Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa)

RESEARCH ARTICLE Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa) Quangang Liu1, Zhanchao Wang1, Xuemei Xu2, Haizhen Zhang1, Chenghao Li1* 1 State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China, 2 Library of Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China * Abstract Background OPEN ACCESS Citation: Liu Q, Wang Z, Xu X, Zhang H, Li C (2015) Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa). PLoS ONE 10(8): e0134753. doi:10.1371/journal.pone.0134753 C2H2 zinc-finger (C2H2-ZF) proteins are a large gene family in plants that participate in various aspects of normal plant growth and development, as well as in biotic and abiotic stress responses. To date, no overall analysis incorporating evolutionary history and expression profiling of the C2H2-ZF gene family in model tree species poplar (Populus trichocarpa) has been reported. Principal Findings Copyright: © 2015 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Here, we identified 109 full-length C2H2-ZF genes in P. trichocarpa, and classified them into four groups, based on phylogenetic analysis. The 109 C2H2-ZF genes were distributed unequally on 19 P. trichocarpa linkage groups (LGs), with 39 segmental duplication events, indicating that segmental duplication has been important in the expansion of the C2H2-ZF gene family. Promoter cis-element analysis indicated that most of the C2H2-ZF genes contain phytohormone or abiotic stress-related cis-elements. The expression patterns of C2H2-ZF genes, based on heatmap analysis, suggested that C2H2-ZF genes are involved in tissue and organ development, especially root and floral development. Expression analysis based on quantitative real-time reverse transcription polymerase chain reaction indicated that C2H2-ZF genes are significantly involved in drought, heat and salt response, possibly via different mechanisms. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Conclusions Editor: Manoj Prasad, National Institute of Plant Genome Research, INDIA Received: March 4, 2015 Accepted: July 13, 2015 Published: August 3, 2015 Funding: The authors have no support or funding to report. Competing Interests: The authors have declared that no competing interests exist. This study provides a thorough overview of the P. trichocarpa C2H2-ZF gene family and presents a new perspective on the evolution of this gene family. In particular, some C2H2ZF genes may be involved in environmental stress tolerance regulation. PtrZFP2, 19 and 95 showed high expression levels in leaves and/or roots under environmental stresses. PLOS ONE | DOI:10.1371/journal.pone.0134753 August 3, 2015 1 / 25 C2H2 Zinc-Finger Family and Poplar (Populus trichocarpa) Additionally, this study provided a solid foundation for studying the biological roles of C2H2ZF genes in Populus growth and development. These results form the basis for further investigation of the roles of these candidate genes and for future genetic engineering and gene functional studies in Populus. Introduction Zinc-finger proteins (ZFPs) are the largest family of transcription regulators in plants [1]. The term “zinc finger” (ZF) refers to a protein domain, in which a zinc ion is surrounded by cysteine (Cys) residues and/or the histidine (His) residues to stabilize its three-dimensional structure, which comprises a two-stranded antiparallel beta sheet and a helix. Based on the number and location of the Cys and His residues, the ZFPs are divided into different types: C2H2, C2HC, C2HC5, C2C2, CCCH, C3HC4, C4, C4HC3, C6, and C8 [2,3]. The first plant-specific ZFP was identified in Petunia and interacts with the promoter region of the 5-enolpyruvylshikimate-3-phosphate synthase gene (EPSPS) [4]. Subsequently, further zinc-finger transcription factors (TFs) have been identified in other plants and their contributions to important biological processes during vegetative growth, reproductive development and stress responses have been noted [5–8]. The C2H2 ZFPs, also called the TFIIIA-type ZFPs, can be represented as X2-Cys-X(2–4)Cys-X12-His-X(3–5)-His, where X represents any amino acid and where the precise spacing varies between the two cysteines and between the two histidines [9]. Among the ZFP types, C2H2-ZFPs are one of the most widespread transcription factor families in eukaryotes [10]. In silico analysis has shown that C2H2-ZF genes represent ~3% of all genes in mammals, ~2.3% in Diptera and ~0.8% in Saccharomyces cerevisiae [11,12]. In plants, the C2H2 zinc-finger gene family is large. There are 176, 189 and 124 members in Arabidopsis, rice and foxtail millet, respectively [13–15]. Compared with other eukaryote C2H2-ZFPs, there are two main structural features in most of the plant C2H2 ZFPs. First, in plant multiple-fingered C2H2-ZFPs, the zinc-finger domains are separated by long spacers that vary in length and sequence, whereas the C2H2-ZFPs of yeast and animals are mostly clustered and separated by a short spacer (six to eight amino acids) [16,17]. Second, most plant C2H2-ZFPs include an invariant sequence, QALGGH, located inside the zinc-finger helices, whereas yeast and animal C2H2-ZFPs do not have this motif [1]. C2H2-ZFPs differ widely in their structures and functions. Many ZFPs function as TFs, and although these proteins are thought to mainly interact with DNA or chromatin, some are also thought to bind to RNA and proteins [18–20]. Therefore C2H2-ZFPs not only participate in transcriptional regulation, but also act in RNA metabolism and in other biological activities. They are involved in a wide range of processes, including plant growth and development, and in biotic and abiotic stress responses in plants. A number of C2H2-ZFPs are involved in trichome initiation, seed germination, floral organogenesis, primary microRNA biogenesis and heat stress in Arabidopsis [21–25]; cold, drought, oxidative and salt stress in rice [26,27]; cold and drought stress in soybean [28]; pathogen defense in Capsicum annuum [29]; and osmotic, cold and mechanical stress in poplar [30]. These studies showed that C2H2-ZFPs are likely to be associated with multiple physiological processes and stress responses. Poplar (Populus trichocarpa) is a valuable forest resource, making it an important commercial and ecological species [31]. P. trichocarpa is also a model plant, whose whole genome sequence is available [32]. Compared with the extensive studies of C2H2-ZF genes in many PLOS ONE | DOI:10.1371/journal.pone.01 (...truncated)