Pyruvate Orthophosphate Dikinase B (PPDKB) Deficiency Impairs Starch Biosynthesis and Redirects Carbon Flux to Lipid and Amino Acid Synthesis in Rice

doi:10.1016/j.rsci.2026.04.010

Abstract

Abstract:

The central endosperm of a chalky rice mutant JM03, which was isolated from a ⁶⁰Co-irradiated mutant population of the indica rice variety 93-11, contains numerous small, irregularly shaped starch granules with looser packing than those of the wild type (WT). JM03 starch showed lower gelatinization onset and peak temperatures, reduced pasting viscosities, and consistently decreased dynamic rheological parameters compared with WT. Through bulked segregant analysis sequencing (BSA-seq), complementation tests, and immunoblot analysis, we identified PPDKB (Os05g0405000) as the causal gene underlying the JM03 phenotype. Multi-omics analysis of developing endosperm at 15 d after flowering revealed that PPDKB deficiency profoundly redirected central carbon and amino acid metabolism. On the one hand, impaired phosphoenolpyruvate regeneration disrupted the gluconeogenic conversion of hexoses into starch biosynthesis precursors, consequently suppressing starch accumulation through downregulation of all starch synthesis-related genes and enzymes. The impaired starch synthesis diminished sucrose unloading capacity due to reduced expression of sucrose synthase, triggering accumulation of sucrose and other soluble sugars. On the other hand, excess pyruvate diverted metabolic flux towards acetyl-CoA production, stimulating tricarboxylic acid (TCA) cycle activity and enhancing lipid biosynthesis. Meanwhile, amino acid synthesis was enhanced due to increased levels of multiple precursors and genes/enzymes involved in this process. The reduction in starch accumulation, combined with the downregulation of key grain weight regulators, such as mitogen-activated protein kinase 6 and BAHD acyltransferase-like protein, collectively led to a significant reduction in grain weight in JM03. Taken together, our study reveals a functional cross-talk between starch, soluble sugars, protein, and lipids in rice endosperm during seed development in JM03, which provides important germplasm resources and a theoretical basis for genetic improvement of rice yield and quality.

Key words: rice, chalky mutant, pyruvate orthophosphate dikinase, multi-omics, starch, lipid

Deng Bowen, Ying Yining, Pan Jianming, Zhang Tongrui, Xu Feifei, Bao Jinsong. Pyruvate Orthophosphate Dikinase B (PPDKB) Deficiency Impairs Starch Biosynthesis and Redirects Carbon Flux to Lipid and Amino Acid Synthesis in Rice[J]. Rice Science, 2026, 33(4): 514-530.

Figures/Tables 6

Fig. 1. Phenotype of wild type (WT) and mutant JM03. A and C, Appearance of brown rice of WT (A) and JM03 (C). Scale bars, 1 mm. B and D, Seed cross section of WT (B) and JM03 (D). Scale bars, 1 mm. E and F, Scanning electron microscopy observation of the central portion of WT (E) and JM03 (F) seeds. Scale bars, 3 μm. G-M, Head rice rate (G), grain length, width, and thickness (H), 1000-grain weight (I), total starch content (J), apparent amylose content (K), protein content (L), and lipid content (M) of WT and JM03. The asterisks indicate statistical significance between WT and JM03, as determined by the Student’s t-test (*, P < 0.05; **, P < 0.01; ***, P < 0.001).

Fig. 2. Identification of causal gene for chalky endosperm of mutant JM03. A, Bulked segregant analysis sequencing revealed a significant peak nearly to 1.0 with high probability on chromosome 5. B, Western blotting of PPDKB in developing endosperm (10 d after flowering) of wild type (WT) and JM03. Anti-actin was used as the loading control. C, Grain (top) and cross-sections (bottom) appearance of WT, JM03, and complementation lines (#1-#3). Scale bars, 5 mm (top) and 1 mm (bottom), respectively. D, Immunoblot detection of PPDKB and 3× hemagglutinin (HA) in mature seed of WT, JM03, and complementation lines (#1-#4). Line #4 was a negative control in which the transgene was not successfully introduced. Anti-actin was used as the loading control.

Fig. 3. Summary of primary metabolome and differentially accumulated metabolites in wild type (WT) and mutant JM03. A, Class-based clustering of identified metabolites (649 total) using Cytoscape (version 3.9.1). Each circle represents a metabolite. Circle size represents fold change in abundance. Red denotes higher abundance in JM03, and blue denotes higher abundance in WT. B, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment between WT and JM03.

Fig. 4. Identification and functional enrichment of differentially expressed genes (DEGs) and proteins (DEPs) between wild type (WT) and mutant JM03. A and C, Volcano plot of DEGs (A) and DEPs (C) between WT and JM03. FDR, False discovery rate. B and D, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of DEGs (B) and DEPs (D) between WT and JM03.

Fig. 5. Simplified metabolic pathways related to carbon and amino acid metabolism in JM03 endosperm. mRNAs and proteins are shown in the left and right rectangles, respectively. Metabolites are shown in rounded rectangles. Red and blue indicate upregulated and downregulated mRNAs, proteins, or metabolites, respectively. Solid lines represent one-step reactions, and dashed lines represent multi-step reactions. * refers to the results from mature seed. # refers to the results reported by Bao et al (2020b). α-AMY, α-Amylase; β-AMY, β-Amylase; GBSSI, Granule-bound starch synthase I; SSI, SSIIa, SSIIIa, and SSIVb, Soluble starch synthase I, IIa, IIIa, and IVb; BEI, and BEIIb, Starch branching enzyme I and IIb; ISA1, Isoamylase 1; PUL, Pullulanase, Pho1, Plastidial phosphorylase; Dpe, Disproportionating enzyme; AGPase, ADP-glucose pyrophosphorylase; UGPase, UDP-glucose pyrophosphorylase; UGPU, UTP-glucose-1-phosphate uridylyltransferase; ENPP1, Ectonucleotide pyrophosphatase/phosphodiesterase family member 1; α-GT, α-glucanotransferase; α-GC, α-glucosidase; UGE, UDP-glucose 4-epimerase; TPS, Trehalose-6-phosphate synthase; TPP, Trehalose-6-phosphate phosphatase; BGLU, β-Glucosidase; PGM, Phosphoglucomutase; SUS, Sucrose synthase; FRK, Fructokinase; PGI, Phosphoglucose isomerase; SPS, Sucrose phosphate synthase; galA, α-Galactosidase; SPP, Sucrose phosphatase; HK, Hexokinase; RFS, Glycosyltransferase; GH, Glycosyl hydrolases; FBPase, Fructose-1,6-bisphosphatase; PFK, 6-Phosphofructokinase; PK, Pyruvate kinase; PPDKB, Pyruvate orthophosphate dikinase, PDC, Pyruvate dehydrogenase complex; Acc, Acetyl-CoA carboxylase; MCAT, Malonyl CoA-(acyl carrier protein) transacylase; KASI, β-Ketoacyl-(acyl carrier protein) synthase; SDR, Short chain dehydrogenase/reductase; KCS, 3-Ketoacyl-CoA synthase; DGK, Diacylglycerol kinase; DGAT, Diacylglycerol acyltransferase; CEPT, Choline/ethanolamine phosphotransferase; PLA2, Phospholipase A2; ALS, Acetolactate synthase; IPMDH, 3-Isopropylmalate dehydratase; trpB, Tryptophan synthase beta chain 2; CM, Chorismate mutase; PDT, Prephenate dehydratase; AlaAT (FLO12), Alanine aminotransferase; ASL, Argininosuccinate lyase; AS, Asparagine synthase; DHDPS, Dihydrodipicolinate synthase; ALT, Alanine transaminase; GS, Glutamine synthetase, GAD, Glutamate decarboxylase; LPC, Lysophosphatidylcholine; LPE, Lysophosphatidyl ethanolamines; PC, Phosphatidylcholine; PE, Phosphatidylethanolamine. Glucose-1P, Glucose-1-phosphate; Glucose-6P, Glucose-6-phosphate; Glycerate-3P, Glycerate-3-phosphate; Frluctose-1, 6P2, Fructose-1,6-biphosphate; Glyceraldehyde-3P, Glyceraldehyde-3-phosphate; Trehalose-6P, Trehalose-6-phosphate; GABA, Gama-aminobutyric acid. Energy and reducing power (e.g., ATP, NADPH, PPi) were omitted from the figure.

Fig. 6. Overview of main component changes in rice endosperm mediated by key metabolic pathways and enzymes in PPDKB mutant JM03. Solid lines represent one-step reactions, and dashed lines represent multi-step reactions. SUS, Sucrose synthase; UDPG, UDP-glucose; G1P, Glucose-1-phosphate; AGPase, ADP-glucose pyrophosphorylase; ADPG, ADP-glucose; GBSSI, Granule-bound starch synthase I; SS, Soluble starch synthase; BE, Starch branching enzyme; DBE, Starch debranching enzyme; F6P, Fructose-6-phosphate; G6P, Glucose-6-phosphate; PGI, Phosphoglucose isomerase; PGM, Phosphoglucomutase; PEP, Phosphoenolpyruvate; PFK, 6-Phosphofructokinase; F1,6P, Fructose-1,6-phosphate; G3P, Glucose-3-phosphate; KCS, 3-Ketoacyl-CoA synthase; SDR, Short chain dehydrogenase/reductase; TCA, Tricarboxylic acid; α-KG, α-Ketoglutarate.

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