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Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
BACKGROUND: Nickel (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 B(12). Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolution...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667541/ https://www.ncbi.nlm.nih.gov/pubmed/19208259 http://dx.doi.org/10.1186/1471-2164-10-78 |
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author | Zhang, Yan Rodionov, Dmitry A Gelfand, Mikhail S Gladyshev, Vadim N |
author_facet | Zhang, Yan Rodionov, Dmitry A Gelfand, Mikhail S Gladyshev, Vadim N |
author_sort | Zhang, Yan |
collection | PubMed |
description | BACKGROUND: Nickel (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 B(12). Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. RESULTS: We 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 B(12)-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 B(12)-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 B(12)-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 B(12)-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. CONCLUSION: Our 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. |
format | Text |
id | pubmed-2667541 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26675412009-04-10 Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization Zhang, Yan Rodionov, Dmitry A Gelfand, Mikhail S Gladyshev, Vadim N BMC Genomics Research Article BACKGROUND: Nickel (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 B(12). Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. RESULTS: We 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 B(12)-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 B(12)-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 B(12)-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 B(12)-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. CONCLUSION: Our 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. BioMed Central 2009-02-10 /pmc/articles/PMC2667541/ /pubmed/19208259 http://dx.doi.org/10.1186/1471-2164-10-78 Text en Copyright © 2009 Zhang et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Zhang, Yan Rodionov, Dmitry A Gelfand, Mikhail S Gladyshev, Vadim N Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization |
title | Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization |
title_full | Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization |
title_fullStr | Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization |
title_full_unstemmed | Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization |
title_short | Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization |
title_sort | comparative genomic analyses of nickel, cobalt and vitamin b12 utilization |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667541/ https://www.ncbi.nlm.nih.gov/pubmed/19208259 http://dx.doi.org/10.1186/1471-2164-10-78 |
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