Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues

Abstract

Background: BAHD acyltransferases are involved in the synthesis and elaboration of a wide variety of secondary metabolites. Previous research has shown that characterized proteins from this family fall broadly into five major clades and contain two conserved protein motifs. Here, we aimed to expand the understanding of BAHD acyltransferase diversity in plants through genome-wide analysis across five angiosperm taxa. We focus particularly on Populus, a woody perennial known to produce an abundance of secondary metabolites.

Results: Phylogenetic analysis of putative BAHD acyltransferase sequences from Arabidopsis, Medicago, Oryza, Populus, and Vitis, along with previously characterized proteins, supported a refined grouping of eight major clades for this family. Taxon-specific clustering of many BAHD family members appears pervasive in angiosperms. We identified two new multi-clade motifs and numerous clade-specific motifs, several of which have been implicated in BAHD function by previous structural and mutagenesis research. Gene duplication and expression data for Populus-dominated subclades revealed that several paralogous BAHD members in this genus might have already undergone functional divergence.

Conclusions: Differential, taxon-specific BAHD family expansion via gene duplication could be an evolutionary process contributing to metabolic diversity across plant taxa. Gene expression divergence among some Populus paralogues highlights possible distinctions between their biochemical and physiological functions. The newly discovered motifs, especially the clade-specific motifs, should facilitate future functional study of substrate and donor specificity among BAHD enzymes.

Figure 1

Phylogeny and Distribution of BAHD Acyltransferases. A: Protein phylogeny of biochemically characterized BAHD acyltransferases and putative BAHD proteins from Arabidopsis, Medicago, Oryza, Populus, and Vitis genomes. Phylogeny was constructed using maximum likelihood analysis. B: Percentage representation of putative BAHD acyltransferases across the five taxa within each phylogenetic clade. Colors correspond to the plant taxa as listed in C. C: Percentage representation of clade membership for putative BAHD acyltransferases within each plant genome.

Figure 2

Phylogenetic Relationship of Clade Ia Members. Expanded view of all Clade Ia sequences from Figure 1A. Bracket indicates region lacking taxon-specific clustering. Filled circles represent putative BAHD acyltransferases, while open circles represent characterized BAHD proteins. Colors correspond to taxa as listed in Figure 1, with gray circles indicating sequences from plants within the Asterids. Populus sequence names are provided in Additional File 1. Loci from the other four genomes have been truncated to accommodate text input limitations (e.g., 1g03495 for At1g03495 of Arabidopsis, AC1253891 for AC125389_1 of Medicago, 01.m08401 for 12001.m08401 of Oryza, G29205001 for GSVIVP00029205001 of Vitis). GenBank accession numbers and full names for previously characterized proteins are provided in Additional File 10.

Figure 3

Phylogenetic Relationship of Clade III Members. Expanded view of all Clade III sequences from Figure 1A. Colors and symbols are the same as in Figures 1 and 2. In addition, pink circles indicate sequences from plants within the Rosids, while teal circle indicates sequence from a basal eudicot.

Figure 4

Phylogenetic Relationship of Clade Va Members. Expanded view of all Clade Va sequences from Figure 1A. Colors and symbols are the same as in Figures 1-3. In addition, red triangles indicate sequences from gymnosperms. Boxed region indicates a poorly resolved branch based on bootstrap analysis.

Figure 5

Conserved Motifs Within Phylogenetic Clades. WebLogo displays of consensus sequences corresponding to MINER-identified motifs, boxed in yellow. Logos are arranged in rows by phylogenetic clade, named at left, and in columns by motif, labelled at the bottom. The three leftmost columns represent motifs conserved across multiple clades. The rightmost column provides examples of clade-specific motifs; motifs in this column are not aligned relative to one another.

Figure 6

Locations of Putative Populus BAHD Acyltransferases on Linkage Groups. Homeologous blocks arising from the salicoid genome duplication event are color-coded across the nineteen linkage groups (chromosomes). BAHD acyltransferases in close proximity to one another are boxed for ease of labelling. Note that proximity on a linkage group does not, by itself, indicate a close phylogenetic relationship.

Figure 7

Expression of BAHD Acyltransferases in Populus Tissues, Organized by Phylogenetic Relationship. A: Expression of BAHD acyltransferase genes across tissues and genotypes. B: Stress responses of BAHD acyltransferase gene expression across tissues and genotypes. Expression data or ratios (stressed vs. control samples) were log-transformed and visualized in heatmaps (see Methods). Genes are organized by phylogenetic relationship and labelled by the clade color in Figure 1. Genotypes analyzed included: P. fremontii × angustifolia clones 1979, 3200, and RM5, and P. tremuloides clones 271 and L4. Tissues analyzed included: young leaf (YL), expanding leaf (EL), root tips (R), and suspension cell cultures (C). Stress treatments included: nitrogen limitation (low N), leaf wounding (wound, sampled either 1 week or 90 hours after wounding), removal of shoot up to leaf plastochron index three (detop, 90 hours after removal), and methyl jasmonate elicitation (MJ) [24]. White text indicates that raw hybridization intensity for either control (for upregulated genes) or stressed treatment (for downregulated genes) samples was below the quantitation limit (see Methods).