Isolation, structural analysis, and expression characteristics of the maize nuclear factor Y gene families

Highlights

• We indicated a total of 50 members of ZmNF-Y gene family in maize genome.

• We analyzed gene structure, protein architecture of ZmNF-Y genes.

• Evolution pattern and phylogenic relationships were analyzed among 50 ZmNF-Y genes.

• Expression pattern of ZmNF-Ys were detected in various maize tissues.

• Transcript levels of ZmNF-Ys were measured under various abiotic and biotic stresses.

Abstract

NUCLEAR FACTOR-Y (NF-Y) has been shown to play an important role in growth, development, and response to environmental stress. A NF-Y complex, which consists of three subunits, NF-YA, NF-YB, and, NF-YC, binds to CCAAT sequences in a promoter to control the expression of target genes. Although NF-Y proteins have been reported in Arabidopsis and rice, a comprehensive and systematic analysis of ZmNF-Y genes has not yet been performed. To examine the functions of ZmNF-Y genes in this family, we isolated and characterized 50 ZmNF-Y (14 ZmNF-YA, 18 ZmNF-YB, and 18 ZmNF-YC) genes in an analysis of the maize genome. The 50 ZmNF-Y genes were distributed on all 10 maize chromosomes, and 12 paralogs were identified. Multiple alignments showed that maize ZmNF-Y family proteins had conserved regions and relatively variable N-terminal or C-terminal domains. The comparative syntenic map illustrated 40 paralogous NF-Y gene pairs among the 10 maize chromosomes. 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.

Introduction

NUCLEAR FACTOR-Y (NF-Y), also called Heme Activator Protein (HAP) or CCAAT-Binding Factor (CBF), is one of the most widespread promoter elements found in numerous genes in fungi, animal, and plants [1]. As a conserved heterotrimer, NF-Y, is composed of three unique subunits: NF-YA (HAP2 or CBF-B), NF-YB (HAP3 or CBF-A), and NF-YC (HAP5 or CBF-C); it specifically recognizes the widespread CCAAT-box, a cis-acting promoter element in eukaryotes [2].

In mammals and yeast, a single gene encodes each of the three NF-Y protein subunits. In contrast, multiple genes encode each subunit in plants. For example, humans and mice encode only one copy of each subunit, whereas Arabidopsis NF-YA, NF-YB, and NF-YC subunit families have 10, 13, and 13 members, respectively [3]. The analysis of these families in rice (Oryza sativa) identified 10, 11, and 7 members for the NF-YA (HAP2), NF-YB(HAP3), and NF-YC(HAP5) families, respectively, whereas these families have developed to 21, 32, and 15 members, respectively, for every subunit in soybeans (Glycine max) [4], [5].

In mammals, the NF-Y complex plays an important role in the control of cell proliferation and the early stages of development [6]. In plants, NF-Y subunits are mainly involved in processes related to the correct development of plant programs, such as embryo development (LEC1 and LEC1-like proteins, in Arabidopsis) [7], ABA-mediated seed germination [8], chloroplast biogenesis [9], photoperiodic regulation of flowering time [10], and primary root elongation [11].

Recent studies have shown that NF-Y genes play a vital role in the response to various abiotic stresses. The over-expression of AtNFYA5 and AtNF-YB1 in Arabidopsis improved plant performance and survival under drought conditions, and over-expression of ZmNF-YB2 (ZmNF-YB13 in this study) in maize improved crop yield under conditions of drought [12], [13]. Additionally AtNF-YC2 was increased in response to numerous environmental stimuli, such as light, heat, and drought stress [14]. De novo transcriptome analysis showed that SiNF-YA1 and SiNF-YB8 were highly stimulated in leaves and roots by drought and salt stresses [15]. Overexpression of GmNFYA3 in Arabidopsis enhanced drought tolerance by reducing leaf water loss and improving sensitivity to high salinity and exogenous ABA [16].

These studies in plants indicated that NF-Y family genes may be important not only for plant development but also for the response and adaptation to stresses; however, a detailed analysis of ZmNF-Y proteins has not yet been performed. To examine the functions of ZmNF-Y genes in this family, transcript levels of the genes were measured in diverse maize tissues and seedling leaves under various abiotic and biotic stresses. The results presented here provide a reference for future studies of NF-Y family genes in maize.