Amino Acid Sequence Of Cytochrome Research Articles

Substitution Trends in the Mitochondrial Cytochrome B Protein Coding Gene and the Corresponding Changes in its Amino Acid Sequence in Catfish Species

The study describes the divergence trends in the partial segment cytochrome b gene (cyt. b) in six catfish species on the basis of the nucleotide substitutions and their location in the triplet codons of the resulting amino acid sequence. The nucleotide sequences of all six species were found A+T rich with average nucleotide frequencies as A: 28.6%; T: 29.3%; G: 13.6%; C: 28.5%, showing an antiguanine bias which was found strongest in R. rita. The transition substitution rate was found highest at 3rd codon position in all the species. The evolutionary divergence follows the trend as highest at 3rd codon position followed by 1st codon position and the least on 2 nd codon position among all species. When amino acid sequences of cytochrome b were aligned, only 12 sites were found with a total 29 amino acid substitutions. which is a resultant of the substitution trend of three codon positions. Majority of the amino acid substitutions were found synonymous and conservative. Three different variability trends are observed in the cyt. b gene which run simultaneously on three different codon positions of triplet codons. Nucleotide substitutions at three codon positions follows the order 3 rd (87) >1st (32) >2nd (03) the frequency of amino acid substitution follows the order 1 st (11) >3rd (04) >2 nd (02); and the frequency of non-conservative amino acid changes found as 2 nd (1:2) >1st (5:11) >3rd (1:4). The study has provided an in-depth understanding of the relative variability and substitution trends in the mitochondrial cytochrome b gene in catfish species at both DNA and protein level.

Amino acid sequence based on Cytochrome b gene in Kejobong goat and its genetic relationships among several local goats in Asia.

Aim:This study aimed to analyze the amino acid sequence of Cytochrome b (Cyt b) gene in Kejobong goat and its genetic relationships with local goats located in Asia.Materials and Methods:A total of 28 heads of Kejobong goat were purposively sampled. The deoxyribonucleic acid (DNA) was extracted from blood using gSYNC DNA mini kit (Geneaid Biotech Ltd.). Cyt b gene was amplified using polymerase chain reaction (PCR) method with CytbCapF and CytbCapR primers. The amplified PCR products were sequenced for further analysis.Results:There were a total 377 amino acid sequences translated from 1140 base pair (bp) of Cyt b gene, 99.20% of it were monomorphic, amino acid alterations were found at site 16th, 121st, and 231st, and Kejobong goat was in the same cluster with Southeast Asian local goats.Conclusion:Most of the amino acid sequence on Cyt b gene in Kejobong goat is monomorphic (99.20%), only a few nucleotide mutations were found that causing amino acid alteration in three sites (0.80%). Kejobong goat has a close genetic relationship to several local goats in Southeast Asian.

Exceptional longevity and exceptionally high metabolic rates in anthropoid primates are linked to a major modification of the ubiquinone reduction site of cytochrome b.

The maximal lifespan of Anthropoid primates (monkeys, apes and humans) exceed the lifespan of most other mammals of equal body mass. Unexpectedly, their exceptional longevity is associated with exceptionally high metabolic rates, in apparent contradiction to the Free Radical Theory of Aging. It was therefore suggested that in anthropoid primates (and several other taxa of mammals and birds) the mitochondrial electron transport complexes evolved to modify the relationship between basal electron transport and superoxide generation to allow for the evolution of exceptional longevity. Cytochrome b, the core protein of the bc1 complex is a major source of superoxide. The amino-acid sequence of cytochrome b evolved much faster in anthropoid than in prosimian primates, and most other mammals, resulting in a large change in the amino-acids composition of the protein. As a result of these changes cytochrome b in anthropoid primates is significantly less hydrophobic and contains more polar residues than other primates and most other mammals. Most of these changes are clustered around the reduction site of uboiquinone. In particular a key positively charged residue, arginine 313, that interacts with propionate D of heme bH, and thus raises its redox potential, is substituted in anthropoid primates with the neutral residue glutamine, most likely resulting in a lower redox potential of heme bH and faster reduction of ubiquinone at high proton motive force. It is suggested that these changes contribute to the observed increased rates of basal metabolism and reduce the rates of superoxide production, thus allowing for increased lifespan.

Molecular genetic evidence of a deep phylogenetic discontinuity between the asian and european races of pygmy wood mouse based on the mitochondrial cytochrome b gene variation

The variation of mitochondrial DNA (mtDNA) cytochrome b gene sequences of pygmy wood mouse Sylvaemus uralensis (Pallas, 1811) from local populations of European Russia, West Siberia, and neighboring countries (Moldova, Kazakhstan, Uzbekistan, and Turkmenistan) has been studied. Phylogenetic analysis based on our results and GenBank data revealed two clusters of haplotypes: the Western clade, which was reliably subdivided into two sequence groups, and the Eastern clade with no significant differentiation. The clusters corresponded exactly to the European and Asian races of pygmy wood mouse recognized previously on the basis of biochemical and karyotypic variation. We suppose that the Asian race can be considered as an independent allopatric species. This concept is supported by the following evidence: the high interrace divergence level suggesting more than 1 Ma of divergent evolution, the absence of common haplotypes and the hiatus between the main peaks of the mismatch distribution, difference in the codon usage frequencies, fixed nucleotide substitutions in cyt b, as well as different amino acid sequences of cytochrome b. Only specimens of the western phylogenetic lineage should be classified as S. uralensis (Pallas, 1811), while S. tokmak, according to its first description (Severtsov, 1873), may be considered as the species uniting specimens of the eastern phylogenetic lineage.

Cytochrome f from the Antarctic psychrophile, Chlamydomonas raudensis UWO 241: structure, sequence, and complementation in the mesophile, Chlamydomonas reinhardtii

Although cytochrome f from the Antarctic psychrophile, Chlamydomonas raudensis UWO 241, exhibits a lower apparent molecular mass (34 kD) than that of the mesophile C. reinhardtii (41 kD) based on SDS-PAGE, both proteins are comparable in calculated molecular mass and show 79% identity in amino acid sequence. The difference in apparent molecular mass was maintained after expression of petA from both Chlamydomonas species in either E. coli or a C. reinhardtii DeltapetA mutant and after substitution of a unique third cysteine-292 to phenylalanine in the psychrophilic cytochrome f. Moreover, the heme of the psychrophilic form of cytochrome f was less stable upon heating than that of the mesophile. In contrast to C. raudensis, a C. reinhardtii DeltapetA mutant transformed with petA from C. raudensis exhibited the ability to undergo state transitions and a capacity for intersystem electron transport comparable to that of C. reinhardtii wild type. However, the C. reinhardtii petA transformants accumulated lower levels of cytochrome b ( 6 ) /f complexes and exhibited lower light saturated rates of O(2) evolution than C. reinhardtii wild type. We show that the presence of an altered form of cytochrome f in C. raudensis does not account for its inability to undergo state transitions or its impaired capacity for intersystem electron transport as previously suggested. A combined survey of the apparent molecular mass, thermal stability and amino acid sequences of cytochrome f from a broad range of mesophilic species shows unequivocally that the observed differences in cytochrome f structure are not related to psychrophilly. Thus, caution must be exercised in relating differences in amino acid sequence and thermal stability to adaptation to cold environments.

The neutral theory of molecular evolution.

IN 1966, I became interested in the amino acid sequences of cytochrome c molecules ([Jukes 1966][1]). I noted that these sequences differed in the cytochromes c of various species to an extent that seemed unnecessary from the standpoint of their function. I stated, “The changes produced in

Phylogenetic relationships of fungal cytochromes c.

The CYC1 gene encoding cytochrome c in the yeast Candida albicans was cloned by complementation of a cytochrome c-deficient mutant of Saccharomyces cerevisiae, and its DNA sequence was determined. The analysis of the amino acid sequences of cytochrome c from 14 fungal species and two isoforms from S. cerevisiae revealed sequences unique to fungi, and revealed a phylogenetic relationship with a pronounced divergence between Schizosaccharomyces pombe and other ascomycetous budding yeast.

A reinvestigation of the covalent structure of Pseudomonas aeruginosa cytochrome c peroxidase

The amino acid sequence of cytochrome c peroxidase from Pseudomonas aeruginosa has been determined using classical chemical degradation techniques combined with accurate mass analysis of all the generated peptides. The sequence obtained is composed of 346 amino acids and confirms the recently published cDNA-derived sequence except at one position [Ridout et al. (1995) FEBS Lett. 365, 152–154]. Based on this sequence, we propose a new model for the binding of the peroxide and the cytochrome electron donor to CCP which is in essence the reverse of the one proposed by Ellfolk et al. [Biochim. Biophys. Acta 1080 (1991) 175–178].

A New Type of Cytochrome c from Synechocystis PCC6803

Summary A gene encoding a c-type cytochrome, designated cytM , was discovered 3.4 kbp downstream from the desA gene in the genome of Synechocystis PCC6803. The amino acid sequence derived from the nucleotide sequence exhibits about 35 % similarity to the amino acid sequences of cytochromes c -553 from other cyanobacteria and eukaryotic algae, but it also includes regions typical of soluble c -type cytochromes from eukaryotic mitochondria. The molecular mass of the putative mature protein was estimated to be 8.3 kDa, and the isoelectric point was calculated to be 7.3. The amino-terminal region of the putative product of the cytM gene is hydrophobic, suggesting that this domain may be a transit peptide or a membrane anchor. Both photosynthesis and respiration in a mutant with a disrupted cytM gene were as efficient as they were in the wild-type strain.

Cloning and correct expression in E. coli of the petJ gene encoding cytochrome c6 from Synechocystis 6803

Cytochrome c 6 from the cyanobacterium Synechocystis 6803 has been isolated and purified to electrophoretic homogeneity. The gene coding for such a heme protein ( petJ) has been cloned and properly expressed in E. coli. This procedure yields a protein preparation completely identical to that obtained from the cyanobacterial cells. The N-terminal amino acid sequences of cytochrome c 6 synthesized in both organisms are the same, thus allowing us to conclude that the petJ gene product is correctly processed in E. coli. To the best of our knowledge, this is the first time that any cytochrome C 6 is produced in the enterobacterium. The identical physicochemical and kinetic properties of the proteins isolated from both sources confirm that expression of the petJ gene in E. coli is an adequate tool to address the study of Synechocystis cytochrome c 6, by site-directed mutagenesis in a parallel way to that carried out with plastocyanin from the same organism.

Amino acid sequences of cytochromes c 2 and c′ from the moderately halophilic purple phototrophic bacterium Rhodospirillum salexigens

Rhodospirillum salexigens is a moderately halophilic 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 c 2, similar in size to mitochondrial cytochrome c. While clearly of the same 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 c 2 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 occured more than once in purple bacteria.

The Phylogenetic Utility of Cytochrome b: Lessons from Bufonid Frogs

The mitochondrial cytochrome b gene is widely used in systematic studies to resolve divergences of many different ages. To investigate phylogenetic relationships among frogs of the large family Bufonidae, and to explore the utility of cytochrome b for this purpose, approximately one-third of the gene was sequenced from representatives of this group. Samples were chosen to represent a range of divergence levels within Bufonidae: (1) deep (= old), among species from around the world; (2) middle, among North American species; and (3) shallow (= young), within a single species group (the Bufo boreas group). The inferred amino acid sequences of cytochrome b are highly similar in these frogs although most pairwise comparisons of the nucleotide sequences are 15-20% different. Consequently insufficient information is available to generate robust phylogenetic hypotheses for the older divergences; silent differences are saturated and yet almost no informative replacement differences exist. Among the younger divergences, silent differences are not saturated and some resolution is possible. These results show that (1) the amino acid sequence of cytochrome b evolves differently in Bufonidae than expected based on other vertebrates, (2) it consequently provides surprisingly little information about old divergences in Bufonidae, and (3) phylogenetic studies applying particular genes to new groups should begin with preliminary surveys of exemplar taxa representing the range of divergence times within the group to estimate the likely phylogenetic utility of that gene in that group.

Incipient mitochondrial evolution in yeasts: II. The complete sequence of the gene coding for cytochrome b in Saccharomyces douglasii reveals the presence of both new and conserved introns and discloses major differences in the fixation of mutations in evolution

We have determined the complete sequence of the mitochondrial gene coding for cytochrome b in Saccharomyces douglasii. The gene is 6310 base-pairs long and is interrupted by four introns. The first one (1311 base-pairs) belongs to the group ID of secondary structure, contains a fragment open reading frame with a characteristic GIY … YIG motif, is absent from Saccharomyces cerevisiae and is inserted in the same site in which introns 1 and 2 are inserted in Neurospora crassa and Podospora anserina, respectively. The next three S. douglasii introns are homologous to the first three introns of S. cerevisiae, are inserted at the same positions and display various degrees of similarity ranging from an almost complete identity (intron 2 and 4) to a moderate one (intron 3). We have compared secondary structures of intron RNAs, and nucleotide and amino acid sequences of cytochrome b exons and intron open reading frames in the two Saccharomyces species. The rules that govern fixation of mutations in exon and intron open reading frames are different: the relative proportion of mutations occurring in synonymous codons is low in some introns and high in exons. The overall frequency of mutations in cytochrome b exons is much smaller than in nuclear genes of yeasts, contrary to what has been found in vertebrates, where mitochondrial mutations are more frequent. The divergence of the cytochrome b gene is modular: various parts of the gene have changed with a different mode and tempo of evolution.

The primary structure of cytochrome c from the nematode Caenorhabditis elegans

The complete amino acid sequence of cytochrome c from the nematode Caenorhabditis elegans was determined. The native protein displays the same spectral properties in the oxidized and reduced states as horse heart cytochrome c. The apoprotein consists of 110 amino acid residues and differs from human cytochrome c by 44 substitutions, one internal deletion, five N-terminal additions and two C-terminal additions. One of the substitutions is the replacement of an 'invariant' phenylalanine residue at position 15 by tyrosine. The N-terminal sequence extension contains a short peptide motif, which is highly homologous with a peptide fragment present at the N-terminus of annelid and insect cytochrome c sequences. From the number of amino acid changes and the evolutionary rate of cytochrome c it would appear that nematodes diverged from a line leading to man about 1.4 billion years ago. When similar data based on the amino acid sequences of the histones H1, H2A, H2B and H3 are taken into account, the average estimate is 1.1 +/- 0.1 billion years.

Cross-linking studies of the cholesterol hydroxylation system from bovine adrenocortical mitochondria.

Cytochrome P-450SCC and adrenodoxin were cross-linked with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. The sample containing 94% of cross-linked complex and 6% of free cytochrome P-450SCC was obtained after purification on cholate-Sepharose. Cytochrome P-450SCC in cross-linked complex completely preserves its high-spin form in the presence of Tween 20 or pregnenolone. Utilization of radioactively labelled adrenodoxin, chemical cleavage of cytochrome P-450SCC from cross-linked complex with o-iodosobenzoic acid and HPLC for separation of peptides allow us to conclude that the complex of cytochrome P-450SCC with adrenodoxin was cross-linked through two amino acid sequences of cytochrome P-450SCC-Leu-88-Thr-107 and Leu-368-Gly-416. The cross-linked complex of adrenodoxin reductase, adrenodoxin and cytochrome P-450SCC with an apparent molecular mass of 114 kDa was obtained with N-succinimidyl-6-(4'-azido-2'-nitrophenylamino)hexanoate. The composition of cross-linked complex was determined by immunoblotting and by evaluation of radioactivity using preliminary N-ethyl[2,3-14C]maleimide-modified adrenodoxin. From this data it appears that the ternary complex may exist in solution.

The amino acid sequence of cytochrome c553 from Microcystis aeruginosa

Cytochrome c 553 is an electron donor to P700 in the photosynthetic electron transfer chain of cyanobacteria and eukaryotic algae. We have purified this cytochrome from the cyanobacterium Microcystis aeruginosa and determined its amino acid sequence. When the amino acid sequence of this protein is compared to sequences of cytochromes c 553 from other organisms, one sees that the evolution of net charge is more pronounced than the evolution of overall structure, further documenting a pronounced shift in the isoelectric point of this protein during the evolution of cyanobacteria. Cyanobacteria and algae also contain cytochrome c 550 ( M r 15,500) which is quite different from cytochrome c 553 ( M r 10,500). When the amino acid sequence of cytochrome c 553 is compared to that of cytochrome c 550, two regions of similar sequence are recognized.

Amino acid sequence of cytochrome c fromAspergillus niger

Cytochrome c from Aspergillus niger consists of two forms, a major one (80%) with 111 amino acid residues and a minor one (20%) with 108 residues, missing the three N-terminal residues of the major one. The primary sequence of A. niger cytochrome c was determined by standard spinning-cup Edman degradation of purified peptides and of pairs of peptides, from which the desired sequence was readily deduced by subtraction of common sequencies. Except for the extension and some variability at the N-terminal sequence, the A. niger protein conforms well with other cytochrome c structures.

CDNA and deduced amino acid sequences of cytochrome c from Chlamydomonas reinhardtii: unexpected functional and phylogenetic implications.

We have isolated complementary DNA (cDNA) clones for apocytochrome c from the green alga Chlamydomonas reinhardtii and shown that they are encoded by a single nuclear gene termed cyc. Cyc mRNA levels are found to depend primarily on the presence of acetate as a reduced carbon source in the culture medium. The deduced amino acid sequence shows that, apart from the probable removal of the initiating methionine, C. reinhardtii apocytochrome c is synthesized in its mature form. Its structure is generally similar to that of cytochromes c from higher plants. Several punctual deviations from the general pattern of cytochrome c sequences that is found in other organisms have interesting structural and functional implications. These include, in particular, valines 19 and 39, asparagine 78, and alanine 83. A phylogenetic tree was constructed by the matrix method from cytochrome c data for a representative range of species. The results suggest that C. reinhardtii diverged from higher plants approximately 700-750 million years ago; they also are not easy to reconcile with the current attribution of Chlamydomonas reinhardtii and Enteromorpha intestinalis to a unique phylum, because these two species probably diverged from one another at about the same time as they diverged from the line leading to higher plants.

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.