Expect the Unexpected Enrichment of “Hidden Proteome” of Seeds and Tubers by Depletion of Storage Proteins

Abstract

Dynamic resolution of seed and tuber protein samples is highly limited due to the presence of high-abundance storage proteins (SPs). These proteins inevitably obscure the low-abundance proteins (LAPs) impeding their identification and characterization. To facilitate the detection of LAPs, several methods have been developed during the past decade, enriching the proteome with extreme proteins. Most of these methods, if not all, are based on the specific removal of SPs which ultimately magnify the proteome coverage. In this mini-review, we summarize the available methods that have been developed over the years for the enrichment of LAPs either from seeds or tubers. Incorporation of these methods during the protein extraction step will be helpful in understanding the seed/tuber biology in greater detail.

Advances in the Biology of Seed and Vegetative Storage Proteins Based on Two-Dimensional Electrophoresis Coupled to Mass Spectrometry

“…Dedicated protein extraction protocols can alleviate in part some of the limitations of the standard 2-DE system, including the analysis of low-abundant proteins and membrane proteins [ 98 , 102 , 104 , 105 ]. It is noteworthy that plant tissues contain relatively lower amounts of proteins than other organisms and a large number of biological compounds that interfere notably with the extraction, solubilization and separation of proteins by 2-DE, such as cell walls, lipids, polysaccharides, polyphenols and large quantities of proteases.…”

Protein Extraction Methods Shape Much of the Extracted Proteomes

“…Third, complex protein samples can be pre-fractionated to deplete high-abundance proteins, to enhance the detection of “missing” low-abundant proteins (LAPs). For example, the depletion of RuBisCO in leaves (Kim et al, 2013 ; Gupta and Kim, 2015 ) and of storage proteins in seeds (Xiong et al, 2014 ) and tubers (Wu et al, 2012 ; Kim et al, 2015 ; Lee et al, 2015 ; Gupta et al, 2016 ) significantly improved the separation and detection of LAPs.…”

High Abundance Proteins: Proteomer’s Thorns in the Flesh?

“…These high abundance proteins are products of the genes which are present in large copy numbers and inevitably impede the identification and characterization of low abundance proteins. Biomarkers or signaling/regulatory proteins are generally low-abundance in nature and are masked by the presence of these abundant proteins which are present in numbers 10 5 -10 6 copies per cell [2,7,8]. As an example, 22 most abundant proteins, in the human blood plasma, constitute approximately 99% of the total plasma proteome with low-abundance proteins present as only 1% [9].…”

“…Several methods have been developed in the last two decades to enrich and identify the low-abundance proteome [2,8]. Most of these methods, if not all, depend on the specific depletion of high-abundance proteins, thus enriching the low-abundance proteins in the remaining fraction [10,11].…”