BMC Evolutionary Biology, 8:232
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Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida 32610-0245 (N.G., L.C.H.); Department of Zoology, University of Florida, Gainesville, Florida 32611-8525 (E.L.B.)
ADP-glucose pyrophosphorylase (AGPase), which catalyses a rate limiting
step in starch synthesis, is a heterotetramer comprised of two
identical large and two identical small subunits in plants. Although
the large and small subunits are equally sensitive to activity-altering
amino acid changes when expressed in a bacterial system, the overall
rate of non-synonymous evolution is ~2.7-fold greater for the large
subunit than for the small subunit. Herein, we examine the basis for
their different rates of evolution, the number of duplications in both
large and small subunit genes and document changes in the patterns of
AGPase evolution over time.
We found that the first duplication in the AGPase large subunit family
occurred early in the history of land plants, while the earliest small
subunit duplication occurred after the divergence of monocots and
eudicots. The large subunit also had a larger number of gene
duplications than did the small subunit. The ancient duplications in
the large subunit family raise concern about the saturation of
synonymous substitutions, but estimates of the absolute rate of AGPase
evolution were highly correlated with estimates of omega (the
non-synonymous to synonymous rate ratio). Both subunits showed evidence
for positive selection and relaxation of purifying selection after
duplication, but these phenomena could not explain the different
evolutionary rates of the two subunits. Instead, evolutionary
constraints appear to be permanently relaxed for the large subunit
relative to the small subunit. Both subunits exhibit branch-specific
patterns of rate variation among sites.
These analyses indicate that the higher evolutionary rate of the plant
AGPase large subunit reflects permanent relaxation of constraints
relative to the small subunit and they show that the large subunit
genes have undergone more gene duplications than small subunit genes.
Candidate sites potentially responsible for functional divergence
within each of the AGPase subunits were investigated by examining
branch-specific patterns of rate variation. We discuss the phenotypes
of mutants that alter some candidate sites and strategies for examining
candidate sites of presently unknown function.