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Although the pathways that produce most secondary compounds have not yet been elucidated, it is clear that there are possibly
hundreds of thousands of different enzymes
involved in secondary metabolism in plants.
There are many known instances in secondary
metabolism in which the synthesis of multiple
products can be catalyzed by a single enzyme,
either from different substrates12,13 or, more
rarely, even from the same substrate14.
However, in most cases that have been investigated, the enzymes in plant secondary metabolism are specific for a given substrate and
produce a single product.
Plant genomes are variously estimated to
contain 20 00060 000 genes, and perhaps
1525% of these genes encode enzymes
for secondary metabolism15,16. Clearly, the
genome of a given plant species encodes only
a small fraction of all the enzymes that would
be required to synthesize the entire set of
secondary metabolites found throughout the
plant kingdom. This article focuses on the
molecular evolutionary mechanisms that are
responsible for generating the great diversity
of plant secondary metabolites.
Gene duplication is not the only
mechanism of evolution of new genes
in secondary metabolism
It is believed that, at least in primary metabolism, new genes almost always arise by gene
duplication followed by divergence17,18. This
leaves the organism with one gene that
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439
(a)
OH
HO
(b)
OH
O
OH
HO
OH
OH
OH
O
OH
HO
H
OMe
OMe
OH
Rutin
Rotenone
(c)
(d) O
OH
N
OMe
OMe
Linalool
(e)
MeO
Berberine
OH
(f)
OH
DIMBOA
N
H
Brassilexin
Fig. 1. Examples of plant secondary metabolites and their proposed function in the plant from
which they were isolated. (a) Rutin, obtained from Forsythia intermedia, thought to act as a visual
pollinator attractant. (b) Rotenone, obtained from Derris elliptica, thought to act as an
insect feeding deterrent. (c) Linalool, obtained from Clarkia breweri, thought to act as an olfactory
pollinator attractant. (d) Berberine, obtained from Berberis wilsoniae, thought to act as a
defense toxin. (e) DIMBOA, obtained from Zea mays, thought to act as a defense toxin.
(f) Brassilexin, obtained from Brassica spp., thought to act as an antifungal toxin.
There are many examples of a specific secondary compound that is restricted to one
plant lineage and is not found in related lineages, especially the ancestral one (such an
observation should always be considered provisional because it is of course possible that
other lineages will later be found to make such
a compound). This represents prima facie evidence that the ability to synthesize this compound arose within this lineage.
Molecular evidence for the origin of a
new gene encoding the enzyme that catalyzes
the formation of this compound requires
analysis of the presence of the gene in this
and related plant lineages, as well as a comparison of its sequence similarity to other
related genes. For example, the gene from
Clarkia breweri (family Onagraceae) that
encodes the enzyme IEMT [which catalyzes
the methylation of (iso)eugenol to give
(iso)methyleugenol and is involved in floral
scent biosynthesis] has been shown to have
arisen from the gene encoding the enzyme
COMT (which methylates caffeic acid to
give ferulic acid and is involved in lignin
biosynthesis) some time after the divergence
of the order Myrtales22 (Fig. 2). However,
such data are rare.
The number of changes in the primary
sequence of an enzyme that are required to
alter its substrate specificity or its mode of
action can vary. Sequence comparisons of
related extant enzymes do not address this
issue directly because enzymes accumulate
neutral changes over time, making the
Table 1. Selected plant gene families with at least some members that are
involved in plant secondary metabolism
Enzyme gene family
No. of copies
in Arabidopsis
2-Oxoglutarate-dependent
dioxygenases
Flavone synthase
.10
Acyl transferases
Acetyl-CoA:benzylalcohol acetyl
transferase
.70
Carboxymethyl methyltransferases
S-adenosylmethionine:salicylic acid
methyl transferase
.20
Cytochromes p450
DIBOA hydroxylase
.100
Glutathione-S-transferases
.20
.10
NADPH-dependent dehydrogenases
Isoflavone reductase
.50
O-Methyl transferases
(Iso)eugenol O-methyltransferase
.20
Polyketide synthases
Stilbene synthase
.10
Terpene synthases
Linalool synthase
.20
441
subsp. trichocarpa
Myrtales
IEMT
Fig. 2. Phylogenetic tree consisting of COMT (which methylates caffeic acid to give ferulic
acid and is involved in lignin biosynthesis) sequences from several species and including the
Clarkia breweri IEMT sequence, showing that Clarkia IEMT evolved from Clarkia COMT
after the origination of the order Myrtales. Modified from Ref. 22.
As discussed above, changes in gene expression are often crucial, although not sufficient
by themselves, for the evolution of
new genes (and new pathways).
(a)
However, such changes can often be
confused with the origin of a new
A
B
D
E
C
gene. For example, C. breweri synthesizes linalool in its petals whereas
New enzyme
its close relative Clarkia concinna
V
W
X
Y
Z
does not, even though C. concinna
possesses the same enzyme respon(b)
sible for linalool synthesis, linalool
synthase (LIS), as C. breweri does.
A
B
D
E
However, in C. concinna, LIS is
found only in the stigma and at a
C
much lower level of expression than
V
W
Y
Z
in C. breweri2,27. Thus, if a plant
species is found to synthesize a secondary compound in a particular
Fig. 3. Two methods by which new biochemical
organ and its relatives do not synthepathways can originate: (a) through the formation
size this compound in that same
of a new enzyme that links two pre-existing pathorgan, it is important to verify
ways; (b) through co-expression in the same comwhether these relatives produce
partment of selected enzymes from two pathways
such a compound elsewhere in the
that share the same intermediate.
plant. If they do, this probably means
that no new biosynthetic genes have
-Selinene synthase (
)
)
Myrcene synthase (
Pinene synthase (
Gymnosperms
(+)-Sabinene synthase (
Convergent and repeated evolution in
secondary metabolism
1,8-Cineole synthase (
Angiosperms
Fig. 4. Phylogenetic tree of terpene synthases from gymnosperms and angiosperms showing
that limonene synthases evolved separately in these two plant lineages. Modified from
Ref. 37.
443
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