Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis
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RESEARCH ARTICLE
Open Access
Genome-wide survey of soybean papainlike cysteine proteases and their expression analysis in root nodule symbiosis Songli Yuan1†, Danxia Ke2,3†, Rong Li1, Xiangyong Li3, Lei Wang3, Haifeng Chen1, Chanjuan Zhang1, Yi Huang1, Limiao Chen1, Qingnan Hao1, Hongli Yang1, Dong Cao1, Shuilian Chen1, Wei Guo1, Zhihui Shan1, Zhonglu Yang1, Xiaojuan Zhang1, Dezhen Qiu1, Yuefeng Guan4* and Xinan Zhou1*
Abstract Background: Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood. Results: In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication. Phylogenetic analysis among different species showed that the lineage differentiation of GmPLCPs occurred after family expansion, and large tandem repeat segment were specifically in soybean. The expression patterns of GmPLCPs in symbiosis-related tissues and nodules identified RNS-related GmPLCPs and provided insights into their putative symbiotic functions in soybean. The symbiotic function analyses showed that a RNS-related GmPLCP gene (Glyma.04G190700) really participate in nodulation and nodule development. Conclusions: Our findings improved our understanding of the functional diversity of legume PLCP family genes, and provided insights into the putative roles of the legume PLCPs in nodulation, nodule development and senescence. Keywords: Genome-wide survey, Nodule development and senescence, Papain-like cysteine protease, Root nodule symbiosis, Soybean
Background Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes associated with plant-pathogen/pest interactions, seed germination, development, immunity, senescence, cyclization and stress responses [1–8]. PLCPs * Correspondence: [email protected]; [email protected] † Songli Yuan and Danxia Ke contributed equally to this work. 4 FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China 1 Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China Full list of author information is available at the end of the article
belong to C1A CysProt (family C1, clan CA), and are a typical member of plant cysteine proteases [3, 9]. These enzymes are produced as inactive precursors with a signal peptide, an auto-inhibitory prodomain and an active protease domain [1]. Besides, some PLCPs carry a GRAN do
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