BioEnergy Research

, 2:217

A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production

Authors

  • Hui Shen
    • Plant Biology DivisionSamuel Roberts Noble Foundation
    • Bioenergy Science Center (BESC)
  • Yanbin Yin
    • Computational Systems Biology Lab, Department of Biochemistry and Molecular BiologyUniversity of Georgia
    • Institute of BioinformaticsUniversity of Georgia
    • Bioenergy Science Center (BESC)
  • Fang Chen
    • Plant Biology DivisionSamuel Roberts Noble Foundation
    • Bioenergy Science Center (BESC)
    • Computational Systems Biology Lab, Department of Biochemistry and Molecular BiologyUniversity of Georgia
    • Institute of BioinformaticsUniversity of Georgia
    • Bioenergy Science Center (BESC)
    • Plant Biology DivisionSamuel Roberts Noble Foundation
    • Bioenergy Science Center (BESC)
Article

DOI: 10.1007/s12155-009-9047-9

Cite this article as:
Shen, H., Yin, Y., Chen, F. et al. Bioenerg. Res. (2009) 2: 217. doi:10.1007/s12155-009-9047-9

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.

Keywords

NAM/NAC proteinTranscription factorSecondary cell wallStress toleranceBiomassCellulosic ethanolPhylogeny

Supplementary material

12155_2009_9047_MOESM1_ESM.pdf (12.1 mb)
Fig. S1Intron-exon analysis of different NAC subfamilies. (a) to (h) show the intron-exon analysis for the NAC-a to NAC-h subfamilies, respectively. The available intron-exon structures are plotted on the phylogentic tree. Open box, exon; solid black box, exons that encode NAC AE domain regions; Line, intron; 0, 1 and 2, intron phase. (PDF 12349 kb)
12155_2009_9047_MOESM2_ESM.pdf (12.1 mb)
Fig. S2The motif clades and subgroups for the NAC-a subfamily. Subgroups are a-1 to a-9; motif clades are a-sc1 to a-sc20. Red/blue colored tree I.D. indicates NAC proteins from dicots and monocots, light blue PpNACs and green SmNACs. The bootstrap values of the branches are shown in black numbers. The MEME motifs are shown as different colored boxes; the solid red, pink, light blue, blue and yellow boxes at the N-terminal indicate the NAC domain region. (PDF 12349 kb)
12155_2009_9047_MOESM3_ESM.pdf (12.1 mb)
Fig. S3The motif clades and subgroups for the NAC-g subfamily. Subgroups are g-1 to g-9; motif clades are g-sc1 to g-sc11. Red/blue colored tree I.D. indicates NAC proteins from dicots and monocots, light blue PpNACs and green SmNACs. The bootstrap values of the branches are shown in black numbers. The MEME motifs are shown as different colored boxes; the solid red, pink, light blue, blue and yellow boxes at the N-terminal indicate the NAC domain region. (PDF 12349 kb)
12155_2009_9047_MOESM4_ESM.pdf (12.1 mb)
Fig. S4Sequence-specific MEME motifs for NAC-c (NST and VND) proteins. (a) MEME motif layout patterns identified in the NAC-c subfamily. (b-d) Logos and clade specific sequences for motifs C.M7, C.M6 and C.M9. (e) Logos and comparison of different clade -specific sequences for motif C.M10. Most of the NST proteins have the sequence specific C.M7 (c-sc8, c-sc9 and csc10), C.M6 (a-sc8, c-sc9 and c-sc10) and C.M9 (a-sc8, c-sc9 and c-sc10) motifs. (PDF 12349 kb)
12155_2009_9047_MOESM5_ESM.pdf (12.1 mb)
Fig. S5Sequence-specific MEME motifs for NAC-g (SND) proteins. (a) MEME motif layout patterns identified in the NAC-g subfamily. (b-e) Logos and comparison of different clade - specific sequences for motifs g.M7, g.M19, g.M25 and g.M47. (PDF 12349 kb)
12155_2009_9047_MOESM6_ESM.pdf (12.1 mb)
Fig. S6Tissue coexpression analysis of selected Arabidopsis NAC genes. All the ANACs identified in this study together with marker genes related to plant cell-wall development and biomass production were analyzed by the GENEVESTIGATOR program for tissue coexpression patterns. Hierarchical clustering was calculated by Pearson correlation. Red box, lignin biosynthetic gene pattern, with the dotted red box showing the pattern for monolignol synthetic genes. Blue box, the secondary cell-wall polysaccharide biosynthetic gene pattern. Green box, ANAC009, ANAC015, ANAC033, ANAC070 and ANAC094 co-expression pattern. Orange box: ANAC104/AtXND1, ANAC056 and NAC074 co-expression pattern. (PDF 12349 kb)
12155_2009_9047_MOESM7_ESM.xls (187 kb)
Table S1The gene and phylogenetic tree IDs used in this study (XLS 187 kb)
12155_2009_9047_MOESM8_ESM.xls (508 kb)
Table S2Subdomain and motif analyses for the 1,232 NAC proteins (XLS 507 kb)
12155_2009_9047_MOESM9_ESM.pdf (12.1 mb)
Table S3Functionally characterized NAC proteins and NAC subfamilies. (PDF 12349 kb)
12155_2009_9047_MOESM10_ESM.pdf (12.1 mb)
Table S4Comparison of the three phylogenetic classifications of NAC genes. (PDF 12349 kb)
12155_2009_9047_MOESM11_ESM.pdf (12.1 mb)
Table S5List of the Arabidopsis NAC genes selected for coexpression analysis (PDF 12349 kb)

Copyright information

© Springer Science+Business Media, LLC. 2009