Two structurally different cytochromes c from Bacillus azotoformans: on the evolution of gram-positive bacteria

Bacillus stearothermophilus qcr operon encoding rieske FeS protein, cytochrome b6, and a novel-type cytochrome c1 of quinol-cytochrome c reductase

The gcr of Bacillus stearothermophilus K1041 encoding three subunits of the quinol-cytochrome c oxidoreductase (cytochrome reductase, b6c1 complex) was cloned and sequenced. The gene (qcrA) for a Rieske FeS protein of 19,144 Da with 169 amino acid residues, and the gene (qcrC) for cytochrome c1 of 27,342 Da with 250 amino acid residues were found at adjacent upstream and downstream sides of the previously reported qcrB (petB) for cytochrome b6 of subunit 25,425 Da with 224 residues (Sone, N., Sawa, G., Sone, T., and Noguchi, S. (1995) J. Biol. Chem. 270, 10612-10617). The three structural genes for thermophilic Bacillus cytochrome reductase form a transcriptional unit. In the deduced amino acid sequence for the FeS protein, the domain including four cysteines and two histidines binding the 2Fe-2S cluster was conserved. Its N-terminal part more closely resembled the cyanobacteria-plastid type than the proteobacteria-mitochondria type when their sequences were compared. The amino acid sequence of cytochrome c1 was not similar to either type; the thermophilic Bacillus cytochrome c1 is composed of an N-terminal part corresponding to subunit IV with three membrane-spanning segments, and a C-terminal part of cytochrome c reminiscent of cytochrome c-551 of thermophilic Bacillus. The subunit IV in the enzyme of cyanobacteria and plastids is the counterpart of C-terminal part of cytochrome b of proteobacteria and mitochondria. These characteristics indicate that Bacillus cytochrome b6c1 complex is unique.

The cytochrome bc complex (menaquinone:cytochrome c reductase) in Bacillus subtilis has a nontraditional subunit organization

We have identified an operon in Bacillus subtilis, designated qcr, that is thought to encode a quinone: cytochrome c reductase. Northern (RNA blot) analysis suggests a tricistronic operon. The operon is located at about 200 degrees on the B. subtilis map. Disruption of the operon leads to loss of a 22-kDa cytochrome c from membrane preparations. The structure of the putative protein products of the qcr operon suggests a protein complex that is closely related to but distinct from known cytochrome bc1 and b6f complexes, which catalyze electron transfer from a quinol to a c-type cytochrome or to plastocyanin. QcrA is similar to Rieske-type iron-sulfur proteins; QcrB is similar in size and sequence to b-type cytochromes from b6f complexes; and QcrC has a novel structure that resembles a fusion of a subunit IV (found in b6f complexes) to a cytochrome c. Transcription of the operon is induced at the end of exponential growth from a sigma A-like promoter. This transition state induction appears to be dependent on the downregulation of abrB expression, which is mediated by Spo0A activation. As bacteria move from the transition state into sporulation, transcription of the operon is reduced in a sigma F-dependent manner.

Membrane-bound Bacillus cytochromes c and their phylogenetic position among bacterial class I cytochromes c

Gram-positive bacteria lack a periplasmic compartment and contain only membrane-bound cytochromes c. There are at least two types. One is found in subunit II of cytochrome oxidase, and the other is small cytochrome c which is also membrane-bound because of an unprocessed signal sequence or post-translational acylation at the N-terminal end of the protein. These Bacillus cytochromes c are compared with known class I cytochromes c, and a phylogenetic tree has been constructed by the neighbour-joining method.

Cytochrome c-551 of the thermophilic bacterium PS3, DNA sequence and analysis of the mature cytochrome

The structural gene for cytochrome c-551 was isolated from genomic DNA of the thermophilic bacterium PS3. The amino acid sequence of cytochrome c-551 as deduced from the DNA sequence consists of 111 amino acid residues and contains one heme c-binding site (-CASCH-) located approximately in the middle of the polypeptide. The N-terminus of isolated cytochrome c-551 was blocked, but treatment with Rhizopus lipase and molecular weight measurement of the mature and lipase-treated forms by ion spray mass spectroscopy suggest that the mature c-551 may have 93 or 94 amino acid residues with a diacylated glycerol-cysteine at the N-terminal region. The first 17 or 18 amino acid residues in the N-terminal region of the nascent polypeptide, rich in hydrophobic and basic amino acid residues, may be a signal peptide to translocate the major portion of cytochrome c-551 to the extracellular surface and to be processed. Similarity of amino acid sequence of this protein is discussed in relation to other c-type cytochromes of bacilli as well as bacterial small cytochromes c such as Pseudomonas aeruginosa cytochrome c-551 and cytochrome c6 of cyanobacteria.

Physico-chemical characterisation of membrane-bound and water-soluble forms of Bacillus subtilis cytochrome c-550

Cytochrome c-550 of the Gram-positive bacterium, Bacillus subtilis, is a membrane-bound 13-kDa protein encoded by the cccA gene. The cytochrome has been proposed to be comprised of an N-terminal membrane anchor domain (about 30 residues) which spans the cytoplasmic membrane in an alpha-helical conformation and a C-terminal heme domain (about 70 residues) which is located on the outside of the cytoplasmic membrane. Cytochrome c-550 was purified in the presence of Triton X-100 and characterised. In the reduced state it shows absorption maxima at 415, 521, 550 nm and in the oxidised state a Soret band at 408 nm and a weak band at about 695 nm. The latter absorption band, together with data from amino acid sequence comparisons, strongly suggest His64 and Met99 as the fifth and sixth axial ligands to the heme iron in cytochrome c-550. The midpoint redox potential of the cytochrome, +178 mV, was pH-independent in the pH range 6.0-7.9. Oxidised cytochrome c-550 showed an EPR signal at gmax = 3.41, which is unusual for low-spin cytochromes c with His/Met axial ligation. The heme domain was isolated as a tryptic fragment of 74 residues and as a protein-A-cytochrome-c-550 hybrid protein. Both these forms were water-soluble and showed thermodynamic and spectroscopic properties indistinguishable from the membrane-bound form of cytochrome c-550 and are suitable for structural analysis of the heme domain by X-ray crystallography or NMR techniques. Polypeptide analysis of the membrane-bound and water-soluble tryptic fragment confirmed that B. subtilis cytochrome c-550 in the membrane consists of 120 amino acid residues and has a two-domain structure.

Metabolic pathways in Paracoccus denitrificans and closely related bacteria in relation to the phylogeny of prokaryotes

Denitrification and methylotrophy in Paracoccus denitrificans are discussed. The properties of the enzymes of denitrification: the nitrate-nitrite antiporter, nitrate reductase, nitrite reductase, nitric oxide reductase and nitrous oxide reductase are described. The genes for none of these proteins have yet been cloned and sequenced from P. denitrificans. A number of sequences are available for enzymes from Escherichia coli, Pseudomonas stutzeri and Pseudomonas aeruginosa. It is concluded that pathway specific c-type cytochromes are involved in denitrification. At least 40 genes are involved in denitrification. In methanol oxidation at least 20 genes are involved. In this case too pathway specific c-type cytochromes are involved. The sequence homology between the quinoproteins methanol dehydrogenase, alcoholde-hydrogenase and glucose dehydrogenase is discussed. This superfamily of proteins is believed to be derived from a common ancestor. The moxFJGI operon determines the structural components of methanol dehydrogenase and the associated c-type cytochrome. Upstream of this operon 3 regulatory proteins were found. The moxY protein shows the general features of a sensor protein and the moxX protein those of a regulatory protein. Thus a two component regulatory system is involved in both denitrification and methylotrophy. The phylogeny of prokaryotes based on 16S rRNA sequence is discussed. It is remarkable that the 16S rRNA of Thiosphaera pantotropha is identical to that of P. denitrificans. Still these bacteria show a number of differences. T. pantotropha is able to denitrify under aerobic circumstances and it shows heterotrophic nitrification. Nitrification and heterotrophic nitrification are found in species belonging to the beta-and gamma-subdivisions of purple non-sulfur bacteria. Thus the occurrence of heterotrophic nitrification in T. pantotropha, which belongs to the alpha-subdivision of purple non-sulfur bacteria is a remarkable property. Furthermore T. pantotropha contains two nitrate reductases of which the periplasmic one is supposed to be involved in aerobic denitrification. The nitrite reductase is of the Cu-type and not of the cytochrome cd1 type as in P. denitrificans. Also the cytochrome b of the Qbc complex of T. pantotropha is highly similar to its counterpart in P. denitrificans. It is hypothesized that the differences between these two organisms which both contain large megaplasmids is due to a combination of loss of genetic information and plasmid-coded properties. The distribution of a number of complex metabolic systems in eubacteria and in a number of species belonging to the alpha-group of purple non sulphur bacteria is reviewed.(ABSTRACT TRUNCATED AT 400 WORDS)

Sequence variability in bacterial cytochromes c

Cytochromes c are proteins that can be defined both phenotypically and by their possession of a characteristic sequence motif. Many sequences from bacterial sources are known, and new ones are being reported every year. An analysis can be made as to what fraction of new sequences are members of already known classes or subclasses, and how many map into previously uninhabited regions of sequence space.