Comparative genomic analysis of nickel homeostasis in cable bacteria.
BMC Genomics
; 25(1): 692, 2024 Jul 15.
Article
in En
| MEDLINE
| ID: mdl-39009997
ABSTRACT
BACKGROUND:
Cable bacteria are filamentous members of the Desulfobulbaceae family that are capable of performing centimetrescale electron transport in marine and freshwater sediments. This longdistance electron transport is mediated by a network of parallel conductive fibres embedded in the cell envelope. This fibre network efficiently transports electrical currents along the entire length of the centimetrelong filament. Recent analyses show that these fibres consist of metalloproteins that harbour a novel nickelcontaining cofactor, which indicates that cable bacteria have evolved a unique form of biological electron transport. This nickeldependent conduction mechanism suggests that cable bacteria are strongly dependent on nickel as a biosynthetic resource. Here, we performed a comprehensive comparative genomic analysis of the genes linked to nickel homeostasis. We compared the genomeencoded adaptation to nickel of cable bacteria to related members of the Desulfobulbaceae family and other members of the Desulfobulbales order.RESULTS:
Presently, four closed genomes are available for the monophyletic cable bacteria clade that consists of the genera Candidatus Electrothrix and Candidatus Electronema. To increase the phylogenomic coverage, we additionally generated two closed genomes of cable bacteria Candidatus Electrothrix gigas strain HY106 and Candidatus Electrothrix antwerpensis strain GW34, which are the first closed genomes of their respective species. Nickel homeostasis genes were identified in a database of 38 cable bacteria genomes (including 6 closed genomes). Gene prevalence was compared to 19 genomes of related strains, residing within the Desulfobulbales order but outside of the cable bacteria clade, revealing several genomeencoded adaptations to nickel homeostasis in cable bacteria. Phylogenetic analysis indicates that nickel importers, nickelbinding enzymes and nickel chaperones of cable bacteria are affiliated to organisms outside the Desulfobulbaceae family, with several proteins showing affiliation to organisms outside of the Desulfobacterota phylum. Conspicuously, cable bacteria encode a unique periplasmic nickel export protein RcnA, which possesses a putative cytoplasmic histidinerich loop that has been largely expanded compared to RcnA homologs in other organisms.CONCLUSION:
Cable bacteria genomes show a clear genetic adaptation for nickel utilization when compared to closely related genera. This fully aligns with the nickeldependent conduction mechanism that is uniquely found in cable bacteria.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Phylogeny
/
Genome, Bacterial
/
Genomics
/
Homeostasis
/
Nickel
Language:
En
Journal:
BMC Genomics
Journal subject:
GENETICA
Year:
2024
Document type:
Article
Affiliation country: