Inactivation of rice starch branching enzyme IIb triggers broad and unexpected changes in metabolism by transcriptional reprogramming

Significance

The properties of starch can be modified by manipulating enzymes that extend the polymer backbone, add new branches, or remove them. The effects of such interventions on wider metabolism are rarely investigated but could help to predict the best metabolic engineering strategies. We mutated the rice gene OsSBEIIb encoding starch branching enzyme IIb, which is required for the synthesis of densely branched amylopectin in the endosperm. We investigated the effect on starch properties, seed morphology, and the expression of starch biosynthesis genes in the endosperm and leaf, observing broad transcriptional reprogramming. The mutation also had a wide effect on general primary and secondary metabolism in the endosperm, causing the accumulation of sugars, fatty acids, amino acids, and phytosterols.

Abstract

Starch properties can be modified by mutating genes responsible for the synthesis of amylose and amylopectin in the endosperm. However, little is known about the effects of such targeted modifications on the overall starch biosynthesis pathway and broader metabolism. Here we investigated the effects of mutating the OsSBEIIb gene encoding starch branching enzyme IIb, which is required for amylopectin synthesis in the endosperm. As anticipated, homozygous mutant plants, in which OsSBEIIb was completely inactivated by abolishing the catalytic center and C-terminal regulatory domain, produced opaque seeds with depleted starch reserves. Amylose content in the mutant increased from 19.6 to 27.4% and resistant starch (RS) content increased from 0.2 to 17.2%. Many genes encoding isoforms of AGPase, soluble starch synthase, and other starch branching enzymes were up-regulated, either in their native tissues or in an ectopic manner, whereas genes encoding granule-bound starch synthase, debranching enzymes, pullulanase, and starch phosphorylases were largely down-regulated. There was a general increase in the accumulation of sugars, fatty acids, amino acids, and phytosterols in the mutant endosperm, suggesting that intermediates in the starch biosynthesis pathway increased flux through spillover pathways causing a profound impact on the accumulation of multiple primary and secondary metabolites. Our results provide insights into the broader implications of perturbing starch metabolism in rice endosperm and its impact on the whole plant, which will make it easier to predict the effect of metabolic engineering in cereals for nutritional improvement or the production of valuable metabolites.