Professor
Department Chair
Molecular mechanisms of starch assembly and disassembly
Plant functional genomics
Research Interests
The overall goal of the joint laboratory of Alan Myers and Martha
James is to provide a comprehensive understanding of starch metabolism
in higher plants. This problem is important owing to the facts that
more than half of the calories in the human diet worldwide originate
from starch, and that starch offers a renewable source of chemical
energy and industrial raw material. Starch biosynthesis also is of
fundamental interest considering that the process is central in the
conversion of electromagnetic energy to chemical energy utilized by
our biosphere. Also of interest is how enzymes are able to catalyze
the formation of a homopolymer with a specific architecture.
The molecular architecture of starch is integrally related to its
biologica functions. In the glucose homopolymers of starch, amylopectin
and amylose, glucose units are linked in linear chains by alpha-1,4
glycoside bonds, and these are joined to each other at branch points
formed by alpha-1,6 glycoside bonds. About 5% of the glucose residues
in amylopectin have branch linkages. The branches are clustered in
specific regions that are separated by areas that lack such linkages.
This architecture allows packing of linear chains into semicrystalline
regions, which in turn form starch granules. This close packing allows
large amounts of glucose to be stored for later use, for example,
in leaves at night or seeds during germination. The central
question for our laboratory is how the biosynthetic enzymes can catalyze
chain growth and branch linkage formation so that the highly specific
architecture of amylopectin arises.
Our research involves all of the enzymes coded for by plant genomes
that can be identified as factors involved in starch assembly or disassembly.
The enzymes involved include: 1) starch synthases (SS), which form
linear glucose chains, 2) starch branching enzymes (BE), which form
branch linkages, 3) starch debranching enzymes (DBE), which eliminate
branch linkages, 4) alpha- and beta- amylases, which hydrolyze alpha-1,4
glycoside bonds, 5) starch phosphorylases, which catalyze phosphorolysis
of alpha-1,4 bonds, and 6) disproportionating enzymes (DE), which
exchange portions of linear chains. All together about 30 such enzymes
are potentially involved in starch metabolism, because multiple isoforms
of each catalytic activity are conserved in plants.
The model organisms used in the lab are maize and Arabidopsis, with
the former serving to study storage starch metabolism and the latter
for leaf starch. Earlier work in this project revealed that genetic
elimination of one of the four conserved DBE genes caused a decrease
in starch content, and accumulation of an abnormal glucan polymer
in which the architectural specificity was lost. This observation
is not intuitive, because a DBE would be expected to be required for
degradation of starch, not for starch biosynthesis. Following up on
this work, one major goal in the lab is to discover the specific function
of DBEs in the assembly of starch.
Most recently the lab has undertaken a functional genomics project
making use of the complete sequence of the Arabidopsis genome to study
starch metabolism in comprehensive sense. The Arabidopsis 2010 Program
of the NSF supports this work. Project goals include collecting loss
of function mutations for each of the 30 genes referred to in the
preceding paragraph, generation of isoform specific antibodies capable
of detecting any of the proteins, detailed descriptions of the effects
of each mutation on starch accumulation and degradation, recombination
and purification of all 30 enzymes, characterization of temporal and
spatial gene expression patters for each gene in the study set, protein-protein
interaction studies among members of the pathway, and global mRNA
profiling in each of the mutants. This set of comprehensive tools
is a necessary step towards a clear mechanistic understanding of the
complex and critical processes of starch assembly and disassembly.
