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Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana

Abstract

Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. Here, as an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite-gene associations led to the identification of N-malonyl-D-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5'-phosphate for its activity. In conclusion, this study thus identifies a new d-amino acid racemase gene family and advances our knowledge of plant d-amino acid metabolism that is currently largely unexplored. As a result, it also demonstrates thatmore » exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.« less

Authors:
 [1];  [2];  [2];  [2];  [1]
  1. North Carolina State Univ., Kannapolis, NC (United States); North Carolina State Univ., Raleigh, NC (United States)
  2. Purdue Univ., West Lafayette, IN (United States)
Publication Date:
Research Org.:
Purdue Univ., West Lafayette, IN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1348406
Grant/Contract Number:  
FG02-07ER15905
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 112; Journal Issue: 37; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; d-amino acid; genome-wide association; natural variation; racemase; secondary metabolism

Citation Formats

Strauch, Renee C., Svedin, Elisabeth, Dilkes, Brian, Chapple, Clint, and Li, Xu. Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana. United States: N. p., 2015. Web. doi:10.1073/pnas.1503272112.
Strauch, Renee C., Svedin, Elisabeth, Dilkes, Brian, Chapple, Clint, & Li, Xu. Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana. United States. doi:10.1073/pnas.1503272112.
Strauch, Renee C., Svedin, Elisabeth, Dilkes, Brian, Chapple, Clint, and Li, Xu. Mon . "Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana". United States. doi:10.1073/pnas.1503272112. https://www.osti.gov/servlets/purl/1348406.
@article{osti_1348406,
title = {Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana},
author = {Strauch, Renee C. and Svedin, Elisabeth and Dilkes, Brian and Chapple, Clint and Li, Xu},
abstractNote = {Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. Here, as an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite-gene associations led to the identification of N-malonyl-D-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5'-phosphate for its activity. In conclusion, this study thus identifies a new d-amino acid racemase gene family and advances our knowledge of plant d-amino acid metabolism that is currently largely unexplored. As a result, it also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.},
doi = {10.1073/pnas.1503272112},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 37,
volume = 112,
place = {United States},
year = {2015},
month = {8}
}

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Cited by: 15 works
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