Gel-free quantitative proteomic approach to identify cotyledon proteins in soybean under flooding stress.

UNLABELLED Flooding stress causes growth inhibition and ultimately death in most crop species by limiting of energy production. To better understand plant responses to flooding stress, here, flooding-responsive proteins in the cotyledons of soybean were identified using a gel-free quantitative proteomic approach. One hundred forty six proteins were commonly observed in both control and flooding-stressed plants, and 19 were identified under only flooding stress conditions. The main functional categories were protein and development-related proteins. Protein-protein interaction analysis revealed that zincin-like metalloprotease and cupin family proteins were found to highly interact with other proteins under flooding stress. Plant stearoyl acyl-carrier protein, ascorbate peroxidase 1, and secretion-associated RAS superfamily 2 were down-regulated, whereas ferretin 1 was up-regulated at the transcription level. Notably, the levels of all corresponding proteins were decreased, indicating that mRNA translation to proteins is impaired under flooding conditions. Decreased levels of ferritin may lead to a strong deregulation of the expression of several metal transporter genes and over-accumulation of iron, which led to increased levels of reactive oxygen species, resulting to detoxification of these reactive species. Taken together, these results suggest that ferritin might have an essential role in protecting plant cells against oxidative damage under flooding conditions. BIOLOGICAL SIGNIFICANCE This study reported the comparative proteomic analysis of cotyledon of soybean plants between non-flooding and flooding conditions using the gel-free quantitative techniques. Mass spectrometry analysis of the proteins from cotyledon resulted in the identification of a total of 165 proteins under flooding stress. These proteins were assigned to different functional categories, such as protein, development, stress, redox, and glycolysis. Therefore, this study provides not only the comparative proteomic analysis but also the molecular mechanism underlying the flooding responsive protein functions in the cotyledon.

[1]  Setsuko Komatsu,et al.  Label-free quantitative proteomic analysis of abscisic acid effect in early-stage soybean under flooding. , 2013, Journal of proteome research.

[2]  N. Hooper,et al.  Families of zinc metalloproteases , 1994, FEBS letters.

[3]  Sixue Chen,et al.  Mechanisms of plant salt response: insights from proteomics. , 2012, Journal of proteome research.

[4]  W. Bode,et al.  Structural features of a superfamily of zinc-endopeptidases: the metzincins. , 1995, Current opinion in structural biology.

[5]  M. Jackson,et al.  Physiology, Biochemistry and Molecular Biology of Plant Root Systems Subjected to Flooding of the Soil , 2003 .

[6]  D. Son,et al.  Functional characterization of orchardgrass cytosolic Hsp70 (DgHsp70) and the negative regulation by Ca2+/AtCaM2 binding. , 2012, Plant physiology and biochemistry : PPB.

[7]  R. Sairam,et al.  Waterlogging-induced increase in sugar mobilization, fermentation, and related gene expression in the roots of mung bean (Vigna radiata). , 2009, Journal of plant physiology.

[8]  R. Matthews,et al.  Oxidative Stress Inactivates Cobalamin-Independent Methionine Synthase (MetE) in Escherichia coli , 2004, PLoS biology.

[9]  Liran Carmel,et al.  Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like Phosphatase Family* , 2006, Journal of Biological Chemistry.

[10]  J. Vliegenthart,et al.  Fatty Acid Hydroperoxide Lyase: A Plant Cytochrome P450 Enzyme Involved in Wound Healing and Pest Resistance , 2001, Chembiochem : a European journal of chemical biology.

[11]  Guanghui Wang,et al.  Global protein identification and quantification technology using two-dimensional liquid chromatography nanospray mass spectrometry. , 2003, Analytical chemistry.

[12]  P. Gane,et al.  Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily , 2000, Microbiology and Molecular Biology Reviews.

[13]  Kuang Yu Chen,et al.  Tandem affinity purification revealed the hypusine‐dependent binding of eukaryotic initiation factor 5A to the translating 80S ribosomal complex , 2006, Journal of cellular biochemistry.

[14]  L. Gómez-Gómez,et al.  Differential expression of the S-adenosyl-L-methionine synthase genes during pea development. , 1998, Plant physiology.

[15]  D. Cyr,et al.  Eukaryotic homologues of Escherichia coli dnaJ: a diverse protein family that functions with hsp70 stress proteins. , 1993, Molecular biology of the cell.

[16]  John Quackenbush,et al.  Genesis: cluster analysis of microarray data , 2002, Bioinform..

[17]  S. Komatsu,et al.  Proteomic and Biochemical Analyses of the Cotyledon and Root of Flooding-Stressed Soybean Plants , 2013, PloS one.

[18]  S. Suri,et al.  A heat-activated MAP kinase (HAMK) as a mediator of heat shock response in tobacco cells. , 2007, Plant, cell & environment.

[19]  Silas P. Rodrigues,et al.  Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants. , 2012, Journal of proteomics.

[20]  Elizabeth C. Theil,et al.  Evidence for conservation of ferritin sequences among plants and animals and for a transit peptide in soybean. , 1990, The Journal of biological chemistry.

[21]  Ricard,et al.  Evidence for the critical role of sucrose synthase for anoxic tolerance of maize roots using a double mutant , 1998, Plant physiology.

[22]  P. Saglio,et al.  Glycolytic Flux and Hexokinase Activities in Anoxic Maize Root Tips Acclimated by Hypoxic Pretreatment , 1996, Plant physiology.

[23]  Y. Zuily-Fodil,et al.  Omega-3 fatty acid desaturase (FAD3, FAD7, FAD8) gene expression and linolenic acid content in cowpea leaves submitted to drought and after rehydration , 2009 .

[24]  D. Lin,et al.  A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development , 2010, Proteome Science.

[25]  R. Brändle,et al.  Impact of post-anoxia stress on membrane lipids of anoxia-pretreated potato cells. A re-appraisal. , 2000, Plant physiology.

[26]  S. Komatsu,et al.  Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots , 2011, Plant Molecular Biology.

[27]  S. Komatsu,et al.  Proteomics techniques for the development of flood tolerant crops. , 2012, Journal of proteome research.

[28]  Setsuko Komatsu,et al.  Expression and Function of Proteins during Development of the Basal Region in Rice Seedlings* , 2005, Molecular & Cellular Proteomics.

[29]  T. Colmer,et al.  Waterlogging Tolerance Among a Diverse Range of Trifolium Accessions is Related to Root Porosity, Lateral Root Formation and ‘Aerotropic Rooting’ , 2001 .

[30]  Zhangcheng Tang,et al.  Proteomic analysis of salt stress‐responsive proteins in rice root , 2005, Proteomics.

[31]  P. M. Wilson,et al.  The metabolism of flood-tolerant plants. , 1987 .

[32]  S. Komatsu,et al.  Organ-specific proteome analysis for identification of abiotic stress response mechanism in crop , 2013, Front. Plant Sci..

[33]  X. Gidrol,et al.  Accumulation of reactive oxygen species and oxidation of cytokinin in germinating soybean seeds. , 1994, European journal of biochemistry.

[34]  P. Shewry,et al.  Seed storage proteins: structures and biosynthesis. , 1995, The Plant cell.

[35]  H. Kato‐Noguchi,et al.  Ethanolic fermentation and anoxia tolerance in four rice cultivars. , 2007, Journal of plant physiology.

[36]  E. Cahoon,et al.  A Multifunctional Acyl-Acyl Carrier Protein Desaturase from Hedera helix L. (English Ivy) Can Synthesize 16- and 18-Carbon Monoene and Diene Products* , 2005, Journal of Biological Chemistry.

[37]  R. Crawford.  Plant life in aquatic and amphibious habitats , 1987 .

[38]  Soojin Lee,et al.  Mechanisms for regulation of Hsp70 function by Hsp40 , 2003, Cell stress & chaperones.

[39]  Zichao Li,et al.  Analysis of Gene Expression Profile Induced by Water Stress in Upland Rice (Oryza sativa L. var. IRAT109) Seedlings using Subtractive Expressed Sequence Tags Library , 2007 .

[40]  R. Crichton,et al.  Iron storage in Saccharomyces cerevisiae , 1988, FEBS letters.

[41]  K. Iwamoto,et al.  Light-enhanced induction of ascorbate peroxidase in Japanese radish roots during postgerminative growth , 1999 .

[42]  Anne Osbourn,et al.  From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants. , 2011, The Plant journal : for cell and molecular biology.

[43]  M. Sachs,et al.  Differential regulation of enolase during anaerobiosis in maize. , 1998, Plant physiology.

[44]  W. Frankenberger,et al.  Production and stability of ethylene in soil , 1990, Biology and Fertility of Soils.

[45]  F. Cellier,et al.  Ferritins control interaction between iron homeostasis and oxidative stress in Arabidopsis. , 2009, The Plant journal : for cell and molecular biology.

[46]  J. C. Chen,et al.  Differential Proteolysis of Glycinin and beta-Conglycinin Polypeptides during Soybean Germination and Seedling Growth. , 1986, Plant physiology.

[47]  T. Sakurai,et al.  Genome sequence of the palaeopolyploid soybean , 2010, Nature.

[48]  S. Komatsu,et al.  Quantitative proteomics reveals the role of protein phosphorylation in rice embryos during early stages of germination. , 2014, Journal of proteome research.

[49]  I. Delgadillo,et al.  Purification and characterization of a novel plant metalloproteinase , 1999 .

[50]  S. Komatsu,et al.  Identification of flooding stress responsible cascades in root and hypocotyl of soybean using proteome analysis , 2010, Amino Acids.

[51]  H. de Kroon,et al.  Does disturbance favour weak competitors? Mechanisms of changing plant abundance after flooding , 2004 .

[52]  Yuefei Xu,et al.  Protective effect of nitric oxide on light-induced oxidative damage in leaves of tall fescue. , 2010, Journal of plant physiology.

[53]  Antoine H P America,et al.  Comparative LC‐MS: A landscape of peaks and valleys , 2008, Proteomics.

[54]  D. Moorhead,et al.  Increasing risk of great floods in a changing climate , 2002, Nature.

[55]  G. Muszyńska,et al.  Phosphorylation of Maize Eukaryotic Translation Initiation Factor 5A (eIF5A) by Casein Kinase 2 , 2009, The Journal of Biological Chemistry.

[56]  S. Komatsu,et al.  Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress , 2010, Amino Acids.

[57]  A. Shutov,et al.  Seed storage proteins of spermatophytes share a common ancestor with desiccation proteins of fungi , 1995, Journal of Molecular Evolution.

[58]  E. Dennis,et al.  Enhanced Low Oxygen Survival in Arabidopsis through Increased Metabolic Flux in the Fermentative Pathway1 , 2003, Plant Physiology.

[59]  K. Shinozaki,et al.  Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings , 2011, Plant Molecular Biology.

[60]  M. Freeling,et al.  The Shrunken gene on chromosome 9 of Zea mays L is expressed in various plant tissues and encodes an anaerobic protein , 1986, Molecular and General Genetics MGG.

[61]  D. Bar-Sagi,et al.  The Ras superfamily of GTPases 1 , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[62]  G. Boru,et al.  Oxygen use from solution by wheat genotypes differing in tolerance to waterlogging , 2003, Euphytica.

[63]  M. Margis-Pinheiro,et al.  Rice ascorbate peroxidase gene family encodes functionally diverse isoforms localized in different subcellular compartments , 2006, Planta.

[64]  M. Jackson,et al.  Plant adaptations to anaerobic stress , 1997 .

[65]  S. Komatsu,et al.  Comparative proteomic analysis of early-stage soybean seedlings responses to flooding by using gel and gel-free techniques. , 2010, Journal of proteome research.

[66]  M. M. Bradford.  A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[67]  F. Bakker,et al.  Phylogeny, function, and evolution of the cupins, a structurally conserved, functionally diverse superfamily of proteins. , 2001, Molecular biology and evolution.

[68]  L. Voesenek,et al.  PLANT HORMONES REGULATE FAST SHOOT ELONGATION UNDER WATER: FROM GENES TO COMMUNITIES , 2004 .

[69]  M. Iwaya-Inoue,et al.  Regulation of soybean seed germination through ethylene production in response to reactive oxygen species. , 2013, Annals of botany.

[70]  H. Selistre‐de‐Araujo,et al.  Identification of metalloprotease gene families in sugarcane , 2001 .