What this entity is
Canonical name: Tryptophan biosynthesis. 1
Known aliases: No aliases were reported in the source document. 1
Stable external identifier: Gene Ontology term GO:0000162. 1
Tryptophan biosynthesis is a functional category identified through interproscan Gene Ontology annotation in antimicrobial-resistance (AMR) cofitness neighborhoods. 1
Evidence from AMR cofitness networks
Tryptophan biosynthesis was significantly enriched in AMR cofitness neighborhoods in 3 organisms among GO terms enriched in at least 3 organisms at FDR (false discovery rate) < 0.05, with a mean odds ratio of 5.3. 1
By AMR mechanism, tryptophan biosynthesis was enriched for efflux-resistance genes in 5 organisms. 1
The enrichment supports the broader observation that amino acid biosynthesis occurs in AMR support networks, but it does not establish direct transcriptional co-regulation; the signal may instead reflect shared dispensability under Fitness Browser laboratory conditions, including media containing amino acid supplements. 1
The report identifies a fitness-matched permutation using random non-AMR genes with the same mean-fitness distribution as the key analysis needed to distinguish genuine co-regulation from shared dispensability. 1
Evidence from FW300-N2E3 metabolic integration
In pseudomonas-fw300-n2e3, GapMind predicted a complete tryptophan biosynthesis pathway, and Fitness Browser experiments showed growth on tryptophan; this supports the pathway’s physiological relevance beyond the AMR-neighborhood enrichment. 2
FW300-N2E3 also increased tryptophan in its WoM exometabolome and had 231 genes with significant fitness effects on tryptophan. This refines the AMR interpretation: broad biosynthetic fitness signals can accompany both pathway requirement and extracellular metabolite release, while the report treats the production-plus-growth-but-no-species-level-catabolism pattern as a hypothesis of overflow, cross-feeding, or signaling rather than evidence that FW300-N2E3 cannot grow on tryptophan. 2
The 231-gene fitness landscape includes pleiotropic requirements, so it does not by itself establish that all significant genes are tryptophan-specific; separating housekeeping from substrate-specific effects remains necessary. 2
Related pages
This entity is discussed in AMR Co-Fitness Support Networks and Metabolic Consistency of Pseudomonas FW300-N2E3 Across Four KBase Data Lakehouse Databases, and relates to condition-specific-fitness, gene-essentiality, metabolic-model-gapfilling, multi-omics-integration, pangenome-integration, and histidine biosynthesis. 1,2