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Prediction of coronavirus 3C-like protease cleavage sites using machine-learning algorithms

Virologica Sinica 2022年第3期37卷 437-444页

作者： Huiting Chen Zhaozhong Zhu Ye Qiu Xingyi Ge Heping Zheng Yousong Peng Bioinformatics Center College of BiologyHunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangsha410082China

The coronavirus 3C-like(3CL)protease,a cysteine protease,plays an important role in viral infection and immune ***,there is still a lack of effective tools for determining the cleavage sites of the 3CL *** study systematically investigated the diversity of the cleavage sites of the coronavirus 3CL protease on the viral polyprotein,and found that the cleavage motif were highly conserved for viruses in the genera of Alphacoronavirus,Betacoronavirus and *** residue preferences were observed at the neighboring positions of the cleavage sites.A random forest(RF)model was built to predict the cleavage sites of the coronavirus 3CL protease based on the representation of residues in cleavage motifs by amino acid indexes,and the model achieved an AUC of 0.96 in *** RF model was further tested on an independent test dataset which were composed of cleavage sites on 99 proteins from multiple coronavirus *** achieved an AUC of 0.95 and predicted correctly 80%of the cleavage ***,1,352 human proteins were predicted to be cleaved by the 3CL protease by the RF *** proteins were enriched in several GO terms related to the cytoskeleton,such as the microtubule,actin and ***,a webserver named 3CLP was built to predict the cleavage sites of the coronavirus 3CL protease based on the RF ***,the study provides an effective tool for identifying cleavage sites of the 3CL protease and provides insights into the molecular mechanism underlying the pathogenicity of coronaviruses.

关键词： Coronavirus 3C-like protease cleavage sites Machine-learning algorithms 3CLP webserver

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cleavage of the Carboxyl-Terminus of LEACS2, a Tomato 1-Aminocyclopropane-l-Carboxylic Acid Synthase Isomer, by a 64-kDa Tomato Metalloprotease Produces a Truncated but Active Enzyme

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Journal of Integrative Plant Biology 2005年第11期47卷 1352-1363页

作者： Jian-Feng LI Robert QI Liang-Hu QU Autar K Mattoo Ning LI Department of Biology The Hong Kong University of Science and Technology Hong Kong SAR China Key Laboratory of Gene Engineering of the Ministry of Education Zhongshan University Guangzhou 510275 China Department of Biochemistry The Hong Kong University of Science and Technology Hong Kong SAR China Sustainable Agricultural Systems Laboratory United States Department of Agriculture-Agriculture Research Service Beltsville Maryland 20705-2350 USA

1-Aminocyclopropane-1-carboxylic acid （ACC） synthase （ACS） is the principal enzyme in phytohormone ethylene biosynthesis. Previous studies have shown that the hypervariable C-terminus of ACS is proteolytically processed in vivo. However, the protease responsible for this has not yet been identified. In the present study, we investigated the processing of the 55-kDa full-length tomato ACS （LeACS2） into 52-, 50- and 49-kDa truncated isoforms in ripening tomato （Lycopersicon esculentum Mill. cv. Cooperation 903） fruit using the sodium dodecyl sulfate-boiling method. Meanwhile, an LeACS2-processing protease was purified via multi-step column chromatography from tomato fruit. Subsequent biochemical analysis of the 64-kDa purified protease revealed that it is a metalloprotease active at multiple cleavage sites within the hypervariable C-terminus of LeACS2. N-terminal sequencing and matrix-assisted laser desorption/ionization time-of-flight analysis indicated that the LeACS2-processing metalloprotease cleaves at the C-terminal sites Lys^438, Glu^447, Lys^448, Asn^456, Ser^460, Ser^462, Lys^463, and Leu^474, but does not cleave the N- terminus of LeACS2. Four C-terminus-deleted （26-50 amino acids） LeACS2 fusion proteins were overproduced and subjected to proteolysis by this metalloprotease to identify the multiple cleavage sites located on the N-terminal side of the phosphorylation site Ser^460. The results indisputably confirmed the presence of cleavage sites within the region between the α-helix domain （H14） and Ser^460 for this metalloprotease. Furthermore, the resulting C-terminally truncated LeACS2 isoforms were active enzymatically. Because this protease could produce LeACS2 isoforms in vitro similar to those detected in vivo, it is proposed that this metalloprotease may be involved in the proteolysis of LeACS2 in vivo.

关键词： 1-aminocyclopropane-1-carboxylic acid synthase cleavage sites metalloprotease proteolytic processing.

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