Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.

The NAC domain was originally characterized from consensus sequences from petunia NAM and from Arabidopsis ATAF1, ATAF2, and CUC2. Genes containing the NAC domain (NAC family genes) are plant-specific transcriptional regulators and are expressed in various developmental stages and tissues. We performed a comprehensive analysis of NAC family genes in Oryza sativa (a monocot) and Arabidopsis thaliana (a dicot). We found 75 predicted NAC proteins in full-length cDNA data sets of O. sativa (28,469 clones) and 105 in putative genes (28,581 sequences) from the A. thaliana genome. NAC domains from both predicted and known NAC family proteins were classified into two groups and 18 subgroups by sequence similarity. There were a few differences in amino acid sequences in the NAC domains between O. sativa and A. thaliana. In addition, we found 13 common sequence motifs from transcriptional activation regions in the C-terminal regions of predicted NAC proteins. These motifs probably diverged having correlations with NAC domain structures. We discuss the relationship between the structure and function of the NAC family proteins in light of our results and the published data. Our results will aid further functional analysis of NAC family genes.

[1]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[2]  J. Mol,et al.  The No Apical Meristem Gene of Petunia Is Required for Pattern Formation in Embryos and Flowers and Is Expressed at Meristem and Primordia Boundaries , 1996, Cell.

[3]  S. D. de Vries,et al.  The CUP-SHAPED COTYLEDON3 Gene Is Required for Boundary and Shoot Meristem Formation in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012203. , 2003, The Plant Cell Online.

[4]  E. Meyerowitz,et al.  A Homolog of NO APICAL MERISTEM Is an Immediate Target of the Floral Homeotic Genes APETALA3/PISTILLATA , 1998, Cell.

[5]  R. R. Samaha,et al.  Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. , 2000, Science.

[6]  S. Rhee,et al.  TAIR: a resource for integrated Arabidopsis data , 2002, Functional & Integrative Genomics.

[7]  T. Boller,et al.  Differential induction of two potato genes, Stprx2 and StNAC, in response to infection by Phytophthora infestans and to wounding , 2001, Plant Molecular Biology.

[8]  N. Chua,et al.  Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. , 2000, Genes & development.

[9]  S. Takada,et al.  Involvement of CUP-SHAPED COTYLEDON genes in gynoecium and ovule development in Arabidopsis thaliana. , 2000, Plant & cell physiology.

[10]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[11]  K. Nicholas,et al.  GeneDoc: Analysis and visualization of genetic variation , 1997 .

[12]  D. Grierson,et al.  Cloning and characterization of tomato leaf senescence-related cDNAs , 1997, Plant Molecular Biology.

[13]  H Fujisawa,et al.  Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. , 1997, The Plant cell.

[14]  Alex Bateman,et al.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites , 2001, Nucleic Acids Res..

[15]  T. Gojobori,et al.  The genome sequence and structure of rice chromosome 1 , 2002, Nature.

[16]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[17]  K. Hibara,et al.  The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. , 2001, Development.

[18]  J. Kawai,et al.  Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice , 2003, Science.

[19]  Tzung-Fu Hsieh,et al.  Molecular characterization of AtNAM: a member of theArabidopsis NAC domain superfamily , 2002, Plant Molecular Biology.

[20]  M. Ueguchi-Tanaka,et al.  Molecular analysis of the NAC gene family in rice , 2000, Molecular and General Genetics MGG.

[21]  F. Qu,et al.  HRT Gene Function Requires Interaction between a NAC Protein and Viral Capsid Protein to Confer Resistance to Turnip Crinkle Virus , 2000, Plant Cell.

[22]  W. J. Lucas,et al.  Phloem long-distance transport of CmNACP mRNA: implications for supracellular regulation in plants. , 1999, Development.

[23]  Yujun Zhang,et al.  Sequence and analysis of rice chromosome 4 , 2002, Nature.

[24]  M. Aida,et al.  Shoot apical meristem and cotyledon formation during Arabidopsis embryogenesis: interaction among the CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS genes. , 1999, Development.

[25]  C. Gutiérrez,et al.  GRAB proteins, novel members of the NAC domain family, isolated by their interaction with a geminivirus protein , 1999, Plant Molecular Biology.

[26]  T. Eulgem,et al.  The WRKY superfamily of plant transcription factors. , 2000, Trends in plant science.

[27]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[28]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.