Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries.
Journal
Environmental microbiology
ISSN: 1462-2920
Titre abrégé: Environ Microbiol
Pays: England
ID NLM: 100883692
Informations de publication
Date de publication:
08 2020
08 2020
Historique:
received:
16
06
2020
accepted:
19
06
2020
pubmed:
22
6
2020
medline:
9
2
2021
entrez:
22
6
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32564477
doi: 10.1111/1462-2920.15138
doi:
Substances chimiques
phosphoenolpyruvate phosphatase
EC 3.1.3.-
Acid Phosphatase
EC 3.1.3.2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3561-3571Subventions
Organisme : Ministerio de Ciencia e Innovación
ID : RTI2018-094370-B-I00
Pays : International
Informations de copyright
© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.
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