Plant Molecular Biology

, Volume 70, Issue 4, pp 421–442 | Cite as

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

Article

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.

Keywords

Acyl CoA-dependent acyltransfease BAHD enzymes Populus trichocarpa Arabidopsis thaliana Gene expression 

Notes

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.

Supplementary material

11103_2009_9482_MOESM1_ESM.eps (1.6 mb)
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 (4.8 mb)
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 (29 kb)
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 (1004 kb)
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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© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  1. 1.Department of BiologyBrookhaven National LaboratoryUptonUSA

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