One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees

Abstract

Bacteria use metallo-β-lactamase enzymes to hydrolyse lactam rings found in many antibiotics, rendering them ineffective. Metallo-β-lactamase activity is thought to be polyphyletic, having arisen on more than one occasion within a single functionally diverse homologous superfamily. Since discovery of multiple origins of enzymatic activity conferring antibiotic resistance has broad implications for the continued clinical use of antibiotics, we test the hypothesis of polyphyly further; if lactamase function has arisen twice independently, the most recent common ancestor (MRCA) is not expected to possess lactam-hydrolysing activity. Two major problems present themselves. Firstly, even with a perfectly known phylogeny, ancestral sequence reconstruction is error prone. Secondly, the phylogeny is not known, and in fact reconstructing a single, unambiguous phylogeny for the superfamily has proven impossible. To obtain a more statistical view of the strength of evidence for or against MRCA lactamase function, we reconstructed a sample of 98 MRCAs of the metallo-β-lactamases, each based on a different tree in a bootstrap sample of reconstructed phylogenies. InterPro sequence signatures and homology modelling were then used to assess our sample of MRCAs for lactamase functionality. Only 5 % of these models conform to our criteria for metallo-β-lactamase functionality, suggesting that the ancestor was unlikely to have been a metallo-β-lactamase. On the other hand, given that ancestral proteins may have had metallo-β-lactamase functionality with variation in sequence and structural properties compared with extant enzymes, our criteria are conservative, estimating a lower bound of evidence for metallo-β-lactamase functionality but not an upper bound.Electronic supplementary materialThe online version of this article (doi:10.1007/s00239-014-9639-7) contains supplementary material, which is available to authorized users.

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

“…Cross-validation was used to optimize the true positive rate to identify previously undescribed B1BL genes. For full-length genes, the method correctly classified all tested B1BL genes (an estimated true positive rate of 100%), while the false positive rate (FPR) was very low, even for closely related genes from the MBL superfamily [23] (an FPR of 0% for all tested gene groups within the MBL superfamily). For metagenomic data, using a fragment length of 100 nucleotides, the method showed a true positive rate of 89% and a FPR of 4% and 0% for the MBL superfamily and random genomic fragments, respectively.…”

“…Thus, if these genes were to become mobilized and spread to pathogenic bacteria, they may constitute a threat to human health in the future [45]. Furthermore, the large increase in known chromosomal B1BL genes will enable more detailed phylogenetic studies of the B1 subclass of metallo-β-lactamases [23], an essential step to further elucidate the evolution and origins of mobile B1BL genes.…”

“…Further examination of environmental and commensal bacteria in search of potentially new B1BLs is therefore important and would enable the identification and surveillance of potent genes before they are mobilized and horizontally transferred into pathogens. Expanding the number of known chromosomal and mobile B1BL genes would also provide a more detailed phylogenetic view of this gene class and facilitate the further elucidation of their origin and evolutionary history [23]. …”

A metallo-beta-lactamase with both beta-lactamase and ribonuclease activity is linked with traduction in giant viruses

“…The giant virus mRNAs should be protected from such a degradation, which may be explained by the encapsidation of RNA transcripts into giant virions that was detected for some of these viruses 27 . Bioinformatic analyses suggested that the tupanvirus MBL fold protein may belong to the RNase Z group that was proposed to be one of the two main groups of the MBL superfamily with that encompassing MBLs 1 . RNase Z enzymes perform tRNA maturation by catalyzing the endoribonucleolytic removal of the 3’ extension of tRNA precursors that do not contain a chromosomally-encoded CCA determinant 28–30 .…”

“…The metallo-beta-lactamase (MBL) superfamily encompasses a large set of enzymes, including MBL and ribonuclease (RNase) Z enzymes 1 . These enzymes are pleitropic proteins that can hydrolyze a wide range of substrates, among which beta-lactams, and DNA or RNA 2,3 .…”