The Arabidopsis thaliana Nuclear Factor Y Transcription Factors

Abstract

Nuclear factor Y (NF-Y) is an evolutionarily conserved trimeric transcription factor complex present in nearly all eukaryotes. The heterotrimeric NF-Y complex consists of three subunits, NF-YA, NF-YB, and NF-YC, and binds to the CCAAT box in the promoter regions of its target genes to regulate their expression. Yeast and mammal genomes generally have single genes with multiple splicing isoforms that encode each NF-Y subunit. By contrast, plant genomes generally have multi-gene families encoding each subunit and these genes are differentially expressed in various tissues or stages. Therefore, different subunit combinations can lead to a wide variety of NF-Y complexes in various tissues, stages, and growth conditions, indicating the potentially diverse functions of this complex in plants. Indeed, many recent studies have proved that the NF-Y complex plays multiple essential roles in plant growth, development, and stress responses. In this review, we highlight recent progress on NF-Y in Arabidopsis thaliana, including NF-Y protein structure, heterotrimeric complex formation, and the molecular mechanism by which NF-Y regulates downstream target gene expression. We then focus on its biological functions and underlying molecular mechanisms. Finally, possible directions for future research on NF-Y are also presented.

Keywords: Arabidopsis; CCAAT box; abiotic response; flowering time; hypocotyl elongation; nuclear factor Y.

FIGURE 1

Nuclear factor Y (NF-Y) protein structure. The NF-YA conserved region is composed of two α-helices. The A1 helix is in the N-terminal of the core region and functions in interaction with NF-YB and NF-YC. The A2 is in the C-terminal and functions in specific recognition of the CCAAT element. The Histone Fold Domain (HFD) domain of the NF-YB and NF-YC proteins contains the DNA-binding domain and protein-protein interaction domain. The diagram shows AtNF-YA1, AtNF-YB1, and AtNF-YC1 as examples.

FIGURE 2

Two molecular mechanisms by which NF-Y modulates gene expression. (A) The NF-YB-YC heterodimers translocate into the nucleus and interact with NF-YA to form an active heterotrimer. This heterotrimer binds to the CCAAT box in the promoter regions of the target genes and mediates their expression. (B) The NF-YB-YC heterodimer interacts with the transcription factor (TF) to form a NF-YB-YC-TF heterotrimer and binds to specific cis-element (indicated by XXX). NF-YA can competitively inhibit the interaction of the TF with NF-YB/NF-YC.

FIGURE 3

Nuclear factor Y regulates hypocotyl elongation through PIF4. At dawn, Phytochrome interacting factor 4 (PIF4) is degraded by the 26S proteasome. At dusk, the transcription level of PIF4 is repressed by evening complex (ELF4-ELF3-LUX). Therefore, NF-YB9/LEC1 cannot be recruited to the promoter of IAA19. At midnight, the transcription level of PIF4 increases along with decreased abundance of the ELF4-ELF3-LUX complex. Meanwhile, NF-YB9/LEC1 is recruited to the promoter of IAA19 through its interaction with PIF4, thus increasing the transcription level of IAA19 and promotes hypocotyl elongation.

FIGURE 4

Nuclear factor Y controls flowering time. (A) In the photoperiod pathway, the NF-Y complex can interact with CONSTANS (CO) protein, then binds the promoter region of FT and enhances its transcription. In the gibberellin (GA) signaling pathway, DELLA interacts with FLC and enhances transcriptional repression of FT and SUPPRESOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) by FLC. DELLA also represses the interaction of CO with NF-YB2, thus preventing the CO-NF-Y complex from promoting expression of FT and SOC1. (B) A diagram indicating the detailed molecular mechanism is shown in the region in gray in (A). NF-YA1, YA4, and YB1 repress the expression of FT and thus delay flowering; NF-YC1 increases the transcription of FT and SOC1, thus promoting flowering. NF-YB2/B3 and YC3/YC4/YC9 can form a complex with CO and regulate the expression of FT. Moreover, NF-YA2/YB2 and NF-YB3/YC9 interact with CO and regulate the expression of SOC1. (C) CO and NF-Y regulate FT expression. At dawn, NF-YA1-YB-YC form a heterotrimeric complex that binds to the promoter of FT thus repressing its transcription. At dusk, CO competes with NF-YA1 to form a heterotrimeric complex NF-YB-YC-CO to promote the transcription of FT.