title: Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters.
abstract: The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokaryotes. For functional annotation of genes, we used two comparative genomic approaches: identification of regulatory signals and analysis of the genomic positions of genes encoding candidate nickel/cobalt transporters. The nickel-responsive repressor NikR regulates many nickel uptake systems, though the NikR-binding signal is divergent in various taxonomic groups of bacteria and archaea. B(12) riboswitches regulate most of the candidate cobalt transporters in bacteria. The nickel/cobalt transporter genes are often colocalized with genes for nickel-dependent or coenzyme B(12) biosynthesis enzymes. Nickel/cobalt transporters of different families, including the previously known NiCoT, UreH, and HupE/UreJ families of secondary systems and the NikABCDE ABC-type transporters, showed a mosaic distribution in prokaryotic genomes. In silico analyses identified CbiMNQO and NikMNQO as the most widespread groups of microbial transporters for cobalt and nickel ions. These unusual uptake systems contain an ABC protein (CbiO or NikO) but lack an extracytoplasmic solute-binding protein. Experimental analysis confirmed metal transport activity for three members of this family and demonstrated significant activity for a basic module (CbiMN) of the Salmonella enterica serovar Typhimurium transporter.
authors.affiliation: The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA. rodionov@burnham.org
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
authors.forename: Peter
authors.initials: P
authors.lastname: Hebbeln
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: Thomas
authors.initials: T
authors.lastname: Eitinger
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D003035:Cobalt / Q000378:metabolism*; D003038:Cobamides; D019295:Computational Biology; D029968:Escherichia coli Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D023281:Genomics; D009532:Nickel / Q000378:metabolism*; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics / Q000378:metabolism*; D012097:Repressor Proteins / Q000378:metabolism
chemical_list: D018528:ATP-Binding Cassette Transporters; D001426:Bacterial Proteins; D003038:Cobamides; D029968:Escherichia coli Proteins; C402409:NikR protein, E coli; D012097:Repressor Proteins; D003035:Cobalt; D009532:Nickel