Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain.
Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA.
Environ Microbiol. 2020 Aug;22(8):3561-3571. doi: 10.1111/1462-2920.15138. Epub 2020 Jul 16.
Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr-B-Phos, Pfr-C-Phos and Pfr-GAP, to describe the three groups of acid phosphatases. These sequence-based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.
对超过 4000 个注释的细菌酸性磷酸酶进行了系统发育分析。我们的分析将这些酶分为以下三种类型：（1）B 类酸性磷酸酶，与其他类型的酶关系较远，（2）C 类酸性磷酸酶和（3）通用酸性磷酸酶（GAP）。虽然 B 类磷酸酶仅在少数细菌科中发现，包括已知的病原体，但 C 类酸性磷酸酶和 GAP 蛋白存在于各种微生物中，这些微生物栖息在土壤、淡水和海洋环境中。作为我们分析的一部分，我们开发了三种模式，分别命名为 Pfr-B-Phos、Pfr-C-Phos 和 Pfr-GAP，以描述这三组酸性磷酸酶。然后，这些基于序列的模式被用于扫描基因组和宏基因组，以鉴定大量以前未知的酸性磷酸酶。数据库中注释为假设蛋白的许多蛋白也被这些模式鉴定为可能的酸性磷酸酶。为了验证这些计算机模拟结果，我们从基因组 DNA 或从宏基因组文库中或根据从宏基因组数据中恢复的蛋白质序列在体外合成的候选酸性磷酸酶基因进行克隆。表达这些基因中的一些，然后对蛋白质进行酶分析，进一步证实了使用我们的模式进行序列相似性搜索可以成功鉴定以前未知的酸性磷酸酶。
