ArticleBMC genomics2009
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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Who cites it
142 citing papers in PubMed, 285 citations in OpenAlex.
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- Adapting Komagataella phaffii Cultivation Media to REACH Regulations.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Cobamide metabolism, regulation, and adaptation inJournal of bacteriology · 2025Review
- The Corrinoid Model for Dissecting Microbial Community Interactions Across Scales.Annual review of microbiology · 2025Review
- Structural investigations connect the disordered N-terminal extension of HypB to the activities of HypB and SlyD in E. coli.Protein science : a publication of the Protein Society · 2025Article
- Comparative genome analyses reveal insights into the marine adaptation of a novel bacterium Pontimicrobium maritimus sp. nov., isolated from seawater.Scientific reports · 2025Article
- Computational Strategies to Enhance Vitamin BCurrent microbiology · 2025Review
- Emerging antibiotic resistance by various novel proteins/enzymes.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Review
- Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.Microbiology and molecular biology reviews : MMBR · 2025Review
- Comprehensive model for predicting toxic equivalents (TEQ) reduction due to dechlorination of polychlorinated dibenzo-p-dioxin and dibenzofurans (PCDD/F congeners).Journal of hazardous materials · 2024Article
- Absence of farnesol salvage inApplied and environmental microbiology · 2024Article
- A novel regulatory interplay between atypical B12 riboswitches and uORF translation in Mycobacterium tuberculosis.Nucleic acids research · 2024Article
- Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov.BMC microbiology · 2024Article
- Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin BbioRxiv : the preprint server for biology · 2024Article
- Physiological and morphological plasticity in response to nitrogen availability of a yeast widely distributed in the open ocean.FEMS microbiology ecology · 2024Article
82 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundNickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited.
resultsWe carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH), ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina) and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts) have a tendency for loss of Ni/Co utilization.
conclusionOur data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three domains of life, yet only a limited number of user proteins.
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