title: Protamine sulfate precipitation method depletes abundant plant seed-storage proteins: A case study on legume plants.
abstract: Depletion of abundant proteins is one of the effective ways to improve detection and identification of low-abundance proteins. Our previous study showed that protamine sulfate precipitation (PSP) method can deplete abundant ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from leaf proteins and is suitable for their in-depth proteome investigation. In this study, we provide evidence that the PSP method can also be effectively used for depletion of abundant seed-storage proteins (SSPs) from the total seed proteins of diverse legume plants including soybean, broad bean, pea, wild soybean, and peanut. The 0.05% protamine sulfate (PS) was sufficient to deplete major SSPs from all legumes tested except for peanut where 0.1% PS was required. SDS-PAGE, Western blotting and 2DE analyses of PS-treated soybean and peanut seed proteins showed enriched spots in PS-supernatant than total proteins. Coefficient of variation percentage (%CV) and principal component analysis of 2DE spots support the reproducibility, suitability, and efficacy of the PSP method for quantitative and comparative seed proteome analysis. MALDI-TOF-TOF successfully identified some protein spots from soybean and peanut. Hence, this simple, reproducible, economical PSP method has a broader application in depleting plant abundant proteins including SSPs in addition to RuBisCO, allowing discussion for comprehensive proteome establishment and parallel comparative studies in plants.
authors: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea.
authors: Yu Ji
authors: YJ
authors: Kim
authors: Department of Plant Microbe Interaction, Max Planck Institute for Plant Breeding Research, Köln, Germany.
authors: Yiming
authors: Y
authors: Wang
authors: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea.
authors: Ravi
authors: R
authors: Gupta
authors: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea.
authors: So Wun
authors: SW
authors: Kim
authors: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea.
authors: Chul Woo
authors: CW
authors: Min
authors: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea.
authors: Yong Chul
authors: YC
authors: Kim
authors: Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, South Korea.
authors: Ki Hun
authors: KH
authors: Park
authors: Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.|GRADE Academy Private Limited, Birgunj, Nepal.
authors: Ganesh Kumar
authors: GK
authors: Agrawal
authors: Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.|GRADE Academy Private Limited, Birgunj, Nepal.|Organization for Educational Initiatives, University of Tsukuba, Tsukuba, Ibaraki, Japan.|Department of Anatomy I, Showa University School of Medicine, Tokyo, Japan.
authors: Randeep
authors: R
authors: Rakwal
authors: Department of Herbal Medicine Resource, Kangwon National University, Samcheok, South Korea.
authors: Myoung-Gun
authors: MG
authors: Choung
authors: Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, South Korea.
authors: Kyu Young
authors: KY
authors: Kang
authors: Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea.
authors: Sun Tae
authors: ST
authors: Kim
mesh_terms: D010367:Arachis / Q000378:metabolism; D011232:Chemical Precipitation; D015180:Electrophoresis, Gel, Two-Dimensional; D007887:Fabaceae / Q000378:metabolism*; D010940:Plant Proteins / Q000378:metabolism; D025341:Principal Component Analysis; D011479:Protamines / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D055314:Seed Storage Proteins / Q000378:metabolism*; D012639:Seeds / Q000378:metabolism; D013025:Glycine max / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D011479:Protamines; D055314:Seed Storage Proteins
keywords: Legume seeds; Plant proteomics; Protamine sulfate precipitation method; Seed proteome; Seed storage proteins