CCAAT-HAP5 Family from Maize

Required domains for CCAAT-HAP5 family:NF-YCPF00808

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Nuclear factor-Y (NF-Y) is a class of transcription factor that plays decisive roles in diverse developmental pathways in plants and other eukaryotes. These are also present in other eukaryotes as known as CCAAT-binding factor (CBF) or heme activator protein (HAP).  NF-Y specifically recognizes the regulatory CCAAT element found in either orientation in the proximal and distal enhancer regions of many genes. In higher eukaryotes, this element is found in about 30% of the promoters, preferentially in the −60/−100 region. The CCAAT box acts in concert with neighboring elements, and its bending by NF-Y is thought to be a major mechanism required for transcription activation.

NF-Y is a heterotrimeric complex composed of NF-YA (CBF-B,HAP2), NF-YB (CBF-A, HAP3), and NF-YC (CBF-C, HAP5). Each subunit contains a core region (defined by pFAM00808) that has been highly conserved throughout evolution and that is sufficient for subunit interactions and CCAAT binding, whereas the flanking regions, which include the activation domains, are much less conserved.  The NF-YA subunit is further defined by the pFAM02045 motif. The NF-YB subunit is further sub-grouped into LEC (Leafy cotyledon) and non-LEC categories. NF-YC and NF-YB core regions are homologous in sequence to histones H2A and H2B, respectively, and are required for heterodimerization, a prerequisite for NF-YA association and CCAAT binding.  The interaction between several of these subunits has been shown in maize using yeast-2-hybrid (Yang et al., 2022).

The presence of multiple forms of each HAP homolog in Arabidopsis compared with the single genes in yeast and vertebrates suggests that the HAP2/3/5 complex may play diverse roles in gene transcription in higher plants. In maize, there are 50 ZmNF-Y (14 ZmNF-YA (HAP2), 18 ZmNF-YB (HAP3), and 18 ZmNF-YC (HAP5)) genes as determined by analysis of the entire genome (Zhang et al. 2016, PMID: 27498027). Microarray data showed that the ZmNF-Y genes had tissue-specific expression patterns in various maize developmental stages and in response to biotic and abiotic stresses. The results suggested that ZmNF-YB2, 4, 8, 10, 13, and 16 and ZmNF-YC6, 8, and 15 were induced, while ZmNF-YA1, 3, 4, 6, 7, 10, 12, and 13, ZmNF-YB15, and ZmNF-YC3 and 9 were suppressed by drought stress. ZmNF-YA3, ZmNF-YA8 and ZmNF-YA12 were upregulated after infection by the three pathogens, while ZmNF-YA1 and ZmNF-YB2 were suppressed. These results indicate that the ZmNF-Ys may have significant roles in the response to abiotic and biotic stresses  (Zhang et al. 2016, Zhang et al., 2023).

NF-Y subunit C13 (ZmNF-YC13) was highly expressed in the leaf base zone of maize plants. ZmNF-YC13 overexpressing plants showed upright leaves with narrow leaf angle and larger LOV, while ZmNF-YC13 knockout plants had larger leaf angle and smaller LOV compared with wild-type plants.  It was found that ZmNF-YC13 functions as a transcriptional regulator and, together with ZmNF-YBs and ZmNF-YA3, affects plant architecture by regulating the expression of ZmWRKY76 and ZmBT2, which repress the expression of cytochrome P450 family members in PLASTOCHRON branch (Mei et al., 2021).

The maize ZmNF-YC2 gene was isolated by map-based cloning and confirmed to encode the nuclear transcription factor Y subunit C-2 protein and a positive regulator of flowering time in maize under long-day conditions. ZmNF-YC2 was found to promote the expression of ZmNF-YA3 while ZmNF-YA3 negatively regulates the transcription of ZmAP2. ZmAP2 suppresses the expression of ZMM4 to delay flowering time. A gene regulatory model of flowering time was then developed in maize using ZmNF-YC2, ZmNF-YA3, ZmAP2, ZMM4, and other key genes. The cascading regulation by ZmNF-YC2 of maize flowering time has not been reported in other species (Su et al., 2021).

Last updated June 2023 by John Gray


Mei X, Nan J, Zhao Z, Yao S, Wang W, Yang Y, Bai Y, Dong E, Liu C, Cai Y. Maize transcription factor ZmNF-YC13 regulates plant architecture. J Exp Bot. 2021 Jun 22;72(13):4757-4772. doi: 10.1093/jxb/erab157. PMID: 33831218.

Su H, Chen Z, Dong Y, Ku L, Abou-Elwafa SF, Ren Z, Cao Y, Dou D, Liu Z, Liu H, Tian L, Zhang D, Zeng H, Han S, Zhu F, Du C, Chen Y. Identification of ZmNF-YC2 and its regulatory network for maize flowering time. J Exp Bot. 2021 Dec 4;72(22):7792-7807. doi: 10.1093/jxb/erab364. PMID: 34338753.

Zhang H, Liu S, Ren T, Niu M, Liu X, Liu C, Wang H, Yin W, Xia X. Crucial Abiotic Stress Regulatory Network of NF-Y Transcription Factor in Plants. Int J Mol Sci. 2023 Feb 23;24(5):4426. doi: 10.3390/ijms24054426. PMID: 36901852; PMCID: PMC10002336.





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