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BAHD superfamily of acyl-CoA dependent acyltransferases in Populus and Arabidopsis: bioinformatics and gene expression

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Abstract

Plant acyl-CoA dependent acyltransferases constitute a large specific protein superfamily, named BAHD. Using the conserved sequence motifs of BAHD members, we searched the genome sequences of Populus and Arabidopsis, and identified, respectively, 94- and 61-putative genes. Subsequently, we analyzed the phylogeny, gene structure, and chromosomal distribution of BAHD members of both species; then, we profiled expression patterns of BAHD genes by “in silico” northern- and microarray-analyses based on public databases, and by RT-PCR. While our genomic- and bioinformatic- analyses provided full sets of BAHD superfamily genes, and cleaned up a few existing annotation errors, importantly it led to our recognizing several unique Arabidopsis BAHD genes that inversely overlapped with their neighboring genes on the genome, and disclosing a potential natural anti-sense regulation for gene expressions. Systemic gene-expression profiling of BAHD members revealed distinct tissue-specific/preferential expression patterns, indicating their diverse biological functions. Our study affords a strong knowledge base for understanding BAHD members’ evolutionary relationships and gene functions implicated in plant growth, development and metabolism.

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Acknowledgments

Authors would like to thank Dr. Gray Tuskan in Oak Ridge National Laboratory for providing additional P. trichocarpa plantlets. This work was supported by the DOE -USDA joint Plant Feedstock Genomics program (Project no: Bo-135) and the Laboratory Directed Research and Development program (LDRD-07-047) of Brookhaven National Laboratory under contract with Department of Energy to C.J.L.

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  1. Department of Biology, Brookhaven National Laboratory, Upton, NY, 11973, USA

    Xiao-Hong Yu, Jin-Ying Gou & Chang-Jun Liu

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Correspondence to Chang-Jun Liu.

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11103_2009_9482_MOESM1_ESM.eps

Supplementary Figure 1 Phylogenic analysis of Populus and Arabidopsis putative BAHD superfamily proteins. The neighbor-joining tree was constructed using aligned full-length amino-acid sequences of 77 Populus-, 52 Arabidopsis-BAHD members, and 51 function-known acyl-CoA dependent acyltransferases from other species as described in Fig. 1. (EPS 1675 kb)

11103_2009_9482_MOESM2_ESM.eps

Supplementary Figure 2 “In silico” northern analysis of poplar BAHD genes expressed in wood tissues. The data was retrieved from PopulusDB EST databases (http://www.populus.db.umu.se/). (EPS 4880 kb)

11103_2009_9482_MOESM3_ESM.pdf

Supplementary Figure 3 Quantitative RT-PCR analysis of PtACT38, 58 and 81 in different tissues of P. trichocarpa. The expressions were normalized with the leaf expression level in each sample. (PDF 29 kb)

11103_2009_9482_MOESM4_ESM.eps

Supplementary Figure 4 Microarray data of Arabidopsis BAHD gene expression. The gene expressions of BAHD members cluster hierarchically with irx 3-4, irx7, irx 8 and irx9 genes. Results are shown as heat maps in blue/white coding, where the darker blue represents the stronger expression. At1g31490, its expression is correlated closely to that of polysaccharide genes, as highlighted in bold. (EPS 1005 kb)

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Yu, XH., Gou, JY. & Liu, CJ. BAHD superfamily of acyl-CoA dependent acyltransferases in Populus and Arabidopsis: bioinformatics and gene expression. Plant Mol Biol 70, 421–442 (2009). https://doi.org/10.1007/s11103-009-9482-1

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