Mitochondrial cytochrome b: evolution and structure of the protein

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

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Volume 1143, Issue 3, 26 July 1993, Pages 243-271

https://doi.org/10.1016/0005-2728(93)90197-N Get rights and content

Abstract

Cytochrome b is the central redox catalytic subunit of the quinol: cytochrome c or plastocyanin oxidoreductases. It is involved in the binding of the quinone substrate and it is responsible for the transmembrane electron transfer by which redox energy is converted into a protonmotive force. Cytochrome b also contains the sites to which various inhibitors and quinone antagonists bind and, consequently, inhibit the oxidoreductase.

Ten partial primary sequences of cytochrome b are presented here and they are compared with sequence data from over 800 species for a detailed analysis of the natural variation in the protein. This sequence information has been used to predict some aspects of the structure of the protein, in particular the folding of the transmembrane helices and the location of the quinone- and heme-binding pockets.

We have observed that inhibitor sensitivity varies greatly among species. The comparison of inhibition titrations in combination with the analysis of the primary structures has enabled us to identify amino acid residues in cytochrome b that may be involved in the binding of the inhibitors and, by extrapolation, quinone/quinol.

The information on the quinone-binding sites obtained in this way is expected to be both complementary and supplementary to that which will be obtained in the future by mutagenesis and X-ray crystallography.

References (256)

G. Hauska et al.
Biochim. Biophys. Acta
(1983)
S. De Vries et al.
Biochim. Biophys. Acta
(1987)
A. Crofts et al.
Biochim. Biophys. Acta
(1992)
W.R. Widger et al.
P. Mitchell
FEBS Lett.
(1975)
M. Wikström et al.
R.W. Mansfield et al.
Biochim. Biophys. Acta
(1990)
C.H. Yun et al.
J. Biol. Chem.
(1992)
M. Saraste
FEBS Lett.
(1984)
R. Brasseur
J. Biol. Chem.
(1988)

J. Mol. Evol.

(1989)

P.L. Dutton

B.L. Trumpower

Microbiol. Rev.

(1990)

W.A. Cramer et al.

G. Hauska et al.

J. Bioenerg. Biomembr.

(1988)

P. Mitchell

P.R. Rich

J. Bioenerg. Biomembr.

(1986)

F. Daldal et al.

EMBO J

(1989)

B. Chance et al.

M. Degli Esposti et al.

Eur. J. Biochem.

(1989)

W.R. Widger et al.

A. Crofts et al.

M. Degli Esposti et al.

A. Crofts et al.

T.D. Kocher et al.

A. Meyer et al.

Nature

(1990)

A. Meyer et al.

J. Mol. Evol.

(1990)

D.M. Irwin et al.

J. Mol. Evol.

(1991)

Cited by (359)

Mutational landscape of mitochondrial cytochrome b and its flanking tRNA genes associated with increased mitochondrial DNA copy number and disease risk in children with autism
2024, Gene Reports
Autism, the severe form of Autism Spectrum Disorder (ASD), is a genetically heterogeneous wide spectrum of impairments characterized by social dysfunction, restricted contact, and communication. Out of 80 children (aged 3 to 10 years) enrolled, 50 were diagnosed with autism (according to M-CHAT-R), while the remaining 30 were healthy children. Lactic acid and ammonia levels were measured using an autoanalyzer and children with autism had significantly higher levels than controls. The Cytb and its adjacent tRNA genes for glutamine, threonine, and proline (MT-TE, MT-TT, MT-TP) were amplified by PCR, purified, and sequenced by Sanger sequencing. A total of 57 variants (19 non-synonymous and 31 synonymous SNPs in Cytb, and seven tRNA gene variants) were identified and Cytb-specific mtDNA copy numbers were determined. There was no significant association between any Cytb variants and disease outcomes, but three of them (15067T>C, 15202C>T, 15262T>C) were linked to higher lactic acid levels and two (14753C>T, 15262T>C) to higher ammonia levels. When docked with Cytb ligands PEE, Heme1, and Heme2, 15341T>C and 15773G>A had the most detrimental impact on protein structure, with higher RMSD than the reference protein complexes. The mtDNA copy number was significantly higher in children with autism than in healthy children, although after adjusting confounding factors the difference was found to be insignificant. Out of two detrimental variants, 15341T>C, along with two additional variants, 15049C>T and 15796T>C, were found to be associated with an increased Cytb-specific mtDNA copy number. Additionally, synonymous SNPs showed codon-usage variations (RSCU). Although no association of variants in Cytb and its adjacent tRNA gene was found with autism, a cluster of variants has been found to affect protein structure and translation rate (as indicated by alteration of RSCU values), which may impair normal activity of electron transport chain (ETC) which is reflected by the significant change in lactic acid and ammonia levels. Children with autism showed increased mtDNA copy number to compensate the impact of these mutational consequences. In conclusion, the electron transport chain complexes should be investigated further in a large sample size to strengthen this finding.
Molecular phylogenetic analysis of Echinococcus multilocularis from horses raised in Canada or Japan, using mitochondrial cytochrome b gene–targeted PCR
2024, Food and Waterborne Parasitology
Alveolar echinococcosis is a zoonotic disease caused by a larval-stage Echinococcus multilocularis infection. Geographical haplotyping targeting the parasite's mitochondrial cytochrome b (cob) gene has been reported for isolates from definitive and intermediate hosts (wild canids and rodents); however, there are limited reports on strain typing for the dead-end host, the horse, which could act as a sentinel for E. multilocularis. Accordingly, we investigated the diversity of E. multilocularis in isolates obtained from slaughtered Japanese and Canadian horses originating from the Iburi and Hidaka regions in Hokkaido and from Alberta, respectively, with PCR and haplogroup analyses targeting cob gene sequences obtained. Seventy horses were diagnosed with alveolar echinococcosis based on histopathology and cob-gene PCR testing. The E. multilocularis detected in these horses was classified as either an Asian (for Hokkaido-raised horses) or a European (for Alberta-raised horses) haplogroup, based on the obtained cob-gene sequence analysis. In addition, haplotype network analysis revealed that E. multilocularis isolated from Hokkaido-raised horses is highly homologous to Kazakhstan isolates, and E. multilocularis isolated from Alberta-raised horses is highly homologous to Austrian isolates. The results of this study suggest that cob-gene-targeted PCR analysis could be useful for the geographical genetic characterization of E. multilocularis isolated from horses.
DNA-based detection of pork content in food
2023, Heliyon
Determination of halal food is essential in ensuring the tranquillity of consumers, especially Muslims. Halal products mean they are free from prohibited ingredients according to Islamic law. One ingredient that is prohibited is food products containing pork and its derivatives. An accurate verification method with a fast result is necessary to meet this requirement for halal food. DNA quantification of pork is now believed to be able to make accurate and quick decisions, as DNA acts as a reservoir or biological characterization of all living things, including pigs, according to specific characteristics of molecular and connection settings. Various DNA-based methods developed include PCR, biosensor and CRISPR methods. This review discussed various DNA-based methods, including PCR, biosensor and CRISPR, to detect pork content in food. Among these methods, CRISPR is considered the easiest, fastest and most accurate. Therefore, it is important to develop this method further in the future. In this article, we provide a short review on DNA-based methods for detection of pork content in food products.
High dietary lipid level promotes low salinity adaptation in the marine euryhaline crab (Scylla paramamosain)
2023, Animal Nutrition
The physiological processes involved in adaptation to osmotic pressure in euryhaline crustaceans are highly energy demanding, but the effects of dietary lipids (fat) on low salinity adaptations have not been well evaluated. In the present study, a total of 120 mud crabs (Scylla paramamosain, BW = 17.87 ± 1.49 g) were fed control and high-fat (HF) diets, at both medium salinity (23‰) and low salinity (4‰) for 6 wk, and each treatment had 3 replicates with each replicate containing 10 crabs. The results indicated that a HF diet significantly mitigated the reduction in survival rate, percent weight gain and feed efficiency induced by low salinity (P < 0.05). Low salinity lowered lipogenesis and activated lipolysis resulting in lipid depletion in the hepatopancreas of mud crabs (P < 0.05). Thus, HF diets enhanced the process of lipolysis to supply more energy. In the gills, low salinity and the HF diet increased the levels of mitochondrial biogenesis markers, the activity of mitochondrial complexes, and the expression levels of genes related to energy metabolism (P < 0.05). Consequently, the positive effects of the HF diet on energy metabolism in mud crabs at low salinity promoted osmotic pressure regulation. Specifically, significantly higher haemolymph osmotic pressure and inorganic ion content, as well as higher osmotic pressure regulatory enzyme activity in gills, and gene and protein expression levels of NaK-ATPase were observed in crabs fed the HF diet at low salinity (P < 0.05). In summary, high dietary lipid levels improved energy provision to facilitate mitochondrial biogenesis, which increased ATP provision for osmotic pressure regulation of mud crabs. This study also illustrates the importance of dietary lipid nutrition supplementation for low salinity adaptations in mud crabs.
Investigation of protein-ligand binding motions through protein conformational morphing and clustering of cytochrome bc1-aa3 super complex
2023, Journal of Molecular Graphics and Modelling
Citation Excerpt :
Cytochrome bc1-aa3 super complex plays a fundamental role in the mycobacterial ETC, and disruption of this super complex leads to serious growth defects [8]. The QcrB component in ETC is essential in the cellular respiratory chain for the transportation of electrons across the membrane through multi-subunits of the cytochrome-bc1 complex to finally transfer the electrons to the cytochrome-aa3 complex for the reduction of oxygen [11,12]. During electron transfer, the QcrB subunit converts redox energy into proton motive force by pumping the protons into the periplasmic space.
Cytochrome b (QcrB) is considered an essential subunit in the electron transport chain that coordinates the action of the entire cytochrome bc1 oxidase. It has been identified as an attractive drug target for a new promising clinical candidate Q203 that depletes the intracellular ATP levels in the bacterium, Mycobacterium tuberculosis. However, single point polymorphism (T313A/I) near the quinol oxidation site of QcrB developed resistance to Q203. In the present study, we analyze the structural changes and drug-resistance mechanism of QcrB due to the point mutation in detail through conformational morphing and molecular docking studies. By morphing, we generated conformers between the open and closed state of the electron transporting cytochrome bc1-aa3 super complex. We clustered them to identify four intermediate structures and relevant intra- and intermolecular motions that may be of functional relevance, especially the binding of Q203 in wild and mutant QcrB intermediate structures and their alteration in developing drug resistance. The difference in the binding score and hydrogen bond interactions between Q203 and the wild-type and mutant intermediate structures of QcrB from molecular docking studies showed that the point mutation T313A severely affected the binding affinity of the candidate drug. Together, the findings provide an in-depth understanding of QcrB inhibition in different conformations, including closed, intermediate, and open states of cytochrome bc1-aa3 super complex in Mycobacterium tuberculosis at the atomic level. We also obtain insights for designing QcrB and cytochrome bc1-aa3 inhibitors as potential therapeutics that may combat drug resistance in tuberculosis.
Effect of starvation on the antioxidative pathway, autophagy, and mitochondrial function in the intestine of Chinese perch Siniperca chuatsi
2022, Aquaculture
The intestine is a main organ responsible for energy and nutrition absorption and digestion and is an important immune barrier in fish. In recent years, the intestinal health of fish has gained increasing attention in the aquaculture industry. The intestine is a direct target organ of starvation and is highly sensitive to nutritional changes. However, the adaptive responses of the fish intestine to starvation are not well studied. The present study aimed to reveal the effects of starvation on antioxidant systems, autophagy, and mitochondrial function in the intestine of Chinese perch. Therefore, Chinese perch (250 ± 22 g) were starved for 0, 7, and 14 days. Our results indicate that the contents of reactive oxygen species (ROS) and malondialdehyde (MDA) were significantly increased in the intestine of Chinese perch after 7 days and 14 days of starvation, indicating that starvation could induce oxidative stress in the intestine. Meanwhile, the activities and mRNA expression of antioxidative enzymes, including superoxide dismutases (SOD), glutathione peroxidases (GPx), and catalases (CAT), were upregulated in the intestine after the starvation treatment, which might be a compensatory response to oxidative stress. Starvation also increased the expression of nrf2 in the intestine, thereby resulting in the upregulation of antioxidative gene expression. However, the glutathione content and its generation in the intestine were decreased under starvation stress. The ultrastructural analysis of the intestine demonstrated that starvation induced autophagy in the intestine of Chinese perch. The RT–qPCR analysis showed that starvation induced the mRNA expression of genes involved in autophagosome membrane initiation, autophagosome membrane expansion, vesicle recycling, and cargo recruitment, including beclin1, ulk1, beclin1, lc3a, atg4, atg5, atg7, p62, and atg9. Mitochondria are the main ATP-generating organelles and target organelles for ROS. The present study indicates that starvation induced a decrease in the ATP content in the intestine of Chinese perch. In addition, starvation downregulated the expression of mitochondrial oxidative phosphorylation-related and mitochondrial ATP generation-related genes (cox1, atp5f1, atp5a1, and mt-cyb) in the intestine of Chinese perch, suggesting that starvation could suppress mitochondrial energy synthesis. Taken together, our data demonstrate that starvation can induce oxidative stress, disrupt antioxidant systems, and cause autophagy and mitochondrial dysfunction in the intestine of Chinese perch. These results provide insight into the mechanisms by which starvation disrupts intestinal homeostasis in fish.

View all citing articles on Scopus

View full text

ReviewMitochondrial cytochrome b: evolution and structure of the protein

Abstract

Biochim. Biophys. Acta

Biochim. Biophys. Acta

Biochim. Biophys. Acta

FEBS Lett.

Biochim. Biophys. Acta

J. Biol. Chem.

FEBS Lett.

J. Biol. Chem.

J. Biol. Chem.

J. Mol. Biol.

J. Biol. Chem.

J. Biol. Chem.

Comp. Biochem. Physiol.

J. Mol. Biol.

J. Mol. Biol.

Biochim. Biophys. Acta

J. Biol. Chem.

J. Mol. Biol.

J. Biol. Chem.

J. Mol. Biol.

J. Biol. Chem.

Biochim. Biophys. Acta

J. Mol. Biol.

Biochim. Biophys. Acta

J. Biol. Chem.

Trends Biochem. Sci.

Trends Biochem. Sci.

Annu. Rev. Biochem.

J. Mol. Evol.

Microbiol. Rev.

J. Bioenerg. Biomembr.

J. Bioenerg. Biomembr.

EMBO J

Eur. J. Biochem.

Nature

J. Mol. Evol.

J. Mol. Evol.

Review
Mitochondrial cytochrome b: evolution and structure of the protein