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Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen.

Ridge PG, Zhang Y, Gladyshev VN - PLoS ONE (2008)

Bottom Line: We found that copper use is widespread among prokaryotes, but also identified several phyla that lack cuproproteins.We present evidence that organisms living in oxygen-rich environments utilize copper, whereas the majority of anaerobic organisms do not.The data are consistent with the idea that proteins evolved to utilize copper following the oxygenation of the Earth.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, USA.

ABSTRACT
Copper is an essential trace element in many organisms and is utilized in all domains of life. It is often used as a cofactor of redox proteins, but is also a toxic metal ion. Intracellular copper must be carefully handled to prevent the formation of reactive oxygen species which pose a threat to DNA, lipids, and proteins. In this work, we examined patterns of copper utilization in prokaryotes by analyzing the occurrence of copper transporters and copper-containing proteins. Many organisms, including those that lack copper-dependent proteins, had copper exporters, likely to protect against copper ions that inadvertently enter the cell. We found that copper use is widespread among prokaryotes, but also identified several phyla that lack cuproproteins. This is in contrast to the use of other trace elements, such as selenium, which shows more scattered and reduced usage, yet larger selenoproteomes. Copper transporters had different patterns of occurrence than cuproproteins, suggesting that the pathways of copper utilization and copper detoxification are independent of each other. We present evidence that organisms living in oxygen-rich environments utilize copper, whereas the majority of anaerobic organisms do not. In addition, among copper users, cuproproteomes of aerobic organisms were larger than those of anaerobic organisms. Prokaryotic cuproproteomes were small and dominated by a single protein, cytochrome c oxidase. The data are consistent with the idea that proteins evolved to utilize copper following the oxygenation of the Earth.

Show MeSH
Occurrence of cuproproteins in bacteria.Phylogenetic tree was adapted from [37]. Reported is the total number of bacteria for each phylum and the numbers of bacteria that utilize a given cuproprotein. Numbers across the top refer to the cuproproteins in Table 1. The last two columns (Users and Nonusers) refer to the number of organisms in the specific phylum that are users and nonusers, respectively. Fields colored in red represent phyla where all bacteria belonging to that phylum were classified as either users or nonusers. The “# Cuproproteins” column shows the total number of cuproproteins utilized by all bacteria belonging to a particular phylum.
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pone-0001378-g001: Occurrence of cuproproteins in bacteria.Phylogenetic tree was adapted from [37]. Reported is the total number of bacteria for each phylum and the numbers of bacteria that utilize a given cuproprotein. Numbers across the top refer to the cuproproteins in Table 1. The last two columns (Users and Nonusers) refer to the number of organisms in the specific phylum that are users and nonusers, respectively. Fields colored in red represent phyla where all bacteria belonging to that phylum were classified as either users or nonusers. The “# Cuproproteins” column shows the total number of cuproproteins utilized by all bacteria belonging to a particular phylum.

Mentions: The numbers in the first column are the numbers used in Figures 1–3 to identify the cuproproteins.


Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen.

Ridge PG, Zhang Y, Gladyshev VN - PLoS ONE (2008)

Occurrence of cuproproteins in bacteria.Phylogenetic tree was adapted from [37]. Reported is the total number of bacteria for each phylum and the numbers of bacteria that utilize a given cuproprotein. Numbers across the top refer to the cuproproteins in Table 1. The last two columns (Users and Nonusers) refer to the number of organisms in the specific phylum that are users and nonusers, respectively. Fields colored in red represent phyla where all bacteria belonging to that phylum were classified as either users or nonusers. The “# Cuproproteins” column shows the total number of cuproproteins utilized by all bacteria belonging to a particular phylum.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2147054&req=5

pone-0001378-g001: Occurrence of cuproproteins in bacteria.Phylogenetic tree was adapted from [37]. Reported is the total number of bacteria for each phylum and the numbers of bacteria that utilize a given cuproprotein. Numbers across the top refer to the cuproproteins in Table 1. The last two columns (Users and Nonusers) refer to the number of organisms in the specific phylum that are users and nonusers, respectively. Fields colored in red represent phyla where all bacteria belonging to that phylum were classified as either users or nonusers. The “# Cuproproteins” column shows the total number of cuproproteins utilized by all bacteria belonging to a particular phylum.
Mentions: The numbers in the first column are the numbers used in Figures 1–3 to identify the cuproproteins.

Bottom Line: We found that copper use is widespread among prokaryotes, but also identified several phyla that lack cuproproteins.We present evidence that organisms living in oxygen-rich environments utilize copper, whereas the majority of anaerobic organisms do not.The data are consistent with the idea that proteins evolved to utilize copper following the oxygenation of the Earth.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, USA.

ABSTRACT
Copper is an essential trace element in many organisms and is utilized in all domains of life. It is often used as a cofactor of redox proteins, but is also a toxic metal ion. Intracellular copper must be carefully handled to prevent the formation of reactive oxygen species which pose a threat to DNA, lipids, and proteins. In this work, we examined patterns of copper utilization in prokaryotes by analyzing the occurrence of copper transporters and copper-containing proteins. Many organisms, including those that lack copper-dependent proteins, had copper exporters, likely to protect against copper ions that inadvertently enter the cell. We found that copper use is widespread among prokaryotes, but also identified several phyla that lack cuproproteins. This is in contrast to the use of other trace elements, such as selenium, which shows more scattered and reduced usage, yet larger selenoproteomes. Copper transporters had different patterns of occurrence than cuproproteins, suggesting that the pathways of copper utilization and copper detoxification are independent of each other. We present evidence that organisms living in oxygen-rich environments utilize copper, whereas the majority of anaerobic organisms do not. In addition, among copper users, cuproproteomes of aerobic organisms were larger than those of anaerobic organisms. Prokaryotic cuproproteomes were small and dominated by a single protein, cytochrome c oxidase. The data are consistent with the idea that proteins evolved to utilize copper following the oxygenation of the Earth.

Show MeSH