NAC transcription factor: Difference between revisions

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 crystallography[http://en.wikipedia.org/wiki/X-ray_crystallography] 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  <ref name="ncbi">www.ncbi.nlm.nih.gov/pubmed/21337010</ref> <ref>http://www.springerlink.com/content/8p88600115713107/fulltext.pdf</ref>. 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  <ref>http://www.springerlink.com/content/r27215773758j405/fulltext.pdf</ref>. The NAC domain-fold also modulates dimerization through Leu14–Thr23 and Glu26–Tyr31 residues, which form a short antiparallel b-sheet at the dimer

[[Image:999.png|thumb|right|200px|The figure obtained from [19] showing the circumstance when NAC domain interact with DNA]]Additionally, the NAC domain also modulates protein binding that may determine fate and function of the NAC protein  <ref>http://www.ibt.unam.mx/computo/pdfs/ubiquita/sinat5.pdf</ref> <ref>http://www.biochemj.org/bj/371/0097/3710097.pdf</ref> <ref name="plantc">http://www.plantcell.org/content/22/4/1249.full.pdf+html</ref>. Especially for VNDs, the VNI can directly interact with VND7, and as such, VND7 can directly interact with VND1-5  <ref name="plantc">http://www.plantcell.org/content/22/4/1249.full.pdf+html</ref>  <ref name="online">http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04514.x/pdf</ref>  Such contacts may also be crucial for plant–pathogen interaction or stress tolerance  <ref>http://www.springerlink.com/content/p82h815356615752/fulltext.pdf</ref> <ref>http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2006.02932.x/pdf</ref>. The D subunit of some NAC domains contains a highly hydrophobic negative regulatory domain which acts to suppress transcriptional activity  <ref>http://www.springerlink.com/content/x3t8826465j44p32/fulltext.pdf</ref>  . 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  <ref>http://www.springerlink.com/content/x3t8826465j44p32/fulltext.pdf</ref> <ref>http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04687.x/pdf</ref>. Furthermore, recent protein structure analyses have shown that NAC domain can change in conformation when binds with DNA  <ref>http://www.biochemj.org/bj/imps/pdf/BJ20111742.pdf</ref>.