SoyProLow: A protein database enriched in low abundant soybean proteins |
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| Authors: | Mona Tavakolan Nadim W Alkharouf Benjamin F Matthews Savithiry S Natarajan |
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| Institution: | 1.Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA;2.USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA |
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| Abstract: | Soybeans are an important legume crop that contain 2 major storage proteins, β-conglycinin and glycinin, which account about 70-
80% of total seed proteins. These abundant proteins hinder the isolation and characterization of several low abundant proteins in
soybean seeds. Several protein extraction methodologies were developed in our laboratory to decrease these abundant storage
proteins in seed extracts and to also decrease the amount of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RuBisCO), which is
normally very abundant in leaf extracts. One of the extraction methodologies used 40% isopropanol and was more effective in
depleting soybean storage proteins and enhancing low abundant seed proteins than similar methods using 10-80% isopropanol.
Extractions performed with 40% isopropanol decreased the amount of storage proteins and revealed 107 low abundant proteins
when using the combined approaches of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and Mass Spectrometry
(MS). The separation of proteins was achieved by iso-electric focusing (IEF) and 2D-PAGE. The proteins were analyzed with MS
techniques to provide amino acid sequence. The proteins were identified by comparing their amino acid sequences with those in
different databases including NCBI-non redundant, UniprotKB and MSDB databases. In this investigation, previously published
results on low abundant soybean seed proteins were used to create an online database (SoyProLow) to provide a data repository
that can be used as a reference to identify and characterize low abundance proteins. This database is freely accessible to individuals
using similar techniques and can be for the subsequent genetic manipulation to produce value added soybean traits. An intuitive
user interface based on dynamic HTML enables users to browse the network and the profiles of the low abundant proteins.Availabilityhttp://bioinformatics.towson.edu/Soybean_low_abundance_proteins_2D_Gel_DB/Gel1.aspx |
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