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SoyProLow: A protein database enriched in low abundant soybean proteins.

Tavakolan M, Alkharouf NW, Matthews BF, Natarajan SS - Bioinformation (2014)

Bottom Line: 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 proteins were identified by comparing their amino acid sequences with those in different databases including NCBI-non redundant, UniprotKB and MSDB databases.This database is freely accessible to individuals using similar techniques and can be for the subsequent genetic manipulation to produce value added soybean traits.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA.

ABSTRACT

Unlabelled: 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.

Availability: http://bioinformatics.towson.edu/Soybean_low_abundance_proteins_2D_Gel_DB/Gel1.aspx.

No MeSH data available.


Related in: MedlinePlus

A snapshot from the SoyProLow online database displaying the search field. The numbers on the image representsproteins that have been separated by 2D-PAGE. When the user types the number ID of the protein of interest, the database returnsthe detailed annotation (if available) for that protein along with other relevant information such as the PI (isoelectric point).
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Related In: Results  -  Collection


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Figure 1: A snapshot from the SoyProLow online database displaying the search field. The numbers on the image representsproteins that have been separated by 2D-PAGE. When the user types the number ID of the protein of interest, the database returnsthe detailed annotation (if available) for that protein along with other relevant information such as the PI (isoelectric point).

Mentions: In our published studies, the results showed that isopropanoldepleted most of the β-conglycinin subunits, however, someglycinin isomers were observed (Figure 1, spots 1-14). Glycininconsists of acidic (A) and basic (B) polypeptides with fivesubunits G1, G2, G3, G4 and G5 [9]. Beilinson et al. [10]identified two additional glycinin subunits in soybean varietyResnik. The five major subunits are classified into two groupsbased on their physical properties. Group I consists of G1(A1aBx), G2 (A2B1a), and G3 (A1aB1b) and group II containsG4 (A5A4B3) and G5 (A3B4). In this study, isopropanolsolubilized a higher proportion of group I glycinin subunitsthan group II subunits. In addition, we observed ten spots(spots 15-24) of soybean lectins in isopropanol extracts. It hasbeen reported that soybean lectins (agglutinins), which areanti-nutritional and also carbohydrate-binding proteins, arepresent in moderate levels in soybean, peas and clover [11].Nine protein spots were identified as dehydrin (spots 25-33)and 14 spots (spots 34-47) were identified as maturationassociated proteins. Dehydrins are a family of lateembryogenesis-abundant proteins (LEA) that normallyaccumulate during the later stages of seed maturation and playan important role in membrane and protein stability [12,13].Various seed maturation proteins (SMPs) are also synthesizedduring the later stages of seed development.


SoyProLow: A protein database enriched in low abundant soybean proteins.

Tavakolan M, Alkharouf NW, Matthews BF, Natarajan SS - Bioinformation (2014)

A snapshot from the SoyProLow online database displaying the search field. The numbers on the image representsproteins that have been separated by 2D-PAGE. When the user types the number ID of the protein of interest, the database returnsthe detailed annotation (if available) for that protein along with other relevant information such as the PI (isoelectric point).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4209371&req=5

Figure 1: A snapshot from the SoyProLow online database displaying the search field. The numbers on the image representsproteins that have been separated by 2D-PAGE. When the user types the number ID of the protein of interest, the database returnsthe detailed annotation (if available) for that protein along with other relevant information such as the PI (isoelectric point).
Mentions: In our published studies, the results showed that isopropanoldepleted most of the β-conglycinin subunits, however, someglycinin isomers were observed (Figure 1, spots 1-14). Glycininconsists of acidic (A) and basic (B) polypeptides with fivesubunits G1, G2, G3, G4 and G5 [9]. Beilinson et al. [10]identified two additional glycinin subunits in soybean varietyResnik. The five major subunits are classified into two groupsbased on their physical properties. Group I consists of G1(A1aBx), G2 (A2B1a), and G3 (A1aB1b) and group II containsG4 (A5A4B3) and G5 (A3B4). In this study, isopropanolsolubilized a higher proportion of group I glycinin subunitsthan group II subunits. In addition, we observed ten spots(spots 15-24) of soybean lectins in isopropanol extracts. It hasbeen reported that soybean lectins (agglutinins), which areanti-nutritional and also carbohydrate-binding proteins, arepresent in moderate levels in soybean, peas and clover [11].Nine protein spots were identified as dehydrin (spots 25-33)and 14 spots (spots 34-47) were identified as maturationassociated proteins. Dehydrins are a family of lateembryogenesis-abundant proteins (LEA) that normallyaccumulate during the later stages of seed maturation and playan important role in membrane and protein stability [12,13].Various seed maturation proteins (SMPs) are also synthesizedduring the later stages of seed development.

Bottom Line: 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 proteins were identified by comparing their amino acid sequences with those in different databases including NCBI-non redundant, UniprotKB and MSDB databases.This database is freely accessible to individuals using similar techniques and can be for the subsequent genetic manipulation to produce value added soybean traits.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA.

ABSTRACT

Unlabelled: 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.

Availability: http://bioinformatics.towson.edu/Soybean_low_abundance_proteins_2D_Gel_DB/Gel1.aspx.

No MeSH data available.


Related in: MedlinePlus