Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza
© Chen et al.; licensee BioMed Central Ltd. 2014
Received: 8 May 2014
Accepted: 3 September 2014
Published: 16 September 2014
Terpenoids constitute the largest class of secondary metabolites made by plants and display vast chemical diversity among and within species. Terpene synthases (TPSs) are the pivotal enzymes for terpenoid biosynthesis that create the basic carbon skeletons of this class. Functional divergence of paralogous and orthologous TPS genes is a major mechanism for the diversification of terpenoid biosynthesis. However, little is known about the evolutionary forces that have shaped the evolution of plant TPS genes leading to terpenoid diversity.
The orthologs of Oryza Terpene Synthase 1 (OryzaTPS1), a rice terpene synthase gene involved in indirect defense against insects in Oryza sativa, were cloned from six additional Oryza species. In vitro biochemical analysis showed that the enzymes encoded by these OryzaTPS1 genes functioned either as (E)-β-caryophyllene synthases (ECS), or (E)-β-caryophyllene & germacrene A synthases (EGS), or germacrene D & germacrene A synthases (DAS). Because the orthologs of OryzaTPS1 in maize and sorghum function as ECS, the ECS activity was inferred to be ancestral. Molecular evolutionary detected the signature of positive Darwinian selection in five codon substitutions in the evolution from ECS to DAS. Homology-based structure modeling and the biochemical analysis of laboratory-generated protein variants validated the contribution of the five positively selected sites to functional divergence of OryzaTPS1. The changes in the in vitro product spectra of OryzaTPS1 proteins also correlated closely to the changes in in vivo blends of volatile terpenes released from insect-damaged rice plants.
In this study, we found that positive Darwinian selection is a driving force for the functional divergence of OryzaTPS1. This finding suggests that the diverged sesquiterpene blend produced by the Oryza species containing DAS may be adaptive, likely in the attraction of the natural enemies of insect herbivores.
Plants produce diverse secondary metabolites that are not essential for growth and development but play important roles in plant interactions with other organisms ,. With over 25,000 representatives , terpenoids constitute the largest class of plant secondary metabolites ,. Synthesized as the components of resins, complex oils, or volatile mixtures (such as floral scents) , terpenoids are involved in diverse biological processes ranging from plant defense to reproduction and symbiosis ,,. Despite the collective diversity of terpenoids in the plant kingdom, for any given plant species, only a subset of terpenoids are produced, some of which may be unique to the taxon ,. Such taxon-specific diversity may be important for the specific biological functions of terpenoids. Therefore, understanding the evolutionary mechanisms underlying the diversification of terpenoid biosynthesis is important for us to understand plant adaptation to specialized niches.
The wealth of structural diversity of plant terpenoids can be mainly attributed to an enzyme class known as terpene synthases (TPSs). TPSs convert the isoprenyl diphosphate precursors geranyl diphosphate (GPP), farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP) to a multitude of cyclic and acyclic monoterpenes (C10), sesquiterpenes (C15) and diterpenes (C20), respectively ,. The unusual reaction mechanism of TPSs involves the formation of intermediate carbocations that can have multiple metabolic fates, depending on the termination mechanisms ,. As a result, a single TPS can catalyze the formation of multiple terpene products from a single substrate. Therefore, the enormous diversity of plant terpenoids is partly due to the ability of some plant TPSs producing multiple products.
The principal cause of plant terpenoid diversity is the large number of TPSs with different product specificities. In most sequenced plant genomes that have been analyzed, TPSs constitute mid-sized gene families with 30-100 members which are most likely to have evolved through gene duplication followed by functional divergence. These genes can be further divided into subfamilies based on their evolutionary relatedness with individual families generally associated with the formation of a specific class of terpenoids, such as monoterpenes, sesquiterpenes or diterpenes . The individual members in specific TPS subfamilies usually share a specific type of isoprenyl diphosphate as substrate, but exhibit large variations in product profiles . The biochemical basis for such functional divergence has been studied using biochemical and structural approaches. The product profiles of many TPSs have been interconverted by mutating only a small number of amino acid residues within or around the active site cavity -. On the other hand, numerous remote substitutions that result in the repositioning of key residues within the active site cavity can lead to enzymes with moderate level of sequence homology catalyzing similar biochemical reactions . In addition to individual sites, epistasis, which is defined as context dependence for mutational effects, also plays a critical role on product specificity of terpene synthases . Other mechanisms such as losing the N-terminal domain  or fusing two functional domains  have been proposed to be involved in evolving new terpene synthase genes.
In contrast, our knowledge of the molecular evolutionary basis underlying functional divergence of TPSs is very limited. The evolution of the large TPS gene family probably occurred largely through gene duplication followed by functional divergence, but the driving forces behind this process have not been well investigated. In contrast, positive Darwinian selection has been identified to be an important driving force for the evolution of a number of genes of plant secondary metabolism for functional diversification. Such examples include the methylthioalkylmalate synthases involved in the glucosinolate biosynthesis , the shikimate kinase (SK) of the shikimate pathway , the methyltransferases of the SABATH family important for the production of methyl esters , the dihydroflavonol-4-reductase (DFR) involved in anthocyanin biosynthesis  and the homospermidine synthase involved in pyrrolizidine alkaloid biosynthesis . While it may be sensible to propose that positive selection has also played a role in the functional diversification of TPSs, no such evidence has been presented.
We have chosen rice (Oryza) as a model plant to study the molecular evolution of TPS genes for two main reasons. First, rice plants produce a mixture of approximately 20 volatile monoterpenes and sesquiterpenes with a clear biological function. Produced upon herbivore damage, they serve in attracting the natural enemies of herbivores . Second, the molecular basis of volatile terpene production in rice has been well characterized. Three TPS genes Os02g02930, Os08g07100 and Os08g04500 are responsible for production of the majority of the terpenes released from insect-damaged rice plants . This study focused on the sesquiterpene synthase Os08g04500 from O. sativa and its orthologs from selected Oryza species. Os08g04500 produces predominantly (E)-β-caryophyllene and germacrene A . The orthologs of Os08g04500 in maize (TPS23)  and sorghum (SbTPS4)  which also play a role in attracting herbivore enemies produce only (E)-β-caryophyllene as their major product. The common ancestry of these three grasses indicates that functional divergence of the Os08g04500/TPS23/SbTPS4 orthologs has occurred, and such functional changes may have happened within the Oryza genus as well. Biochemical characterization and molecular evolutionary analysis of the orthologs of Os08g04500 (collectively designated as OryzaTPS1) from multiple Oryza species implied that positive Darwinian selection is one evolutionary force driving the functional divergence of OryzaTPS1s.
Functional conservation and divergence of OryzaTPS1s
To detect sequence divergence of OryzaTPS1 in rice, OryzaTPS1s were cloned from six additional Oryza species including O. glaberrima (African cultivated rice), O. rufipogon (a perennial wild relative of O. sativa), O. nivara (an annual wild relative of O. sativa), O. barthii (a wild relative of O. glaberrima), O. glumaepatula and O. officinalis (Additional file 1). All these seven species are diploids. The seven OryzaTPS1s cloned from the seven Oryza species displayed 96-99% similarity at the protein sequence level (Additional file 2). The related sequences have been deposited in the GenBank under accessions KJ415250 to KJ415255.
Molecular evolutionary analysis of OryzaTPS1s
Molecular evolutionary analysis of OryzaTPS1s
Positively selected sitesa
ω0 = 0.6296
ω0 = 0.5532; ωD = 999.0000
Yes (P < 0.05)
ω0 = 0; ω1 = 1
Yes (vs neutral) (P < 0.05)
318 L (0.976*)
Functional validation of the five positively selected sites
To better illustrate the contribution to the functional evolution from each mutant, the product profiles of all the mutants were subject to a clustering analysis based on relative abundance of the four sesquiterpene products. As shown in Figure 4, of the five single mutants, one (ObTPS1-C429G) showed a reduced proportion of (E)-β-caryophyllene and an elevated amount of germacrene A, but not germacrene D, while the other four displayed the wild-type phenotype. The products of three double mutants (ObTPS1-F318L + C429G, ObTPS1-C429G + V433I and ObTPS1-F318L + V433I) included germacrene D (the chromatogram of ObTPS1-F318L + V433I is shown in Figure 4 as an instance) with the first two mutants also producing significant amounts of germacrene A (Figure 4). The triple mutant ObTPS1-F318L + C429G + V433I produced comparable amounts of germacrene A, germacrene D and (E)-β-caryophyllene (Figure 4) and might represent the sequence of an intermediate stage gene prior to full functional divergence. Noticeably, all the proteins were grouped into two major clades. The first clade contained the proteins producing no or just minor amounts of germacrene D while the second clade contained OrTPS1 and four ObTPS1 mutants (1 triple mutant, 2 quadruple mutants and the quintuple mutant) harboring all the following switches: F318L, C429G, and V433I, further supporting the key role of these three switches in the function evolution. Finally, the quintuple mutant gave a product profile similar to that of ObTPS1-F318L + C429G + V433I rather than a true DAS (Figure 4), and thus changes at additional residue(s) are necessary for a complete functional switch from ECS to DAS.
Biological impact of OryzaTPS1 evolution
This study has demonstrated that positive Darwinian selection is an evolutionary force driving the functional divergence of terpene synthases, the pivotal enzymes for the biosynthesis of the largest class of secondary metabolites made by plants. OryzaTPS1, a terpene synthase found in rice species that produces a mixture of volatile sesquiterpenes, was subject to an overall purifying selection. This pattern is consistent with the evolution of TPS23 in maize, which may suggest that the evolution of the indirect defense traits may have been constrained in grasses. However, it was shown by phylogenetic analysis and functional characterization to have diverged from being an (E)-β-caryophyllene synthase (ECS) making a few other minor products to being an (E)-β-caryophyllene/germacrene A synthase (EGS) or a germacrene D and A synthase (DAS) (Figures 1 & 2) and molecular evolutionary analysis revealed that at least the evolution from ECS to DAS was driven by positive Darwinian selection. Functional divergence from ECS en route to DAS was partially achieved by the effects of mutations at five, particularly three, positively selected codon positions identified through the analysis using the branch-site models of the PAML package (Figures 3 & 4).
It is not particularly surprising that even a quintuple mutant of ECS in which all five target residues have been exchanged did not exhibit exact DAS activity (Figure 4). This suggests that one or more additional amino acids are involved in the activity divergence. Some of those amino acids may have been under positive selection. If so, the failure to detect the signature of positive selection could be due to the relatively small sampling size. On the other hand, the genus Oryza is relatively small with about 20 species; the seven species analyzed in this study account for most of the diploid Oryza species. Two of the five sites identified to be under positive selection exerted minimal, if any, effect on functional changes from ECS to DAS (Figure 4). One explanation for this phenomenon is epistasis, namely the function of these sites can only be manifested with the changes of additional amino acids in the appropriate context . Further systemic creation and analysis of additional mutants may help clarify these possibilities.
It should be acknowledged that the evolutionary trajectory for functional divergence of OryzaTPS1s could have occurred in a number of scenarios. If only the seven Oryza species studied in this paper are considered, O. officinalis is sister to the other six species based on the canonical Oryza species tree . Because OoTPS1 from O. officinalis was an EGS, one scenario could be that the ancestral activity of the other six OryzaTPS1s is EGS. In this case, it would suggest that DAS evolved from EGS, which earlier had evolved from ECS. The functional divergence from ECS to EGS was relatively minor, affecting only the relative abundance of germacrene A (Figure 1). The five amino acid residues in ECSs and EGSs that correspond to the five sites under positive selection in DAS were highly similar, providing additional evidence on the importance of these sites on the evolution of the new activity DAS. However, it is still highly possible that DAS evolved from ECS, as inferred in this study, which would represent the ancestral activity of the six OryzaTPS1s sister to OoTPS1. In this case, the EGS activity of OoTPS1 would have evolved from an ECS after the split of O. officinalis from the common ancestor of the other six Oryza species. Functional characterization of OryzaTPS1s from additional Oryza species may provide better answer to this question.
The evidence for positive selection driving the diversification of secondary metabolite biosynthesis has been detected in a number of enzyme systems, such as methylthioalkylmalate synthases involved in glucosinolate biosynthesis  and dihydroflavonol-4-reductases involved in anthocyanin biosynthesis . In all such cases, positive selection has exerted its effect on duplicated genes. In contrast, the positive selection-driven functional divergence of OryzaTPS1 in rice appears to have occurred without the direct involvement of gene duplication. In the sequenced O. sativa cultivar Nipponbare, OryzaTPS1 (Os08g04500 or OsTPS1) and its closest paralog Os08g07100 (50% identity at the amino acid level, Additional file 8) have been demonstrated to be derived from a duplication event that occurred before the divergence of rice (Oryza), maize and sorghum . Os08g04500 and Os08g07100 make two completely different sets of terpene products . Analysis of the whole genome sequence available for another Oryza species O. glaberrima also supported that OryzaTPS1 (gene ID ORGLA08G0019200 in this species) has not been duplicated in rice after the divergence of rice from the common ancestor of maize and sorghum as its closest paralog in this species (gene ID ORGLA08G0035300 in this species) also only possessed 48% similarity at the amino acid level to OryzaTPS1. Analysis of the genome sequences of other Oryza species analyzed in this study will be needed to provide undisputable evidence that the positive selection-driven functional divergence of OryzaTPS1 occurred without the direct involvement of gene duplication.
The divergence of OryzaTPS1 to new biochemical functions was apparent not only from in vitro enzyme assays (Figure 1), but also from whole plant volatile collection. There were strong correlations between the sesquiterpene profiles of individual OryzaTPS1 enzymes and the sesquiterpenes emitted from the plant from which the corresponding OryzaTPS1 was cloned (Figure 5), indicating that functional evolution of OryzaTPS1 directly impacts the phenotype of the plant. What is the biological significance of these alterations in sesquiterpene volatile emission? The volatile sesquiterpenoids emitted from insect-damaged rice and maize plants function in indirect defense as chemical cues to attract natural enemies, such as parasitic wasps ,,. Herbivore enemies have demonstrated the ability to perceive differences in terpene volatile profiles ,. Therefore, the changes in rice sesquiterpene emission profiles caused by functional divergence of OryzaTPS1 may reflect the changing spectra of insect herbivores and their natural enemies present in the environments of different species. For instance, (E)-β-caryophyllene serves as a signal not only for the indirect defense above ground ,, but also for that below ground . However, based on the current literature, germacrene A and germacrene D are specific signals for the indirect defense above ground -. Thus, it's likely that evolution from ECS to DAS & EGS in certain rice lineages is driven by more serious insect challenges above ground.
The detection of positive selection as an evolutionary force driving the functional divergence of OryzaTPS1 (Figure 2) presents the first case that we are aware of in which positive selection drove the evolution of terpene synthase genes for the diversification of terpenoid biosynthesis. This study also strengthens the view that the interactions of plants with their herbivores and pathogens evolve rapidly. In the arms race with pests, plants are continually evolving novel defenses as adaptive traits under positive selection, reflected by such disparate examples as the evolution of glucosinolate biosynthetic genes  and plant resistance (R) genes  for direct defense against insect herbivores and defense against microbial pathogens, respectively. The functional divergence of the terpene synthase gene OryzaTPS1 driven by positive selection implies the adaptive evolution of indirect defense against herbivorous insects.
This study reports that positive Darwinian selection is a driving force for the functional divergence of OryzaTPS1. As the evolution of OryzaTPS1 is well correlated with changes in terpene emission profiles of Oryza plants, these results may imply that the sesquiterpene volatile blend produced by the Oryza species that contains DAS may be adaptive, likely in the attraction of the natural enemies of insect herbivores. This study gains us further insight into the mechanisms shaping the diversity of plant secondary metabolism.
Plants growth and insect treatment
Seeds of the selected Oryza species (Additional file 1) were obtained from the National Plant Germplasm Systems of the USDA Agricultural Research Service (http://www.ars-grin.gov/npgs/). Seeds were de-hulled and germinated at 28°C in the dark for 3 days. Seedlings were planted at eight plants per 200 ml glass jar, and grown at 28°C with 16 h of light per day. The eggs of Spodoptera frugiperda were purchased from Benzon Research Inc (PA, USA). Newly emerged larvae of S. frugiperda were transferred to 37.5 ml cups containing pinto-bean-based artificial diet as a food source in an incubator (28°C). For plant treatment, two second-instar larvae were placed on the leaves of a single 2-week-old rice seedling. After overnight (when approximately 20% of the leaf area had been consumed), insects were removed and the rice plants were subjected to volatile collection and tissue collection for RNA extraction.
Related sequences were obtained and analyzed through the Rice Genome Annotation Project website (http://rice.plantbiology.msu.edu/index.shtml) and http://www.gramene.org/Oryza_glaberrima/Info/Index.
Full-length cDNA cloning
Total RNA was isolated from rice tissues using Qiagen Plant RNeasy Mini Kit. cDNAs were synthesized through GE Healthcare First-Strand cDNA Synthesis Kit. Full-length cDNAs of the TPS genes were cloned into the vector pEXP5-CT/TOPO (Invitrogen, Carlsbad, CA, USA) and fully sequenced. The primers used for CDS cloning were: 5'- ATGGCAACCTCTGTTCCGAG-3' (forward) and 5'-CAGTCACGCTTCATTAGAAG-3' (reverse).
Protein expression in E. coli and terpene synthase assay
An E. coli BL21 Codon Plus strain (Invitrogen), transformed with the appropriate expression construct (including a vector control), was used for protein expression. Expression was induced by addition of isopropyl-1-thio-d-galactopyranoside to a final concentration of 1 mm. The cells were collected by centrifugation at 4000 g for 6 min, and disrupted by a 4 × 30 sec treatment with a sonicator in chilled extraction buffer (50 mm Mopso, pH 7.0, with 5 mm MgCl2, 5 mm sodium ascorbate, 0.5 mm PMSF, 5 mm dithiothreitol and 10% v/v glycerol). The cell fragments were removed by centrifugation at 14 000 g, and the supernatant was desalted into assay buffer (10 mm Mopso, pH 7.0, 1 mm dithiothreitol, 10% v/v glycerol) by passage through a Econopac 10DG column (Bio-Rad). Enzyme assays were performed in a Teflon®-sealed, screw-capped 1 ml GC glass vial containing 50 μl of the bacterial extract and 50 μl assay buffer with 10 μm (E, E)-FPP, 10 mm MgCl2, 0.2 mm NaWO4 and 0.1 mm NaF. An SPME (solid phase micro-extraction) fiber consisting of 100 μm polydimethylsiloxane (Supelco) was placed into the headspace of the vial for 60 min incubation at 30°C and then inserted into the injector of the gas chromatograph for analysis of the adsorbed reaction products. Volatiles were analyzed on a Shimadzu 17A gas chromatograph coupled to a Shimadzu (http://www.shimadzu.com) QP5050A quadrupole mass selective detector. Separation was performed on a Restek SHR5XLB column (30 m × 0.25 mm internal diameter × 0.25 μm thickness, Shimadzu). Helium was used as the carrier gas (flow rate of 5 ml min-1), a splitless injection (injection injector temperature 250°C) was used, and a temperature gradient of 5°C min-1 from 40°C (3 min hold) to 240°C was applied. Products were identified by comparison of retention times and mass spectra with those of authentic reference compounds obtained from Fluka, Sigma (http://www.sigmaaldrich.com/) and W. König at the University of Hamburg.
Plant volatile collection and identification
Volatiles emitted from insect-damaged rice plants and control rice plants were collected in an open headspace sampling system (Analytical Research Systems, Gainesville, FL, USA). Eight plants grown in a single glass jar wrapped with aluminum foil were placed in a glass chamber with a removable O-ring snap lid with an air outlet port. Charcoal-purified air entered the chamber at a flow rate of 0.8 l min-1 from the top through a Teflon® hose. Volatiles were collected for 4 h by pumping air from the chamber through a Super Q volatile collection trap (Analytical Research Systems). Volatiles were eluted with 40 μl of CH2Cl2, and 1-octanol was added as an internal standard for quantification. Volatile identification was conducted as described above.
Hierarchical clustering analysis
Hierarchical clustering analysis was performed in MATLAB using the clustergram function in the bioinformatics toolbox. The Mahalanobis Distance was used to calculate the distance matrix, from which the hierarchical clusters were generated using complete linkage method. The color bar in each figure showed the relative abundance of the four sesquiterpene products (from 0% to 100%).
To perform phylogeny reconstruction, the protein sequence alignment was performed by using the MAFFT program . The phylogenetic tree based on the alignment was reconstructed using the maximum likelihood method in MEGA5  with 1,000 replicates of bootstrap analysis.
Molecular evolutionary analysis
Molecular evolution of OryzaTPS1s was analyzed using the codeml program in the PAML 4.4 package . An unrooted phylogenetic tree reconstructed using the maximum likelihood method and a canonical species tree  containing the seven Oryza species included in this study were subjected to the analysis. A series of branch models were tested: the one ratio model for all the lineages and the two-ratio model for the A and D lineages respectively (labeled in the phylogenetic tree) where the original enzyme functional evolution occurred. Likelihood ratio tests (LRT) were conducted to determine which model fitted the data better. The D lineage was tested for a signature of positive selection using the branch-sites test. The positive sites with high posterior probabilities (>0.95) were obtained through Bayes Empirical Bayes analysis.
For site-directed mutagenesis, the QuickChange site-directed mutagenesis kit (Stratagene, La Jolla, USA) was used according to the manufacturer's instructions. Mutated genes were fully sequenced.
Homology-based structural modeling
Protein structure modeling was performed with the SWISS-MODEL service (http://www.expasy.org/swissmod/SWISS-MODEL.html)  using the previously determined structure of 5-epi-aristolochene synthase M4 mutant (, PDB id, 3lz9) as the modeling template. Models were visualized and analyzed using the program PyMOL.
Author contributions: HC, TGK, JG and FC conceived the project. HC performed gene cloning, enzymes assays, volatile collection from plants and mutagenesis studies. G-LL performed phylogenetic and molecular evolutionary analysis. TGK performed enzyme assays and structure modeling. Q-DJ conducted the clustering analysis. HC and FC wrote the manuscript and all other authors provided critical comments and revisions. All authors read and approved the final manuscript.
This work was supported by an Innovation grant from the University of Tennessee Experimental Station (to F.C.) and funds from the Max Planck Society (to TGK and JG).
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