CCAAT-HAP2 Family from Maize

Required domains for CCAAT-HAP2 family:PF02045

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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) which are all required for CCAAT binding. 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).

Members of the miR169 miRNA family are highly conserved in plants and they regulate the expression of genes encoding the universal transcription factor subunit NUCLEAR FACTOR-Y subunit A (NF-YA) via transcript cleavage. The miR169/NF-YA module plays a critical role during plant development and in plant responses to abiotic stress. The expression patterns of zma-miR169s and their target ZmNF-YA genes in maize leaves were found to change in response to the three stress treatments. The expression of most zma-miR169 genes was downregulated by PEG and upregulated by ABA. In response to salt stress, zma-miR169 genes were upregulated initially and subsequently downregulated (Luan et al., 2015). A study in maize roots yielded similar results (Luan et al., 2014).

NF-Y transcription factors also play a role in regulating maize flowering time and stress response in maize. Genome-wide analysis showed that ZmNF-YA3 bound to >6000 sites in the maize genome, 2259 of which are associated with genic sequences. ZmNF-YA3 was found to interact with CONSTANS-like (CO-like) and flowering promoting factor1 (FPF1) through yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Quantitative real-time reverse transcription-PCR (qRT-PCR) combined with yeast one-hybrid assay and EMSA suggested that NF-YA3 could promote early flowering by binding to the FLOWERING LOCUS T-like12 (FT-like12) promoter in maize (Su et al., 2018).

The ZmNFYA01 and ZmNFYA06 TFs may regulate maize disease resistance by affecting the transcription levels of ZmPRs. After inoculation with Setosphaeria turcica and Cochliobolus heterostrophus, the lesion areas of nfya01 and nfya06 were significantly larger than that of B73, indicating that ZmNFYA01 and ZmNFYA06 positively regulated maize disease resistance (Lv et al., 2022).

Last updated June 2023 by John Gray


Zhang Z, Li X, Zhang C, Zou H, Wu Z. Isolation, structural analysis, and expression characteristics of the maize nuclear factor Y gene families. Biochem Biophys Res Commun. 2016 Sep 16;478(2):752-8. doi: 10.1016/j.bbrc.2016.08.020. Epub 2016 Aug 4. PMID: 27498027.

Luan M, Xu M, Lu Y, Zhang L, Fan Y, Wang L. Expression of zma-miR169 miRNAs and their target ZmNF-YA genes in response to abiotic stress in maize leaves. Gene. 2015 Jan 25;555(2):178-85. doi: 10.1016/j.gene.2014.11.001. Epub 2014 Nov 5. PMID: 25445264.

Luan M, Xu M, Lu Y, Zhang Q, Zhang L, Zhang C, Fan Y, Lang Z, Wang L. Family-wide survey of miR169s and NF-YAs and their expression profiles response to abiotic stress in maize roots. PLoS One. 2014 Mar 14;9(3):e91369. doi: 10.1371/journal.pone.0091369. PMID: 24633051; PMCID: PMC3954700.

Lv M, Cao H, Wang X, Zhang K, Si H, Zang J, Xing J, Dong J. Identification and expression analysis of maize NF-YA subunit genes. PeerJ. 2022 Nov 7;10:e14306. doi: 10.7717/peerj.14306. PMID: 36389434; PMCID: PMC9648346.

Yang Y, Wang B, Wang J, He C, Zhang D, Li P, Zhang J, Li Z. Transcription factors ZmNF-YA1 and ZmNF-YB16 regulate plant growth and drought tolerance in maize. Plant Physiol. 2022 Sep 28;190(2):1506-1525. doi: 10.1093/plphys/kiac340. PMID: 35861438; PMCID: PMC9516732.

Su H, Cao Y, Ku L, Yao W, Cao Y, Ren Z, Dou D, Wang H, Ren Z, Liu H, Tian L, Zheng Y, Chen C, Chen Y. Dual functions of ZmNF-YA3 in photoperiod-dependent flowering and abiotic stress responses in maize. J Exp Bot. 2018 Oct 12;69(21):5177-5189. doi: 10.1093/jxb/ery299. PMID: 30137393.

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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