Genome-Wide Identification and Classification of Soybean C2H2 Zinc Finger Proteins and Their Expression Analysis in Legume-Rhizobium Symbiosis

Songli Yuan; Xiangyong Li; Rong Li; Lei Wang; Chanjuan Zhang; Limiao Chen; Qingnan Hao; Xiaojuan Zhang; Haifeng Chen; Zhihui Shan; Zhonglu Yang; Shuilian Chen; Dezhen Qiu; Danxia Ke; Xinan Zhou

doi:10.3389/fmicb.2018.00126

Genome-Wide Identification and Classification of Soybean C2H2 Zinc Finger Proteins and Their Expression Analysis in Legume-Rhizobium Symbiosis

Front Microbiol. 2018 Feb 6:9:126. doi: 10.3389/fmicb.2018.00126. eCollection 2018.

Authors

Songli Yuan^{1

2}, Xiangyong Li³, Rong Li^{1

2}, Lei Wang³, Chanjuan Zhang^{1

2}, Limiao Chen^{1

2}, Qingnan Hao^{1

2}, Xiaojuan Zhang^{1

2}, Haifeng Chen^{1

2}, Zhihui Shan^{1

2}, Zhonglu Yang^{1

2}, Shuilian Chen^{1

2}, Dezhen Qiu^{1

2}, Danxia Ke³, Xinan Zhou^{1

2}

Affiliations

¹ Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, China.
² Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China.
³ Bioinformatics Laboratory, College of Life Sciences, Xinyang Normal University, Xinyang, China.

Abstract

Root nodule symbiosis (RNS) is one of the most productive and economical systems for nitrogen fixation, and previous studies have shown that several nodule-specific C2H2-zinc finger proteins (ZFPs) play important roles in symbiosis establishment and nodule function. However, C2H2-ZFPs are the most widespread ZFPs in eukaryotes, and a great variation of structure and function exist among the family members. It remains largely unclear whether or not special types of C2H2-ZF genes participate in symbiosis, especially in soybean. In the present study, we performed a genome-wide survey of soybean C2H2-ZF genes, and 321 soybean C2H2-ZF genes were identified and classified into 11 clearly distinguishable subsets (Gm-t1-SF, Gm-t2-SF, Gm-1i-Q-SF, Gm-1i-M-SF, Gm-1i-Z-SF, Gm-1i-D-SF, Gm-2i-Q-SF, Gm-2i-M-SF, Gm-2i-Mix-SF, Gm-3i-SF, and Gm-4i-SF) based on the arrangements, numbers, and types of C2H2-ZF domains. Phylogenetic and gene ontology analyses were carried out to assess the conserved sequence and GO function among these subsets, and the results showed that the classification of soybean C2H2-ZFPs was reasonable. The expression profile of soybean C2H2-ZFPs in multiple tissues showed that nearly half of soybean C2H2-ZFPs within different subsets had expressions in nodules, including a clustering branch consisting of 11 Gm-1i-Q-SF genes specifically expressed in symbiotic-relative tissues. RNA-Seq was used to identify symbiosis-related soybean C2H2-ZFPs, and the expression pattern of the soybean C2H2-ZFPs in roots and nodules at different development stages showed that soybean C2H2-ZFPs mainly played roles in nodule development or nodule function rather than nodulation signal transduction, and nearly half of these genes had high expressions and/or different expression patterns during soybean nodule development, especially for the six clustering branches of genes consisting of different subsets of C2H2-ZFPs. Furthermore, the selected symbiosis-related soybean C2H2-ZFPs might function in legume-rhizobium symbiosis through regulating or interacting with other key proteins. Taken together, our findings provided useful information for the study on classification and conservative function of C2H2-ZFPs, and offered solid evidence for investigation of rhizobium symbiosis-related C2H2-ZFPs in soybean or other legumes.

Keywords: C2H2 zinc finger proteins; classification; gene expression; root nodule symbiosis; soybean.