Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality

The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to...

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Published inMicroorganisms (Basel) Vol. 11; no. 8; p. 1933
Main Authors Maatouk, Mohamad, Merhej, Vicky, Pontarotti, Pierre, Ibrahim, Ahmad, Rolain, Jean-Marc, Bittar, Fadi
Format Journal Article
LanguageEnglish
Published Basel MDPI AG 28.07.2023
MDPI
Subjects
Annotations
Antibiotic resistance
Antibiotics
Bacteria
Bacteriology
Beta lactamases
beta-lactamase
Biochemistry, Molecular Biology
Candidate Phyla Radiation
Coding
computer simulation
Emerging diseases
Enzymes
functional diversity
Genes
Genetic aspects
genetic variation
Genomes
Genomics
Human health and pathology
Infectious diseases
Kinases
Life Sciences
massive analysis
metallo-beta-lactamase fold
Metallo-β-lactamase
Metallography
Microbiology and Parasitology
Microorganisms
Physiological aspects
Proteins
Radiation
sequence homology
sequence similarity network
Substrates
France
functional diversity
massive analysis
bacteria
metallo-beta-lactamase fold
Candidate Phyla Radiation
sequence similarity network
protein domains
enzyme promiscuity
Online AccessGet full text
ISSN2076-2607
2076-2607
DOI10.3390/microorganisms11081933

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Abstract The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.
AbstractList The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.
The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) ( n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.
The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.
Audience Academic
Author Maatouk, Mohamad
Bittar, Fadi
Merhej, Vicky
Ibrahim, Ahmad
Pontarotti, Pierre
Rolain, Jean-Marc
AuthorAffiliation 3 Centre National de la Recherche Scientifique (CNRS-SNC5039), 13009 Marseille, France
1 Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; mohamad.maatouk@etu.univ-amu.fr (M.M.); pierre.pontarotti@univ-amu.fr (P.P.); ahmad.ibrahim@etu.univ-amu.fr (A.I.); jean-marc.rolain@univ-amu.fr (J.-M.R.)
2 Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
AuthorAffiliation_xml – name: 2 Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
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– name: 1 Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; mohamad.maatouk@etu.univ-amu.fr (M.M.); pierre.pontarotti@univ-amu.fr (P.P.); ahmad.ibrahim@etu.univ-amu.fr (A.I.); jean-marc.rolain@univ-amu.fr (J.-M.R.)
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Keywords functional diversity
massive analysis
bacteria
metallo-beta-lactamase fold
Candidate Phyla Radiation
sequence similarity network
protein domains
enzyme promiscuity
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Snippet The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among...
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SubjectTerms Annotations
Antibiotic resistance
Antibiotics
Bacteria
Bacteriology
Beta lactamases
beta-lactamase
Biochemistry, Molecular Biology
Candidate Phyla Radiation
Coding
computer simulation
Emerging diseases
Enzymes
functional diversity
Genes
Genetic aspects
genetic variation
Genomes
Genomics
Human health and pathology
Infectious diseases
Kinases
Life Sciences
massive analysis
metallo-beta-lactamase fold
Metallo-β-lactamase
Metallography
Microbiology and Parasitology
Microorganisms
Physiological aspects
Proteins
Radiation
sequence homology
sequence similarity network
Substrates
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Title Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality
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Volume 11
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