Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran.
Department of Recombinant Hepatitis B Vaccine, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran.
Database (Oxford). 2021 May 18;2021. doi: 10.1093/database/baab029.
Sus scrofa or pig was domesticated thousands of years ago. Through various indigenous breeds, different phenotypes were produced such as Chinese inbred miniature minipig or Wuzhishan pig (WZSP), which is broadly used in the life and medical sciences. The whole genome of WZSP was sequenced in 2012. Through a bioinformatics study of pig carbonic anhydrase (CA) sequences, we detected some β- and γ-class CAs among the WZSP CAs annotated in databases, while β- or γ-CAs had not previously been described in vertebrates. This finding urged us to analyze the quality of whole genome sequence of WZSP for the possible bacterial contamination. In this study, we used bioinformatics methods and web tools such as UniProt, European Bioinformatics Institute, National Center for Biotechnology Information, Ensembl Genome Browser, Ensembl Bacteria, RSCB PDB and Pseudomonas Genome Database. Our analysis defined that pig has 12 classical α-CAs and 3 CA-related proteins. Meanwhile, it was approved that the detected CAs in WZSP are categorized in the β- and γ-CA families, which belong to Pseudomonas spp. and Acinetobacter spp. The protein structure study revealed that the identified β-CA sequence from WZSP belongs to Pseudomonas aeruginosa with PDB ID: 5JJ8, and the identified γ-CA sequence from WZSP belongs to P. aeruginosa with PDB ID: 3PMO. Bioinformatics and computational methods accompanied with bacterial-specific markers, such as 16S rRNA and β- and γ-class CA sequences, can be used to identify bacterial contamination in mammalian DNA samples.
家猪（Sus scrofa）在几千年前就已被驯化。通过各种本地品种，产生了不同的表型，例如中国近交小型迷你猪或五指山猪（WZSP），它广泛应用于生命科学和医学科学。2012 年，WZSP 的全基因组被测序。通过对猪碳酸酐酶（CA）序列的生物信息学研究，我们在数据库中注释的 WZSP CA 中检测到了一些β-和γ-类 CA，而β-或γ-CA 以前在脊椎动物中没有被描述过。这一发现促使我们分析 WZSP 全基因组序列的质量，以确定是否存在细菌污染。在这项研究中，我们使用了生物信息学方法和 UniProt、欧洲生物信息学研究所、美国国家生物技术信息中心、Ensembl 基因组浏览器、Ensembl 细菌、RSCB PDB 和假单胞菌基因组数据库等网络工具。我们的分析定义了猪有 12 种经典的α-CA 和 3 种 CA 相关蛋白。同时，也证实了在 WZSP 中检测到的 CA 属于β-CA 和γ-CA 家族，分别属于假单胞菌属和不动杆菌属。蛋白质结构研究表明，从 WZSP 中鉴定出的β-CA 序列属于铜绿假单胞菌，其 PDB ID 为 5JJ8，而从 WZSP 中鉴定出的γ-CA 序列属于铜绿假单胞菌，其 PDB ID 为 3PMO。生物信息学和计算方法结合细菌特异性标志物，如 16S rRNA 和β-和γ-类 CA 序列，可用于鉴定哺乳动物 DNA 样本中的细菌污染。
