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.The transition metals nickel and cobalt are essential cofactors for a number of prokaryotic enzymes involved in a variety of metabolic processes (36,41). Among the known nickeldependent enzymes are urease (8), [NiFe] hydrogenase, carbon monoxide dehydrogenase (Ni-CODH) (35), acetyl-coenzyme A decarbonylase/synthase (21), superoxide dismutase SodN (22), methyl-coenzyme M reductase (20), and glyoxylase I (50). In contrast to the diverse roles of nickel in microbial metabolism, cobalt is mainly found in the corrin ring of coenzyme B 12 , a cofactor involved in methyl group transfer and in rearrangement reactions (36). Since in natural environments, soluble Ni 2ϩ and Co 2ϩ are usually present only in trace amounts, the synthesis of the respective metalloenzymes requires high-affinity uptake of metal ions. Until recently, two major types of microbial high-affinity nickel and cobalt transporters were known: ATP-binding cassette (ABC) systems and secondary permeases of the NiCoT family (reviewed in reference 24).The NikABCDE system of Escherichia coli belongs to the nickel/peptide/opine ABC transporter family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and -C), and two ATPases (NikD and -E) (43). The molecular basis of selective high-affinity binding of Ni 2ϩ remains elusive, although crystal structures of E. coli NikA have been determined by two approaches (10, 31).The two studies uncovered that N...

Structural and mechanistic insights into prokaryotic energy-coupling factor transporters

“…This early work also showed that the energy for transport was supplied by the hydrolysis of ATP 2 . These observations date from the pre-genomics era and, although some of the binding proteins were purified and their amino acid compositions determined 3,4 , the molecular identity of the transport systems remained elusive until the 2000s [6][7][8][9][10][11][12][13][14] .…”

In silico description of cobalt and nickel assimilation systems in the genomes of methanogens

“…Many bacterial species possess transporters from only one family, and few species have a redundant set of nickel/ cobalt transporters from different families (Rodionov et al 2006). Methanogens have typical transporter for capable and selective transport of these metal ions.…”

“…Kessler et al (1997) reported that tungsten has specifically to inhibit diazotrophic growth of Methanococcus maripaludis in the presence of molybdenum. The mechanism of nickel and cobalt uptake in many bacteria and most archaea is not known, although, for instance in methanogenes, Ni-and Co-containing enzymes are essential for energy metabolism and anabolism (Rodionov et al 2006). Moreover, a little effort has been made on investigating the cellular systems of methanogens for controlling uptake and distribution of metal ions prevent toxic accumulation and subsequent oxidative damage of macromolecules.…”

Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake

“…11,13 The UreH group includes Ni-specific permeases whose corresponding genes are associated with gene clusters for urease or Ni-superoxide dismutase in the genome of Bacillus and also in several proteobacteria and cyanobacteria. 5,14 Finally, members of the HupE/UreJ family are widespread among bacteria, and are usually encoded within hydrogenase or urease gene clusters. 5 In some cyanobacteria the hupE-like genes are preceded by B 12 riboswitches, thus suggesting a preference for cobalt ions.…”

“…5,14 Finally, members of the HupE/UreJ family are widespread among bacteria, and are usually encoded within hydrogenase or urease gene clusters. 5 In some cyanobacteria the hupE-like genes are preceded by B 12 riboswitches, thus suggesting a preference for cobalt ions. 15 Rhizobium leguminosarum HupE was the first member of the HupE/UreJ family specifically a Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.…”