The amino acid sequence of cytochrome c' from the purple sulphur bacterium Chromatium vinosum

Martin David Kamen (1913-2002): discoverer of carbon 14, and of new cytochromes in photosynthetic bacteria

Martin Kamen was a giant of twentieth century science. Trained as a physical chemist, he was the co-discoverer of radioactive Carbon 14, which has transformed many areas of science as a tracer and as a way to date artifacts. He later switched to the study of metabolism and biochemistry and made important contributions to the understanding of nitrogen fixation and photosynthesis. Finally, he studied cytochromes, primarily from anoxygenic photosynthetic bacteria.

Structural and functional insights into thermally stable cytochrome c' from a thermophile

Thermophilic Hydrogenophilus thermoluteolus cytochrome c′ (PHCP) exhibits higher thermal stability than a mesophilic counterpart, Allochromatium vinosum cytochrome c′ (AVCP), which has a homo‐dimeric structure and ligand‐binding ability. To understand the thermal stability mechanism and ligand‐binding ability of the thermally stable PHCP protein, the crystal structure of PHCP was first determined. It formed a homo‐dimeric structure, the main chain root mean square deviation (rmsd) value between PHCP and AVCP being 0.65 Å. In the PHCP structure, six specific residues appeared to strengthen the heme‐related and subunit–subunit interactions, which were not conserved in the AVCP structure. PHCP variants having altered subunit–subunit interactions were more severely destabilized than ones having altered heme‐related interactions. The PHCP structure further revealed a ligand‐binding channel and a penta‐coordinated heme, as observed in the AVCP protein. A spectroscopic study clearly showed that some ligands were bound to the PHCP protein. It is concluded that the dimeric PHCP from the thermophile is effectively stabilized through heme‐related and subunit–subunit interactions with conservation of the ligand‐binding ability.

Brief Summary

We report the X‐ray crystal structure of cytochrome c′ (PHCP) from thermophilic Hydrogenophilus thermoluteolus. The high thermal stability of PHCP was attributed to heme‐related and subunit–subunit interactions, which were confirmed by a mutagenesis study. The ligand‐binding ability of PHCP was examined by spectrophotometry. PHCP acquired the thermal stability with conservation of the ligand‐binding ability. This study furthers the understanding of the stability and function of cytochromes c.

PDB Code(s): 5B3I

The distance between bacterial species in sequence space

Despite the revolution caused by information from macromolecular sequences, the basis of bacterial classification remains the genus and the species. How do these terms relate to the variety of bacteria that exist on earth? In this paper, the inter- and intraspecies differences in amino acid sequence of several bacterial electron transport proteins, cytochromes c, and blue copper proteins are compared. For the soil and water organisms studied, bacterial species can be classed as "tight" when there is little intraspecies variation, or "loose" when this variation is large. For this set of proteins and organisms, interspecies variation is much larger than that within a species. Examples of "tight" species are Pseudomonas aeruginosa and Rhodobacter sphaeroides, while Pseudomonas stutzeri and Rhodopseudomonas palustris are loose species. The results are discussed in the context of the origin and age of bacterial species, and the distribution of genomes in "sequence space." The situation is probably different for commensal or pathogenic bacteria, whose population structure and evolution are linked to the properties of another organism.

Molecular cloning and sequencing of cytochrome c' from the phototrophic purple sulfur bacterium Chromatium vinosum

The gene for cytochrome c' from Chromatium vinosum was cloned from a HindIII-SalI digest of genomic DNA. A 1.4 kbp fragment containing the gene was sequenced in both directions using the Sanger dideoxy method. The cytochrome c' gene codes for a 154-residue peptide, of which the last 131 amino acids match the previously determined sequence of the protein. The remaining 23 residues represent a signal sequence that is cleaved from the polypeptide upon translocation to the periplasmic space. An additional open reading frame on the other strand of the fragment codes for a peptide that contains four regions that are homologous to corresponding regions of the cytochrome b-type subunit of several Ni-Fe hydrogenases.

Amino acid sequences of cytochromes c2 and c' from the moderately halophilic purple phototrophic bacterium Rhodospirillum salexigens

Rhodospirillum salexigens is a moderately halophilic purple phototrophic bacterium which grows optimally in 8% NaCl. The amino acid sequences of the two principal soluble cytochromes c have been determined. One of these is a cytochrome c2, similar in size to mitochondrial cytochrome c. While clearly of the same sequence class as mitochondrial cytochrome c and the proteins from several other Gram-negative bacteria, it does not show particular affinity to any already known sequence in terms of the percentage sequence identity. The other protein is a cytochrome c', but is also a divergent member of this widespread group. The lack of appreciable sequence identity to other species is probably due to a limit of divergence which has been reached for the majority of purple bacterial species. However, the numbers of insertions and deletions and their locations in cytochromes c2 and c' suggest that R salexigens may be related to Rhodospirillum molischianum. Like other electron transport proteins from halophiles, both of these cytochromes are notable for their high content of arginine as compared with lysine and both are acidic. However, they do not show any particular sequence homology to electron transport proteins that have been characterized from the extremely halophilic phototrophes of the genus Ectothiorhodospira. Thus, it appears that adaptation to halophilic habitats has independently occurred more than once in purple bacteria.

Amino acid sequences of Euglena viridis ferredoxin and cytochromes c

The Order Euglenida comprises many species and perhaps 40 genera, but almost all biochemical and genetic studies have been limited to a single species. Euglena gracilis, because of its ease of growth in the laboratory. Sequence studies of chloroplast and mitochondrial proteins from E. gracilis show that they have diverged widely from other eukaryotic lines. In the present paper we report the sequences of three proteins from another euglenoid, Euglena viridis, using material isolated from a natural bloom. The mitochondrial cytochrome c shows more than 90% sequence identity with that from E. gracilis, and contains the same characteristic features. The chloroplast cytochrome c6 has diverged to a greater extent and shows only 77% identity. The chloroplast ferredoxin from E. viridis is similar in sequence to those of cyanobacteria and algal chloroplasts, with sequence identities of up to 75%. Details of the purification, analysis and sequence determination experiments on the peptides have been deposited as Supplementary Publication SUP 50163 (32 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1991) 273, 5.

Rattlesnake cytochrome c. A re-appraisal of the reported amino acid sequence

The amino acid sequence of rattlesnake cytochrome c was originally reported in 1965, and was one of the earlier sequences to be studied. When compared with other mitochondrial cytochromes c, the snake sequence was soon seen to be anomalous. There were several positions in which the snake protein resembled human cytochrome c, although comparable anomalies were not reported for the protein from other reptiles such as lizard and turtle. Explanations of these results have included accelerated evolution in the snake lineage, paralogy rather than orthology, and faulty determination of the sequence, and the rattlesnake is now often omitted from cytochrome c phylogenetic trees. We have re-investigated the sequence of the snake protein, and believe that the correct sequence differs in nine places from that used for evolutionary theorizing since 1965. Four of these differences are near the haem-attachment site, in a region that was only analysed for amino acid composition in the original investigation. The other five differences are towards the C-terminus of the molecule, and can be explained as being due to the wrong ordering of amino acids within peptides that had been satisfactorily purified. Despite these corrections, the rattlesnake cytochrome c sequence still more closely resembles human cytochrome c than it does that of any other protein we know. We believe that this is an example of convergent evolution, although it does appear that there has been accelerated change in the line connecting the rattlesnake to the ancestral vertebrate line. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50162 (16 pages) at the British Library Document Supply Centre, Boston Spa. Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1991) 273, 5.

Two distinct azurins function in the electron-transport chain of the obligate methylotroph Methylomonas J

Methylomonas J is an obligate methylotroph although it is unable to grow on methane. Like Pseudomonas AM1, it produces two blue copper proteins when growing on methylamine, one of which is the recipient of electrons from the methylamine dehydrogenase. When grown on methanol, only the other blue copper protein is produced. We have determined the amino acid sequences of these blue copper proteins, and show that they are both true azurins. The sequences are clearly homologous to those of the proteins characterized from fluorescent pseudomonads and various species of Alcaligenes, and can be aligned with them and with each other without the need to postulate any internal insertions or deletions in the sequences. The iso-1 azurin, the one produced during both methanol and methylamine growth, shows 59-65% identity with these other azurins, whereas the iso-2 protein shows only 47-53% identity. The proteins show 52% identity with each other. The two functionally equivalent blue copper proteins from Pseudomonas AM1 belong to two sequence classes that are quite distinct from the true azurins. Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50151 (23 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1989) 257, 5.

Amino acid sequences of cytochrome c-554(548) and cytochrome c' from a halophilic denitrifying bacterium of the genus Paracoccus

The amino acid sequences of the cytochromes c-554(548) and c' from the moderately halophilic bacterium Paracoccus sp., I.A.M. 203 (= A.T.C.C. 12084, N.C.I.B. 8669) have been determined. Cytochrome c-554(548) consists of a single polypeptide chain of 83 residues, and dimerizes strongly. The most similar protein of known sequence is the N-terminal half of the dihaem cytochrome c4, and other related proteins include the cytochrome c-554(547) of Thiobacillus neapolitanus and the cytochrome c-553 of Desulfovibrio vulgaris. Cytochrome c', which has a single polypeptide chain of 132 residues, is similar in sequence to cytochromes c' from phototrophic and denitrifying bacteria, but only shows about 36% sequence identity to the most similar protein of known sequence. Both of the Paracoccus proteins have a considerable excess of acidic amino acid side chains over basic ones, and a higher proportion of their basic amino acids is arginine than is usual in cytochromes c. Both these characteristics seem to be adaptations to increase the stability of the proteins in an environment of high ionic strength. Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication 50140 (24 pp.) at the British Library (Lending Division), Boston Spa, Yorkshire LS23 7BQ, U.K. from which copies are available on prepayment.

The amino acid sequence of the cytochrome c2 from the phototrophic bacterium Rhodopseudomonas globiformis

The amino acid sequence of the principal soluble cytochrome c from the phototrophic acidophilic bacterium Rhodopseudomonas (or Rhodopila) globiformis was determined. By the criteria of percentage sequence identity and fewness of internal insertions and deletions it is more similar in sequence to some mitochondrial cytochromes c than to any known bacterial cytochrome. The organism does not have any properties that commend it as being particularly similar to postulated prokaryotic precursors of the mitochondrion. We consider that the relatively high degree of sequence similarity is an instance of convergence, and is an example of the limitations that are imposed on attempts to deduce distant evolutionary relationships from sequence information. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50136 (12 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment [see Biochem. J. (1987) 241, 5].

The amino acid sequence of cytochrome c-555 from the methane-oxidizing bacterium Methylococcus capsulatus

The amino acid sequence of the cytochrome c-555 from the obligate methanotroph Methylococcus capsulatus strain Bath (N.C.I.B. 11132) was determined. It is a single polypeptide chain of 96 residues, binding a haem group through the cysteine residues at positions 19 and 22, and the only methionine residue is a position 59. The sequence does not closely resemble that of any other cytochrome c that has yet been characterized. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50131 (12 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment.

The primary structures of Pseudomonas AM1 amicyanin and pseudoazurin. Two new sequence classes of blue copper proteins

The amino acid sequences of two blue copper proteins from the pink facultative methylotroph Pseudomonas AM1 (N.C.I.B. 9133) were determined. They each consist of a single polypeptide chain and bind one copper atom. Amicyanin contains 99 and pseudoazurin 123 residues. Copper-binding sites, consisting of the side chains of two histidine, one cysteine and one methionine residues, can be recognized in each protein by analogy with azurin and plastocyanin, but the spacings of the ligand residues are different, and other sequence similarity is limited. Proteins that are in the pseudoazurin sequence class can be recognized in some strains of Alcaligenes, and probably also in Paracoccus denitrificans. Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50130 (23 pp.) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1985) 225, 5.

The amino acid sequence of the cytochrome c-554(547) from the chemolithotrophic bacterium Thiobacillus neapolitanus

An amino acid sequence is proposed for the cytochrome c-554(547) from the bacterium Thiobacillus neapolitanus N.C.I.B. 8539). It consists of a polypeptide chain of 91 residues, with a pair of haem-attachment cysteine residues at positions 15 and 18. There is similarity in sequence with each of the halves of the sequence of the dihaem cytochromes c4 and with a cytochrome c-554(548) from a halophilic strain of Paracoccus. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50127 (11 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1985) 225, 5.

The amino acid sequence of the dihaem cytochrome c4 from the bacterium Azotobacter vinelandii

An amino acid sequence is proposed for the cytochrome c4 from the bacterium Azotobacter vinelandii strain OP. It is a single polypeptide chain of 190 residues, with two sets of haem-attachment cysteine residues at positions 14/17 and 119/122. Proteins with similar sequences are also present in denitrifying pseudomonads. There is similarity in sequence between the two halves of the cytochrome c4 molecule, and each half also shows similarity to the sequences of certain monohaem cytochromes c isolated from organisms that are not obviously closely related to A. vinelandii. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50125 (17 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment.

Amino acid sequences of bacterial cytochromes c' and c-556

The cytochrome c' are electron transport proteins widely distributed in photosynthetic and aerobic bacteria. We report the amino acid sequences of the proteins from 12 different bacterial species, and we show by sequences that the cytochromes c-556 from 2 different bacteria are structurally related to the cytochromes c'. Unlike the mitochondrial cytochromes c, the heme binding site in the cytochromes c' and c-556 is near the COOH terminus. The cytochromes c-556 probably have a methionine sixth heme ligand located near the NH2 terminus, whereas the cytochromes c' may be pentacoordinate. Quantitative comparison of cytochrome c' and c-556 sequences indicates a relatively low 28% average identity.

Cytochromes c-556 from three genetic races of Agrobacterium. Purification and comparison of their properties

1. The soluble cytochromes c-556 from three strains of Agrobacterium tumefaciens, B6, II Chrys and Apple 185 have been purified to homogeneity. The strains are representative members of the three main genetic races of Agrobacterium. The purity of the final preparations was established by electrophoresis with an without sodium dodecyl sulphate, by analytical isoelectric focusing and ultracentrifugation, and by N-terminal analysis. 2. Properties of these cytochromes were compared wih those of cytochrome c-556 from A. tumefaciens, strain B2a, a member of the same genetic race as strain B6. The four cytochromes are monohaem proteins with molecular weights of about 12300 (determined by four different methods). The isoelectric points of those from strains B6 and B2a are identical at pH 5.5, but they differ from the cytochromes of the other genetic races: cytochrome c-556 from strain Apple 185 is more acidic (ph 5.2) and that from strain II Chrys more basic (pH 6.2). The cytochromes from strains b6 and B2a have very similar but not identical amino acid compositions; both of them differ more from Apple 185 than from II Chrys c-556. 3. Comparison of the tryptic, chymotryptic and thermolytic fingerprints of cytochrome c-556 from strains B2a and II Chrys reveals strong homology between the primary structures of these cytochromes. Therefore and because of the sequence identity of the first eight residues, the cytochromes c-556 from strains II Chrys, B6 and B2a are most likely C-terminal haem-bound, of the same type as the cytochrome c' from photosynthetic bacteria.