Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response

Truyen N. Quach,Hanh T. M. Nguyen,Babu Valliyodan,Henry T. Nguyen,Dong Xu,Trupti Joshi

doi:10.1007/s00438-014-0978-2

Abstract

Nuclear factor-Y (NF-Y), a heterotrimeric transcription factor, is composed of NF-YA, NF-YB and NF-YC proteins. In plants, there are usually more than 10 genes for each family and their members have been identified to be key regulators in many developmental and physiological processes controlling gametogenesis, embryogenesis, nodule development, seed development, abscisic acid (ABA) signaling, flowering time, primary root elongation, blue light responses, endoplasmic reticulum (ER) stress response and drought tolerance. Taking the advantages of the recent soybean genome draft and information on functional characterizations of nuclear factor Y (NF-Y) transcription factor family in plants, we identified 21 GmNF-YA, 32 GmNF-YB, and 15 GmNF-YC genes in the soybean (Glycine max) genome. Phylogenetic analyses show that soybean’s proteins share strong homology to Arabidopsis and many of them are closely related to functionally characterized NF-Y in plants. Expression analysis in various tissues of flower, leaf, root, seeds of different developmental stages, root hairs under rhizobium inoculation, and drought-treated roots and leaves revealed that certain groups of soybean NF-Y are likely involved in specific developmental and stress responses. This study provides extensive evaluation of the soybean NF-Y family and is particularly useful for further functional characterization of GmNF-Y proteins in seed development, nodulation and drought adaptation of soybean.Electronic supplementary materialThe online version of this article (doi:10.1007/s00438-014-0978-2) contains supplementary material, which is available to authorized users.

Highlights

Nuclear factor Y (NF-Y) is a transcription factor (TF) complex that binds the CCAAT element to regulate gene expression
Soybean Nod factor (NF)-Y protein sequences were downloaded from three current databases of soybean transcription factors
The second soybean transcription database, SoybeanTFDB, used Hidden Markov Model (HMM) of PFAM to search against the modeled proteome data of annotated genes in Glyma1 from Phytozome database with a threshold of E < 1e-5 and a verification from domain searches using InterProScan and Blastp for putative homologous genes (Mochida et al 2010)

Summary

Introduction

Nuclear factor Y (NF-Y) is a transcription factor (TF) complex that binds the CCAAT element to regulate gene expression. Subunit assembly is well studied in animals and is conserved in plants (Romier et al 2003; Calvenzani et al 2012; Hackenberg et al 2012). Sequence analysis of mammalian genome showed 25–30 % of the genes having NF-Y binding sites in their promoters (Mantovani 1998). The CCAAT box is typically found in both forward and reverse orientations between 60 and 100 bp upstream of transcription start site in mammalian genes and may be present in multiple copies with variable distances (Mantovani 1998). In a survey of a promoter sequence population, the CCAAT box element appeared highly associated with TATA-less promoters (Mantovani 1998)

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Conclusion