skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

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:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1416648
Alternate Identifier(s):
OSTI ID: 1436660
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
PLoS Genetics
Additional Journal Information:
Journal Name: PLoS Genetics Journal Volume: 14 Journal Issue: 1; Journal ID: ISSN 1553-7404
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

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., 2018. 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. Thu . "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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1371/journal.pgen.1007147

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655
journal, September 2003


Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions
journal, November 2011


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

Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014

  • Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1223

The thrH Gene Product of Pseudomonas aeruginosa Is a Dual Activity Enzyme with a Novel Phosphoserine:Homoserine Phosphotransferase Activity
journal, December 2003

  • Singh, S. Kumar; Yang, Kun; Karthikeyan, Subramanian
  • Journal of Biological Chemistry, Vol. 279, Issue 13
  • DOI: 10.1074/jbc.M311393200

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

Syntrophic exchange in synthetic microbial communities
journal, April 2014

  • Mee, M. T.; Collins, J. J.; Church, G. M.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 20
  • DOI: 10.1073/pnas.1405641111

Comparative genomics of the lactic acid bacteria
journal, October 2006

  • Makarova, K.; Slesarev, A.; Wolf, Y.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 42
  • DOI: 10.1073/pnas.0607117103

From one amino acid to another: tRNA-dependent amino acid biosynthesis
journal, February 2008

  • Sheppard, K.; Yuan, J.; Hohn, M. J.
  • Nucleic Acids Research, Vol. 36, Issue 6
  • DOI: 10.1093/nar/gkn015

Novel proteins for homocysteine biosynthesis in anaerobic microorganisms
journal, November 2014

  • Rauch, Benjamin Julius; Gustafson, Andrew; Perona, John J.
  • Molecular Microbiology, Vol. 94, Issue 6
  • DOI: 10.1111/mmi.12832

Dimeric dUTPases, HisE, and MazG belong to a New Superfamily of all-α NTP Pyrophosphohydrolases with Potential “House-cleaning” Functions
journal, March 2005

  • Moroz, Olga V.; Murzin, Alexey G.; Makarova, Kira S.
  • Journal of Molecular Biology, Vol. 347, Issue 2
  • DOI: 10.1016/j.jmb.2005.01.030

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

Sinorhizobium meliloti Cells Require Biotin and either Cobalt or Methionine for Growth
journal, August 2001


Accelerated Profile HMM Searches
journal, October 2011


Homocysteine Is Biosynthesized from Aspartate Semialdehyde and Hydrogen Sulfide in Methanogenic Archaea
journal, May 2015


Improving Microbial Genome Annotations in an Integrated Database Context
journal, February 2013


Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes
journal, December 1995


Protein Thiocarboxylate-Dependent Methionine Biosynthesis in Wolinella succinogenes
journal, January 2011

  • Krishnamoorthy, Kalyanaraman; Begley, Tadhg P.
  • Journal of the American Chemical Society, Vol. 133, Issue 2
  • DOI: 10.1021/ja107424t

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

The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20
journal, October 2014


Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein
journal, May 2016

  • Rauch, Benjamin Julius; Perona, John J.
  • Journal of Bacteriology, Vol. 198, Issue 14
  • DOI: 10.1128/JB.00141-16

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life
journal, June 2012

  • Thole, Sebastian; Kalhoefer, Daniela; Voget, Sonja
  • The ISME Journal, Vol. 6, Issue 12
  • DOI: 10.1038/ismej.2012.62

Genome Streamlining in a Cosmopolitan Oceanic Bacterium
journal, August 2005


Harnessing the landscape of microbial culture media to predict new organism–media pairings
journal, October 2015

  • Oberhardt, Matthew A.; Zarecki, Raphy; Gronow, Sabine
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9493

Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway
journal, June 2014

  • de Crécy-Lagard, Valérie
  • Computational and Structural Biotechnology Journal, Vol. 10, Issue 16
  • DOI: 10.1016/j.csbj.2014.05.008

Genetics and Regulation of the Major Enzymes of Alanine Synthesis in Escherichia coli
journal, August 2010

  • Kim, S. H.; Schneider, B. L.; Reitzer, L.
  • Journal of Bacteriology, Vol. 192, Issue 20
  • DOI: 10.1128/JB.00738-10

A universal TagModule collection for parallel genetic analysis of microorganisms
journal, May 2010

  • Oh, Julia; Fung, Eula; Price, Morgan N.
  • Nucleic Acids Research, Vol. 38, Issue 14
  • DOI: 10.1093/nar/gkq419

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
journal, October 2011


BioNumbers—the database of key numbers in molecular and cell biology
journal, October 2009

  • Milo, Ron; Jorgensen, Paul; Moran, Uri
  • Nucleic Acids Research, Vol. 38, Issue suppl_1
  • DOI: 10.1093/nar/gkp889

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

Alternative Pyrimidine Biosynthesis Protein ApbE Is a Flavin Transferase Catalyzing Covalent Attachment of FMN to a Threonine Residue in Bacterial Flavoproteins
journal, April 2013

  • Bertsova, Yulia V.; Fadeeva, Maria S.; Kostyrko, Vitaly A.
  • Journal of Biological Chemistry, Vol. 288, Issue 20
  • DOI: 10.1074/jbc.M113.455402

Influence of Vitamin B12 and Cocultures on the Growth of Dehalococcoides Isolates in Defined Medium
journal, March 2007

  • He, J.; Holmes, V. F.; Lee, P. K. H.
  • Applied and Environmental Microbiology, Vol. 73, Issue 9
  • DOI: 10.1128/AEM.02574-06

The redundant aminotransferases in lysine and arginine synthesis and the extent of aminotransferase redundancy in E scherichia coli : Aminotransferase redundancy
journal, October 2014

  • Lal, Piyush Behari; Schneider, Barbara L.; Vu, Khoan
  • Molecular Microbiology, Vol. 94, Issue 4
  • DOI: 10.1111/mmi.12801

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

  • Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1226

Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium
journal, October 2012

  • Carini, Paul; Steindler, Laura; Beszteri, Sara
  • The ISME Journal, Vol. 7, Issue 3
  • DOI: 10.1038/ismej.2012.122

RamA, a Protein Required for Reductive Activation of Corrinoid-dependent Methylamine Methyltransferase Reactions in Methanogenic Archaea
journal, November 2008

  • Ferguson, Tsuneo; Soares, Jitesh A.; Lienard, Tanja
  • Journal of Biological Chemistry, Vol. 284, Issue 4
  • DOI: 10.1074/jbc.M807392200

The essential gene set of a photosynthetic organism
journal, October 2015

  • Rubin, Benjamin E.; Wetmore, Kelly M.; Price, Morgan N.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 48
  • DOI: 10.1073/pnas.1519220112

Persulfide Formation Mediates Cysteine and Homocysteine Biosynthesis in Methanosarcina acetivorans
journal, February 2017


Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments
journal, December 2011


Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria
journal, November 2013