title: Coupling of gel-based 2-DE and 1-DE shotgun proteomics approaches to dig deep into the leaf senescence proteome of Glycine max.
abstract: Leaf senescence is the last stage of leaf development that re-mobilizes nutrients from the source to sink. Here, we have utilized the soybean as a model system to unravel senescence-associated proteins (SAPs). A comparative proteomics approach was used at two contrasting stages of leaf development, namely mature (R3) and senescent (R7). Selection criteria for these two stages were the contrasting differences in their biochemical parameters - chlorophyll, carotenoids and malondialdehyde contents. Proteome analysis involved subjecting the total leaf proteins to 15% poly-ethylene glycol (PEG) pre-fractional method to enrich the low-abundance proteins (LAPs) and their analyses by gel-based 2-DE and 1-DE shotgun proteomics approaches. 2-DE profiling of PEG-supernatant and -pellet fractions detected 153 differential spots between R3 and R7 stages, of which 102 proteins were identified. In parallel, 1-DE shotgun proteomics approach identified 598 and 534 proteins in supernatant and pellet fractions of R3 and R7 stages, respectively. MapMan and Gene Ontology analyses showed increased abundance and/or specific accumulation of proteins related to jasmonic acid biosynthesis and defense, while proteins associated with photosynthesis and ROS-detoxification were decreased during leaf senescence. These findings and the generated datasets further our understanding on leaf senescence at protein level, providing a resource for the scientific community.
  
  
  
  Leaf senescence is a major biological event in the life cycle of plants that leads to the recycling of nutrients. However, the molecular mechanisms underlying leaf senescence still remain poorly understood. Here, we used a combination of gel-based 2-DE and 1-DE shotgun proteomics approaches to dig deeper into the leaf senescence proteome using soybean leaf as a model experimental material. For the identification of low-abundance proteins, polyethylene glycol (PEG) fractionation was employed and both PEG-supernatant and -pellet fractions were utilized for 2-DE and shotgun proteomic analysis. A total of 1234 (102 from 2-DE and 1132 from 1-DE shotgun proteome analysis) proteins were identified which were functionally annotated using GO and MapMan bioinformatics tools. Our results also emphasize the role of jasmonic acid in soybean leaf senescence.
authors.affiliation: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
authors.forename: Ravi
authors.initials: R
authors.lastname: Gupta
authors.affiliation: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
authors.forename: Su Ji
authors.initials: SJ
authors.lastname: Lee
authors.affiliation: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
authors.forename: Cheol Woo
authors.initials: CW
authors.lastname: Min
authors.affiliation: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
authors.forename: So Wun
authors.initials: SW
authors.lastname: Kim
authors.affiliation: Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.
authors.forename: Ki-Hun
authors.initials: KH
authors.lastname: Park
authors.affiliation: Center for Research Facilities, Gyeongsang National University, Jinju, Republic of Korea.
authors.forename: Dong-Won
authors.initials: DW
authors.lastname: Bae
authors.affiliation: Department of Functional Crops, National Institute of Crop Science (NICS), Rural Development Administration (RDA), Miryang 627-803, Republic of Korea.
authors.forename: Byong Won
authors.initials: BW
authors.lastname: Lee
authors.affiliation: Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal.
authors.forename: Ganesh Kumar
authors.initials: GK
authors.lastname: Agrawal
authors.affiliation: Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences and Tsukuba International Academy for Sport Studies (TIAS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan.
authors.forename: Randeep
authors.initials: R
authors.lastname: Rakwal
authors.affiliation: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea. Electronic address: stkim71@pusan.ac.kr.
authors.forename: Sun Tae
authors.initials: ST
authors.lastname: Kim
mesh_terms: D000375:Aging; D019295:Computational Biology; D003517:Cyclopentanes / Q000032:analysis; D015180:Electrophoresis, Gel, Two-Dimensional; D004591:Electrophoresis, Polyacrylamide Gel; D008018:Life Cycle Stages; D054883:Oxylipins / Q000032:analysis; D010937:Plant Growth Regulators / Q000032:analysis; D018515:Plant Leaves / Q000737:chemistry* / Q000502:physiology; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D030262:Soybean Proteins / Q000032:analysis; D013025:Glycine max / Q000737:chemistry*
chemical_list: D003517:Cyclopentanes; D054883:Oxylipins; D010937:Plant Growth Regulators; D020543:Proteome; D030262:Soybean Proteins; C011006:jasmonic acid
keywords: Developmental stages; Glycine max; Low-abundance proteins; Polyethylene glycol; Proteomics; Senescence