Cytochrome b

Cytochrome b is a protein found in the mitochondria of eukaryotic cells. It functions as part of the electron transport chain and is the main subunit of transmembrane cytochrome bc1 and b6f complexes.[1][2]

1l0l opm
Identifiers
SymbolCytochrom_B_N
PfamPF00033
InterProIPR005797
PROSITEPDOC00171
SCOPe3bcc / SUPFAM
TCDB3.D.3
OPM superfamily3
OPM protein3h1j
CDDcd00284

Function

In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (EC 1.10.2.2) — also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is an analogous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase (EC 1.10.99.1), also known as the b6f complex. These complexes are involved in electron transport, the pumping of protons to create a proton-motive force (PMF). This proton gradient is used for the generation of ATP. These complexes play a vital role in cells.[3]

Structure

Cytochrome b/b6[4][5] is an integral membrane protein of approximately 400 amino acid residues that probably has 8 transmembrane segments. In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. Cytochrome b/b6 non-covalently binds two heme groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two heme groups.

Use in phylogenetics

Cytochrome b is commonly used as a region of mitochondrial DNA for determining phylogenetic relationships between organisms, due to its sequence variability. It is considered to be most useful in determining relationships within families and genera. Comparative studies involving cytochrome b have resulted in new classification schemes and have been used to assign newly described species to a genus as well as to deepen the understanding of evolutionary relationships.[6]

Clinical significance

Mutations in cytochrome b primarily result in exercise intolerance in human patients; though more rare, severe multi-system pathologies have also been reported.[7]

Single-point mutations in cytochrome b of Plasmodium falciparum and P. berghei are associated with resistance to the anti-malarial drug atovaquone.[8]

Human genes

Human genes encoding cytochrome b proteins include:

  • CYB5A – cytochrome b5 type A (microsomal)
  • CYB5B – cytochrome b5 type B (outer mitochondrial membrane)
  • CYBASC3 – cytochrome b, ascorbate dependent 3
  • MT-CYB – mitochondrially encoded cytochrome b

References

  1. ^ Howell N (August 1989). "Evolutionary conservation of protein regions in the proton motive cytochrome b and their possible roles in redox catalysis". J. Mol. Evol. 29 (2): 157–69. doi:10.1007/BF02100114. PMID 2509716.
  2. ^ Esposti MD, De Vries S, Crimi M, Ghelli A, Patarnello T, Meyer A (July 1993). "Mitochondrial cytochrome b: evolution and structure of the protein". Biochim. Biophys. Acta. 1143 (3): 243–71. doi:10.1016/0005-2728(93)90197-N. PMID 8329437.
  3. ^ Blankenship, Robert (2009). Molecular Mechanisms of Photosynthesis. Blackwell Publishing. pp. 124–132.
  4. ^ Howell N (1989). "Evolutionary conservation of protein regions in the protonmotive cytochrome b and their possible roles in redox catalysis". J. Mol. Evol. 29 (2): 157–169. doi:10.1007/BF02100114. PMID 2509716.
  5. ^ Esposti MD, Crimi M, Ghelli A, Patarnello T, Meyer A, De Vries S (1993). "Mitochondrial cytochrome b: evolution and structure of the protein". Biochim. Biophys. Acta. 1143 (3): 243–271. doi:10.1016/0005-2728(93)90197-N. PMID 8329437.
  6. ^ Castresana, J. (2001). "Cytochrome b Phylogeny and the Taxonomy of Great Apes and Mammals". Molecular Biology and Evolution. 18 (4): 465–471. doi:10.1093/oxfordjournals.molbev.a003825. PMID 11264397.
  7. ^ Blakely EL, Mitchell AL, Fisher N, Meunier B, Nijtmans LG, Schaefer AM, Jackson MJ, Turnbull DM, Taylor RW (July 2005). "A mitochondrial cytochrome b mutation causing severe respiratory chain enzyme deficiency in humans and yeast". FEBS J. 272 (14): 3583–92. doi:10.1111/j.1742-4658.2005.04779.x. PMID 16008558.
  8. ^ Siregar JE, Syafruddin D, Matsuoka H, Kita K, Marzuki S (June 2008). "Mutation underlying resistance of Plasmodium berghei to atovaquone in the quinone binding domain 2 (Qo(2)) of the cytochrome b gene". Parasitology International. 57 (2): 229–32. doi:10.1016/j.parint.2007.12.002. PMID 18248769.

External links

Chrotomys

The genus Chrotomys contain a unique group of rodents found only in the Philippines, specifically the islands of Luzon, Mindoro, and Sibuyan. Instead of being predominantly herbivorous or omnivorous like other murines, these rats feed predominantly on invertebrates although they do eat some vegetable matter. This vermivory is probably the result of a rat-like animal moving into an ecological niche usually filled by shrews. Shrews and other insectivores are absent on these Philippine islands.

Coenzyme Q – cytochrome c reductase

The coenzyme Q : cytochrome c – oxidoreductase, sometimes called the cytochrome bc1 complex, and at other times complex III, is the third complex in the electron transport chain (EC 1.10.2.2), playing a critical role in biochemical generation of ATP (oxidative phosphorylation). Complex III is a multisubunit transmembrane protein encoded by both the mitochondrial (cytochrome b) and the nuclear genomes (all other subunits). Complex III is present in the mitochondria of all animals and all aerobic eukaryotes and the inner membranes of most eubacteria. Mutations in Complex III cause exercise intolerance as well as multisystem disorders. The bc1 complex contains 11 subunits, 3 respiratory subunits (cytochrome B, cytochrome C1, Rieske protein), 2 core proteins and 6 low-molecular weight proteins.

Ubiquinol—cytochrome-c reductase catalyzes the chemical reaction

QH2 + 2 ferricytochrome c Q + 2 ferrocytochrome c + 2 H+

Thus, the two substrates of this enzyme are quinol (QH2) and ferri- (Fe3+) cytochrome c, whereas its 3 products are quinone (Q), ferro- (Fe2+) cytochrome c, and H+.

This enzyme belongs to the family of oxidoreductases, specifically those acting on diphenols and related substances as donor with a cytochrome as acceptor. This enzyme participates in oxidative phosphorylation. It has four cofactors: cytochrome c1, cytochrome b-562, cytochrome b-566, and a 2-Iron ferredoxin of the Rieske type.

Cytochrome

Cytochromes are proteins containing heme as a cofactor. They are classified according to the type of heme and its mode of binding. Four varieties are recognized by the IUBMB, cytochromes a, cytochromes b, cytochromes c and cytochrome d. Cytochrome function is linked to the reversible redox change from ferrous (Fe(II)) to the ferric (Fe(III)) oxidation state of the iron found in the heme core. In addition to the classification by the IUBMB into four cytochrome classes, several additional classifications such as cytochrome o and cytochrome P450 can be found in biochemical literature.

Cytochrome C1

Cytochrome C1 (also known as Complex III subunit 4) is a protein encoded by the CYC1 gene. Cytochrome is a heme-containing subunit of the cytochrome b-c1 complex, which accepts electrons from Rieske protein and transfers electrons to cytochrome c in the mitochondrial respiratory chain. It is formed in the cytosol and targeted to the mitochondrial intermembrane space. Cytochrome c1 belongs to the cytochrome c family of proteins.

Cytochrome b-245

The Cytochrome b (-245) protein complex is composed of cytochrome b alpha (CYBA) and beta (CYBB) chain.

Cytochrome b5 reductase

Cytochrome-b5 reductase (also known as methemoglobin reductase) is a NADH-dependent enzyme that converts methemoglobin to hemoglobin. It contains FAD and catalyzes the reaction:

NADH + H+ + 2 ferricytochrome b5 = NAD+ + 2 ferrocytochrome b5

The following four human genes encode cytochrome-b5 reductases:

CYB5R1

CYB5R2

CYB5R3

CYB5R4

Diving duck

The diving ducks, commonly called pochards or scaups, are a category of duck which feed by diving beneath the surface of the water. They are part of Anatidae, the diverse and very large family that includes ducks, geese, and swans.

The diving ducks are placed in a distinct tribe in the subfamily Anatinae, the Aythyini. While morphologically close to the dabbling ducks, there are nonetheless some pronounced differences such as in the structure of the trachea. mtDNA cytochrome b and NADH dehydrogenase subunit 2 sequence data indicate that the dabbling and diving ducks are fairly distant from each other, the outward similarities being due to convergent evolution.

Alternatively, the diving ducks are placed as a subfamily Aythyinae in a subfamily Anatidae which would encompass all duck-like birds except the whistling-ducks.

The seaducks commonly found in coastal areas, such as the long-tailed duck (formerly known in the US as oldsquaw), scoters, goldeneyes, mergansers, bufflehead and eiders, are also sometimes colloquially referred to in North America as diving ducks because they also feed by diving; their subfamily (Merginae) is a very distinct one however.

Although the group is cosmopolitan, most members are native to the Northern Hemisphere, and it includes several of the most familiar Northern Hemisphere ducks.

This group of ducks is so named because its members feed mainly by diving, although in fact the Netta species are reluctant to dive, and feed more like dabbling ducks.

These are gregarious ducks, mainly found on fresh water or on estuaries, though the greater scaup becomes marine during the northern winter. They are strong fliers; their broad, blunt-tipped wings require faster wing-beats than those of many ducks and they take off with some difficulty. Northern species tend to be migratory; southern species do not migrate though the hardhead travels long distances on an irregular basis in response to rainfall. Diving ducks do not walk as well on land as the dabbling ducks; their legs tend to be placed further back on their bodies to help propel them when underwater.

Duodenal cytochrome B

Duodenal cytochrome B (Dcytb) also known as cytochrome b reductase 1 is an enzyme that in humans is encoded by the CYBRD1 gene.

Dcytb CYBRD1 was first identified as a ferric reductase enzyme which catalyzes the reduction of Fe3+ to Fe2+ required for dietary iron absorption in the duodenum of mammals. Dcytb mRNA and protein levels in the gut are increased by iron deficiency and hypoxia which acts to promote dietary iron absorption. The effect of iron deficiency and hypoxia on Dcytb levels are medicated via the HIF2 (Hypoxia inducible factor 2) transcription factor which binds to hypoxia response elements within the Dcytb promoter and increases transcription of the gene. DCYTB protein has also been found in other tissues, such as lung epithelial cells and in the plasma membrane of mature red blood cells of scorbutic species (unable to make ascorbate) such as human and guinea pig but not in other species which have retained the ability to synthesise ascorbate like mice and rat. This has led to the notion that Dcytb may have an additional role in ascorbate metabolism in scorbutic species. DCYTB protein has also been found in breast tissue (epithelial and myoepithelial cells) and high DCYTB levels are associated with a favourable prognosis in patients with breast cancer. A single nucleotide polymorphism (SNP) within the DCYTB promoter (SNP rs884409) which reduced functional DCYTB promoter activity was also associated with reduced serum ferrtin levels in a patient cohort with C282Y haemochromatosis.

Exercise intolerance

Exercise intolerance is a condition of inability or decreased ability to perform physical exercise at what would be considered to be the normally expected level or duration. It also includes experiences of unusually severe post-exercise pain, fatigue, nausea, vomiting or other negative effects. Exercise intolerance is not a disease or syndrome in and of itself, but can result from various disorders.

In most cases, the specific reason that exercise is not tolerated is of considerable significance when trying to isolate the cause down to a specific disease. Dysfunctions involving the pulmonary, cardiovascular or neuromuscular systems have been frequently found to be associated with exercise intolerance, with behavioural causes also playing a part.

MT-CYB

Cytochrome b is a protein that in humans is encoded by the MT-CYB gene. Its gene product is a subunit of the respiratory chain protein Ubiquinol Cytochrome c Reductase (UQCR, Complex III or Cytochrome bc1 complex), which consists of the products of one mitochondrially encoded gene, MT-CYB (mitochondrial cytochrome b) and ten nuclear genes: UQCRC1, UQCRC2, Cytochrome c1, UQCRFS1 (Rieske protein), UQCRB, "11kDa protein", UQCRH (cyt c1 Hinge protein), Rieske Protein presequence, "cyt. c1 associated protein", and Rieske-associated protein.

Madagascan warbler

The Madagascan warblers are a newly validated family of songbirds. They were formally named Bernieridae in 2010. The family currently consists of eleven species (in eight genera) of small forest birds. These birds are all endemic to Madagascar.

In 1934, the monophyly of this group was proposed by Finn Salomonsen but the traditional assignments of these birds were maintained, mistaken by their convergent evolution and the lack of dedicated research. The families to which the Malagasy warblers were formerly assigned—Pycnonotidae (bulbuls) and even more so Timaliidae (Old World babblers) and the Old World warbler—were used as "wastebin taxa", uniting unrelated lineages that were somewhat similar ecologically and morphologically.

It was not until the analysis of mtDNA cytochrome b and 16S rRNA (Cibois et al. 1999, 2001) as well as nDNA RAG-1 and RAG-2 exon (Beresford et al. 2005) sequence data, that the long-proposed grouping was accepted.

Mountain chickadee

The mountain chickadee (Poecile gambeli) is a small songbird, a passerine bird in the tit family Paridae. Often, it is still placed in the genus Parus with most other tits, but mtDNA cytochrome b sequence data and morphology suggest that separating Poecile more adequately expresses these birds' relationships. The American Ornithologists' Union has been treating Poecile as a distinct genus for some time.

Adults of both sexes have a black cap joining a black postocular stripe behind distinctive white eyebrows. Their backs and flanks are gray and they have paler gray underparts; they have a short black bill, and a black bib. The typical adult wingspan is 7.5 in (19 cm), and the overall length is 5–6 in (13–15 cm).

Common inhabitants of the mountainous regions of the western United States, their range extends from the southern Yukon to California and Rocky Mountain States in the United States. A few mountain chickadees may migrate locally up the mountains in the summer and down into the mountain foothills in the winter; but this phenomenon is not well documented.

They breed monogamously, producing 1 to 2 broods per year. Incubation by the female is 14 days. The young are altricial, and stay in the nest for 21 days while being fed by both parents.

Their primary diet is insects during the summer and breeding season; conifer seeds and other plant seeds are taken throughout the year. They cling to the undersides of branches and to tree trunks, searching for food in the bark or breaking seeds open by hammering them with their beaks.

Their call is a throaty chick-adee-dee-dee, while their song is a 3- or 4-note descending whistle fee-bee-bay or fee-bee-fee-bee. They travel in pairs or small groups, and may join multi-species feeding flocks after breeding season.

Recent studies have indicated that in mixed flocks, black-capped chickadees become dominant over mountain chickadees.

The specific name honors naturalist William Gambel.

NOX2

NADPH oxidase 2 (Nox2), also known as cytochrome b(558) subunit beta or Cytochrome b-245 heavy chain, is a protein that in humans is encoded by the NOX2 gene (also called CYBB gene). The protein is a super-oxide generating enzyme which forms reactive oxygen species (ROS).

Notocitellus

Notocitellus is a genus of ground squirrels, containing two species. These species are the tropical ground squirrel (Notocitellus adocetus), and the ring-tailed ground squirrel (N. annulatus). Notocitellus was formerly placed in the large ground squirrel genus Spermophilus, as a subgenus or species group. Since DNA sequencing of the cytochrome b gene has shown Spermophilus to be paraphyletic to the marmots, antelope squirrels, and prairie dogs, it is now separated, along with six other genera. The exact relations of this genus are unclear, though a relation to the antelope squirrels is possible.

Otospermophilus

Otospermophilus is a genus of ground squirrels in the family Sciuridae, containing three species. Otospermophilus was formerly placed in the large ground squirrel genus Spermophilus, as a subgenus or species group. Since DNA sequencing of the cytochrome b gene has shown Spermophilus to be paraphyletic to the prairie dogs and marmots, it is now separated, along with six other genera.

Parrotbill

The parrotbills are a group of peculiar birds native to East and Southeast Asia, though feral populations exist elsewhere. They are generally small, long-tailed birds which inhabit reedbeds and similar habitat. They feed mainly on seeds, e.g. of grasses, to which their bill, as the name implies, is well-adapted. Living in tropical to southern temperate climates, they are usually non-migratory.

The bearded reedling or "bearded tit", a Eurasian species long placed here, is more insectivorous by comparison, especially in summer. It also strikingly differs in morphology, and was time and again placed in a monotypic family Panuridae. DNA sequence data supports this.

As names like "bearded tit" imply, their general habitus and acrobatic habits resemble birds like the long-tailed tits. Together with these and others they were at some time placed in the titmouse family Paridae. Later studies found no justification to presume a close relationship between all these birds, and consequently the parrotbills and bearded reedling were removed from the tits and chickadees and placed into a distinct family, Paradoxornithidae. As names like Paradoxornis paradoxus - "puzzling, paradox bird" - suggest, their true relationships were very unclear, although by the latter 20th century they were generally seen as close to Timaliidae ("Old World babblers") and Sylviidae ("Old World warblers").

Since 1990 (Sibley & Ahlquist 1990), molecular data has been added to aid the efforts of discovering the parrotbills' true relationships. As Paradoxornis species are generally elusive and in many cases little-known birds, usually specimens of the bearded reedling which are far more easy to procure were used for the analyses. Often, the entire group was entirely left out of analyses, being small and seemingly insignificant in the large pattern of bird evolution (e.g. Barker et al. 2002, 2004). The bearded reedling tended to appear close to larks in phylogenies based on e.g. DNA-DNA hybridization (Sibley & Ahlquist 1990), or on mtDNA cytochrome b and nDNA c-myc exon 3, RAG-1 and myoglobin intron 2 sequence data (Ericson & Johansson 2003). Placement in a superfamily Sylvioidea which contained birds such as Sylviidae, Timaliidae and long-tailed tits - but not Paridae - was confirmed.

Cibois (2003a) analyzed mtDNA cytochrome b and 12S/16S rRNA sequences of some Sylvioidea, among them several species of Paradoxornis but not the bearded reedling. These formed a robust clade closer to the Sylvia typical warblers and some presumed "Old World babblers" such as Chrysomma sinense than to other birds. The puzzle was finally resolved by Alström et al. (2006), who studied mtDNA cytochrome b and nDNA myoglobin intron 2 sequences of a wider range of Sylvioidea: The bearded reedling was not a parrotbill at all, but forms a distinct lineage on its own, the relationships of which are not entirely resolved at present. The parrotbills' presence in the clade containing Sylvia, on the other hand, necessitates that the Paradoxornithidae are placed in synonymy of the Sylviidae. Cibois (2003b) even suggested that these themselves were to be merged with the remaining Timaliidae and the latter name to be adopted. This has hitherto not been followed and researchers remain equivocal as many taxa in Sylviidae and Timaliidae remain to be tested for their relationships. In any case, it is most likely that the typical warbler-parrotbill group is monophyletic and therefore agrees with the modern requirements for a taxon. Hence, whether to keep or to synonymize it is entirely a matter of philosophy, as the scientific facts would agree with either approach.

The interesting conclusion from an evolutionary point of view is that the morphologically both internally homogenous and compared to each other highly dissimilar typical warblers and parrotbills form the two extremes in the divergent evolution of the Sylviidae. This is underscored by looking at the closest living relatives of the parrotbills in the rearranged Sylviidae: The genus Chrysomma are non-specialized species altogether intermediate in habitus, habitat and habits between the typical warblers and the parrotbills. Presumably, the ancestral sylviids looked much like these birds. How dramatic the evolutionary changes wrought upon the parrotbills in their adaptation to feeding on grass caryopses and similar seeds were can be seen by comparing them with the typical fulvettas, which were formerly considered Timaliidae and united with the alcippes (Pasquet 2006). These look somewhat like drab fairy-wrens and have none of the parrotbills' adaptations to food and habitat. Yet it appears that the typical fulvettas' and parrotbills' common ancestor evolved into at least two parrotbill lineages independently (Cibois 2003a) & (Yeung et al. 2006). Only the wrentit, the only American sylviid, resembles the parrotbills much in habitus, though not in color pattern, and of course, as an insectivore, neither in bill shape.

Petrel

Petrels are tube-nosed seabirds in the bird order Procellariiformes.

Rio Grande ground squirrel

The Rio Grande ground squirrel (Ictidomys parvidens) is a species of squirrel in the family Sciuridae.

All the species of Ictidomys were previously believed to belong to the much larger genus Spermophilus (I. parvidens as a subspecies of Spermophilus mexicanus), but DNA sequencing of the cytochrome b gene showed that this group was paraphyletic to the prairie dogs and marmots, and could therefore no longer be retained as a single genus. As a result, Ictidomys is now considered as a genus in its own right.

Roberto's spiny rat

Roberto's spiny-rat, Proechimys roberti, or Para spiny rat, is a spiny rat species from South America. It is found in Brazil.

Morphological, karyological, and mitochondrial DNA (cytochrome b) data indicate that Proechimys oris is likely a junior synonym of P. roberti.

Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
Globins
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