Shared strategies for β-lactam catabolism in the soil microbiome

Nat Chem Biol. 2018 Jun;14(6):556-564. doi: 10.1038/s41589-018-0052-1. Epub 2018 Apr 30.

Abstract

The soil microbiome can produce, resist, or degrade antibiotics and even catabolize them. While resistance genes are widely distributed in the soil, there is a dearth of knowledge concerning antibiotic catabolism. Here we describe a pathway for penicillin catabolism in four isolates. Genomic and transcriptomic sequencing revealed β-lactamase, amidase, and phenylacetic acid catabolon upregulation. Knocking out part of the phenylacetic acid catabolon or an apparent penicillin utilization operon (put) resulted in loss of penicillin catabolism in one isolate. A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β-lactamase penicillin product. To test the generality of this strategy, an Escherichia coli strain was engineered to co-express a β-lactamase and a penicillin amidase or the put operon, enabling it to grow using penicillin or benzylpenicilloic acid, respectively. Elucidation of additional pathways may allow bioremediation of antibiotic-contaminated soils and discovery of antibiotic-remodeling enzymes with industrial utility.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amidohydrolases / metabolism
  • Burkholderia
  • Cloning, Molecular
  • Gene Expression Regulation, Bacterial
  • Genome
  • Hydrolases / metabolism
  • Microbial Sensitivity Tests
  • Microbiota*
  • Open Reading Frames*
  • Operon
  • Penicillins / metabolism
  • Phenylacetates / metabolism
  • Phylogeny
  • Pseudomonas
  • Soil
  • Soil Microbiology*
  • Transcriptome
  • Up-Regulation
  • beta-Lactamases / metabolism
  • beta-Lactams / metabolism*

Substances

  • Penicillins
  • Phenylacetates
  • Soil
  • beta-Lactams
  • Hydrolases
  • Amidohydrolases
  • amidase
  • beta-Lactamases
  • phenylacetic acid