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

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.

Figure 1. Occurrence of cuproproteins in bacteria.

Phylogenetic tree was adapted from . 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.

Figure 2. Occurrence of cuproproteins in Archaea.

Reported is the occurrence (by phylum) of cuproproteins and Cu exporters in archaea. No importers, repressors, or chaperones were identified in archaea. See legend to Figure 1 for further details.

Figure 3. Occurrence of transporters, repressors and chaperones in bacteria.

Phylogenetic tree was adapted from . Reported are the number of bacteria (by phylum) which utilized a given transporter, repressor, or chaperone. Numbers across the top refer to specific transporters or chaperones (see Table 1 for protein names). Columns 10–17 are exporters, column 18 is the sole importer, columns 19–20 are chaperones, and column 21 is a transporter whose exact function has not been characterized. The last four columns report the number of exporters, importers, and chaperones present in each phyla.

Figure 4. Bacterial cuproproteomes.

Phylogenetic tree adapted from . Numbers across the top (1–5) show the size of cuproproteomes (i.e., the number of cuproproteins in a phylum or organism). Displayed is the number of organisms from each phylum with the cuproproteome of the particular size.

Figure 5. Archaeal cuproproteomes.

See the legend to Figure 4.

Figure 6. Occurrence of Cu users and nonusers among bacteria differing in their dependence on oxygen.

Bacteria were divided based on their oxygen requirement into anaerobic, aerobic, facultative, and microaerophilic. Shown are the numbers of users/nonusers for each of these groups of organisms.

Figure 7. Occurrence of Cu users and nonusers among archaea differing in their dependence on oxygen.

Archaea were divided based on their oxygen requirement into anaerobic, aerobic, facultative, and microaerophilic. Shown are the numbers of users/nonusers for each of these groups of organisms.