A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production
- 1.3k Downloads
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.
KeywordsNAM/NAC protein Transcription factor Secondary cell wall Stress tolerance Biomass Cellulosic ethanol Phylogeny
This work was supported by grants to RAD and YX from the US Department of Energy Bioenergy Research Centers, through the Office of Biological and Environmental Research in the DOE Office of Science.
- 1.Ferrell JE, Wright LL, Tuskan GA (1995) Research to develop improved production methods for woody and herbaceous biomass crops. Paper presented at the conference: 2. Meeting on biomass of the Americas, Portland, Oregon, 21–24 Aug 1995Google Scholar
- 2.McLaughlin S, Bouto J, Bransby D, Conger B, Ocumpaugh W, Parrish D et al (1999) Developing switchgrass as a bioenergy crop. ASHS, Alexandria, pp 282–299Google Scholar
- 19.Fang Y, You J, Xie K, Xie W, Xiong L (2008) Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Gen Genet 280:547–563Google Scholar
- 33.Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yichuan 29:1023–1026Google Scholar
- 47.Liu Z, Shao FX, Tang GY, Shan L, Bi YP (2009) Cloning and characterization of a transcription factor ZmNAC1 in maize (Zea mays). Yichuan 31:199–205Google Scholar
- 58.Takada S, Hibara K, Ishida T, Tasaka M (2001) The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. Development 7:1127–1135Google Scholar
- 71.Tran LSP, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K et al (2004) Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell 16:2481–2498CrossRefPubMedGoogle Scholar
- 78.Das MK, Fuentes RG, Taliaferro CM (2004) Genetic variability and trait relationships in switchgrass. Crop Sci 44:443–448Google Scholar