Phylogenetic studies of two rubredoxins from sulfate reducing bacteria

Abstract

The sequences of two rubredoxins isolated from the sulfate reducing bacteria: Desulfovibrio vulgaris and Desulfovibrio gigas have been elucidated. They have similar sequences but many more differences occur than would be expected from two bacteria of the same genus. Of the 52 sites, only 37 are occupied by identical residues. The primary structures are compared with those of the anaerobic bacteria rubredoxins of Clostridium pasteurianum, Micrococcus aerogenes, Pseudomonas oleovorans and Peptostreptococcus elsdenii: only 12 identities are found, mostly in the two clusters that contain two iron-bound cysteines each. A phylogenetic tree based on the primary structures is presented and possible relations with plant and bacterial ferredoxins are discussed. A secondary and tertiary structure stereochemically compatible with the sequence data, is proposed.

Analysis of the transcriptional unit encoding the genes for rubredoxin (rub) and a putative rubredoxin oxidoreductase (rbo) in Desulfovibrio vulgaris Hildenborough

“…Finally, a homologous rub gene in the absence of a detectable, homologous rbo gene is found in three, whereas the converse is found in a single one of the species of sulfate-reducing bacteria examined. D. gigas, which has a rubredoxin with 71% sequence identity (37 identical residues in a total of 52) with the protein from D. vulgaris Hildenborough (36), the pRubl probe appears sufficiently homologous for the detection of the rub gene on a 1.2-kb EcoRI fragment (Fig. 6A, lane 12; Table 2).…”

“…7). Thus, of the first 36 amino acids of the rbo gene product, 19 are identical to desulforedoxin, whereas conservative amino acid changes are frequently found in the nonidentical positions. The four cysteine residues (C-9, C-12, C-28, and C-29), which have been proposed to coordinate to the iron (18), are among the conserved amino acid residues.…”

“…Rubredoxins are small, electron-carrying proteins (molecular mass, 6 kilodaltons [kDa]), which are found in the cytoplasm of several anaerobic bacteria, e.g., Deslllfovibrio gigas (8), D. vulgaris Hildenborough (7), D. desulfuricans (15), Thermodesulfobacterium commune (24), Clostridium pasteurianum (36), Peptostreptoc occlus elsdenii (4), and Peptococcus aerogenes (3). The amino acid sequences of these rubredoxins have been determined (3,4,7,8,15,36), and the three-dimensional structures of rubredoxins from C. pasteurianum, D. vulgaris, D. gigas, and D. desulfuricans, which has a very low molecular mass (only 5.2 kDa) have been solved (2,13,14,32,(41)(42)(43).…”

“…The amino acid sequences of these rubredoxins have been determined (3,4,7,8,15,36), and the three-dimensional structures of rubredoxins from C. pasteurianum, D. vulgaris, D. gigas, and D. desulfuricans, which has a very low molecular mass (only 5.2 kDa) have been solved (2,13,14,32,(41)(42)(43). The redox center of rubredoxin consists of a single iron atom (redox potential, -50 to 0 mV), coordinated to four cysteinyl sulfurs.…”