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Title: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. Here, we studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes.
Authors:
ORCiD logo [1] ; ORCiD logo [2] ;  [1] ;  [1] ; ORCiD logo [2] ;  [1] ;  [1]
  1. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  2. Univ. of Missouri, Columbia, MO (United States). Dept. of Biochemistry
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Published Article
Journal Name:
PLoS Genetics
Additional Journal Information:
Journal Volume: 14; Journal Issue: 1; Journal ID: ISSN 1553-7404
Publisher:
Public Library of Science
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
OSTI Identifier:
1416648
Alternate Identifier(s):
OSTI ID: 1436660

Price, Morgan N., Zane, Grant M., Kuehl, Jennifer V., Melnyk, Ryan A., Wall, Judy D., Deutschbauer, Adam M., and Arkin, Adam P.. Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. United States: N. p., Web. doi:10.1371/journal.pgen.1007147.
Price, Morgan N., Zane, Grant M., Kuehl, Jennifer V., Melnyk, Ryan A., Wall, Judy D., Deutschbauer, Adam M., & Arkin, Adam P.. Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. United States. doi:10.1371/journal.pgen.1007147.
Price, Morgan N., Zane, Grant M., Kuehl, Jennifer V., Melnyk, Ryan A., Wall, Judy D., Deutschbauer, Adam M., and Arkin, Adam P.. 2018. "Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics". United States. doi:10.1371/journal.pgen.1007147.
@article{osti_1416648,
title = {Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics},
author = {Price, Morgan N. and Zane, Grant M. and Kuehl, Jennifer V. and Melnyk, Ryan A. and Wall, Judy D. and Deutschbauer, Adam M. and Arkin, Adam P.},
abstractNote = {For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. Here, we studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes.},
doi = {10.1371/journal.pgen.1007147},
journal = {PLoS Genetics},
number = 1,
volume = 14,
place = {United States},
year = {2018},
month = {1}
}

Works referenced in this record:

MicrobesOnline: an integrated portal for comparative and functional genomics
journal, November 2009
  • Dehal, P. S.; Joachimiak, M. P.; Price, M. N.
  • Nucleic Acids Research, Vol. 38, Issue suppl_1, p. D396-D400
  • DOI: 10.1093/nar/gkp919

EcoCyc: a comprehensive database resource for Escherichia coli
journal, December 2004
  • Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro
  • Nucleic Acids Research, Vol. 33, Issue suppl_1, p. D334-D337
  • DOI: 10.1093/nar/gki108

Development of a Markerless Genetic Exchange System for Desulfovibrio vulgaris Hildenborough and Its Use in Generating a Strain with Increased Transformation Efficiency
journal, October 2009
  • Keller, K. L.; Bender, K. S.; Wall, J. D.
  • Applied and Environmental Microbiology, Vol. 75, Issue 24, p. 7682-7691
  • DOI: 10.1128/AEM.01839-09

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000
  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006
  • Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
  • Molecular Systems Biology, Vol. 2, Article No. 2006.0008
  • DOI: 10.1038/msb4100050

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons
journal, May 2015
  • Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J.
  • mBio, Vol. 6, Issue 3, Article No. e00306-15
  • DOI: 10.1128/mBio.00306-15