NAC Family from Maize

Required domains for NAC family:PF02365

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NAC transcription factors (NAM (No Apical Meristem), ATAF1,2 (Arabidopsis thaliana ACTIVATING FACTOR1), and CUC2 (cup-shaped cotyledon) are one of the largest plant-specific transcription factor families.  NAC TFs possess a highly conserved N-terminal DNA binding domain (NAC) (PF02365) and a variable C-terminal transcription regulation region (TRR), and can activate or suppress the transcription of multiple target genes. The C-terminal regions of some NAC TFs also contain transmembrane motifs (TMs), which anchor to the plasma membrane. The NAC TF has a highly conserved “WKATGTD” sequence in the DNA-binding domain, similar to the “WRKYGQK” DNA-binding motif from WRKY TFs. NAC proteins, WRKY transcription factors and the mammalian GCM (Glial cell missing) transcription factors, all use a β-strand motif for DNA-binding. The consensus binding site (BS) [T,A] [T,G][T,A,C,G]CGT[G,A] has been proposed from studies of Arabidopsis ANAC019 ( (Olsen et al., 2005, Welner et al., 2012).  The recent structure of the DNA-bound ORE1-NAC domain (from Arabidopsis thaliana NAC092) further reveals the molecular basis for nucleobase recognition and phosphate backbone interactions (Chun et al., 2023).

In Arabidopsis, ATAF1 serves as a core transcriptional activator of senescence by coupling stress-related signaling with photosynthesis- and senescence-related transcriptional cascades (Garapati et al., 2015). Double mutants cuc3/cuc2 or cuc3/cuc1 in A. thaliana and the co-suppression plants of NAM and its homolog genes NAM HOMOLOG-1 (NH-1) and NAM HOMOLOG-3 (NH-3) in Petunia exhibit lateral organ fusion during vegetative development (Souer et al., 1996). Phylogenetic analysis indicates that two distinct NAM and CUC3 precursors already existed prior to the separation of mono- and dicot species (Zimmerman et al., 2005). ZmNAM1 and ZmNAM2 appear to contribute to SAM establishment. The  ZmCUC3 orthologue is associated with boundary specification at the SAM periphery, where it visualizes which fraction of cells in the SAM is committed to a new leaf primordium (Zimmerman et al., 2005).

At least 148 nonredundant NAC genes have been identified in the maize genome using Blast search tools (Peng et al., 2015, Shiragu et al., 2014).  Phylogenetic analysis using stress-related NAC TFs from Arabidopsis, rice, and soybean as seeding sequences identified 24 of 152 ZmNACs (all from Group II) as putative stress-responsive genes (Shiragu et al., 2014). ZmSNAC1 has shown drought tolerance in transgenic Arabidopsis (Lu et al., 2012). Transcriptome analysis in contrasting maize inbred lines revealed five maize NAC genes that appear to operate under drought stress (Ding et al., 2023). Two endosperm-specific NAC transcription factors, ZmNAC128 and ZmNAC130, have a regulatory function in endosperm development. Knockdown of expression of ZmNAC128 and ZmNAC130 with RNA interference (RNAi) causes a shrunken kernel phenotype with significant reduction of starch and protein. It was shown that ZmNAC128 and ZmNAC130 regulate the transcription of Bt2 and then reduce its protein level, a rate-limiting step in starch synthesis of maize endosperm. Lack of ZmNAC128 and ZmNAC130 also reduced accumulation of zeins and nonzeins by 18% and 24% compared with nontransgenic siblings, respectively (Zhang et al., 2019).

Last updated June 2023 by John Gray


Peng X, Zhao Y, Li X, Wu M, Chai W, Sheng L, Wang Y, Dong Q, Jiang H, Cheng B. Genomewide identification, classification and analysis of NAC type gene family in maize. J Genet. 2015 Sep;94(3):377-90. doi: 10.1007/s12041-015-0526-9. PMID: 26440076.

Olsen, A. N., Ernst, H. A., Leggio, L. L., & Skriver, K. (2005). DNA-binding specificity and molecular functions of NAC transcription factors. Plant Science, 169(4), 785-797.

Shiriga K, Sharma R, Kumar K, Yadav SK, Hossain F, Thirunavukkarasu N. Genome-wide identification and expression pattern of drought-responsive members of the NAC family in maize. Meta Gene. 2014 Jun 1;2:407-17. doi: 10.1016/j.mgene.2014.05.001. PMID: 25606426; PMCID: PMC4287890.

Welner DH, Lindemose S, Grossmann JG, Møllegaard NE, Olsen AN, Helgstrand C, Skriver K, Lo Leggio L. DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors. Biochem J. 2012 Jun 15;444(3):395-404. doi: 10.1042/BJ20111742. PMID: 22455904.

Chun I, Kim HJ, Hong S, Kim YG, Kim MS. Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence. Plant Commun. 2022 Dec 23:100510. doi: 10.1016/j.xplc.2022.100510. Epub ahead of print. PMID: 36564947.

Garapati P, Xue GP, Munné-Bosch S, Balazadeh S. Transcription Factor ATAF1 in Arabidopsis Promotes Senescence by Direct Regulation of Key Chloroplast Maintenance and Senescence Transcriptional Cascades. Plant Physiol. 2015 Jul;168(3):1122-39. doi: 10.1104/pp.15.00567. Epub 2015 May 7. PMID: 25953103; PMCID: PMC4741325.

Souer E, van Houwelingen A, Kloos D, Mol J, Koes R. The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Cell. 1996 Apr 19;85(2):159-70. doi: 10.1016/s0092-8674(00)81093-4. PMID: 8612269.

Zimmermann R, Werr W. Pattern formation in the monocot embryo as revealed by NAM and CUC3 orthologues from Zea mays L. Plant Mol Biol. 2005 Jul;58(5):669-85. doi: 10.1007/s11103-005-7702-x. PMID: 16158242.

Lu M, Ying S, Zhang DF, Shi YS, Song YC, Wang TY, Li Y. A maize stress-responsive NAC transcription factor, ZmSNAC1, confers enhanced tolerance to dehydration in transgenic Arabidopsis. Plant Cell Rep. 2012 Sep;31(9):1701-11. doi: 10.1007/s00299-012-1284-2. Epub 2012 May 18. PMID: 22610487.

Zhang Z, Dong J, Ji C, Wu Y, Messing J. NAC-type transcription factors regulate accumulation of starch and protein in maize seeds. Proc Natl Acad Sci U S A. 2019 Jun 4;116(23):11223-11228. doi: 10.1073/pnas.1904995116. Epub 2019 May 20. PMID: 31110006; PMCID: PMC6561305.

Ding N, Zhao Y, Wang W, Liu X, Shi W, Zhang D, Chen J, Ma S, Sun Q, Wang T, Lu M. Transcriptome analysis in contrasting maize inbred lines and functional analysis of five maize NAC genes under drought stress treatment. Front Plant Sci. 2023 Jan 19;13:1097719. doi: 10.3389/fpls.2022.1097719. PMID: 36743547; PMCID: PMC9892906.




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