What this entity is
Shewanella oneidensis is the canonical organism name used for the MR1 strain in the essential-metabolome analysis. 1
Key facts from the essential-metabolome analysis
Shewanella oneidensis (MR1) was one of 7 organisms successfully mapped for the pilot comparison of essential-gene organisms using gapmind pathway-completeness predictions. 1
MR1 had complete predictions for 18 of 18 amino-acid biosynthesis pathways, corresponding to 100% pathway completeness in the analysis. 1 The 18 pathways assessed were arg, asn, chorismate, cys, gln, gly, his, ile, leu, lys, met, phe, pro, thr, trp, tyr, and val; MR1 was complete for all 18. 1
The analysis reported 694 raw gapmind predictions for the MR1 genome, GCF_000146165.2. 1 MR1 was included in a pilot rather than a pan-bacterial assessment because only 7 organisms were mapped successfully from an underlying collection containing 45 organisms. 1
The pathway-capability analysis supports and extends this pilot placement: S. oneidensis was one of the 7 Tier 1 organisms with matching GapMind and Fitness Browser data, among 48 Fitness Browser organisms considered. 2 The broader analysis classified organism–pathway pairs by both GapMind capability and experimentally observed fitness dependency, thereby refining the interpretation of MR1’s complete pathway calls rather than treating completeness as proof of requirement. 2
Fitness and functional-dark-matter integration
The functional-dark-matter analysis refines the pilot’s pathway-completeness view by placing MR1 in a broader Fitness Browser prioritization: MR-1 contributed 25 of the top 100 phenotype-bearing dark-gene candidates across 22 organisms. 3
MR-1 202463 was among the highest-ranked fitness-active candidates, with |fit| = 6.4 under stress and a YGGT domain prediction. 3 The analysis also identified the MR-1 K03306 paralog trio 199738, 203545, and 202450, with nitrogen-associated fitness effects of 5.5, 4.0, and 3.9 respectively. 3
This supports using MR1 as an experimental priority beyond the rich-media essential-metabolome pilot: the first three experiments in a greedy set-cover sequence—MR-1 stress, nitrogen source, and carbon source—would address 111 of the top 500 dark genes (20.8%). 3 These fitness results do not establish that the complete amino-acid pathways identified by gapmind are individually required for viability; they instead add condition-specific evidence for other, poorly characterized genes. 3
The truly-dark-gene analysis refines this prioritization by using a stricter set: genes hypothetical in both the original pipeline and Bakta. MR-1 contributed 8 of the top 100 candidates in that separate ranking across 19 organisms; this is not a contradiction of the earlier count of 25 because the analyses rank different dark-gene populations. 4 The MR-1-specific candidates and their underlying evidence are detailed in Truly Dark Genes — What Remains Unknown After Modern Annotation?. 4
Interpretation and limitations
The MR1 result contributes to the observation that 17 of 18 amino-acid biosynthesis pathways were present in all 7 analyzed organisms, although the small and phylogenetically restricted sample limits generalization to bacteria as a whole. 1
The pathway calls were computational gapmind predictions rather than experimental measurements, and complete or likely_complete calls can miss non-canonical pathways, divergent enzymes, or genes absent from genome annotations. 1 The essential-gene context came from rich-media tnseq experiments, meaning nutrient supplementation could make biosynthetic genes appear non-essential; the analysis therefore does not establish that MR1’s complete pathways are individually required for viability. 1
The functional-dark-matter rankings also require caution because Fitness Browser condition coverage is uneven, and MR-1 has 121 historical conditions; deeper condition coverage can produce more specific phenotypes and higher prioritization scores. 3 The new capability–dependency framework reinforces this caution: across its 161 organism–pathway pairs, complete pathways could lack fitness defects under standard conditions yet become important under other tested conditions, while the condition-specific median threshold may itself drive some reclassifications. 2
The truly-dark ranking should likewise be interpreted as a prioritization rather than a demonstrated function: the report notes that short genes can be harder to measure for fitness and that strong phenotypes may reflect polar effects on downstream genes. 4
Related pages
- Essential Metabolome: GapMind Pathway Analysis Across Essential-Gene Organisms — source report for the essential-metabolome pilot. 1
- Functional Dark Matter — Experimentally Prioritized Novel Genetic Systems — source report for experimentally prioritized dark-gene systems. 3
- Metabolic Capability vs Dependency — source report linking pathway capability with fitness dependency. 2
- Truly Dark Genes — What Remains Unknown After Modern Annotation? — source report distinguishing persistent hypothetical genes from annotation-lag genes. 4
- metabolic-model-gapfilling — cross-project context for GapMind pathway-completeness analysis. 1
- gene-essentiality — context for essential-gene measurements and pathway completeness. 1
- condition-specific-fitness — context for rich-media conditions and nutrient-dependent fitness interpretation. 1