title: Analysis of initial changes in the proteins of soybean root tip under flooding stress using gel-free and gel-based proteomic techniques.
abstract: Flooding has a severe negative effect on soybean cultivation in the early stages of growth. To obtain a better understanding of the response mechanisms of soybean to flooding stress, initial changes in root tip proteins under flooding were analyzed using two proteomic techniques. Two-day-old soybeans were treated with flooding for 3, 6, 12, and 24h. The weight of soybeans increased during the first 3h of flooding, but root elongation was not observed. Using gel-based and gel-free proteomic techniques, 115 proteins were identified in root tips, of which 9 proteins were commonly detected by both methods. The 71 proteins identified by the gel-free proteomics were analyzed by a hierarchical clustering method based on induction levels during the flooding, and the proteins were divided into 5 clusters. Additional interaction analysis of the proteins revealed that ten proteins belonging to cluster I formed the center of a protein interaction network. mRNA expression analysis of these ten proteins showed that citrate lyase and heat shock protein 70 were down-regulated, whereas calreticulin was up-regulated in initial phase of flooding. These results suggest that flooding stress to soybean induces calcium-related signal transduction, which might play important roles in the early responses to flooding.
  
  
  CONCLUSIONS
  Flooding has a severe negative effect on soybean cultivation, particularly in the early stages of growth. To better understand the response mechanisms of soybean to the early stages of flooding stress, two proteomic techniques were used. Two-day-old soybeans were treated without or with flooding for 3, 6, 12, and 24h. The fresh weight of soybeans increased during the first 3h of flooding stress, but the growth then slowed and no root elongation was observed. Using gel-based and gel-free proteomic techniques, 115 proteins were identified in root tips, of which 9 proteins were commonly detected by both methods. The 71 proteins identified by the gel-free proteomics were analyzed by a hierarchical clustering method based on induction levels during the flooding stress, and 5 protein clusters were recognized. Protein interaction analysis revealed that ten proteins belonging to cluster I formed the center of a protein interaction network. mRNA expression analysis of these ten proteins showed that citrate lyase and heat shock protein 70 were down-regulated in response to flooding stress, whereas calreticulin was up-regulated. These results suggest that flooding stress to soybean induces calcium-related signal transduction, which might play important roles in the early responses to flooding.
authors.affiliation: University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
authors.forename: Xiaojian
authors.initials: X
authors.lastname: Yin
authors.affiliation: Maebashi Institute of Technology, Maebashi 371-0816, Japan.
authors.forename: Katsumi
authors.initials: K
authors.lastname: Sakata
authors.affiliation: University of Tsukuba, Tsukuba 305-8572, Japan.
authors.forename: Yohei
authors.initials: Y
authors.lastname: Nanjo
authors.affiliation: University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan. Electronic address: skomatsu@affrc.go.jp.
authors.forename: Setsuko
authors.initials: S
authors.lastname: Komatsu
mesh_terms: D002118:Calcium / Q000378:metabolism; D020013:Calcium Signaling; D015180:Electrophoresis, Gel, Two-Dimensional; D004734:Energy Metabolism; D055868:Floods; D005782:Gels / Q000737:chemistry*; D018506:Gene Expression Regulation, Plant; D018517:Plant Roots / Q000378:metabolism*; D025941:Protein Interaction Mapping; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000378:metabolism; D013025:Glycine max / Q000378:metabolism*
chemical_list: D005782:Gels; D012333:RNA, Messenger; D002118:Calcium
keywords: Flooding stress; Protein–protein interaction; Proteomics; Root tips; Soybean