Dataset for: Pre-pandemic artificial MERS analog of polyfunctional SARS-CoV-2 S1/S2 furin cleavage site domain is unique among spike proteins of genus Betacoronavirus

Data File Descriptions and Methods [betacov_matching_IPR042578.fasta]: Representative set of 2,465 betacoronavirus S protein overlapping homologous superfamily sequences retreived in fasta format on 4 December 2022 from the InterPro repository at https://www.ebi.ac.uk/interpro/entry/InterPro/IPR042578/. [betacov_matching_IPR042578_motif.fasta]: Extracted 98,122 furin cleavage site (FCS) motifs of 20 amino acid length, including overlapping sequences, using the FindFur algorithm as described by (Gu, 2020) and deposited on 15 December 2020 at the GitHub software repository at https://github.com/chwisteeng/FindFur. These sequences were individually checked for The/Ser O-glycosite residue pairs with the standard prediction software NetOGlyc4.0 (Steentoft et al., 2013) as available at https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/. The bioinformatics nuclear localization signal (NLS) predictions, specifically including the positive hits for pat7 in SARS-CoV-2 and in MERS_MA30 CoV, used the PSORT algorithm available as a webservice at https://wolfpsort.hgc.jp/ which is based on the work of Nakai and Horton (Nakai and Horton, 1999). [betacov_s1s2_nls_pat7_furin_blastp.txt]: Comprehensive sequence database searches using were performed using the NCBI protein BLAST (BLASTP) algorithm with webservice available at https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins. The following BLASTP search parameters and settings were used: Word size=2; Expect value=200000; Hitlist size=500; Gapcosts=9,1; Matrix=PAM30; Filter string=F; Genetic Code=1;Window Size=40; Threshold=11; Composition-based stats=0; Database Posted date=Jan 19, 2023 2:59 AM; Number of letters=17,117,563; Number of sequences=10,766; Entrez query: Includes: Betacoronavirus (taxid:694002); Excludes: SARS-CoV-2 (taxid:2697049). The six polyfunctional input query consensus motif sequences were TXXPR(K/H/R)XRSX and TXXPRX(K/H/R)RSX. [table_s1s2_hits_betacov_polyf.pdf]: Compiled summary table of hits (PDF) representing S1/S2 spike domains across genus Betacoronavirus. [table_s1s2_hits_betacov_polyf.xlsx]: Compiled summary table of hits (MS Excel) representing S1/S2 spike domains across genus Betacoronavirus. References Gu, C., 2020. FindFur: A Tool for Predicting Furin Cleavage Sites of Viral Envelope Substrates. Master’s Thesis, San Jose State University, CA, USA. doi: 10.31979/etd.4ahv-9jya Nakai, K., Horton, P., 1999. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24, 34–36. doi: 10.1016/s0968-0004(98)01336-x Steentoft, C., Vakhrushev, S.Y., Joshi, H.J., Kong, Y., Vester-Christensen, M.B., Schjoldager, K.T.-B.G., Lavrsen, K., Dabelsteen, S., Pedersen, N.B., Marcos-Silva, L., Gupta, R., Bennett, E.P., Mandel, U., Brunak, S., Wandall, H.H., Levery, S.B., Clausen, H., 2013. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J 32, 1478–1488. doi: 10.1038/emboj.2013.79数据文件说明与方法 [betacov_matching_IPR042578.fasta]：2022年12月4日从InterPro数据库（InterPro）获取2465条代表性β冠状病毒（betacoronavirus）刺突蛋白（S protein）重叠同源超家族序列，以FASTA格式（FASTA）存储，获取来源为https://www.ebi.ac.uk/interpro/entry/InterPro/IPR042578/。 [betacov_matching_IPR042578_motif.fasta]：基于Gu（2020）提出的FindFur算法，提取得到98122条长度为20个氨基酸的弗林蛋白酶切割位点（furin cleavage site, FCS）基序（包含重叠序列），并于2020年12月15日上传至GitHub软件仓库https://github.com/chwisteeng/FindFur。随后使用标准预测软件NetOGlyc4.0（Steentoft等，2013，https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/）对所有序列逐一校验苏氨酸/丝氨酸O-糖基化位点残基对。核定位信号（nuclear localization signal, NLS）的生物信息学预测（特指针对SARS-CoV-2及MERS_MA30 CoV中pat7的阳性命中结果）采用了基于Nakai与Horton（1999）研究开发的PSORT算法，其网络服务地址为https://wolfpsort.hgc.jp/。 [betacov_s1s2_nls_pat7_furin_blastp.txt]：采用NCBI蛋白质BLAST（BLASTP）算法（网络服务地址：https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins）开展全面的序列数据库搜索。本次搜索使用的BLASTP参数设置如下：单词长度（Word size）=2；期望阈值（Expect value）=200000；命中列表大小（Hitlist size）=500；间隙代价（Gapcosts）=9,1；矩阵（Matrix）=PAM30；过滤字符串（Filter string）=F；遗传密码（Genetic Code）=1；窗口大小（Window Size）=40；阈值（Threshold）=11；基于组成的统计值（Composition-based stats）=0；数据库发布日期：2023年1月19日 2:59；总字符数：17,117,563；总序列数：10,766；Entrez查询条件：包含β冠状病毒属（分类学ID：694002），排除SARS-CoV-2（分类学ID：2697049）。本次搜索使用的6条多功能输入查询共有基序序列为TXXPR(K/H/R)XRSX和TXXPRX(K/H/R)RSX。 [table_s1s2_hits_betacov_polyf.pdf]：涵盖β冠状病毒属S1/S2刺突结构域命中结果的汇总统计表（PDF格式）。 [table_s1s2_hits_betacov_polyf.xlsx]：涵盖β冠状病毒属S1/S2刺突结构域命中结果的汇总统计表（Microsoft Excel格式）。 ## 参考文献 1. 顾晨，2020。FindFur：病毒包膜底物弗林蛋白酶切割位点预测工具。美国加利福尼亚州圣何塞州立大学硕士学位论文。DOI: 10.31979/etd.4ahv-9jya 2. 中井健、霍顿P，1999。PSORT：一种检测蛋白质分选信号并预测其亚细胞定位的程序。《生物化学趋势》（Trends in Biochemical Sciences），24卷，34-36页。DOI: 10.1016/s0968-0004(98)01336-x 3. 斯滕托夫特C等，2013。通过SimpleCell技术精准绘制人类O-GalNAc糖蛋白质组图谱。《EMBO期刊》（EMBO Journal），32卷，1478-1488页。DOI: 10.1038/emboj.2013.79