The Journal of antimicrobial chemotherapy · 2026
Phylogenetic diversification of the PoxtA ribosomal protection determinant.
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Almeida Lara M, Zorzi Felipe M, Araujo Kawany M, Silva Joas L, Moreno Andrea M, Bispo Paulo, Gilmore Michael S
Аннотация
OBJECTIVES: Three ATP-binding cassette subfamily F (ABC-F) PoxtA protein sequences are currently represented in NCBI's Pathogen Detection Reference Gene Catalog (WP_002415638.1, WP_209691075.1, and WP_094899500.1), while the number of publicly available sequences has steadily increased. We therefore conducted a curated survey of PoxtA homologue diversity, distribution, amino acid variability, and dissemination-associated genetic contexts.
METHODS: WP accessions were retrieved using BLASTp nr and a corresponding data package was obtained from NCBI Datasets v18.0.1. Proteins were aligned with MAFFT v7.525, clustered with CD-HIT v4.8.1, and maximum likelihood trees inferred in IQ-TREE v2.4.0. Gene occurrence derived from GCF assemblies containing host or source metadata. Genetic contexts were then investigated through sequence alignments of genomic regions extracted from these datasets.
RESULTS: Among 83 non-redundant PoxtA-related WP accessions retrieved, 21 homologues clustered with canonical RefSeq PoxtA proteins, while the remaining proteins were more distantly related to ABC-F. Predominantly associated with Bacillota, homologues exhibited broad distribution across clinical, agricultural, food-associated, and environmental sources. Substitutions potentially affecting their ribosome interactions were identified mainly within the Arm subdomain and the antibiotic-resistance domain. Genomes encoding homologues exhibited diverse genetic contexts, including partial conservation of Tn6657, intact Tn6246 and Tn8026 structures, and atypical contexts carrying additional resistance genes.
CONCLUSIONS: Homologue diversification suggests ongoing adaptation and highlights an expanding repertoire of amino acid substitutions with yet unresolved structural and functional impacts. Genetic contexts likely underlie intra- and interspecies horizontal dissemination of homologue genes by promoting co-selection under antimicrobial selective pressures.
METHODS: WP accessions were retrieved using BLASTp nr and a corresponding data package was obtained from NCBI Datasets v18.0.1. Proteins were aligned with MAFFT v7.525, clustered with CD-HIT v4.8.1, and maximum likelihood trees inferred in IQ-TREE v2.4.0. Gene occurrence derived from GCF assemblies containing host or source metadata. Genetic contexts were then investigated through sequence alignments of genomic regions extracted from these datasets.
RESULTS: Among 83 non-redundant PoxtA-related WP accessions retrieved, 21 homologues clustered with canonical RefSeq PoxtA proteins, while the remaining proteins were more distantly related to ABC-F. Predominantly associated with Bacillota, homologues exhibited broad distribution across clinical, agricultural, food-associated, and environmental sources. Substitutions potentially affecting their ribosome interactions were identified mainly within the Arm subdomain and the antibiotic-resistance domain. Genomes encoding homologues exhibited diverse genetic contexts, including partial conservation of Tn6657, intact Tn6246 and Tn8026 structures, and atypical contexts carrying additional resistance genes.
CONCLUSIONS: Homologue diversification suggests ongoing adaptation and highlights an expanding repertoire of amino acid substitutions with yet unresolved structural and functional impacts. Genetic contexts likely underlie intra- and interspecies horizontal dissemination of homologue genes by promoting co-selection under antimicrobial selective pressures.