Shared strategies for β-lactam catabolism in the soil microbiome

Terence S. Crofts, Bin Wang, Aaron Spivak, Tara A. Gianoulis, Kevin J. Forsberg, Molly K. Gibson, Lauren A. Johnsky, Stacey M. Broomall, C. Nicole Rosenzweig, Evan W. Skowronski, Henry S. Gibbons, Morten O. A. Sommer, Gautam Dantas*

*Corresponding author for this work

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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.
Original languageEnglish
JournalNature Chemical Biology
Volume14
Pages (from-to)556-564
ISSN1552-4450
DOIs
Publication statusPublished - 2018

Cite this

Crofts, T. S., Wang, B., Spivak, A., Gianoulis, T. A., Forsberg, K. J., Gibson, M. K., Johnsky, L. A., Broomall, S. M., Rosenzweig, C. N., Skowronski, E. W., Gibbons, H. S., Sommer, M. O. A., & Dantas, G. (2018). Shared strategies for β-lactam catabolism in the soil microbiome. Nature Chemical Biology, 14, 556-564. https://doi.org/10.1038/s41589-018-0052-1