Cassava root membrane proteome reveals activities during storage root maturation

Abstract

Cassava (Manihot esculenta Crantz) is one of the most important crops of Thailand. Its storage roots are used as food, feed, starch production, and be the important source for biofuel and biodegradable plastic production. Despite the importance of cassava storage roots, little is known about the mechanisms involved in their formation. This present study has focused on comparison of the expression profiles of cassava root proteome at various developmental stages using two-dimensional gel electrophoresis and LC-MS/MS. Based on an anatomical study using Toluidine Blue, the secondary growth was confirmed to be essential during the development of cassava storage root. To investigate biochemical processes occurring during storage root maturation, soluble and membrane proteins were isolated from storage roots harvested from 3-, 6-, 9-, and 12-month-old cassava plants. The proteins with differential expression pattern were analysed and identified to be associated with 8 functional groups: protein folding and degradation, energy, metabolism, secondary metabolism, stress response, transport facilitation, cytoskeleton, and unclassified function. The expression profiling of membrane proteins revealed the proteins involved in protein folding and degradation, energy, and cell structure were highly expressed during early stages of development. Integration of these data along with the information available in genome and transcriptome databases is critical to expand knowledge obtained solely from the field of proteomics. Possible role of identified proteins were discussed in relation with the activities during storage root maturation in cassava.

Exploring dynamic protein-protein interactions in cassava through the integrative interactome network

“…For each predicted PPI, Pearson correlation analysis was performed to examine the concurrent expression of a protein pair in order to support the interaction. The five time-series datasets of Naconsie et al 49 , Li et al 52 , Amuge et al 69 , An et al 63 and Wang et al 70 used in this study could support 4,742 interactions in MePPI-U ( Table 2). The remaining PPIs in the network would have to be validated when more applicable time-series expression datasets become available.…”

“…The coverage of proteins in MePPI-U supported by expression data. All 24,590 proteins in MePPI-U were matched with published cassava protein and/or gene expression data [49][50][51][52][53][54][62][63][64][65][66][67][68][69][70] to support their existence in MePPI-U. 56 revealed greater numbers of biological processes covered by putative PPIs in MePPI-U, especially post-translational modification and signaling (Fig.…”

“…From these datasets, seven represent protein expression in cassava roots (fibrous and storage roots), leaves, embryos and plantlets at different development stages [49][50][51][52][53][54]62 and eight are gene expression in the form of either microarray-based datasets [63][64][65][66] or RNA-seq-based datasets [67][68][69][70] . Subsequently, co-expression patterns of the interacting protein pairs were determined using information from five time-series expression datasets of Naconsie et al 49 , An et al 63 , Li et al 64 , Amuge et al 69 and Wang et al 70 . The co-expression analysis was conducted only for highly expressed genes or proteins that exhibit expression levels greater than 80 percentile rank to ensure the existence of the interacting proteins.…”

“…Cassava yield and production are, thus, crucial for securing food sufficiency worldwide. To elucidate cellular regulations involved in starch biosynthesis as well as crop yield, protein expression in various conditions, for example during root development 49 , drought stress 50 , and in specific tissues [51][52][53][54] , has been studied. However, the interaction among these expressed proteins, which is believed to be key to the regulatory processes underlying observed phenotypes, is still unclear.…”

Transgenic technologies in cassava for nutritional improvement and viral disease resistance: a key strategy for food security in Africa

“…Although thousands of proteins have been identified by different proteomics approaches, only few of them have known functions, e.g., post-harvest physiological deterioration [22] and carotenoid sequestration [23] . Apparently, active expression of proteins (e.g., membrane proteins) is essentially related to storage root development [24][25][26][27] . Different protein profiles were also reported in distinct cultivars [28] .…”