NAC transcription factor: Difference between revisions
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</ref>. VNDs are grouped in NAC-c subfamily<ref>http://csbl.bmb.uga.edu/~yinyb/ | </ref>. VNDs are grouped in NAC-c subfamily<ref>http://csbl.bmb.uga.edu/~yinyb/ | ||
</ref>. 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 <ref>www.ncbi.nlm.nih.gov/pubmed/15708345</ref> <ref name ="nature">http://www.nature.com/embor/journal/v5/n3/pdf/7400093.pdf</ref>. 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. | </ref>. 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 <ref>www.ncbi.nlm.nih.gov/pubmed/15708345</ref> <ref name ="nature">http://www.nature.com/embor/journal/v5/n3/pdf/7400093.pdf</ref>. 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. | ||
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== Conserved NAC domain == | == Conserved 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 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 | 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 | ||
interface stabilized by salt bridges formed by Arg19 and Glu26 <ref name ="nature">http://www.nature.com/embor/journal/v5/n3/pdf/7400093.pdf</ref> <ref name="ncbi">www.ncbi.nlm.nih.gov/pubmed/21337010</ref> . This domain also contains mono or bipartite nuclear localization signals with the lysine residues in subdomain D playing crucial roles for nuclear shuttling <ref name="MPLANT">http://www.springerlink.com/content/qq1584g690243n16/fulltext.pdf | interface stabilized by salt bridges formed by Arg19 and Glu26 <ref name ="nature">http://www.nature.com/embor/journal/v5/n3/pdf/7400093.pdf</ref> <ref name="ncbi">www.ncbi.nlm.nih.gov/pubmed/21337010</ref> . This domain also contains mono or bipartite nuclear localization signals with the lysine residues in subdomain D playing crucial roles for nuclear shuttling <ref name="MPLANT">http://www.springerlink.com/content/qq1584g690243n16/fulltext.pdf | ||
</ref> <ref>http://www.springerlink.com/content/r27215773758j405/fulltext.pdf</ref>. | </ref> <ref>http://www.springerlink.com/content/r27215773758j405/fulltext.pdf</ref>. | ||
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>. | [[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>. | ||
== Diverged C-terminal domain == | == Diverged C-terminal domain == | ||