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Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds

ABSTRACT: The low phytic acid trait in soybeans can be conferred by loss-of-function mutations in genes encoding myo-inositol phosphate synthase and two epistatically interacting genes encoding multidrug-resistance protein ABC transporters. However, perturbations in phytic acid biosynthesis are associated with poor seed vigor. Since the benefits of the low phytic acid trait, in terms of end-use quality and sustainability, far outweigh the negatives associated with poor seed performance, a fuller understanding of the molecular basis behind the negatives will assist crop breeders and engineers in producing variates with low phytic acid and better germination rate. The gene regulatory network for developing low and normal phytic acid soybean seeds was previously constructed, with genes modulating a variety of processes pertinent to phytic acid metabolism and seed viability being identified. In this study, a comparative time series analysis of low and normal phytic acid soybeans was carried out to investigate the transcriptional regulatory elements governing the transitional dynamics from dry seed to germinated seed. Gene regulatory networks were reverse engineered from time series transcriptomic data of three distinct genotypic subsets composed of low phytic acid soybean lines and their normal phytic acid sibling lines. Using a robust unsupervised network inference scheme, putative regulatory interactions were inferred for each subset of genotypes. These interactions were further validated by published regulatory interactions found in Arabidopsis thaliana and motif sequence analysis. Results indicate that low phytic acid seeds have increased sensitivity to stress, which could be due to changes in phytic acid levels, disrupted inositol phosphate signaling, disrupted phosphate ion homeostasis, and altered myo-inositol metabolism. Putative regulatory interactions were identified for the latter two processes. Changes in abscisic acid signaling candidate transcription factors putatively regulating genes in this process were identified as well. Analysis of the gene regulatory networks reveal altered regulation in processes that may be affecting the germination of low phytic acid soybean seeds. Therefore, this work contributes to the ongoing effort to elucidate molecular mechanisms underlying altered seed viability, germination and field emergence of low phytic acid crops, understanding of which is necessary in order to mitigate these problems.

ORGANISM(S): Glycine max

PROVIDER: GSE172018 | GEO | 2021/06/17

REPOSITORIES: GEO

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Project description:Germination offers advantages to improve legume protein digestibility as it disintegrates seed structure and hydrolyzes proteins and anti-nutrients. Seed permeability (related to polyphenol content of seed coats) is an important factor affecting the duration of seed germination and its impact in protein digestibility and bioactivity. The objective was to compare the effect of seed germination on protease activity, structure and proteolysis of four selected legumes with contrasting seed coat polyphenol profiles (gray zero tannin [GZL], beluga [BL] and dehulled red [DL] lentils; and zero tannin/low vicine-convicine fava bean [ZF]). Protein hydrolysis was characterized during germination and digestion with respect to proteins, peptides and free amino acids (FAA). In vitro antihypertensive and antioxidant activities of digests were investigated, and peptidomic characterization (HPLC-MS/MS) and identification of bioactive fragments in intestinal digests were performed. Regardless of seed type, germination increased protease activity and reduced levels of phytic acid, trypsin inhibitors and tannins (only in BL). Significant proteolysis of the 7S and 11S globulins and concomitant increase peptides and FAA was observed in all sprouted legumes. Digestion kinetics in sprouts revealed a faster generation of FAA and peptides than in dry seeds, with changes more evident for DL associated to faster imbibition, germination and sprout growth. In contrast, BL sprouts showed the lowest protein digestibility, likely due to lower protease activity levels, seed structure disintegration and higher anti-nutrient levels in comparison to GZL, DL and ZF. Moreover, digestion of sprouts resulted in a higher number of resistant peptides in DL and ZF that matched with previously reported bioactive sequences, suggesting a promising health potential of legume sprouts that was confirmed in vitro. Results suggested that the germination process improved protein digestibility and health promoting potential of lentil and fava bean proteins although these changes were more evident in DL due to its rapid imbibition, faster germination and sprout development. This study will provide important information for either plant breeders to develop legume varieties with permeable seed coats or food producers that could use dehulled seeds for efficient production of sprouts as sustainable food sources of plant proteins with improved nutritional and healthy properties.

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Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds

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