Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. (September 2018)

• Record Type: Journal Article
• Authors: Silveira, Melise Chaves; Azevedo da Silva, Rangeline; Faria da Mota, Fábio; Catanho, Marcos; Jardim, Rodrigo; R Guimarães, Ana Carolina; de Miranda, Antonio B
• Is Part Of: Evolutionary bioinformatics online. Volume 14(2018)
• Publication Date: 2018-09
• Subjects: β-lactamase -- class -- subclass -- identification -- sequence similarity; Bioinformatics -- Periodicals; Evolutionary computation -- Periodicals; Genetic programming (Computer science) -- Periodicals; Computational Biology; Evolution, Molecular; Bioinformatics; Electronic journals; Periodicals; Fulltext; Internet Resources; Periodicals; Periodicals; 576.8
• DOI: 10.1177/1176934318797351
• Languages: English
• ISSNs: 1176-9343

Abstract

Β-lactamases, the enzymes responsible for resistance to β-lactam antibiotics, are widespread among prokaryotic genera. However, current β-lactamase classification schemes do not represent their present diversity. Here, we propose a workflow to identify and classify β-lactamases. Initially, a set of curated sequences was used as a model for the construction of profiles Hidden Markov Models (HMM), specific for each β-lactamase class. An extensive, nonredundant set of β-lactamase sequences was constructed from 7 different resistance proteins databases to test the methodology. The profiles HMM were improved for their specificity and sensitivity and then applied to fully assembled genomes. Five hierarchical classification levels are described, and a new class of β-lactamases with fused domains is proposed. Our profiles HMM provide a better annotation of β-lactamases, with classes and subclasses defined by objective criteria such as sequence similarity. This classification offers a solid base to the elaboration of studies on the diversity, dispersion, prevalence, and evolution of the different classes and subclasses of this critical enzymatic activity.