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Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.

Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN - BMC Genomics (2009)

Bottom Line: 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.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588-0664, USA. yzhang@genomics.unl.edu

ABSTRACT

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 B12. 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 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.

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.

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Related in: MedlinePlus

Multiple alignment of a newly predicted B12-dependent protein family. All detected sequences were used to generate the alignment. Residues shown in white on black or grey are conserved in homologs. Location of the distant homolog of B12-binding domain (COG5012) is indicated.
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Figure 4: Multiple alignment of a newly predicted B12-dependent protein family. All detected sequences were used to generate the alignment. Residues shown in white on black or grey are conserved in homologs. Location of the distant homolog of B12-binding domain (COG5012) is indicated.

Mentions: Through our analysis, a novel B12-dependent protein family was predicted in prokaryotes. Orthologs of this protein were detected in 11 sequenced bacteria belonging to four evolutionarily distant phyla (Firmicutes/Clostridia, Firmicutes/Lactobacillales, Chloroflexi and Thermotogae). A distant homolog of the B12-binding domain (COG5012, found in MetH and other methyltransferases) was detected in its N terminus (Fig. 4). Structure prediction using HHpred [55] suggested that the N-terminus may contain a TIM-barrel-like structure involved in B12 binding (data not shown). Analysis of genome context of this putative B12-dependent protein showed that it is always adjacent to NAD/NADP octopine/nopaline dehydrogenase (pfam02317), which acts on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. Additional enzyme candidates included D-alanine:D-alanine ligase and asparagine synthase (glutamine-hydrolyzing), which were located in the vicinity of the gene for the novel B12-dependent protein in several organisms. Further experiments are needed to confirm their dependence on B12.


Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.

Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN - BMC Genomics (2009)

Multiple alignment of a newly predicted B12-dependent protein family. All detected sequences were used to generate the alignment. Residues shown in white on black or grey are conserved in homologs. Location of the distant homolog of B12-binding domain (COG5012) is indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667541&req=5

Figure 4: Multiple alignment of a newly predicted B12-dependent protein family. All detected sequences were used to generate the alignment. Residues shown in white on black or grey are conserved in homologs. Location of the distant homolog of B12-binding domain (COG5012) is indicated.
Mentions: Through our analysis, a novel B12-dependent protein family was predicted in prokaryotes. Orthologs of this protein were detected in 11 sequenced bacteria belonging to four evolutionarily distant phyla (Firmicutes/Clostridia, Firmicutes/Lactobacillales, Chloroflexi and Thermotogae). A distant homolog of the B12-binding domain (COG5012, found in MetH and other methyltransferases) was detected in its N terminus (Fig. 4). Structure prediction using HHpred [55] suggested that the N-terminus may contain a TIM-barrel-like structure involved in B12 binding (data not shown). Analysis of genome context of this putative B12-dependent protein showed that it is always adjacent to NAD/NADP octopine/nopaline dehydrogenase (pfam02317), which acts on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. Additional enzyme candidates included D-alanine:D-alanine ligase and asparagine synthase (glutamine-hydrolyzing), which were located in the vicinity of the gene for the novel B12-dependent protein in several organisms. Further experiments are needed to confirm their dependence on B12.

Bottom Line: 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.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588-0664, USA. yzhang@genomics.unl.edu

ABSTRACT

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 B12. 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 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.

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.

Show MeSH
Related in: MedlinePlus