Genome Analysis

A milestone for the understanding of the physiology of Streptomyces will be the completed nucleotide sequence determination of the 8-Mb linear genome of S. coelicolor (Streptomyces coelicolor Genome Project, http://www.sanger.ac.uk/Projects/S_coelicolor/, Sanger Centre, UK). This project has been initiated after the generation of a cosmid library covering the genome (59). The ongoing annotation at the Sanger Centre provides the community with a first impression of the proteins encoded on this, for bacterial standards, large genome. The availability of the genome sequence facilitates more detailed searches for specific proteins and families of proteins. Blast searches using the sequences of known copper proteins and copper-binding motifs have been used to make an inventory of putative copper proteins in S. coelicolor. This inventory can provide better guidance to the experiments aimed at the understanding of the close relationship between copper ions and morphogenesis in Streptomyces.

In microorganisms, copper-containing proteins can roughly be divided in three categories: (1) electron-transfer proteins, (2) redox enzymes, and (3) copper-transport and homeostasis proteins. The first two categories of copper proteins have redox active copper centers. The function of proteins belonging to the latter group is transport and/or storage of copper ions and keeping copper redox inactive. In this way, these proteins protect the cell from the lethal effects of free-copper ions and they can deliver the copper ion at the site where it is required. Each of these categories of copper-containing proteins is characterized by one or more amino acid motifs, including the copper ligands. Representative proteins of each category and the known amino acid sequence motifs have been used to screen the S. coelicolor genome database for putative copper proteins. No hits have been found with searches for electron-transfer proteins, but several hits were recorded in the other two categories. Search criteria were, among others, copper-binding sites (type I, type II, or type III), heavy-metal-associated motif (HMA), and cysteine-rich sequences such as in metallothioneins (60) and in the copper fist domain of Macl (61). The most convincing examples of putative copper-binding proteins in S. coelicolor are discussed in the following subsections and are listed in Table 1. The localization of these proteins is depicted in Fig. 9. It must be emphasized that the similarity searches deliver an indication of copper binding as a cofactor and a prediction of the function of the proteins. Detailed biochemical and genetic studies should provide definite proof of their copper-binding capacity and their role in physiology.

Q = copper-binding site(s) Fig. 9. Localization of putative copper proteins in S. coelicolor. Table 1

Putative Copper-Binding and/or Transporting Proteins in S. coelicolor

Database no.

Putative classification

Localization

Motif

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