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

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.

Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

“…Similar to ELF6 and REF6, MtrunA17_Chr1g0199511/Medtr1g094740 and Mtrun A17_Chr3g0116441/Medtr3g075210 also had an array of four C2H2 motifs located at the C-terminus, including a degraded C2H2, which has also been found in ELF6 and REF6 [16]. MtrunA17_Chr1g0199511/ Medtr1g094740 and MtrunA17_Chr3g0116441/Medtr3 g075210 are highly similar to soybean Glyma.20G1 81000 and Glyma.04G191900, the C2H2 arrays which have recently been reported [27].…”

“…In the M. truncatula genome, 67 ZFPs harbored multiple C2H2 motifs, including 38 ZFPs containing two C2H2s, 16 ZFPs containing three C2H2s, 9 ZFPs containing four C2H2s, MtTRM1 (five C2H2s), 2 ZFPs containing six C2H2s and MtTFIIIA (nine C2H2s). ZFPs with multiple C2H2s have been widely found in other plant species [1,15,16,27]. Based on the spacer length between motifs, the organization of C2H2s can be classified into dispersedly distributed motifs or tandem arrays [16,27].…”

“…ZFPs with multiple C2H2s have been widely found in other plant species [1,15,16,27]. Based on the spacer length between motifs, the organization of C2H2s can be classified into dispersedly distributed motifs or tandem arrays [16,27]. Using this method, we classified the 67 ZFPs with multiple C2H2s into two subgroups, i.e., 15 ZFPs contained tandem C2H2s and 52 ZFPs lacked tandem C2H2s.…”

Cys2/His2 Zinc-Finger Proteins in Transcriptional Regulation of Flower Development

“…Soybean C2H2-ZFP genes are defined and classified into 11 distinguishable subsets on the basis of arrangements, numbers, and types of C2H2-ZF domains. Phylogenetic and gene ontology analyses further confirmed the rationality of classification [ 46 ]. Similar to Arabidopsis , the C2H2-ZFP family of maize is divided into three subgroups (A, B, and C) [ 44 ].…”

“…The development of high-throughput sequencing technology and genome-wide analysis technology has enabled the analysis of the C2H2-ZFP family of several species. In plants, genome-wide analysis detected 124 C2H2-ZFPs in foxtail millet, 122 in sorghum [ 42 ], 109 in poplar [ 43 ], 211 in maize [ 44 ], 188 in tobacco [ 45 ], and 321 in soybean [ 46 ]. In foxtail millet, 78% of C2H2-ZFPs comprise QALGGH motifs and are designated as Q-type ZFs [ 42 ].…”