A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Productio
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A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production Hui Shen & Yanbin Yin & Fang Chen & Ying Xu & Richard A. Dixon
Published online: 16 October 2009 # Springer Science + Business Media, LLC. 2009
Abstract NAM, ATAF, and CUC2 (NAC) proteins are encoded by one of the largest plant-specific transcription factor gene families. The functions of many NAC proteins relate to different aspects of lignocellulosic biomass production, and a small group of NAC transcription factors has been characterized as master regulators of plant cell wall development. In the present study, a total of 1,232 NAC protein sequences from 11 different organisms were analyzed by sequence phylogeny based on protein DNA-binding domains. We included eight whole genomes (Arabidopsis, rice, poplar, grape, sorghum, soybean, moss (Physcomitrella patens), and spike moss (Selaginella moellendorffii)) and three not yet fully sequenced genomes (maize, switchgrass, and Medicago
truncatula) in our analyses. Ninety-two potential PvNAC genes from switchgrass and 148 PtNAC genes from poplar were identified. The 1,232 NAC proteins were phylogenetically classified into eight subfamilies, each of which was further divided into subgroups according to their tree topology. The phylogenetic subgroups were then grouped into different clades each sharing conserved motif patterns in the C-terminal sequences, and those that may function in plant cell wall development were further identified through motif grouping and gene expression pattern analysis using publicly available microarray data. Our results provide a bioinformatic baseline for further functional analyses of candidate NAC genes for improving cell wall and environmental tolerance traits in the bioenergy crops switchgrass and poplar.
Hui Shen and Yanbin Yin contributed equally to this study.
Keywords NAM/NAC protein . Transcription factor . Secondary cell wall . Stress tolerance . Biomass . Cellulosic ethanol . Phylogeny
Electronic supplementary material The online version of this article (doi:10.1007/s12155-009-9047-9) contains supplementary material, which is available to authorized users. H. Shen : F. Chen : R. A. Dixon (*) Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA e-mail: [email protected] Y. Yin : Y. Xu (*) Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA e-mail: [email protected] Y. Yin : Y. Xu Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA H. Shen : Y. Yin : F. Chen : Y. Xu : R. A. Dixon Bioenergy Science Center (BESC), Oak Ridge, TN, USA
Introduction The generation of renewable bioenergy from plant biomass has ecological and economic implications of national and global importance. Selection of suitable plant materials for bioenergy production has been conducted in the USA through the Bioenergy Feedstock Development Program at the Oak Ridge National Laboratory since 19
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