Mitochondrial cytochrome b: evolution and structure of the protein

Esposti, Mauro Degli; Vries, Simon de; Crimi, Massimo; Ghelli, Anna; Patarnello, Tomaso; Meyer, Axel

doi:10.1016/0005-2728(93)90197-n

Cited by 375 publications

(317 citation statements)

References 218 publications

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“…We assume that these deletions or insertions may be corrected by the RNA editing process, possibly by adding zero, one, or two U residues just downstream of the position 22 bp in the edited region. This assumption is supported by the observations that (1) non-edited regions of all tested species/strains encoded a highly homologous stretch of 351 amino acids, (2) most amino acid substitutions are biochemically conservative, and (3) conserved amino acids in a wide variety of species (Degli Esposti et al 1993) were also conserved in all the species/strains analysed in this study. The fact that most of the amino acid substitutions were found in the transmembrane regions is congruent with previous studies of the Cyt b gene of different species.…”

Section: Phylogenetic Trees Inferred From Cyt B Gene Sequencessupporting

confidence: 75%

“…The fact that most of the amino acid substitutions were found in the transmembrane regions is congruent with previous studies of the Cyt b gene of different species. (Degli Esposti et al 1993 ;Farias et al 2001).…”

Section: Phylogenetic Trees Inferred From Cyt B Gene Sequencesmentioning

confidence: 99%

“…The cytochrome b (Cyt b) gene is contained in the mitochondrial genome of a wide variety of living forms and encodes the central catalytic subunit of an enzyme present in the respiratory chain of mitochondria. The gene has been widely used for phylogenetic studies and identification of animals and plants (Irwin, Kocher & Wilson, 1991 ;Degli Esposti et al 1993).…”

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Sequence variation of the Cytochrome b gene of various human infecting members of the genus Leishmania and their phylogeny

et al. 2004

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S U M M A R YThe Cytochrome b (Cyt b) gene has proved to be useful for identification and classification of many mammals and plants. In order to evaluate the utility of this gene for discrimination of Leishmania parasites as well as for exploring their phylogenetic relationships, we determined the nucleotide sequences of the Cyt b gene from 13 human-infecting Leishmania species (14 strains) from the New and Old Worlds. The Cyt b genes, approximately 1080 base pairs, were found to be A/T rich, and their 5k terminal-editing regions were highly conserved. The nucleotide sequence variation among them was enough to discriminate parasite species; 245 nucleotide positions were polymorphic and 190 positions were parsimony informative. The phylogenetic relationships based on this gene, showed good agreement with the classification of Lainson & Shaw (1987) ) tropica complex and the placement of L. tarentolae in another genus. These data show that the Cyt b gene is useful for phylogenetic study of Leishmania parasites.

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Section: Phylogenetic Trees Inferred From Cyt B Gene Sequencessupporting

confidence: 75%

Section: Phylogenetic Trees Inferred From Cyt B Gene Sequencesmentioning

confidence: 99%

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confidence: 99%

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Sequence variation of the Cytochrome b gene of various human infecting members of the genus Leishmania and their phylogeny

et al. 2004

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“…There are numerous examples for proteins for which "reliable experimental information" obtained from different groups is contradictory. To list a few controversial cases: ( I ) nicotinic acetylcholine receptor channel: four a-helices versus two a-helices and two P-strands (Hucho et al, 1994); (2) P-type ATPases: 8 versus 10 a-helices (Stokes et al, 1994); (3) a-subunit of the FO channel Escherichia coli: topology our (Lewis et al, 1990) versus topology in (Bjorbaek et al, 1990); (4) mitochondrial cytochrome b: 7-9 a-helices (Degli Esposti et al, 1993). One consequence of this is that prediction methods are likely t o become more accurate as reliable experimental information about integral membrane proteins is being added to the databases.…”

Section: Accuracy Of Prediction Methodsmentioning

confidence: 99%

Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy

1996

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Previously, we introduced a neural network system predicting locations of transmembrane helices (HTMs) based on evolutionary profiles (PHDhtm, Rost B, Casadio R, Fariselli P, Sander C, 1995, Protein Sci 4:521-533). Here, we describe an improvement and an extension of that system. The improvement is achieved by a dynamic programming-like algorithm that optimizes helices compatible with the neural network output. The extension is the prediction of topology (orientation of first loop region with respect to membrane) by applying to the refined prediction the observation that positively charged residues are more abundant in extra-cytoplasmic regions. Furthermore, we introduce a method to reduce the number of false positives, i.e., proteins falsely predicted with membrane helices. The evaluation of prediction accuracy is based on a cross-validation and a double-blind test set (in total 131 proteins). The final method appears to be more accurate than other methods published: (1) For almost 89% (+.3%) of the test proteins, all HTMs are predicted correctly. (2) For more than 86% (*3%) of the proteins, topology is predicted correctly. (3) We define reliability indices that correlate with prediction accuracy: for one half of the proteins, segment accuracy raises to 98%; and for two-thirds, accuracy of topology prediction is 95%. (4) The rate of proteins for which HTMs are predicted falsely is below 2% (k 1070). Finally, the method is applied to 1,616 sequences of Haemophilus influenzae. We predict 19% of the genome sequences to contain one or moreHTMs. This appears to be lower than what we predicted previously for the yeast VI11 chromosome (about 25%).Keywords: .dynamic programming; genome analysis; Haemophilus influenzae; postprocessing neural network output; secondary structure prediction; structure prediction for integral membrane proteins; topology prediction for helical transmembrane proteins Integral membrane proteins comprise an important class of proteins for which experimental techniques for 3D structure determination are often not applicable. Fortunately, theoretical prediction of structural aspects is simpler for membrane proteins than for globular proteins because the lipid bilayer imposes strong constraints on the degrees of freedom for the 3D struc-

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“…The two cytochromes b (both with bis-histidine axial ligation) in quinol:cytochrome c reductase (complex III) have such a function. The arrange-ment of the heme groups in the membrane-integral domain of these two enzymes is, however, very different [43]. In quinol:-cytochrome c reductase the two heroes are ligated by only two transmembrane helices; each pair of histidines on the two helices are 13 14 residues apart.…”

Section: Implications From the Sequence Comparisons And The Modelmentioning

confidence: 99%

A structural moDAl for the membrane‐integral domain of succinate:quinone oxidoreductases

Hägerhäll¹,

Hederstedt²

1996

FEBS Letters

123

102

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Many succinate:quinone oxidoreductases in bacteria and mitochondria, i.e. succinate:quinone reductases and fumarate reductases, contain in the membrane anchor a cytochrome b whose structure and function is poorly understood. Based on biochemical data and polypeptide sequence information, we show that the anchors in different organisms are related despite an apparent diversity in polypeptide and heine composition. A general structural model for the membrane-integral domain of the anchors is proposed. It is an antiparallel four-helix bundle with a novel arrangement of hexa-coordinated protoheme IX. The structure can be applied to a larger group of membraneintegral cytochromes of b-type and has evolutionary and functional implications.

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Mitochondrial cytochrome b: evolution and structure of the protein

Cited by 375 publications

References 218 publications

Sequence variation of the Cytochrome b gene of various human infecting members of the genus Leishmania and their phylogeny

Sequence variation of the Cytochrome b gene of various human infecting members of the genus Leishmania and their phylogeny

Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy

A structural moDAl for the membrane‐integral domain of succinate:quinone oxidoreductases

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