, C., Mastrandrea, M.D., Falcon, W.P., and Naylor, R.L. (2008). Prioritizing climate change adaptation needs for food security in 2030. Science 319: 607-610.
Loscalzo, J., and Freedman, J. (1986). Purification and characterization of human platelet glutathione-S-transferase. Blood 67: 1595-1599.
Mitprasat, M., Roytrakul, S., Jiemsup, S., Boonseng, O., and Yokthongwattana, K. (2011). Leaf proteomic analysis in cassava (Manihot esculenta, Crantz) during plant development, from planting of stem cutting to storage root formation. Planta 233: 1209-1221.
Montagnac, J.A., Davis, C.R., and Tanumihardjo, S.A. (2009). Nutritional value of cassava for use as a staple food and recent advances for improvement. Comprehensive Reviews in Food Science and Food Safety 8: 181-194.
Mueller, L.A., Zhang, P., and Rhee, S.Y. (2003). AraCyc: A biochemical pathway database for Arabidopsis. Plant Physiol. 132: 453-460.
Niggeweg, R., Michael, A.J., and Martin, C. (2004). Engineering plants with increased levels of the antioxidant chlorogenic acid. Nat. Biotechnol. 22: 746-754.
Owiti, J., Grossmann, J., Gehrig, P., Dessimoz, C., Laloi, C., Hansen, M.B., Gruissem, W., and Vanderschuren, H. (2011). iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration. Plant J. 67: 145-156.
Prochnik, S., Marri, P.R., Desany, B., Rabinowicz, P.D., Kodira, C., Mohiuddin, M., Rodriguez, F., Fauquet, C., Tohme, J., Harkins, T., Rokhsar, D.S., and Rounsley, S. (2012). The cassava genome: Current progress, future directions. Trop. Plant Biol. 5: 88-94.
Raju, P.D.R., and Neelima, G. (2012). Image segmentation by using histogram tresholding. International Journal of Computer Science Engineering and Technology 2: 776-779.
Reilly, K., Bernal, D., Cortés, D.F., Gómez-Vásquez, R., Tohme, J., and Beeching, J.R. (2007). Towards identifying the full set of genes expressed during cassava post-harvest physiological deterioration. Plant Mol. Biol. 64: 187-203.
Reilly, K., Gómez-Vásquez, R., Buschmann, H., Tohme, J., and Beeching, J.R. (2004). Oxidative stress responses during cassava post-harvest physiological deterioration. Plant Mol. Biol. 56: 625-641.
Reilly, K., Han, Y., Tohme, J., and Beeching, J.R. (2001). Isolation and characterisation of a cassava catalase expressed during postharvest physiological deterioration. Biochim. Biophys. Acta 1518: 317-323.
Rickard, J.E. (1985). Physiological deterioration of cassava roots. J. Sci. Food Agric. 36: 167-176.
Rodriguez Milla, M.A., Maurer, A., Rodriguez Huete, A., and Gustafson, J.P. (2003). Glutathione peroxidase genes in Arabidopsis are ubiquitous and regulated by abiotic stresses through diverse signaling pathways. Plant J. 36: 602-615.
Rommens, C.M., Richael, C.M., Yan, H., Navarre, D.A., Ye, J., Krucker, M., and Swords, K. (2008). Engineered native pathways for high kaempferol and caffeoylquinate production in potato. Plant Biotechnol. J. 6: 870-886.
Roxas, V.P., Lodhi, S.A., Garrett, D.K., Mahan, J.R., and Allen, R.D. (2000). Stress tolerance in transgenic tobacco seedlings that overexpress glutathione S-transferase/glutathione peroxidase. Plant Cell Physiol. 41: 1229-1234.
Rubery, P.H., and Fosket, D.E. (1969). Changes in phenylalanine ammonia-lyase activity during xylem differentiation in Coleus and soybean. Planta 87: 54-62.
Saito, K. (2004). Sulfur assimilatory metabolism: The long and smelling road. Plant Physiol. 136: 2443-2450.
Sanchez, T., Chavez, A.L., Ceballos, H., Rodriguez-Amaya, D., Nestel, P., and Ishitani, M. (2006). Reduction or delay of postharvest physiological deterioration in cassava roots with higher carotenoid content. J. Sci. Food Agric. 86: 634-639.
Sayre, R., et al. (2011). The BioCassava Plus Program: Biofortification of cassava for sub-Saharan Africa. Annu. Rev. Plant Biol. 62: 251-272.
Schmelz, E.A., Kaplan, F., Huffaker, A., Dafoe, N.J., Vaughan, M.M., Ni, X., Rocca, J.R., Alborn, H.T., and Teal, P.E. (2011). Identity, regulation, and activity of inducible diterpenoid phytoalexins in maize. Proc. Natl. Acad. Sci. USA 108: 5455-5460.
Sheffield, J., Taylor, N., Fauquet, C., and Chen, S. (2006). The cassava (Manihot esculenta Crantz) root proteome: Protein identification and differential expression. Proteomics 6: 1588-1598.
Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996). Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68: 850-858.
Silva, J.C., Gorenstein, M.V., Li, G.Z., Vissers, J.P., and Geromanos, S.J. (2006). Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition. Mol. Cell. Proteomics 5: 144-156.
Stupak, M., Vanderschuren, H., Gruissem, W., and Zhang, P. (2006). Biotechnological approaches to cassava protein improvement. Trends Food Sci. Technol. 17: 634-641.
Sun, T.P., and Kamiya, Y. (1997). Regulation and cellular localization of ent-kaurene synthesis. Physiol. Plant. 101: 701-708.
Tanaka, Y., Data, E.S., Hirose, S., Taniguchi, T., and Uritani, I. (1983). Biochemical changes in secondary metabolites in wounded and deteriorated cassava roots. Agric. Biol. Chem. 47: 693-700.
Vanderschuren, H., Alder, A., Zhang, P., and Gruissem, W. (2009). Dose-dependent RNAi-mediated geminivirus resistance in the tropical root crop cassava. Plant Mol. Biol. 70: 265-272.
Vanderschuren, H., Lentz, E., Zainuddin, I., and Gruissem, W. (2013). Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement. J. Proteomics 93: 5-19.
Vanholme, R., Demedts, B., Morreel, K., Ralph, J., and Boerjan, W. (2010). Lignin biosynthesis and structure. Plant Physiol. 153: 895-905.
Velikova, V., Yordanov, I., and Edreva, A. (2000). Oxidative stress and some antioxidant systems in acid rain-treated bean plants: Protective role of exogenous polyamines. Plant Sci. 151: 59-66.
Vizcaíno, J.A., et al. (2013). The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013. Nucleic Acids Res. 41: D1063-D1069.
Vogt, T. (2010). Phenylpropanoid biosynthesis. Mol. Plant 3: 2-20.
Wang, K.L., Li, H., and Ecker, J.R. (2002). Ethylene biosynthesis and signaling networks. Plant Cell 14 (suppl.): S131-S151.
Wenham, J.E. (1995). Postharvest Deterioration of Cassava: A Biotechnological Perspective. FAO Plant Production and Protection Paper 130. (Rome: FAO).
Wheatley, C.C., and Schwabe, W.W. (1985). Scopoletin involvement in post-harvest physiological deterioration of cassava root (Manihot esculenta Crantz). J. Exp. Bot. 36: 783-791.
Xu, J., Duan, X., Yang, J., Beeching, J.R., and Zhang, P. (2013). Enhanced reactive oxygen species scavenging by overproduction of superoxide dismutase and catalase delays postharvest physiological deterioration of cassava storage roots. Plant Physiol. 161: 1517-1528.
Yin, L., Wang, S., Eltayeb, A.E., Uddin, M.I., Yamamoto, Y., Tsuji, W., Takeuchi, Y., and Tanaka, K. (2010). Overexpression of dehydroascorbate reductase, but not monodehydroascorbate reductase, confers tolerance to aluminum stress in transgenic tobacco. Planta 231: 609-621.
Yoshimura, K., Miyao, K., Gaber, A., Takeda, T., Kanaboshi, H., Miyasaka, H., and Shigeoka, S. (2004). Enhancement of stress tolerance in transgenic tobacco plants overexpressing Chlamydomonas glutathione peroxidase in chloroplasts or cytosol. Plant J. 37: 21-33.
