ArticlePLoS genetics2018
Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 115 citations in OpenAlex.
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- Methionine synthesis and glycine betaine demethylation are intricately intertwined in cosmopolitan marine bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- DmdA-independent lag phase shortening in Phaeobacter inhibens bacteria under stress conditions.The FEBS journal · 2025Article
- Convergence in Amino Acid Outsourcing Between Animals and Predatory Bacteria.International journal of molecular sciences · 2025Article
- Bacterial Amino Acid Auxotrophies Enable Energetically Costlier Proteomes.International journal of molecular sciences · 2025Article
- Boolean matrix logic programming for active learning of gene functions in genome-scale metabolic network models.Machine learning · 2025Article
- Exploring interspecific interaction variability in microbiota: A review.Engineering microbiology · 2024Review
- Interactive tools for functional annotation of bacterial genomes.Database : the journal of biological databases and curation · 2024Article
- Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage.FEMS microbiology ecology · 2024Article
- Phenotypic and genomic characterization ofApplied and environmental microbiology · 2024Article
- Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities.Nature communications · 2024Article
- Biosynthetic and catabolic pathways control amino acid δFrontiers in microbiology · 2024Article
- Development of a rapid and highly accurate method forISME communications · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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. 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.
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