Dpe2/phs1 revealed unique starch metabolism with three distinct phases characterized by different starch granule numbers per chloroplast, allowing insights into the control mechanism of granule number regulation by gene co-regulation and metabolic profiling

Abstract

An Arabidopsis mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial glucan Phosphorylase 1 (PHS1) revealed a unique starch metabolism. Dpe2/phs1 has been reported to have only one starch granule number per chloroplast when grown under diurnal rhythm. For this study, we analyzed dpe2/phs1 in details following the mutant development, and found that it showed three distinct periods of granule numbers per chloroplast, while there was no obvious change observed in Col-0. In young plants, the starch granule number was similar to that in Col-0 at first, and then decreased significantly, down to one or no granule per chloroplast, followed by an increase in the granule number. Thus, in dpe2/phs1, control over the starch granule number is impaired, but it is not defective in starch granule initiation. The data also indicate that the granule number is not fixed, and is regulated throughout plant growth. Furthermore, the chloroplasts revealed alterations during these three periods, with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism was perpetuated when starch degradation was further impaired through an additional lack of Isoamylase 3 (ISA3) or Starch excess 4 (SEX4). Transcriptomic studies and metabolic profiling revealed the co-regulation of starch metabolism-related genes and a clear metabolic separation between the periods. Most senescence-induced genes were found to be up-regulated more than twice in the starch-less mature leaves. Thus, dpe2/phs1 is a unique plant material source, with which we may study starch granule number regulation to obtain a more detailed understanding.

Transcriptomics of Leaf Development in the Endangered Dioecious Magnolia kwangsiensis: Molecular Basis Underpinning Specialized Metabolism Genes

“…These identified genes—each displaying distinctive features and enzymatic functions relevant to polysaccharide biosynthesis—are postulated to have substantial roles in developing starch granules within the species’ leaf tissues. The noteworthy genes include Chr01.2399, annotated as a 1,4-α-glucan-branching enzyme, which is implicated in the generation of branch points in the polysaccharide chain during the creation of glycogen [ 32 , 33 ]; Chr02.481, identified as Isoamylase 3 ( ISA3 ), exhibits homology to enzymes known for their capacity to cleave α-1,6 glycosidic bonds in amylopectin [ 32 , 34 ]; Chr02.4751 is associated with the ADP-glucose synthesis pathway and has been denoted as encoding a protein that catalyzes the synthesis of the activated glycosyl donor, ADP-glucose from Glc-1-P and ATP [ 35 , 36 ]; and Chr04.195, which is part of the glycosyltransferase 1 family under the bacterial plant glycogen synthase subfamily [ 37 , 38 ]. The discovery of these genes aligns with previous research from other trees that glycosyltransferase is critical to plant development, enriching our current understanding of the exact member of genes that regulate the leaf tissue’s unique metabolic demands in M. kwangsiensis .…”

Genome-Wide Association Study of Metabolic Traits in the DuckweedSpirodela polyrhiza

“…Three SNPs associated with the contents of L-Tyrosine, Chlorogenic acid and IAA were linked to SpUGT89B1, SpCYP71AU50 and SpMYBC1, three genes functioning in secondary metabolite biosynthesis (Yamaguchi et al 2014;Caputi et al 2012;Ke et al 2021) (Figure 3 B, D, E). A SNP within SpDPE2, which is functionally involved in starch metabolism is associated with IAA content (Li et al 2022) (Figure 3E). For SVs, contents of L-Glutamine and L-Serine were associated with a 94 bp intronic deletion in the Ubiquitin-carboxyterminal hydrolase 7 SpUBP7 (Figure 4A-C).…”