What this entity is
Canonical name: Methanococcus maripaludis. 1
Known alias: M. maripaludis. 1
Strains represented: JJ and S2. 1,2
Stable identifier reported: SNIPE-associated locus MMJJ_RS01635; no organism-level stable identifier was provided in the report. 1
Methanococcus maripaludis is an organism represented in the Fitness Browser and the only organism in that dataset reported to contain a complete two-domain SNIPE architecture. 1 The truly dark genes analysis further identifies Methanococcus strains S2 and JJ as accounting for 55% of truly dark genes, and Methanococcus_JJ contributes 13 of the top 100 prioritized candidates. 3 This refines the organism’s context: its representation in Fitness Browser also makes it a major source of unresolved gene-function candidates, although the dark-gene analysis does not establish their functions. 3
The conservation-versus-fitness analysis supports the importance of this Fitness Browser representation: Methanococcus maripaludis S2 showed the strongest essential-gene core-conservation enrichment among the compared organisms, with OR=5.21. 2 This result applies to S2 and therefore refines the separate SNIPE evidence from strain JJ rather than identifying the SNIPE locus as the enriched gene set. 2
Evidence from the SNIPE analysis
The SNIPE protein at locus MMJJ_RS01635 contained PF13250/DUF4041, PF13455/Mug113, and PF10544, providing the only complete PF13250-plus-PF13455 architecture detected among the surveyed Fitness Browser organisms. 1 The relevant domain families are PF13250/DUF4041 and PF13455/Mug113. 1
The Fitness Browser provided 129 experiments for this protein. 1 Its minimum measured fitness was -1.16 under formate/acetate conditions, and it was dispensable under most tested conditions. 1
PF13455 occurred in 7 genes across 6 Fitness Browser organisms, including Methanococcus maripaludis, but only Methanococcus maripaludis carried the complete PF13250-plus-PF13455 architecture. 1
Interpretation and limitation
The Methanococcus maripaludis result demonstrates that a complete SNIPE-like domain architecture occurs in an archaeal Fitness Browser organism, but it does not establish that the Enterobacterales phage-lambda ManYZ transporter mechanism operates in archaea. 1 The concentration of unresolved genes in Methanococcus strains supports prioritizing archaeal-specific annotation and experimental follow-up, but the dark-gene results do not by themselves establish horizontal transfer, gene function, or a connection to SNIPE. 3
The S2 conservation signal likewise indicates an association between inferred essentiality and core-genome conservation, not a strain-independent property of every Methanococcus maripaludis gene; essentiality was inferred from RB-TnSeq under the library’s represented growth conditions. 2
Related pages
- SNIPE Defense System in the KBase Data Lakehouse Pangenome — source report describing the SNIPE architecture and Fitness Browser evidence. 1
- Truly Dark Genes — What Remains Unknown After Modern Annotation? — source report distinguishing annotation-lag genes from persistent hypothetical genes and prioritizing candidates. 3
- Conservation vs Fitness — Linking FB Genes to Pangenome Clusters — source report linking Fitness Browser essentiality to pangenome conservation. 2
- phage-defense-syndromes-and-arms-race — cross-project synthesis of SNIPE-mediated phage defense and its proposed transporter trade-off. 1
- kescience-fitnessbrowser — dataset supplying the organism’s fitness measurements. 1
- snipe-defense-system — SNIPE defense system investigated in the report. 1