GSE201804
Interpreting gene co-regulation and metabolic profiling in the unique starch metabolism of Arabidopsis dpe2/phs1 mutant reveals insights into control mechanism of the starch granule number
An Arabidopsis double mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial Glucan phosphorylase (PHS1) revealed a unique starch metabolism. Dpe2/phs1 was reported to have a dwarf growth phenotype, an uneven starch distribution in the rosettes, and a strongly reduced starch granule number per chloroplast when grown under diurnal rhythm. Here we analyzed dpe2/phs1 in more detail and found that it showed three distinct growth periods. In young plants the starch granule number was similar to Col-0, then the starch granule number decreased massively down to one or no granule per chloroplast followed by an increase of the granule number. Thus, in dpe2/phs1 the control over the starch granule number is impaired and it is not defective in starch granule initiation. The data also show that the granule number is not fixed and is regulated over the entire plant growth. Further, also the chloroplasts revealed alterations during these three periods with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism perpetuated if starch degradation is further impaired by additionally lack of Isoamylase 3 and Starch excess 4. Transcriptomic studies and metabolic profiling of dpe2/phs1 revealed a gene co-regulation of most starch metabolism related genes and a clear metabolic separation. Further most senescence-induced genes were found to up-regulated more than 2-fold in the starch-less mature leave. Thus, dpe2/phs1 is a unique source to understand especially the starch granule number regulation in detail. We performed gene expression profiling analysis using data obtained from RNA-seq of 3 stages from both Col-0 and dpe2/phs1. Overall design: Comparative gene expression profiling analysis of RNA-seq data for 3 stages, designated as the Prior Period; young and mature leaves of the Retard Period; and the Recovery Period from both Col-0 and dpe2/phs1.