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Multi-omics Analysis of Spiroplasma eriocheiris Non-coding RNAs (ncRNAs) and Their Virulence Targets |
OU Jiang-tao1,**(),LUAN Xiao-qi1,2,BIAN Yun-xia1,JIANG Qi-cheng1,MENG Yu-suo1,DONG Hui-zi1,WANG Zi-sheng1,**() |
1 College of Ocean and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China 2 School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China |
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Abstract China is the one of the largest aquaculture countries in the world, and the annual economic loss caused by diseases of crustaceans is about 7 billion RMB per year. Among them, Spiroplasma is one of the important pathogenic bacteria of crustaceans, which can cause large-scale death of crustaceans, and has been listed as a Class III epidemic disease of the Ministry of Agriculture. Non coding RNAs (ncRNAs) are widespread in bacteria. They recognize target mRNAs mainly through base pairing and regulate gene expression at the post transcriptional level. Some ncRNAs affect protein function by interacting with proteins. Recent studies have shown that bacterial ncRNAs play an important role in virulence regulation. In order to study the molecular regulatory role of Spiroplasma ncRNAs in crustaceans, it is necessary to systematically screen and identify the ncRNAs and virulence targets related to Spiroplasma infection. Through comparative genome, differential transcriptome, quantitative proteome, system biology analysis, and combined analysis of molecular interaction and bioinformatics methods, this study showed that 54 ncRNAs of Spiroplasma were obtained by integrating genome and transcriptome. Under the conditions of infection in vivo and culture in vitro, 11 and 28 significantly different ncRNAs were obtained by digital gene expression profiling. Four biological software tools were used to predict ncRNA targets, and 423 targets were obtained by intersection. Using quantitative proteomic analysis, 68 differential virulence proteins were identified, which were the same as 21 out of the 30 virulence targets of ncRNAs. Six main hub-ncRNAs were found by network biology analysis. Using RNA pull-down, prokaryotic chain specific sequencing and LC-MS/MS comprehensive analysis, 53 interacting RNAs and 120 interacting proteins of ncRNA SR05 were found. The relevant research results can lay a foundation for interpreting the pathogenic mechanism of Spiroplasma and its interaction mechanism with the host, and provide a scientific basis for the comprehensive prevention and treatment of this disease in crustaceans.
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Received: 12 September 2022
Published: 07 December 2022
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