Comprehensive genomic survey, structural classification and expression analysis of C2H2 zinc finger protein gene family in Brassica rapa L.

RESEARCH ARTICLE Comprehensive genomic survey, structural classification and expression analysis of C2H2 zinc finger protein gene family in Brassica rapa L. Intikhab Alam1, Khadija Batool2, Dong-Li Cui1, Yan-Qing Yang1, Yun-Hai Lu ID1* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China, 2 State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Key Lab of Biopesticides and Chemical Biology, Fujian Agriculture and Forestry University, Fuzhou, China * , Abstract OPEN ACCESS Citation: Alam I, Batool K, Cui D-L, Yang Y-Q, Lu Y-H (2019) Comprehensive genomic survey, structural classification and expression analysis of C2H2 zinc finger protein gene family in Brassica rapa L.. PLoS ONE 14(5): e0216071. https://doi. org/10.1371/journal.pone.0216071 Editor: Maoteng Li, Huazhong University of Science and Technology, CHINA Received: December 18, 2018 Accepted: April 12, 2019 Published: May 6, 2019 Copyright: © 2019 Alam 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. Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files. Funding: This work was supported by a start-up fund for distinguished scholars of Fujian Agriculture and Forestry University, No. 114120019 to YHL. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. C2H2 zinc finger protein (ZFP) genes have been extensively studied in many organisms and can function as transcription factors and be involved in many biological processes including plant growth and development and stress responses. In the current study, a comprehensive genomics analysis of the C2H2-ZFP genes in B. rapa was performed. A total of 301 B. rapa putative C2H2-ZFP (BrC2H2-ZFP) genes were identified from the available Brassica genome databases, and further characterized through analysis of conserved amino acid residues in C2H2-ZF domains and their organization, subcellular localization, phylogeny, additional domain, chromosomal location, synteny relationship, Ka/Ks ratio, and expression pattern. We also analyzed the expression patterns of eight B. rapa C2H2-ZFP genes under salt and drought stress conditions by using qRT-PCR technique. Our results showed that about one-third of these B. rapa C2H2-ZFP genes were originated from segmental duplication caused by the WGT around 13 to 17 MYA, one-third of them were highly and consecutively expressed in all tested tissues, and 92% of them were located in nucleus by prediction supporting then their functional roles as transcription factors, of which some may play important roles in plant growth and development. The Ka/Ks ratios of 264 orthologous C2H2-ZFP gene pairs between A. thaliana and B. rapa were all, except two, inferior to 1 (varied from 0.0116 to 1.4919, with an average value of 0.3082), implying that these genes had mainly experienced purifying selection during species evolution. The estimated divergence times of the same set of gene pairs ranged from 6.23 to 38.60 MY, with an average value of 18.29 MY, indicating that these gene members have undergone different selective pressures resulting in different evolutionary rates during species evolution. In addition, a few of these B. rapa C2H2-ZFPs were shown to be involved in stress responses in a similar way as their orthologs in A. thaliana. Comparison between A. thaliana and B. rapa orthologous C2H2-ZFP genes showed that the majority of these C2H2-ZFP gene members encodes proteins with conserved subcellular localization and functional domains between the two species but differed in their expression patterns in five tissues or organs. Thus, our PLOS ONE | https://doi.org/10.1371/journal.pone.0216071 May 6, 2019 1 / 22 Comprehensive analysis of C2H2 zinc finger protein gene family in Brassica rapa study provides valuable information for further functional determination of each C2H2-ZFP gene across the Brassica species, and may help to select the appropriate gene targets for further in-depth studies, and genetic engineering and improvement of Brassica crops. Introduction The zinc finger proteins (ZFPs) are one of the most common groups of proteins widely existing in all eukaryotic organisms. Zinc finger proteins were known to be involved in many cellular processes including DNA-binding, RNA-binding, protein-protein interaction, and protein folding, etc. [1–3], and play important roles in plant growth and development as well as response to various environmental stresses [4–7]. The zinc finger (ZF) structure is maintained by the zinc ion, which coordinates conserved cysteine and/or histidine residues in different combinations. According to the type and order of these zinc coordinated residues, the ZFs can be classified into different types, such as, C2H2, C2C2, and C3H1 domains coordinating one zinc ion, whereas C3HC4 RING finger, PHD and LIM domains coordinating two zinc ions [8–10]. As high as 30 types of ZFs were approved in human genome [9]. The C2H2-ZFs, also called classical ZFs, were the first class to be characterized among all the types of ZFs [9]. The C2H2-ZF domain was defined as about 30 amino acids with two conserved Cys and two His residues which bound to one Zn2+ atom tetrahedrally and form a structure as C-X2-4–C-X3–F-X5-L-X2–H-X3-5–H, where X represents any amino acid [2,11]. Plant C2H2 zinc finger proteins differ from other eukaryotic organisms by a long and diverse space between two zinc fingers, while in animal, the spaces between two tandem repeated zinc fingers are often short (seven amino acid residues) and known as the HC links [8], as it was found in Drosophila and yeast [12]. Additionally, the α-helix in the plant zinc finger domain has a very conserved sequence, QALGGH, which is absent in other organisms, and probably the result of evolution through natural selection for a specific regulatory process unique in plants [7,13]. C2H2-ZFP family has been reported in several plant genomes, including 179 members in Arabidopsis thaliana [14], 189 in rice [15], 321 in soybean [16], 211 in maize [17], 124 in foxtail millet [18], 122 in durum wheat [19], 118 in tobacco [20], and 109 in poplar [21]. Recently, extensive studies showed that most of C2H2-ZFPs functioned as transcription factors and were involved in various biological processes, including plant growth and development, hormone signaling and stress responses in many plants species [4,18,22,23]. For example, in rice ZFP179 is involved in salt (...truncated)