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Edited by Caroline S. Harwood, University of Washington, Seattle, WA, and approved May 22, 2019 (received for review January 15, 2019)
Significance
We identified dozens of hypothetical proteins that we predict to be members of the aryloxyalkanoate dioxygenase (AAD) class of enzymes that degrade both phenoxycarboxylic synthetic auxins and the aryloxyphenoxypropionate classes of herbicides. We provide a structure of a member of this class and characterize 2 AADs with opposite substrate enantioselectivities. These findings have expanded our mechanistic understanding of representative dioxygenases involved in 2,4-dichlorophenoxyacetic acid catabolism, a pathway that has been studied for nearly 40 years. The AAD enzymes, along with tolerance traits to glyphosate and glufosinate, have been successfully deployed as a component of the Enlist weed control system. This combination of herbicide and trait technology has provided tools to combat invasive weeds and to manage resistance development.
Abstract
The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is an active ingredient of thousands of commercial herbicides. Multiple species of bacteria degrade 2,4-D via a pathway initiated by the Fe(II) and α-ketoglutarate (Fe/αKG)-dependent aryloxyalkanoate dioxygenases (AADs). Recently, genes encoding 2 AADs have been deployed commercially in herbicide-tolerant crops. Some AADs can also inactivate chiral phenoxypropionate and aryloxyphenoxypropionate (AOPP) herbicides, albeit with varying substrate enantioselectivities. Certain AAD enzymes, such as AAD-1, have expanded utility in weed control systems by enabling the use of diverse modes of action with a single trait. Here, we report 1) the use of a genomic context-based approach to identify 59 additional members of the AAD class, 2) the biochemical characterization of AAD-2 from Bradyrhizobium diazoefficiens USDA 110 as a catalyst to degrade (S)-stereoisomers of chiral synthetic auxins and AOPP herbicides, 3) spectroscopic data that demonstrate the canonical ferryl complex in the AAD-1 reaction, and 4) crystal structures of representatives of the AAD class. Structures of AAD-1, an (R)-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite (S)-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.
Footnotes
↵1J.R.C. and C.O. contributed equally to this work.
- ↵2To whom correspondence may be addressed. Email: snair{at}illinois.edu.
Author contributions: R.M.C. and S.K.N. designed research; J.R.C., C.O., B.Z., L.J.R., R.M.C., and S.K.N. performed research; T.R.W., B.Z., and L.J.R. contributed new reagents/analytic tools; J.R.C., C.O., B.Z., J.M.B., L.J.R., C.K., R.M.C., and S.K.N. analyzed data; and J.R.C., T.R.W., J.M.B., C.K., R.M.C., and S.K.N. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The structure factors and coordinates have been deposited in the Protein Data Bank, www.wwpdb.org (PDB ID codes 5BKB–5BKE and 5BK9).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1900711116/-/DCSupplemental.
Published under the PNAS license.
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Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants
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