Phylogenetic analysis of the chromate ion transporter (CHR) superfamily

Abstract

Because toxic heavy metals (including chromium) have been abundant on the Earth since the beginning of life, microbes have been exposed to them for nearly four billion years [1]. In response, cells have developed diverse mechanisms that confer heavy metal resistance, such as, for example, the active extrusion of toxic metal cations [2,3]. This constitutes one of the beststudied bacterial mechanisms of resistance to chromium, which is based on the active efflux of chromate driven by the membrane potential [4,5] ChrA is a membrane protein that confers resistance to the toxic ion chromate through the energy-dependent chromate efflux from the cytoplasm. In the protein databases, ChrA is a member of the chromate ion transporter (CHR) superfamily, composed of at least several dozens of members, distributed in the three domains of life. The aim of this work was to perform a phylogenetic analysis of the CHR superfamily. An exhaustive search for ChrA homologous proteins was carried out at the National Center for Biotechnology Information database. One hundred and thirty-five sequences were identified as members of the CHR superfamily [77 long-chain sequences, or bidomains (LCHR), and 58 short-chain sequences, or monodomains (SCHR)], organized mainly as tandem pairs of genes whose resultant proteins probably possess oppositely oriented membrane topology. LCHR sequences were split into amino and carboxyl domains, and the resultant domains were aligned with the SCHR proteins. A phylogenetic tree was reconstructed using four different methods, obtaining similar results. The domains were grouped into three clusters: the SCHR proteins cluster, the amino domain cluster of LCHR proteins and the carboxyl domain cluster of LCHR proteins. These results, as well as differences in the genomic context of CHR proteins, enabled the proteins to be sorted into two families (SCHR and LCHR), and 10 subfamilies. Evidence was found suggesting an ancient origin of LCHR proteins from the fusion of two SCHR protein-encoding genes; however, some secondary events of fusion and fission may have occurred later. The separate distribution of the LCHR and SCHR proteins, differences in the genomic context in both groups and the fact that chromate transport has been demonstrated only in LCHR proteins suggest that the CHR proteins comprise two or more paralogous groups in the CHR superfamily.Abbreviations CHR, chromate ion transporter; ME, minimum evolution; MP, maximum parsimony; NJ, neighbour joining; TMS, transmembrane segment; UPGMA, unweighted pair-group method using arithmetic averages.

Responses of Lactic Acid Bacteria to Heavy Metal Stress

“…The best-studied example is the Pseudomonas aeruginosa ChrA protein, which functions as a chemiosmotic pump that extrudes chromate from the cytoplasm using the proton motive force (Alvarez et al 1999). A broad phylogenic analysis for chrA transporter genes revealed homologous genes in bacteria, archaea, and fungi (Diaz-Perez et al 2007). Several bacilli possess homologous gene sequences, but none of the known chromium-defense genes is present in the sequenced LAB genomes.…”

Short-Chain Chromate Ion Transporter Proteins from Bacillus subtilis Confer Chromate Resistance in Escherichia coli

“…The best-studied example is the Pseudomonas aeruginosa ChrA protein, which functions as a chemiosmotic pump that extrudes chromate from the cytoplasm using the proton motive force (2). ChrA belongs to the chromate ion transporter (CHR) superfamily (11), which includes dozens of homologs from all three domains of life (5). The CHR superfamily is composed of two families of sequences: (i) the short-chain monodomain CHR (SCHR) family, formed by proteins of about 200 amino acid (aa) residues, and (ii) the long-chain bidomain CHR (LCHR) family, comprising proteins of about 400 aa (5).…”

“…ChrA belongs to the chromate ion transporter (CHR) superfamily (11), which includes dozens of homologs from all three domains of life (5). The CHR superfamily is composed of two families of sequences: (i) the short-chain monodomain CHR (SCHR) family, formed by proteins of about 200 amino acid (aa) residues, and (ii) the long-chain bidomain CHR (LCHR) family, comprising proteins of about 400 aa (5). The CHR superfamily is considered to be the first example of the existence of short-unit equivalent ancestral polypeptides, as well as full-length duplicated proteins (5).…”

“…The CHR superfamily is composed of two families of sequences: (i) the short-chain monodomain CHR (SCHR) family, formed by proteins of about 200 amino acid (aa) residues, and (ii) the long-chain bidomain CHR (LCHR) family, comprising proteins of about 400 aa (5). The CHR superfamily is considered to be the first example of the existence of short-unit equivalent ancestral polypeptides, as well as full-length duplicated proteins (5). In fact, some bacterial genomes (e.g., those of Cupriavidus metallidurans and Burkholderia species) encode multiple SCHR and LCHR homologs of different subfamilies (5).…”

“…The CHR superfamily is considered to be the first example of the existence of short-unit equivalent ancestral polypeptides, as well as full-length duplicated proteins (5). In fact, some bacterial genomes (e.g., those of Cupriavidus metallidurans and Burkholderia species) encode multiple SCHR and LCHR homologs of different subfamilies (5). Several proteins of the LCHR family have been demonstrated previously to function as membrane transporters able to extrude chromate ions from the cytoplasm (1, 2, 3, 10), but no function for proteins of the SCHR family has yet been reported.…”