Positive selection drives adaptive diversification of the 4-coumarate: CoA ligase (4CL) gene in angiosperms

Abstract

Lignin and flavonoids play a vital role in the adaption of plants to a terrestrial environment. 4-Coumarate: coenzyme A ligase (4CL) is a key enzyme of general phenylpropanoid metabolism which provides the precursors for both lignin and flavonoids biosynthesis. However, very little is known about how such essential enzymatic functions evolve and diversify. Here, we analyze 4CL sequence variation patterns in a phylogenetic framework to further identify the evolutionary forces that lead to functional divergence. The results reveal that lignin-biosynthetic 4CLs are under positive selection. The majority of the positively selected sites are located in the substrate-binding pocket and the catalytic center, indicating that nonsynonymous substitutions might contribute to the functional evolution of 4CLs for lignin biosynthesis. The evolution of 4CLs involved in flavonoid biosynthesis is constrained by purifying selection and maintains the ancestral role of the protein in response to biotic and abiotic factors. Overall, our results demonstrate that protein sequence evolution via positive selection is an important evolutionary force driving adaptive diversification in 4CL proteins in angiosperms. This diversification is associated with adaption to a terrestrial environment.

Full text

Positive selection drives adaptive diversification of the
4-coumarate: CoA ligase (4CL) gene in angiosperms
Haiyan Sun
1,2,3,4
, Kai Guo
2,3,4
, Shengqiu Feng
2,3,5
, Weihua Zou
2,3,5
, Ying Li
2,3,5
, Chunfen Fan
2,3,5
&
Liangcai Peng
2,3,4,5
1
School of Biology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China
2
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
3
Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China
4
College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
5
College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
Keywords
4-Coumarate: coenzyme A ligase,
diversification, evolution, phylogeny, positive
selection.
Correspondence
Liangcai Peng, National Key Laboratory of
Crop Genetic Improvement, Huazhong
Agricultural University, Wuhan 430070,
China.
Tel: 86-27-87281765;
Fax: 86-27-87280016;
E-mail: lpeng@mail.hzau.edu.cn
Funding Information
The National Transgenic Project
(2009ZX08009-119B), the 111 Project
(B08032), the 973 Specific Pre-project
(2010CB134401) and the Youth Foundation
of Jiangsu Province (BK20140417).
Received: 11 May 2015; Revised: 25 June
2015; Accepted: 25 June 2015
Ecology and Evolution 2015; 5(16):
3413–3420
doi: 10.1002/ece3.1613
Abstract
Lignin and flavonoids play a vital role in the adaption of plants to a terrestrial
environment. 4-Coumarate: coenzyme A ligase (4CL) is a key enzyme of general
phenylpropanoid metabolism which provides the precursors for both lignin and
flavonoids biosynthesis. However, very little is known about how such essential
enzymatic functions evolve and diversify. Here, we analyze 4CL sequence varia-
tion patterns in a phylogenetic framework to further identify the evolutionary
forces that lead to functional divergence. The results reveal that lignin-biosyn-
thetic 4CLs are under positive selection. The majority of the positively selected
sites are located in the substrate-binding pocket and the catalytic center, indi-
cating that nonsynonymous substitutions might contribute to the functional
evolution of 4CLs for lignin biosynthesis. The evolution of 4CLs involved in fla-
vonoid biosynthesis is constrained by purifying selection and maintains the
ancestral role of the protein in response to biotic and abiotic factors. Overall,
our results demonstrate that protein sequence evolution via positive selection is
an important evolutionary force driving adaptive diversification in 4CL proteins
in angiosperms. This diversification is associated with adaption to a terrestrial
environment.
Introduction
Lignin and flavonoids are thought to play vital roles in
the adaptation of plants to terrestrial environments
(Rozemaa et al. 2002; Weng and Chapple 2010; Agati
et al. 2013). The enzyme 4-Coumarate: CoA ligase (4CL;
EC 6.2.1.12) is a key enzyme that functions in an early
step of the general phenylpropanoid pathway. The pro-
tein 4CL converts 4-coumaric acid and other cinnamic
acids, such as caffeic acid and ferulic acid, into the cor-
responding CoA thiol esters, which are then subse-
quently used for the biosynthesis of numerous secondary
metabolites, including flavonoids, isoflavonoids, lignin,
suberins, coumarins and wall-bound phenolics (Ehlting
et al. 1999; Saballos et al. 2012). The 4CL gene family is
typically small. The 4CL family has 4 members in Ara-
bidopsis (Hamberger and Hahlbrock 2004), 5 members
in rice (Gui et al. 2011; Sun et al. 2013), and 4 mem-
bers in soybean (Lindermayr et al. 2002). 4CL isoforms
with different substrate specificities may direct the flow
from general phenylpropanoid metabolism into the dif-
ferent pathways for specific end products (Souza et al.
2008).
In dicots, 4CLs can be divided into two distinct groups:
class I and class II. The disruption of 4CL expression has
demonstrated that class I 4CLs participate in lignin
ª2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use,
distribution and reproduction in any medium, provided the original work is properly cited.
3413

formation, while class II 4CLs impact flavonoid metabo-
lism (Lee et al. 1997; Hu et al. 1998; Ehlting et al. 1999;
Harding et al. 2002; Nakashima et al. 2008). The remark-
able functional diversity of 4CL suggests that it may be
subject to positive Darwinian selection. However, how the
4CL genes evolve and functionally diverge and whether
natural selection plays a role in their evolution have been
poorly studied. In this study, we analyzed nucleotide
divergence in the 4CL genes from 16 species and used
likelihood methods with various evolutionary models to
investigate potential patterns of positive selection.
Methods
Sequence data collection
All known and reported 4CL protein-coding sequences
from dicots, monocots, and gymnosperms (loblolly pine)
were retrieved from the National Center for Biotechnol-
ogy Information (NCBI). In total, 42 4CL protein
sequences from 16 species were collected and are listed in
Table S1.
Phylogenetic analysis
The 4CL protein-coding sequences were aligned using the
program CLUSTALW implemented in MEGA5 (Tamura
et al. 2011) and manually edited. Highly variable regions,
indels, and gaps were excluded. A phylogenetic tree was
constructed using MEGA5 with the neighbor-joining (NJ)
method. The reliability of the branches was evaluated by
1000 bootstrap replicates.
Test for selection
The nonsynonymous–synonymous substitution rate ratio
(x=dN/dS) provides a measure of the selective pressure
at the protein level, where a xof 1, <1, or >1 indicates
neutral evolution, purifying selection, or positive selec-
tion, respectively. The hypothesis of positive selection was
tested using the CODEML program in the PAML v4.3b
package (Yang 2007). Three approaches, branch, site, and
branch-site models, incorporated into the program were
used. In the lineage-specific selection analyses, we
employed the recently developed dynamic programming
procedure to search for the optimal branch-specific model
that had a likelihood equal to or close to the global maxi-
mum likelihood for all of the possible models (Zhang
et al. 2011). In the site-specific selection analyses, the
dataset was fitted to three pairs of codon substitution
models (M2a vs. M1a, M3 vs. M0, and M8 vs. M7). The
branch-site model A was used to detect positively selected
sites along the branches that showed elevated xratios.
The sites under positive selection were identified by the
Bayes Empirical Bayes (BEB) approach.
Results and Discussion
Angiosperm 4CL gene phylogeny
The conserved protein-coding sequences of 42 4CLs from
16 species were used to reconstruct a phylogenetic tree.
Analysis revealed that all of the 4CL genes fell into one of
two general groups: A and B (Fig. 1). Group A contains
representatives from all of the available dicots, including
verified 4CL sequences from Arabidopsis, poplar and soy-
bean. The monocot 4CL isoenzymes in group B form a
highly supported monophyletic group and are thus sepa-
rated from the dicot isoforms. The gymnosperm 4CLs,
the loblolly pine isoforms Lp4CL1 and Lp4CL2, also
formed a separate cluster that was closest to the monocot
isoenzymes.
The functional divergence of the 4CL gene
family
The dicot 4CLs can be divided into two distinct groups
that are designated dicots class I and dicots class II
(Fig. 1). Previous studies have demonstrated that 4CL
genes in dicots class I are associated with lignin accumu-
lation, while dicots class II 4CLs are involved in the meta-
bolism of other phenolic compounds, such as flavonoids.
For example, the genes Pt4CL1,At4CL1,At4CL2,At4CL4,
Gm4CL1, and Gm4CL2 in dicots class I are involved in
lignin formation (Hu et al. 1998; Ehlting et al. 1999; Lin-
dermayr et al. 2002). However, the genes Pt4CL2,At4CL3,
and Gm4CL4 in dicots class II are believed to play a role
in flavonoid biosynthesis (Uhlmann and Ebel 1993; Hu
et al. 1998; Ehlting et al. 1999).
The 4CLs from monocots can also be classified into
two groups, which are designated monocots class I and
monocots class II (Fig. 1). The 4CL genes in monocots
class I are associated with lignin accumulation. For
example, Pv4CL1 in monocots class I is the key 4CL
isoenzyme involved in lignin biosynthesis because RNA
interference of Pv4CL1 reduces the activity of extractable
4CL by 80% leading to a reduction in lignin content
and a decrease in the guaiacyl unit composition (Xu
et al. 2011). The Os4CL3 gene in the same group is also
involved in lignin biosynthesis because suppression of
Os4CL3 expression results in significant lignin reduction,
retarded growth and other morphological changes (Gui
et al. 2011). However, the genes in monocots class II
(Fig. 1) are likely to participate in the flavonoid biosyn-
thetic pathway. For example, based on phylogenetic
analysis, Xu et al. (2011) hypothesized that Pv4CL2 in
3414 ª2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
Evolution of the 4CL Genes H. Sun et al.

monocots class II mainly participates in the flavonoid
biosynthesis pathway in switchgrass. Recent research
(Sun et al. 2013) has demonstrated that the primary
function of Os4CL2 is to channel the activated 4-
coumarate to chalcone synthase and subsequently to
different branched pathways of flavonoid secondary
metabolism leading to flower pigments and UV protec-
tive flavonols and anthocyanins. The remarkable func-
tional diversity of not only dicot but also monocot 4CLs
suggests that 4CL may be subject to positive Darwinian
selection.
Evolutionary patterns among lineages and
among sites
To test the hypothesis that positive selection acts on 4CLs,
we applied branch-specific models to the 4CL dataset. It
was clear that 40RM (40 ratio model) with 40 different x
ratios was the optimal branch model (Table S2). The six
branches where xwas >1 were defined as branches a,b,c,
d,e, and f, respectively (Fig. 1). To examine whether the x
ratio for each branch was significantly greater than the
background ratio, the log-likelihood values were calculated
Figure 1. Phylogenetic relationship between
4CL genes from angiosperms based on the
neighbor-joining method. The branch lengths
are proportional to distances, and the values at
the interior nodes are the bootstrap
percentages derived from 1000 replicates. The
six branches potentially under positive selection
are indicated as a, b, c, d, e, and f,
respectively.
ª2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. 3415
H. Sun et al.Evolution of the 4CL Genes

from two-ratio models that assigned the ratios x
a
,x
b
,x
c
,
x
d
,x
e
, and x
f
to branches a,b,c,d,e, and f, and the ratio
x
0
was assigned to all other branches. All of these two-ra-
tio models were individually compared with the one-ratio
model (M0). The one-ratio model, which assumes the
same xparameter for the entire tree, yielded a log-likeli-
hood value of -28951.48 with an estimated x
0
of 0.089
(Table 1). The low average ratio indicated the dominating
role of purifying selection in the evolution of the 4CL
genes. The two-ratio models for branches a,c,d, and ffit
the data significantly better than the one-ratio model
(Table 2), resulting in the rejection of the null hypothesis
that the 4CL genes evolved at constant rates along the
branches. To test whether the six xratios were signifi-
cantly higher than 1, we calculated the log-likelihood val-
ues using the two-ratio models with x
a
,x
b
,x
c
,x
d
,x
e
,
and x
f
fixed to 1 (Table 1). The likelihood ratio tests were
also implemented for comparing each two-ratio model
and its corresponding fixed two-ratio model. The likeli-
hood ratio tests in Table 2 revealed that the xratios for
branches a,b,c,d,e, and fwere not significantly greater
than one. We therefore conclude that the evolution of the
Table 1. Log-likelihood values and parameter estimates for the 4CL genes.
Model plnL Parameter estimates Positively selected sites
M0: one ratio 1 28951.48 x
0
=0.089 None
Branch specific models
Two ratios (branch a) 2 28949.50 x
0
=0.089, x
a
=3.463
Two ratios (fixed x
a
=1) 1 28949.58 x
0
=0.089, x
a
=1
Two ratios (branch b) 2 28950.10 x
0
=0.088, x
b
=0.273
Two ratios (fix x
b
=1) 1 28950.49 x
0
=0.088, x
b
=1
Two ratios (branch c) 2 28948.26 x
0
=0.088, x
c
=2.270
Two ratios (fixed x
c
=1) 1 28948.29 x
0
=0.088, x
c
=1
Two ratios (branch d) 2 28948.76 x
0
=0.088, x
d
=0.574
Two ratios (fixed x
d
=1) 1 28948.79 x
0
=0.088, x
d
=1
Two ratios (branch e) 2 28950.04 x
0
=0.088, x
e
=∞
Two ratios (fixed x
e
=1) 1 28950.17 x
0
=0.088, x
e
=1
Two ratios (branch f) 2 28939.38 x
0
=0.088, x
f
=∞
Two ratios (fixed x
f
=1) 1 28940.20 x
0
=0.088, x
f
=1
Sites-specific models
M1:neutral (K =2) 1 28731.92 p
0
=0.946 (p
1
=0.054) Not allowed
M2: selection (K =3) 3 28731.92 p
0
=0.946, p
1
=0.011 None
(p
2
=0.042), x
2
=1
M3: discrete (K =2) 3 28260.60 p
0
=0.520 (p
1
=0.480) None
x
0
=0.020, x
1
=0.175
M3: discrete (K =3) 5 28136.31 p
0
=0.408, p
1
=0.456, (p
2
=0.136) None
x
0
=0.010, x
1
=0.108, x
2
=0.320
M7: beta 2 28118.00 p=0.542, q=4.443 Not allowed
M8: beta and x428116.60 p
0
=0.994, p=0.570, q=5.015
(p
1
=0.006), x=1
None
Branch-site model A
Model a 3 28731.43 p
0
=0.912, p
1
=0.052 None
(p
2
+p
3
=0.036), x
2
=9.870
Model fixed x
a
228731.55 p
0
=0.725, p
1
=0.041 Not allowed
(p
2
+p
3
=0.234), x
2
=1
Model c 3 28719.14 p
0
=0.885, p
1
=0.051 82C 291S (at P>0.95)
(p
2
+p
3
=0.064), x
2
=15.947 379M 423T (at P>0.99)
Model fixed x
c
228724.93 p
0
=0.780, p
1
=0.046 Not allowed
(p
2
+p
3
=0.155), x
2
=1
Model d 3 28723.32 p
0
=0.922, p
1
=0.053 79V 202S 211S (at P>0.95)
(p
2
+p
3
=0.024), x
2
=14.873
Model fixed x
d
228726.61 p
0
=0.825, p
1
=0.047 Not allowed
(p
2
+p
3
=0.128), x
2
=1
Model f 3 28716.01 p
0
=0.780, p
1
=0.045 65L 69E 181I 223L
(p
2
+p
3
=0.160), x
2
=∞234K 239K (at P>0.95)
Model fixed x
f
228720.97 p
0
=0.349, p
1
=0.020 Not allowed
(p
2
+p
3
=0.631), x
2
=1
3416 ª2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
Evolution of the 4CL Genes H. Sun et al.

4CL genes in angiosperms is dominated by purifying
selection.
Because the branch model test averages the xratios
across all of the sites and is a very conservative test for
positive selection, we applied site-specific models to the
4CL dataset. The log-likelihood values and the parameter
estimates under models with variable xratios among the
sites are listed in Table 1. Two site classes (M3, K =2) fit
the data significantly better than one site class (M0) by
690.88 log-likelihood units revealing significant variation
in the selective pressure on the sites. However, none of
the site-specific models allowed for the presence of posi-
tively selected sites, such as M2a (selection), M3 (dis-
crete), and M8 (beta and x), suggesting the existence of
positively selected sites with x>1. The majority of the
sites in the 4CL sequences appear to be under strong
selective constraints.
Evidence for positive selection on
lignin-related 4CL genes
Positive selection is difficult to detect because it often
operates episodically on just a few amino acid sites and
purifying selection may mask the signal. Branch-site mod-
els can detect positive selection that affected a small num-
ber of sites along prespecified lineages. We used branch-
site model A to test the hypothesis. As detailed in
Table 3, branch-site model A using branch cas the fore-
ground branch (MAc) resulted in a significantly better fit
to M1a (2DlnL =25.56, df =2, P<0.00) and to null
model A for branch c(2DlnL =11.58, df =1, P<0.00)
(Table 3). This result also suggested that 5.1% of amino
acids are under positive selection in lineage c with
x=15.95 (Table 1). Branch-site model A using branch d
as the foreground branch (MAd) provided a significantly
better fit to M1a (2DlnL =17.2, df =2, P<0.00) and
the null model A for branch d(2DlnL =6.58, df =1,
P<0.00) (Table 3). This result also suggested that 5.3%
of the protein sites are under positive selection in lineage
dwith x=14.873 (Table 1). When the analysis was
repeated with branch fas the foreground branch (MAf),
model A was much more realistic and fit the data signifi-
cantly better than M1a (2DlnL =31.82, df =2, P<0.00)
and the null model A for branch f(2DlnL =9.92, df =1,
P<0.01) (Table 3), which suggested that 4.5% of the
amino acids are under positive selection in lineage fwith
x=∞(Table 1). Model A using branch aas the fore-
ground branch (MAa) did not fit the data better than the
two null models in test 1 and test 2 (Table 3). These evi-
dences are sufficient to support the positive selection
hypothesis on lineages c,d, and f.
Based on the BEB method, four and six candidate sites
for positive selection were identified in dicots and mono-
cots, respectively (Table 1). These positively selected sites
are labeled in Figure 2. Sites 181I, 202S, 211S, 223L, 234K,
and 239K are located in the substrate-binding pocket, and
379M and 423T are located in the in catalytic centers. Sites
65L, 69E, 79V, and 82C are located between the conserved
sequence motifs A2 and A3, which form a phosphate-
binding loop. Site 291S is close to motif A6, which is
important for the formation of a stable tertiary structure.
Thus, amino acid substitutions in these positively selected
sites in the 4CL genes might influence the 4CL substrate
specificity, activity, or secondary structure, which would in
turn have a profound effect on 4CL’s function.
Table 2. Likelihood ratio statistics (2DlnL) for testing branch hypothe-
sis.
M0
(one
ratio)
Fixed
x
a
=1
Fixed
x
b
=1
Fixed
x
c
=1
Fixed
x
d
=1
Fixed
x
e
=1
Fixed
x
f
=1
x
a
free
3.96*0.16
x
b
free
2.76 0.78
x
c
free
6.44*0.06
x
d
free
5.44*0.06
x
e
free
2.88 0.26
x
f
free
24.2** 1.64
*Significant (P<0.05, v
2
=3.84).
**Extremely significant (P<0.01, v
2
=6.63).
Table 3. Likelihood ratio statistics (2DlnL) for testing branch-site hypothesis.
M1a Branch-site MAa (x
a
=1) Branch-site MAc (x
c
=1) Branch-site MAd (x
e
=1) Branch-site MAf (x
e
=1)
MAa 0.98 (0.61) 0.24 (0.89)
MAc 25.56 (2.82E-07)** 11.58 (6.67E-04)**
MAd 17.2 (1.84E-04)** 6.58 (1.03E-02)*
MAf 31.82 (1.23E-07)** 9.92 (7.01E-03)**
*Significant (P<0.05).
**Extremely significant (P<0.01).
ª2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. 3417
H. Sun et al.Evolution of the 4CL Genes

We have demonstrated that 4CL genes in branches c
and f, which are associated with lignin accumulation, are
under positive selection. Interestingly, positive selection is
also detected at the At4CL genes in branch d. However,
the role of these proteins in lignin formation is similar
to other proteins from dicots class I (Hu et al. 1998;
Ehlting et al. 1999). We hypothesize that positive selec-
tion on the At4CL genes may be related to functional
specialization.
Selective constraints on flavonoid-related
4CLs in dicots
The 4CL genes involved in flavonoid biosynthesis (dicots
class II and monocots class II, Fig. 1) have been largely
conserved during plant evolution, suggesting that they are
constrained by purifying selection. Land plants evolved
from green algae in the mid-Ordovician over 450 million
years ago (Langdale 2008). After arriving in terrestrial
environments, the pioneering land plants were confronted
with several major challenges such as ultraviolet irradia-
tion, desiccation stress. The presence of flavonoid in the
earliest land plants and the associated ability to resist UV
irradiations made survival on land possible for the plants
(Rozemaa et al. 2002). Flavonoid evolved prior to the lig-
nin pathway. For example, bryophytes do not synthesize
lignin, but accumulate soluble phenylpropanoids, such as
flavonoids and lignans (Weng and Chapple 2010). Flavo-
noids accumulate in the epidermal layer of extant plants,
which has been shown to absorb over 90% of UV-B radi-
ation (Stafford 1991). These evidences suggested that the
ancestral role of 4CL was to participate in the flavonoid
biosynthesis and that this role was maintained in the
adaption to a terrestrial environment.
Conclusions
4CLs play important roles in both lignin and flavonoid
biosynthesis. 4CLs that play a role in lignin biosynthesis
are subject to positive selection. This positive selection
resulted in a functional divergence after the monocot–
dicot split approximately 200 million years ago. Positive
selection could have been involved in the early stages of
the evolution of the 4CL genes; 4CL rapidly evolves after
speciation events. Strong purifying selection operates on
the novel 4CL genes to maintain the protein’s existing
function. Based on the BEB method, four and six candi-
date sites for positive selection were identified in dicots
and monocots, respectively (Table 1). Most of the posi-
tively selected sites are located in the substrate-binding
pocket and the catalytic centers (Fig. 2). Therefore,
amino acid replacements in these sites might imply a
neofunctionalization. The result is in agreement with our
findings that 4CL genes functionally diversified in angios-
perms (Hu et al. 1998; Ehlting et al. 1999; Gui et al.
2011; Xu et al. 2011; Sun et al. 2013). Although several
positively selected sites were detected using the branch-
site model, we find that the 4CL gene family as a whole
experiences purifying evolution rather than pervasive
selection throughout evolution. The 4CLs involved in fla-
vonoid biosynthesis have been largely conserved during
plant evolution and maintain the ancestral role in
response to biotic or abiotic factors. These findings pro-
vide deeper insights into understanding the evolutionary
Figure 2. The deducted amino acid sequence
for Arabidopsis At4CL1 referred to in this
article. The residues involved in
hydroxycinnamate binding are indicated with
stars, while those involved in enzymatic
functions are labeled with triangles (Hu et al.
2010). The bold-type letters indicate conserved
motifs (Gulick 2009), while those on a gray
background indicate positively selected sites.
3418 ª2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
Evolution of the 4CL Genes H. Sun et al.

mechanisms of 4CL isoforms and their functional diversi-
fication.
Acknowledgments
We thank Dr. Peng Chen and Dr. Liqiang Wang for read-
ing and discussing the manuscript and Dr. Chengjun
Zhang for assistance with statistical analysis. This work
was supported in part by grants from the National Trans-
genic Project (2009ZX08009-119B), the 111 Project
(B08032), the 973 Specific Pre-project (2010CB134401),
and the Youth Foundation of Jiangsu Province
(BK20140417).
Conflict of Interest
None declared.
References
Agati, G., C. Brunetti, M. Di Ferdinando, F. Ferrini, S.
Pollastri, and M. Tattini. 2013. Functional roles of
flavonoids in photoprotection: new evidence, lessons from
the past. Plant Physiol. Biochem. 72:35–45.
Ehlting, J. E., D. Buttner, Q. Wang, C. J. Douglas, I. E.
Somssich, and E. Kombrink. 1999. Three 4-coumarate:
coenzyme A ligases in Arabidopsis thaliana represent two
evolutionarily divergent classes in angiosperms. Plant J.
19:9–20.
Gui, J., J. Shen, and L. Li. 2011. Functional characterization of
evolutionarily divergent 4-coumarate: coenzyme a ligases in
rice. Plant Physiol. 157:574–586.
Gulick, A. M. 2009. Conformational dynamics in the Acyl-
CoA synthetases, adenylation domains of non-ribosomal
peptide synthetases, and firefly luciferase. ACS Chem. Biol.
4:811–827.
Hamberger, B., and K. Hahlbrock. 2004. The 4-coumarate:
CoA ligase gene family in Arabidopsis thaliana comprises
one rare, sinapate-activating and three commonly occurring
isoenzymes. Proc. Natl Acad. Sci. USA 101:2209–2214.
Harding, S. A., J. Leshkevich, V. L. Chiang, and C. J. Tsai.
2002. Differential substrate inhibition couples kinetically
distinct 4-coumarate:coenzyme a ligases with spatially
distinct metabolic roles in quaking aspen. Plant Physiol.
128:428–438.
Hu, W. J., A. Kawaoka, C. J. Tsai, J. Lung, K. Osakabe, H.
Ebinuma, et al. 1998. Compartmentalized expression of two
structurally and functionally distinct 4-coumarate: CoA
ligase genes in aspen. Proc. Natl Acad. Sci. USA 95:5407–
5412.
Hu, Y., Y. Gai, L. Yin, X. Wang, C. Feng, L. Feng, et al. 2010.
Crystal structures of a Populus tomentosa 4-coumarate: CoA
ligase shed light on its enzymatic mechanisms. Plant Cell
22:3093–3104.
Langdale, J. A. 2008. Evolution of developmental mechanisms
in plants. Curr. Opin. Genet. Dev. 18:368–373.
Lee, D., K. Meyer, C. Clint, and C. Douglas. 1997. Antisense
suppression of 4-Coumarate: coenzyme A ligase activity in
Arabidopsis leads to altered lignin subunit composition.
Plant Cell 9:1985–1998.
Lindermayr, C., B. Mollers, J. Fliegmann, A. Uhlmann, and F.
Lottspeich. 2002. Divergent members of a soybean (Glycine
max L.) 4-coumarate:coenzyme A ligase gene family. Eur. J.
Biochem. 269:1304–1315.
Nakashima, J., F. Chen, L. Jackson, G. Shadle, and R. A.
Dixon. 2008. Multi-site genetic modification of
monolignol biosynthesis in alfalfa (Medicago sativa): effects
on lignin composition in specific cell types. New Phytol.
179:738–750.
Rozemaa, J., L. O. Bjorn, J. F. Bornman, A. Gaberscik, D.
P. Hader, T. Trost, et al. 2002. The role of UV-B
radiation in aquatic and terrestrial ecosystems—an
experimental and functional analysis of the evolution of
UV-absorbing compounds. J. Photochem. Photobiol., B
66:2–12.
Saballos, A., S. E. Sattler, E. Sanchez, T. P. Foster, Z. Xin, C.
Kang, et al. 2012. Brown midrib2 (Bmr2) encodes the major
4-coumarate: coenzyme A ligase involved in lignin
biosynthesis in sorghum (Sorghum bicolor (L.) Moench).
Plant J. 70:818–830.
Souza, C. A., B. Barbazuk, S. G. Ralph, G. Bohlmann, B.
Hamberger, and C. J. Douglas. 2008. Genome-wide analysis
of a land plant-specific acyl: coenzymeA synthetase(ACS)
gene family in Arabidopsis, poplar, rice and Physcomitrella.
New Phytol. 179:987–1003.
Stafford, H. A. 1991. Flavonoid evolution: an enzymic
approach. Plant Physiol. 96:680–685.
Sun, H., Y. Li, S. Feng, W. Zou, K. Guo, C. Fan, et al. 2013.
Analysis of five rice 4-coumarate:coenzyme A ligase enzyme
activity and stress response for potential roles in lignin and
flavonoid biosynthesis in rice. Biochem. Biophys. Res.
Commun. 430:1151–1156.
Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and
S. Kumar. 2011. MEGA5: molecular evolutionary genetics
analysis using maximum likelihood, evolutionary distance,
and maximum parsimony methods. Mol. Biol. Evol.
28:2731–2739.
Uhlmann, A., and J. Ebel. 1993. Molecular cloning and
expression of 4-coumarate:coenzyme A ligase, an enzyme
involved in the resistance response of soybean (Glycine
max 1.) against pathogen attack. Plant Physiol. 102:1147–
1156.
Weng, J. K., and C. Chapple. 2010. The origin and
evolution of lignin biosynthesis. New Phytol. 187:
273–285.
Xu, B., L. L. Escamilla-Trevino, N. Sathitsuksanoh, Z. Shen, H.
Shen, Y. H. Zhang, et al. 2011. Silencing of 4-
coumarate:coenzyme A ligase in switchgrass leads to reduced
ª2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. 3419
H. Sun et al.Evolution of the 4CL Genes

lignin content and improved fermentable sugar yields for
biofuel production. New Phytol. 192:611–625.
Yang, Z. 2007. PAML 4: phylogenetic analysis by maximum
likelihood. Mol. Biol. Evol. 24:1586–1591.
Zhang, C., J. Wang, W. Xie, G. Zhou, M. Long, and Q. Zhang.
2011. Dynamic programming procedure for searching
optimal models to estimate substitution rates based on the
maximum-likelihood method. Proc. Natl Acad. Sci. USA
108:7860–7865.
Supporting Information
Additional Supporting Information may be found in the
online version of this article:
Table S1. Members of plant 4-coumarate:coenzyme A
ligase (4CL) genes.
Table S2. Likelihood Ratio Statistics (2DlnL) for Testing
Method1 result.
3420 ª2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
Evolution of the 4CL Genes H. Sun et al.