Genome-wide characterization and expression analysis of citrus NUCLEAR FACTOR-Y (NF-Y) transcription factors identified a novel NF-YA gene involved in drought-stress response and tolerance.

Suzam L S Pereira,Luciana C Cidade,Grazielle M Alcantara,Alex-Alan F De Almeida,Cristina P S Martins,Aurizangela O Sousa,Luciana R Camillo,Marcio G C Costa,Danielle S Camargo,Caroline P Araújo,Jin-Song Zhang

doi:10.1371/journal.pone.0199187

Abstract

Nuclear factor Y (NF-Y) is a ubiquitous transcription factor found in eukaryotes. It is composed of three distinct subunits called NF-YA, NF-YB and NF-YC. NF-Ys have been identified as key regulators of multiple pathways in the control of development and tolerance to biotic and abiotic factors. The present study aimed to identify and characterize the complete repertoire of genes coding for NF-Y in citrus, as well as to perform the functional characterization of one of its members, namely CsNFYA5, in transgenic tobacco plants. A total of 22 genes coding for NF-Y were identified in the genomes of sweet orange (Citrus sinensis) and Clementine mandarin (C. clementina), including six CsNF-YAs, 11 CsNF-YBs and five CsNF-YCs. Phylogenetic analyses showed that there is a NF-Y orthologous in the Clementine genome for each sweet orange NF-Y gene; this was not observed when compared to Arabidopsis thaliana. CsNF-Y proteins shared the same conserved domains with their orthologous proteins in other organisms, including mouse. Analysis of gene expression by RNA-seq and EST data demonstrated that CsNF-Ys have a tissue-specific and stress inducible expression profile. qRT-PCR analysis revealed that CsNF-YA5 exhibits differential expression in response to water deficit in leaves and roots of citrus plants. Overexpression of CsNF-YA5 in transgenic tobacco plants contributed to the reduction of H2O2 production under dehydration conditions and increased plant growth and photosynthetic rate under normal conditions and drought stress. These biochemical and physiological responses to drought stress promoted by CsNF-YA5 may confer a productivity advantage in environments with frequent short-term soil water deficit.

Highlights

Nuclear Factor Y (NF-Y), known as heme activator protein (HAP) or CCAAT-binding factor (CBF), is a heterotrimeric complex transcription factor composed of three distinct subunits called NF-YA (HAP2), NF-YB (HAP3/CBF-A) and NF-YC (HAP5/CBF-C. sinensis (Cs))
BLAST searches using the 30 amino acid sequences of the complete set of A. thaliana NF-Y proteins as query sequences resulted in the identification of a total of 22 different Citrus species NF-Y encoding protein genes (CsNF-Ys) in the sweet orange genome, including six CsNF-YAs, 11 CsNF-YBs and five CsNF-YCs (Table 1)
Phylogenetic analysis showed that there is a NF-Y ortholog in the genome of Clementine mandarin for each sweet orange NF-Y gene, while two CsNF-YAs (CsNF-YA5 and CsNF-YA6), four CsNF-YBs (CsNF-YB1, CsNF-YB2, CsNF-YB5 and CsNF-YB11) and one CsNF-YC (CsNF-YC4) have no close homologs in A. thaliana (S1–S3 Figs and Table 1)

Summary

Introduction

Nuclear Factor Y (NF-Y), known as heme activator protein (HAP) or CCAAT-binding factor (CBF), is a heterotrimeric complex transcription factor composed of three distinct subunits called NF-YA (HAP2), NF-YB (HAP3/CBF-A) and NF-YC (HAP5/CBF-C). Arabidopsis NF-YA genes have been shown to regulate gametogenesis, embryogenesis, seed development and flowering [5,6,7], while in leguminous plants they have been reported as key regulators of organogenesis and development of symbiotic root nodules [8,9,10,11]. NF-YB has been implicated in the regulation of embryogenesis, seed and nodule development [9,12,13,14], flowering time [15,16,17,18], chloroplast biogenesis [19], cell proliferation and endosperm development [20], root elongation [21], photosynthesis [22] and photomorphogenesis [23]. NF-YCs have been likewise found to be involved in the control of flowering time [15,17,18,24], symbiotic nodule development [8,25], root growth [25], photosynthesis [26] and photomorphogenesis [27,28]

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Conclusion