Fig 1.
Overview of all plant specialized terpenoid biosynthetic modules.
Proteins involved in the mevalonic (MVA, shown in black) and methylerythritol phosphate (MEP, shown in purple) pathways synthesize the universal C5-isoprenoid building blocks isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). Those compounds can be isomerized using enzymes of the IPP isomerase class (IDI, shown in turquois). Subsequently, the C5- blocks are transferred by enzymes of the prenyltransferase (PTF, shown in green) group to the isoprenoid intermediates with variable carbon backbone chain lengths (i.e. C10 for geranyl pyrophosphate; C15 for farnesyl pyrophosphate; C20 for geranylgeranyl phosphate and nerolidol diphosphate). Terpene synthase (core-TPS) gene products (shown in red) further catalyze biosynthesis of C10 (mono-), C15 (sesqui-) or C20 (di-) terpenes (end products, shown in yellow). C30 (shown in blue) refers to enzymes catalyzing biosynthesis of specific triterpenes (end products, shown in yellow). Likewise, prenyltransferases are involved in biosynthesis of longer-branched tetra- and polyterpenes (shown in green).
Table 1.
The published terpenoid biosynthetic module in Arabidopsis.
Table 2.
The extended terpenoid phenotypic module in Arabidopsis, including triterpene- specific (C30) synthases.
Fig 2.
Circos ideogram showing 5 Arabidopsis chromosomes with the extended set of genes associated with major terpenoid biosynthetic modules.
A. Gene inventory of the complete terpenoid biosynthetic pathway after initial expansion of published modules. Tandem duplicate supergenes are marked in red. Singletons are marked in green. Ohnolog duplicate gene pairs are marked in blue. Central pie chart shows a 68% tandem duplicate supergenes fraction. B. Subset of prenyltransferases and specific triterpene synthases marked in yellow. Central pie chart shows a 70% tandem duplicate supergenes fraction. C. Subset of core terpene synthase (TPS) genes marked in bright green. Central pie chart shows an 84% tandem duplicate supergenes fraction. D. Subset of genes associated with MEP and MVA pathways, including IPP isomerases, marked in blue. Central pie chart shows a 16% tandem duplicate supergenes fraction.
Table 3.
Tandem Duplicates fractions among terpenoid specialized biosynthetic module in 13A genomes.
Table 4.
Ohnolog duplicates fractions among the terpenoid specialized biosynthetic module in 13A genomes.
Table 5.
Overview of protein domain annotation for the extended set of Arabidopsis terpenoid biosynthetic genesA.
Fig 3.
Illustration showing the complete set of genes associated with all terpenoid biosynthetic modules identified in this study across 17 genome assemblies, based on the HMM-generated profiles of Table 5.
For core-TPS genes, numbers of previously published full-length target genes is included if available. Asterisks indicate number of previously identified full-length TPS open reading frames and hence putative number of functional terpene synthase enzymes. Incomplete protein fragments are not included.
Fig 4.
Phylogenetic relationships among 83 DXS-like proteins.
Brassicaceae and Cleomaceae are marked in blue. Solanaceae are marked in red. Proteins encoded in the basal Angiosperm Amborella are marked in green. The moss Physcomitrella comprises the outgroup and is marked in yellow. DXS-like genes group in three distinct clades since the origin of Angiosperms. Notably, all analyzed Brassicaceae have lost DXS2-like genes. However, the model plant Arabidopsis contains one highly diverged member of clade two that groups closer to clade one than to any other clade two homologs (marked by black arrow).
Fig 5.
(B)LastZ two-way multiple alignment of 40kb-windows harboring the putative Arabidopsis gene transposition duplicate gene pair DXS3 (AT5G11380) (upper lane, marked in purple) and DXS1 (AT4G15560) (lower lane, marked in purple).
Non-syntenic coding sequences are marked in green. Both duplicate copies form a highest-scoring sequence pair (marked in turquoise). Transposon-like sequences are marked in orange. Pseudogenes are marked in blue. Analysis can be regenerated online following the CoGe link https://genomevolution.org/r/eooq (last accessed on December 13th, 2014).
Table 6.
Overview of gene and genome duplication responsible for DXS-like cluster extension; shown are all target genes for four genomesA.
Fig 6.
Comparative tissue-specific expression of all Arabidopsis DXS-like genes relative to the bHLH housekeeping gene.
Values comprise averages of four independent ATH1 microarray experiments (Experiment ID: E-MEXP-2008, see Materials & Methods section). Notably, DXS1 is the only member with annotation to “trichome” plant ontology (PO:0000282). The error bars represent the standard error.
Fig 7.
Transcript levels of S. lycopersicum DXS-like genes in different parts of the plant (leaves, roots, stems, stems without (W/O) trichomes, and isolated stem trichomes) relative to those of the reference gene RCE1 (Solyc10g039370.1.1).
Transcript levels were determined by real-time qPCR with four biological and three technical replicates for each biological sample. The error bars represent the standard error.
Fig 8.
Transcript levels of the S. lycopersicum DXS3 gene in different parts of the plant (leaves, roots, stems, stems without (W/O) trichomes, and isolated stem trichomes) relative to those of the reference gene RCE1 (Solyc10g039370.1.1).
Transcript levels were determined by real-time qPCR with four biological replicates and three technical replicates for each biological sample. The error bars represent the standard error.