Rationale for this project, in general and in the Arabidopsis 2010 program

A significant portion of the metabolic activity in all plants is devoted to synthesis and utilization of starch. Based on sequence homologies, a number of Arabidopsis genes can be clearly assigned as functioning in some aspect of starch assembly or disassembly. Other genes are likely to be involved in these processes that cannot be identified from nucleotide sequence information. Thus, we suggest it is logical and obvious that a concerted genome-scale investigation of starch biosynthesis and degradation will be required to complete the goal of assigning functions to all Arabidopsis genes. Comprehensive understanding of the whole plant absolutely requires a detailed description of the functions of all individual gene products that play a role in starch assembly and disassembly.

Looking beyond Arabidopsis as a model organism, we propose that a critical event in evolution of species on earth was a subtle alteration in the biosynthesis of glycogen that resulted in insoluble starch granules replacing the soluble glucan polymer. This alteration is likely to have occurred in a primordial endosymbiont as it was undergoing conversion into the plastids present today in plants. Glycogen and the glucose homopolymers in starch, i.e., amylose and amylopectin, are practically identical in chemical structure but differ in molecular architecture. Starch granules, which result from the architectural features of amylopectin, provide the ability in plants to store carbohydrates much more efficiently, and for longer periods of time, than is possible in organisms in the other kingdoms. Thus, the function of plant seeds, and the metabolic functions that allow organism-wide utilization of carbohydrates produced by photosynthesis, both depend on starch. We suggest that understanding the specific mechanisms that determine glucose polymer architecture, and the disassembly of such structures, will provide information critical to understanding how plant species arose through evolution.

The availability of the Arabidopsis genome sequence provides for the first time the ability to recognize or identify all of the genes that function in starch metabolism. A consistent observation, detailed in a following section, is that for any known enzymatic activity in these processes there exists multiple isoforms coded for by separate genes. For this reason, the identification of an enzymatic activity, or a general physiological pathway that is affected by a mutation, is not sufficient to determine a gene’s function. Further characterization is required, extending to the precise molecular role of any gene product in determining the chemical characteristics of the organism. Comprehensive functional genomics allows such mechanistic investigation. Thus, Arabidopsis is a desirable system, even a requisite system, in which the investigation of starch assembly and disassembly should be pursued. These arguments apply even though Arabidopsis does not accumulate large amounts of storage starch, and that the same research problem is being actively addressed in crop species in which starch is a major agronomic objective.