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Reid, D. J.

Publications and source records attributed to Reid, D. J..

2 recordsLinked to original sources

A truncated soil phage catechol 1,2-dioxygenase illustrates how viruses preserve and disseminate auxiliary catalytic functions in the soil microbiome

Bacteriophages can rewire host chemistry via auxiliary viral genes (AVGs). Using metagenomic and metatranscriptomic data from the native soil microbiome, we identified transcriptionally active AVGs, including a viral catechol 1,2-dioxygenase (V-C12DO). V-C12DO shares [~]40% sequence identity with its nearest bacterial homologs and lacks the helical dimerization domain. Despite truncation, V-C12DO retains more than [~]25% of the global consensus residues compared to C12DOs across domains of life, including the two tyrosines and two histidines that coordinate the non-heme Fe(III) active site. A 1.7 [A] crystal structure also showed the conservation of the canonical {beta}-sandwich scaffold for the iron. We next confirmed that V-C12DO cleaves catechol and remains highly active across a broad range of temperatures (30-60 {degrees}C), pH (5.5-9), and salinity (up to 2 M), exceeding those of known bacterial CD12Os. This work shows that truncated phage enzymes preserve the core catalytic chemistry and potentially further expand host metabolic versatility across dynamic environmental conditions.

microbiology↗

Comprehensive identification of β-lactam antibiotic polypharmacology in Mycobacterium tuberculosis

Infections with Mycobacterium tuberculosis (Mtb) cause tuberculosis (TB), which requires at least six months of treatment with multiple antibiotics. There is emergent interest in using {beta}-lactam antibiotics to improve treatment outcomes for patients. These drugs target cell wall biosynthesis, but a comprehensive list of enzymes inhibited by {beta}-lactams in Mtb is lacking. In the current study, we sought to identify and characterize Mtb enzymes inhibited by {beta}-lactam antibiotics using physiological conditions representative of both acute and chronic TB disease. We used new activity-based probes based on the {beta}-lactam antibiotic meropenem due to its approval by the World Health Organization for TB treatment. Activity-based probes label enzymes based on both substrate specificity and catalytic mechanism, enabling precise identification of drug targets. We identified previously undiscovered targets of meropenem in addition to known cell wall biosynthetic enzymes. We validated {beta}-lactam binding and hydrolysis for six newly identified targets: Rv1723, Rv2257c, Rv0309, DapE (Rv1202), MurI (Rv1338), and LipD (Rv1923). Our results demonstrate that there are at least 30 enzymes in Mtb vulnerable to inhibition by meropenem. This is many more {beta}-lactam targets than historically described, suggesting that efficacy in Mtb is a direct result of polypharmacology.

biochemistry↗