NAC transcription factor
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Vascular-related NAC-domain transcription facor (VND)is one group of the largest plant-specific transcription factor NAC family. The VND1-VND7 were orginally isolated as genes for which expression levels are elevated during transdifferentiation into trachery elements, in a induction system using Arabidopsis suspension cells [1].In the past several years, VNDs have been intensively investigated in different species and shown to be important switches of the biosynthesis of secondary cell walls that provide textiles, timber, and potentially second-generation bio-fuels for human use[2,3]. VNDs are grouped in NAC-c subfamily [4]. Typically, the proteins in this subfamily share a well conserved N-terminal NAC domain (-150 amino acid;aa) and a diversified C-terminal transcription regulatory region [5,6]. The N-terminal NAC domain is usually responsible for DNA binding and dimerization, and the C-terminal region function in transcription activation , repression and protein binding. X-ray crystallography have exhibited the structure of conserved NAC domains when they form dimer and bind with DNA. However, due to the diversified sequence of C-terminal region, no structure analyses haven't been conducted in the region.
The NAC domainThe NAC domain
The DNA binding activity of NAC proteins is restricted into NAC domain which was divided into five subdomains A-E. The highly conserved positively charged subdomains C and D bind to DNA, whereas subdomain A may be involved in the formation of a functional dimer. X-ray crystallograhy have exhibited the presence of a novel transcription factor fold consisting of a twirled antiparallel β-sheet (β 1-6/7) which is used for DNA binding,located between an N-terminal helix and a short helix [7,8]. Most importantly, Val119-Ser183, lys123 and lys126, along with Lys79, Arg85,and Arg 88 were identified as biochemically crucial for DNA binding. Arg88 is conserved in all NAC proteins but Lys79 and Arg85 could be exchangable but exert different DNA binding affinity [9]. TThe NAC domain-fold also modulates dimerization through Leu14–Thr23 and Glu26–Tyr31 residues, which form a short antiparallel b-sheet at the dimer interface stabilized by salt bridges formed by Arg19 and Glu26 [6,7]. This domain also contains mono or bipartite nuclear localization signals with the lysine residues in subdomain D playing crucial roles for nuclear shuttling [3,10].
Additionally, the NAC domain also modulates protein binding that may determine fate and function of the NAC protein [11-13]. Especially for VNDs, the VNI can directly interact with VND7, and as such, VND7 can directly interact with VND1-5 [13,14] Such contacts may also be crucial for plant–pathogen interaction or stress tolerance [15,16]. The D subunit of some NAC domains contains a highly hydrophobic negative regulatory domain which acts to suppress transcriptional activity [17]. Many transcription factor family including Dof, WRKY, and APETALA, can be suppressed. Based on my alignment analyses, most of VNDs in Arabidopsis and poplar have this domain, but the function of this domain for VNDs remain elusive. The hydrophobicity associated with 'LVFY' residues or some structual interference with DNA-binding or nuclear transport in this region may be responsible for such repression. Thanks to the prescence of this domain, the positively charged Lys79, the exposed side chain of Arg85, and the hydrogen bond network of Arg 88 may mediate DNA binding activity [17,18]. Furthermore, recent protein structure analyses have shown that NAC domain can change in conformation when binds with DNA [19].
1.Kubo et al (2005) Transcription swtiches for protoxylem and metaxylem vessel formation. Gene Dev.16, 1855-1860.
2.Wang et al (2011) On-Off switches for secondary cell wall biosynthesis. Mol plant. doi:10.1093/mp/ssr098
3.Puranik et al. (2012) NAC proteins: regulation and role in stress tolerance. doi:10.1016/j.tplants.2012.2.14
4.Shen et al (2009)A bioinformatic analysis of NAC genes for plant cell wall development in relation to lignocellulosic bioenergy production. Bioener.Res. 2,217-232.
5.Olsen et al (2005) NAC transcription factor : structurally distinct, functionally diverse. Trends Plant Sci. 10,79-87
6.Ernst et al (2004)Structure of the conserved domain of ANAC,a member of the NAC family of transcription factors. EMBO J 5,297-303
7.Chen et al(2011)A structual view of the conserved domain of rice stress-responsive NAC1. Protein cell 2, 55-63
8.Puranik et al. (2011) Molecular cloning and characterization of a membrane associated NAC family gene, SiNAC from foxtail millet. Mol. Biotech.49,138-150.
9.Tran,L.S.P et al. (2009) Molecular characterization of stress-inducable GmNAC genes in soybean.Mol. Genet.Genomics 281.647-664.
10.Le, D.T. et al. (2011) Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress. DNA Res. 18, 263–276
11.Xie, Q. et al. (2002) SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals. Nature 419, 167–170
12. Greve, K. et al. (2003) Interactions between plant RING-H2 and plantspecific NAC (NAM/ATAF1/2/CUC2) proteins: RING-H2 molecular specificity and cellular localization. Biochem. J. 371, 97–108
13.Yamaguchi, M. et al. (2010) VND-INTERACTING2, a NAC domain transcription factor, negatively regulates xylem vessel formation in Arabidopsis. Plant Cell 22, 1249–1263
14.Yamaguchi, M. et al. (2011)VASCULAR-RELATED NAC-DOMAIN7 directly regulates the expression of a broad range of genes for xylem vessel formation. Plant Journal 66, 579-90
15.Xie, Q. et al. (1999) GRAB proteins, novel members of the NAC domain family, isolated by their interaction with a geminivirus protein. Plant Mol. Biol. 39, 647–656
16. Tran, L.S.P. et al. (2007) Co-expression of the stress inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis. Plant J. 49, 46–63
17. Hao, Y.J. et al. (2010) Plant NAC-type transcription factor proteins contain a NARD domain for repression of transcriptional activation. Planta 232, 1033–1043
18.Hao, Y.J. et al. (2011) Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants. Plant J. 68, 302–313
19.Welner, D.H et al.(2012)������� DNA binding by the plant specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors. Biochem J. doi:10.1092