NAC transcription factor: Difference between revisions

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OCA, Hao Chen, David Canner, Michal Harel, Jaime Prilusky, Alexander Berchansky

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 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  <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
-</ref> <ref>http://www.springerlink.com/content/r27215773758j405/fulltext.pdf</ref>[3,10].
+</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>[11-13]. 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>[13,14]  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>[15,16]. 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>  [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  <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>[17,18]. 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>[19].
+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|frame|The figure obtained from [19] showing the circumstance when NAC domain interact with DNA]]
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 == Diverged C-terminal  domain ==
-The transcription regulatory region, generally lying at the highly diverged C-terminal, can either activate  <ref>http://www.plantcell.org/content/16/9/2481.full.pdf+html</ref> <ref>http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2005.02575.x/pdf</ref> <ref>http://www.springerlink.com/content/8101522211447210/fulltext.pdf</ref>[20-22] or repress transcription  <ref name="plantc">http://www.plantcell.org/content/22/4/1249.full.pdf+html</ref> <ref name="jbc">http://www.jbc.org/content/282/50/36292.full.pdf</ref> <ref>http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2005.02488.x/pdf</ref>[13,23,24]. Recently, the C-terminal of a novel  NAC domain protein VNI have been shown to both activate and repress transcription  <ref>http://www.plantcell.org/content/early/2011/06/13/tpc.111.084913.full.pdf+html</ref>[25]. More interestingly, VNI2 transcriptional repression motif can be transformed into the transcription activation domain under high salt conditions. It is therefore likely that the C-terminal domain isn’t only complex in sequence, but confer  the multiple functions.  Based on the sequence analyses, the transcription regulatory region has several  group speciﬁc motifs that are rich in repeats of serine–threonine, proline–glutamine, or acidic residues, for example, the transcription regulatory region of rice NAC proteins was found to contain ten C-terminal motifs  <ref>http://www.biomedcentral.com/content/pdf/1756-0500-4-302.pdf</ref>[27]. Another comprehensive study has revealed that these motifs are conserved for a given subgroup of NAC subfamilies but varies across the different subfamilies<ref name="oxford">http://mplant.oxfordjournals.org/content/early/2011/12/01/mp.ssr098.full.pdf+html
+The transcription regulatory region, generally lying at the highly diverged C-terminal, can either activate  <ref>http://www.plantcell.org/content/16/9/2481.full.pdf+html</ref> <ref>http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2005.02575.x/pdf</ref> <ref>http://www.springerlink.com/content/8101522211447210/fulltext.pdf</ref> or repress transcription  <ref name="plantc">http://www.plantcell.org/content/22/4/1249.full.pdf+html</ref> <ref name="jbc">http://www.jbc.org/content/282/50/36292.full.pdf</ref> <ref>http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2005.02488.x/pdf</ref>. Recently, the C-terminal of a novel  NAC domain protein VNI have been shown to both activate and repress transcription  <ref>http://www.plantcell.org/content/early/2011/06/13/tpc.111.084913.full.pdf+html</ref>. More interestingly, VNI2 transcriptional repression motif can be transformed into the transcription activation domain under high salt conditions. It is therefore likely that the C-terminal domain isn’t only complex in sequence, but confer  the multiple functions.  Based on the sequence analyses, the transcription regulatory region has several  group speciﬁc motifs that are rich in repeats of serine–threonine, proline–glutamine, or acidic residues, for example, the transcription regulatory region of rice NAC proteins was found to contain ten C-terminal motifs  <ref>http://www.biomedcentral.com/content/pdf/1756-0500-4-302.pdf</ref>. Another comprehensive study has revealed that these motifs are conserved for a given subgroup of NAC subfamilies but varies across the different subfamilies<ref name="oxford">http://mplant.oxfordjournals.org/content/early/2011/12/01/mp.ssr098.full.pdf+html
-</ref> [2]. Thus, this region imparts variation to individual functions of NAC proteins. Additionally, because of the excessive low-complexity sequences, transcription regulatory regions have a high degree of intrinsic disorder (ID) and fail to have a single stable three-dimensional structure <ref name="content">http://www.jbc.org/content/286/41/35418.full.pdf+html</ref><ref>http://peer.ccsd.cnrs.fr/docs/00/47/92/44/PDF/PEER_stage2_10.1042%252FBJ20091234.pdf</ref>[28,29]. Such ﬂexibility enables them to interact with different target proteins making them model proteins for systematic analysis of transcription factor functions and structural ID. Some NAC proteins have protein-binding ability in their TRRs  <ref name="jbc">http://www.jbc.org/content/282/50/36292.full.pdf</ref>  <ref name="content">http://www.jbc.org/content/286/41/35418.full.pdf+html</ref> <ref name="mpiz">http://www.mpiz-koeln.mpg.de/26442/Kleinow_Plant_J_23_pdf.pdf</ref>[23,28,30]. An a-helical transmembrane (TM) motif present in some NAC proteins is responsible for plasma membrane or endoplasmic reticulum membrane anchoring  <ref name="mpiz">http://www.mpiz-koeln.mpg.de/26442/Kleinow_Plant_J_23_pdf.pdf</ref>[30]. Up to now, 18 membrane bound NAC proteins have been identiﬁed in Arabidopsis, 11 in soybean, seven in maize (Zea mays), six in grape, ﬁve each in rice, poplar, switchgrass (Panicum virgatum) and sorghum (Sorghum bicolor), and four in Medicago truncatula  <ref> http://signet.korea.ac.kr/webzine/6th/papers/Trends_in_Plant_Science_200810.pdf</ref> <ref>http://ac.els-cdn.com/S0888754309002122/1-s2.0-S0888754309002122-main.pdf?_tid=f675eda8581767131107a56c803e8434&acdnat=1336012303_7e1cc13e64dad88ebd90823905b9ccfb</ref>[31,32], which may play important regulatory roles under environmental cues. However, no VNDs and other NAC proteins relating to cell wall were identified to have transmembrane motif.
+</ref>. Thus, this region imparts variation to individual functions of NAC proteins. Additionally, because of the excessive low-complexity sequences, transcription regulatory regions have a high degree of intrinsic disorder (ID) and fail to have a single stable three-dimensional structure <ref name="content">http://www.jbc.org/content/286/41/35418.full.pdf+html</ref><ref>http://peer.ccsd.cnrs.fr/docs/00/47/92/44/PDF/PEER_stage2_10.1042%252FBJ20091234.pdf</ref>. Such ﬂexibility enables them to interact with different target proteins making them model proteins for systematic analysis of transcription factor functions and structural ID. Some NAC proteins have protein-binding ability in their TRRs  <ref name="jbc">http://www.jbc.org/content/282/50/36292.full.pdf</ref>  <ref name="content">http://www.jbc.org/content/286/41/35418.full.pdf+html</ref> <ref name="mpiz">http://www.mpiz-koeln.mpg.de/26442/Kleinow_Plant_J_23_pdf.pdf</ref>. An a-helical transmembrane (TM) motif present in some NAC proteins is responsible for plasma membrane or endoplasmic reticulum membrane anchoring  <ref name="mpiz">http://www.mpiz-koeln.mpg.de/26442/Kleinow_Plant_J_23_pdf.pdf</ref>. Up to now, 18 membrane bound NAC proteins have been identiﬁed in Arabidopsis, 11 in soybean, seven in maize (Zea mays), six in grape, ﬁve each in rice, poplar, switchgrass (Panicum virgatum) and sorghum (Sorghum bicolor), and four in Medicago truncatula  <ref> http://signet.korea.ac.kr/webzine/6th/papers/Trends_in_Plant_Science_200810.pdf</ref> <ref>http://ac.els-cdn.com/S0888754309002122/1-s2.0-S0888754309002122-main.pdf?_tid=f675eda8581767131107a56c803e8434&acdnat=1336012303_7e1cc13e64dad88ebd90823905b9ccfb</ref>[31,32], which may play important regulatory roles under environmental cues. However, no VNDs and other NAC proteins relating to cell wall were identified to have transmembrane motif.
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 In vascular vessel, VND6 and VND7 control both secondary cell development and programmed cell death of vessels in both root and shoot tissues  <ref name="GENEDEV">http://genesdev.cshlp.org/content/19/16/1855.full.pdf</ref> <ref>http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2008.03533.x/pdf
-</ref>(1,33). The over-expression of VND6 and VND7 can induce ectopic differentiation of two different types of vessel elements: proto-xylem, and meta-xylem vessels. Reversely, the functional repression of VND6 and VND7 can inhibit vessel element formation. Additionally, the excellent works finished by Ye lab showed that the Arabidopsis VND6 and VND7 can complement the NST1NST3 double mutant phenotype, indicating that VNDs share the conserved functions with other secondary cell wall regulators  <ref name="plantbio"> http://www.plantbio.uga.edu/~zhye/2010-SWNTargets.pdf</ref>[34]. Then they found that the poplar VNDs can complement the Arabidopsis cell wall development defective mutant NST1NST3, suggesting that the conserved function of VNDs among different species  <ref>http://www.plantbio.uga.edu/~zhye/2010-PtrWND.pdf</ref>[35]. Recently, the downstream genes of VND6 and VND7 were identified by the excellent works mainly done by Demura lab, Ye lab and Fukuda lab  <ref name="online">http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04514.x/pdf</ref> <ref name="plantbio"> http://www.plantbio.uga.edu/~zhye/2010-SWNTargets.pdf</ref> <ref>http://www.plantcell.org/content/22/10/3461.full.pdf+html</ref>[14,34,36]. Both VND6 and VND7 regulates a battery of genes that are common with the downstream of SND1 (secondary cell wall related NAC domain transcription factor), a well known fiber developmental switch. The common downstream genes of VND6, VND7, and SND1 were MYBs transcription factor that have been identified as important regulators of secondary cell wall biosynthesis. However, VND6 and VND7 regulated LBD (Late organ boundery domain) transcription factor that involved in programmed cell death, indicating the important role of VND6 and VND7 in vessel development. The further elucidation of regulatory ways of VNDs not only promote our knowledge in vessel development, but also facilitate the engineering of plant stocks stem from cell wall suitable for biofuel production.
+</ref>. The over-expression of VND6 and VND7 can induce ectopic differentiation of two different types of vessel elements: proto-xylem, and meta-xylem vessels. Reversely, the functional repression of VND6 and VND7 can inhibit vessel element formation. Additionally, the excellent works finished by Ye lab showed that the Arabidopsis VND6 and VND7 can complement the NST1NST3 double mutant phenotype, indicating that VNDs share the conserved functions with other secondary cell wall regulators  <ref name="plantbio"> http://www.plantbio.uga.edu/~zhye/2010-SWNTargets.pdf</ref>. Then they found that the poplar VNDs can complement the Arabidopsis cell wall development defective mutant NST1NST3, suggesting that the conserved function of VNDs among different species  <ref>http://www.plantbio.uga.edu/~zhye/2010-PtrWND.pdf</ref>. Recently, the downstream genes of VND6 and VND7 were identified by the excellent works mainly done by Demura lab, Ye lab and Fukuda lab  <ref name="online">http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04514.x/pdf</ref> <ref name="plantbio"> http://www.plantbio.uga.edu/~zhye/2010-SWNTargets.pdf</ref> <ref>http://www.plantcell.org/content/22/10/3461.full.pdf+html</ref>. Both VND6 and VND7 regulates a battery of genes that are common with the downstream of SND1 (secondary cell wall related NAC domain transcription factor), a well known fiber developmental switch. The common downstream genes of VND6, VND7, and SND1 were MYBs transcription factor that have been identified as important regulators of secondary cell wall biosynthesis. However, VND6 and VND7 regulated LBD (Late organ boundery domain) transcription factor that involved in programmed cell death, indicating the important role of VND6 and VND7 in vessel development. The further elucidation of regulatory ways of VNDs not only promote our knowledge in vessel development, but also facilitate the engineering of plant stocks stem from cell wall suitable for biofuel production.
 [[Image:1123.png|thumb|frame|The figure and figure legend obtained from [35].Restoration of lignified secondary walls in the interfascicular fibers of stems of the snd1 nst1 double mutant by expression of PtrWNDs. The bottom parts of 8-week-old stems were sectioned and stained for lignin with phloroglucinol-HCl. if, Interfascicular fiber; xy, xylem. Bar in C = 82 mm for C to J.. Of these WNDs, PtrWNB3-6 are included in the group of VNDs]]