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Evolution of bioenergetics
Rieske/cytb complexes are composed by at least two subunits: a cytochrome b and an iron sulfur protein. Cytochrome b is a transmembrane protein with at least 7 membrane spanning helices and two b-hemes. It may be split into two parts and is than named cytochrome b6. The iron-sulfur cluster containing subunit harbours a 2Fe2S cluster ligated by two Cys and two His which results in a characteristic EPR signal and a comparably high redox midpoint potential. The subunit was first described by John S. Rieske and later named after him. The invariable presence of these two subunits leads to the name for the entire family, the Rieske/cytb complexes (Schuetz et al. 2000). An electron acceptor subuint to the Rieske cluster was recruited independently in most phyla and can be used to distinguish different members of the family. Thus a c1-type heme (for its origin see ‘collapsed di-heme’) gave its name to bc1 complexes in proteobacteria and mitochondria, the structurally unrelated cytochrome f to the b6f complexes of cyanobacteria and chloroplasts. Other these two cases various di-, tetra, hexa-, hepta- or octaheme-subunits were found by genome surveys of various Bacteria and b-hemes in Archaea (examples in multi R/b). Additional subunits as the core subuints of bc1 complexes or HAO-subunits in Anammoxbacteria as well as supercomplex formation with oxidases (Wei-Chun et al. 2016, Bergdoll et al. 2016) or NAR (our contribution: van Lis et al. 2011) were reported.
Rieske/cytb complexes integrate most bioenergetic reaction chains at the level of the quinone pool (link to Figure 2 on the Research topics page). They need a redox potential difference of about 200mV between the pool quinone and the electron acceptor that connects them to the terminal oxidase of the chain to be able to turn over. Due to energy shortage, they are therefore not part of the equipment of acetogenic and methanogenic bacteria.
We constructed a phylogenetic tree based on the amino acid sequences of the transmembrane cytochrome b subunit. This tree follows the tree of live to the exception of a few, clearly identified events of lateral gene transfer (Aquificales, Haloarchaea and various phylogentically unrelated Bacteria that cluster in groups A1 and A2) (ten Brink et al. 2013).
A phylogenetic analysis of the Rieske subunit is difficult due to the short length of the subunit sequence and the insertion of variable loops in the protein scaffold (Lebrun et al. 2006). The alignment needs to be guided by the 3D structure of the protein, which limits analysis to crystalized subunits and their closely related relatives. This approach is worthwhile, however, since the Rieske subunit, at variance with cytochrome b possesses a clearly defined outgroup, the Rieske-subunit of arsenite oxidases (Lebrun et al. 2006, Duval et al. 2010). Integration of arsenite oxidase sequences into the alignment allows rooting the Rieske/cytb tree and indicates the pre-LUCA appearance of Rieske/cytb complexes. So far unexplained is the presence of multiple copies of the enzymes in a single organism as observed for example in Haloarchaea, Planctomycetes or deltaproteobacteria.
The electron donor to the Rieske/cytb complexes is a quinol in the quinol oxidizing site of the complex close to the perimplasmic side of the membrane, whereas its electron acceptors are small electron transfer proteins or subunits (like cytochrome c or plastocyanin) in the periplasm and a quinone (of the same chemical type than the electron donor) on the cytoplasmic side of the membrane. Electron transfer over the membrane occurs via two b-type hemes and contributes to the build-up of a transmembrane potential. Electron transfer from quinone to quinone against the pmf is possible, since the quinol in the Qo site thermodynamically bifurcates its electrons and consequently conveys a low redox potential to one electron at expense of the other (for more information on electron bifurcation please visit our 2-electron website). The fundamental principle of the Q-cycle has been formulated by Peter Mitchel in 1975. Fine-tuning of the redox midpoint potentials of all co-factors of the complex to the pool quinone potential is necessary to make the enzyme work and to transform the redox span between the acceptor of the initial electron donor of the chain and the donor to its terminal electron acceptor into pmf. Redox midpoint potentials as determined for all cofactors of the bc1 complex from Rhodobacter sphaeroides, including the two one-electron transitions of the Qo-site quinone, perfectly illustrate this proposal. We investigated a Rieske/cytb complex from a MK-chain and found that all redox potentials are down-shifted by the potential difference between ubiquinone and menaquinone (Bergdoll et al. 2016), nicely confirming the interdependency of the redox midpoint potentials of all co-factors and the universal validity of the Q-cycle scheme.
Resolution of the crystal structure of the b6f complex in 2003 revealed the presence of an unexpected co-factor: a c-type heme, linked to the protein via a single thioester bound in the quinone-reducing side close to the cytoplasmic face of the membrane. This heme is unique among known heme-cofactors in that is has no axial protein ligand. In 2007 we published an EPR characterization of this co-factor and revealed its interaction with the adjacent heme bH (Baymann et al. 2007) and a redox potential identical to the quinone potential. NQNO, a quinone analog and inhibitor of b6f complexes becomes a ligand to heme ci, strongly influencing its redox and EPR properties.
The presence of heme ci in a Rieske/cytb complex can be inferred from the presence of a conserved Cys residue in the sequence. Mapping this Cys-residue on a phylogenetic tree suggests that heme ci appeared in the ancestor of Firmicutes/Heliobacteria/cyanobacteria and was laterally transferred to a number of phylogentically distant species, all featuring cytochrome b6.
We observed that in the presence of heme ci the redox potential difference between heme bH and the quinone pool is bigger than observed in complexes devoid of this cofactor (Bergdoll et al. 2016). Sequence analysis and structure modelization indicates that in organisms outside cyanobacteria a glutamic or aspartic acid in the quinone-binding site forms an axial ligand to heme ci (Ducluzeau et al. 2008). In all complexes we studied so far the redox midpoint potential of this co-factor is the same as the potential of the pool-quinone (Bergdoll et al. 2016). Other these factual observations a role for heme ci remains elusive.
Schütz, M., Brugna, M., Lebrun, E., Baymann, F., Huber, R., Stetter, K.-O., Hauska, G., Toci, R.,
Lemesle-Meunier, D., Tron, P., Schmidt, C. and Nitschke, W. (2000)
J.Mol.Biol. 300, 663-676 [pdf-file]
Early evolution of cytochrome bc-complexes
Kao, W.-C., Kleinschroth, T., Nitschke, W., Baymann, F., Neehaul, Y.,
Hellwig, P., Richers, S., Vonck, J., Bott, M. and Hunte, C. (2016)
Biochim. Biophys. Acta Bioenergetics 1857, 1705-1714
The obligate respiratory supercomplex from Actinobacteria
Bergdoll, L., ten Brink, F., Nitschke, W., Picot, D. and Baymann, F. (2016)
Biochim. Biophys. Acta Bioenergetics 1857, 1569-1579
From low- to high-potential bioenergetic chains:
Thermodynamic constraints of Q-cycle function
van Lis, R., Ducluzeau, A.-L., Nitschke, W. and Schoepp-Cothenet, B. (2011)
The nitrogen cycle in the Archaean; an intricate interplay of enzymatic and abiotic reactions
in: Nitrogen Cycling in Bacteria: Molecular Analysis (Moir, J.W.B., ed.), Chapter I, pp. 1-21
Caister Academic Press, ISBN: 978-1-904455-86-8
ten Brink, F., Schoepp-Cothenet, B., van Lis, R., Nitschke, W. and Baymann, F. (2013)
Biochim.Biophys. Acta Bioenergetics 1827, 1392-1406
Multiple Rieske/cytb complexes in a single organism
Lebrun, E., Santini, J.M., Brugna, M., Ducluzeau, A.-L., Ouchane, S., Schoepp-Cothenet, B., Baymann, F. and Nitschke, W. (2006)
Mol. Biol. Evol. 23, 1180-1191 [pdf-file]
The Rieske protein; a case study on the pitfalls of multiple sequence alignments and
Duval, S., Santini, J.M., Nitschke, W., Hille, R. and Schoepp-Cothenet, B. (2010)
J.Biol.Chem. 285, 20442-20451 [pdf-file]
The small subunit AroB of arsenite oxidase: lessons on the [2Fe-2S]-Rieske protein superfamily
Baymann, F., Giusti, F., Picot, D. and Nitschke, W. (2007)
Proc.Natl.Acad.Sci. USA 104, 519-524 [pdf-file]
The ci/bH-moiety in the cytochrome b6f complex studied by EPR. A pair of strongly interacting hemes
Ducluzeau, A.-L., Chenu, E., Capowiez, L. and Baymann, F. (2008)
Biochim.Biophys.Acta Bioenergetics 1777, 1140-1146 [pdf-file]
The Rieske/cytochrome b complex of Heliobacteria
Last update: September 22, 2020
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