A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land

Abstract

Background: The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified.

Results: We have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL), which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PAL via horizontal gene transfer (HGT) during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments.

Conclusion: Our results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments) suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV.

Figure 1

A schematic representation of phenylpropanoid metabolism. From the general phenylpropanoid pathway (top left, reactions from L-phenylalanine to p-Coumaroyl-CoA) two separated branches lead to the production of lignin monomers (right) and of flavonoids (bottom). Solid arrows indicate a single step enzymatic reaction, dashed arrows multiple sequential enzymatic reactions. Enzymes are reported with a three letter code: PAL, phenylalanine ammonia lyase; TAL, tyrosine ammonia lyase; C4H, cinnamate 4-hydroxylase; 4CL, 4-coumarate CoA ligase; COMT, caffeic acid/5-hydroxyferulic acid O-methyltransferase; HCT/CST, hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyltransferase; C3H, p-coumaroyl shikimate/quinate 3-hydroxylase; CCoAOMT, caffeoyl CoA O-methyltransferase; CCR, (hydroxy)cinnamoyl CoA reductase; CAD, (hydroxy)cinnamyl alcohol dehydrogenase; F5H ferulate 5-hydroxylase; CHS, chalcone synthase; STS, stilbene synthase.

Figure 2

Phylogeny of PAL/TAL/HAL. Unrooted bayesian tree of a representative sampling of PAL/TAL/HAL homologues. Characterized bacterial PALs are shown in red font, while characterized bacterial TALs are shown in blue font. Although it is difficult to decide where the root lies, it is clear that eukaryotic HAL (blue square) and fungi/land plants PAL (orange and green squares, respectively) have distinct origins. Moreover, taxonomic distribution of HAL and PAL orthologues indicates that the ancestor of eukaryotes harbored a HAL (blue arrow) while a PAL was introduced by HGT in the ancestor of Dikarya fungi (orange arrow) and the ancestor of land plants (green arrow). The source of this HGT is likely in a group of sediment/soil bacteria including characterized cyanobacterial PAL and uncharacterized sequences from Methylobacterium sp. and Herpetosiphon aurantiacus (red square). Probable HAL orthologues of Methylobacterium sp. and Herpetosiphon aurantiacus are indicated by red asterisks. The amoebozoan Dictyostelium discoideum appear to have acquired a PAL in the course of a recent HGT from soil bacteria (pink arrow). Numbers at nodes represent posterior probabilities (for clarity only PP relevant for discussion are indicated). The scale bar represents the average number of substitutions per site. The same tree with full accession numbers and PP is provided as Additional file 1. A maximum likelihood analysis gave very similar results and is provided as additional file 2.

Figure 3

An evolutionary scenario for the origin of plant PAL. A HAL coding gene (orange circle) was present in the most recent eukaryotic ancestor, based on its presence in all major eukaryotic supergroups for which sequence data is available (indicated by an asterisk), and it was lost in the ancestor of Dikarya Fungi and in the ancestor of the phylum Plantae (orange crosses). In contrast, the origin of eukaryotic PAL is more recent: (1) origin of PAL in a bacterium (green circle), (2) HGT to fungi -Dikarya or possibly earlier (solid green arrow), (3) HGT from fungi to an ancestor of land plants (dashed green arrow). Alternatively: (1) origin of PAL in a soil bacterium (green circle), (2a) HGT to an ancestor of land plants (solid pink arrow), (3a) HGT from this ancestor to fungi (dashed pink arrow). Extensive HGT of PAL and HAL among and within bacteria and archaea are indicated by double rounded arrows and gene losses by green and orange crosses.