Annotation-aware multidomain validation of NucS and MutS-MutL across 23,435 prokaryotic reference genomes
Abstract
Background: EndoMS/NucS mediates non-canonical mismatch repair in several archaeal and actinobacterial lineages. A 2017 phylogenomic survey found that NucS and canonical MutS-MutL were largely mutually exclusive, with coexistence concentrated in Halobacteria and Deinococcus-Thermus. This study reassessed this pattern in an expanded prokaryotic reference collection and tested how annotation wording relates to complete multidomain protein architecture.
Results: GFF3 annotations from 23,435 NCBI reference genomes (22,606 Bacteria and 829 Archaea) were screened and annotation-positive candidates were evaluated with Pfam profile HMMs. Complete NucS required NucS_N (PF21003) and NucS_C (PF01939) on the same protein; canonical MutS required five defined MutS profiles on one protein without a same-protein PF01713 warning; and MutL required PF01119 plus PF08676. Annotation screening yielded 1,145 apparent coexistence genomes, whereas 470 met all three profile criteria: 421 Halobacteria, 48 Deinococcota and one highly contaminated Lysobacter korlensis assembly. Across 6,270 unique NucS candidate proteins, 5,189 carried both NucS profiles, 111 were NucS_N-only, 901 were NucS_C-only and 69 matched neither. The 682-genome generic “NucS domain-containing” tier contained 680 testable genomes and 717 unique proteins; 685 were NucS_C-only, eight NucS_N-only, five carried both profiles and 19 carried neither. At genome level, 663/680 testable generic-tier genomes (97.50%) contained at least one NucS-associated domain, but only five contained a same-protein two-domain NucS candidate. Explicit nucS annotations showed 99.63% two-domain concordance; canonical MutS and MutL annotation-positive genomes met strong profile criteria in 96.78% and 97.14%, respectively. The Jaccard overlap between two-domain NucS and strong MutS-MutL positives was 2.18%.
Conclusions: The contemporary collection confirms the lineage concentration reported in 2017 rather than identifying a new coexistence lineage. The main advance is an architecture-aware audit showing that broad “NucS domain-containing” annotations are usually valid at the domain level but are poor proxies for complete two-domain NucS. Because annotation-negative genomes were not exhaustively searched, the reported counts are validated positives from an annotation-first workflow, not exhaustive prevalence or gene-loss estimates.
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BibTeX
@article{esfahani2026annotationaware,
title = {{Annotation-aware multidomain validation of NucS and MutS-MutL across 23,435 prokaryotic reference genomes}},
author = {Kiarash Sadeghian Esfahani},
journal = {BMC Genomics},
year = {2026},
month = oct,
doi = {10.1186/s12864-026-13470-8},
url = {https://link.springer.com/article/10.1186/s12864-026-13470-8},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Annotation-aware multidomain validation of NucS and MutS-MutL across 23,435 prokaryotic reference genomes
AU - Kiarash Sadeghian Esfahani
PY - 2026
DA - 2026/10/15
JO - BMC Genomics
DO - 10.1186/s12864-026-13470-8
UR - https://link.springer.com/article/10.1186/s12864-026-13470-8
AB - Background: EndoMS/NucS mediates non-canonical mismatch repair in several archaeal and actinobacterial lineages. A 2017 phylogenomic survey found that NucS and canonical MutS-MutL were largely mutually exclusive, with coexistence concentrated in Halobacteria and Deinococcus-Thermus. This study reassessed this pattern in an expanded prokaryotic reference collection and tested how annotation wording relates to complete multidomain protein architecture. Results: GFF3 annotations from 23,435 NCBI reference genomes (22,606 Bacteria and 829 Archaea) were screened and annotation-positive candidates were evaluated with Pfam profile HMMs. Complete NucS required NucS_N (PF21003) and NucS_C (PF01939) on the same protein; canonical MutS required five defined MutS profiles on one protein without a same-protein PF01713 warning; and MutL required PF01119 plus PF08676. Annotation screening yielded 1,145 apparent coexistence genomes, whereas 470 met all three profile criteria: 421 Halobacteria, 48 Deinococcota and one highly contaminated Lysobacter korlensis assembly. Across 6,270 unique NucS candidate proteins, 5,189 carried both NucS profiles, 111 were NucS_N-only, 901 were NucS_C-only and 69 matched neither. The 682-genome generic “NucS domain-containing” tier contained 680 testable genomes and 717 unique proteins; 685 were NucS_C-only, eight NucS_N-only, five carried both profiles and 19 carried neither. At genome level, 663/680 testable generic-tier genomes (97.50%) contained at least one NucS-associated domain, but only five contained a same-protein two-domain NucS candidate. Explicit nucS annotations showed 99.63% two-domain concordance; canonical MutS and MutL annotation-positive genomes met strong profile criteria in 96.78% and 97.14%, respectively. The Jaccard overlap between two-domain NucS and strong MutS-MutL positives was 2.18%. Conclusions: The contemporary collection confirms the lineage concentration reported in 2017 rather than identifying a new coexistence lineage. The main advance is an architecture-aware audit showing that broad “NucS domain-containing” annotations are usually valid at the domain level but are poor proxies for complete two-domain NucS. Because annotation-negative genomes were not exhaustively searched, the reported counts are validated positives from an annotation-first workflow, not exhaustive prevalence or gene-loss estimates.
SN - 1471-2164
ER -