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BBA - Bioenergetics (v.1827, #2)

Editorial Board (pp. i).

The evolutionary aspects of bioenergetic systems by Wolfgang Nitschke (pp. 61-61).

Turnstiles and bifurcators: The disequilibrium converting engines that put metabolism on the road by Elbert Branscomb; Michael J. Russell (pp. 62-78).

The Submarine Hydrothermal Alkaline Spring Theory for the emergence of life holds that it is the ordered delivery of hydrogen and methane in alkaline hydrothermal solutions at a spontaneously precipitated inorganic osmotic and catalytic membrane to the carbon dioxide and other electron acceptors in the earliest acidulous cool ocean that, through these gradients, drove life into being. That such interactions between hydrothermal fuels and potential oxidants have so far not been accomplished in the lab is because some steps along the necessary metabolic pathways are endergonic and must therefore be driven by being coupled to thermodynamically larger exergonic processes. But coupling of this kind is far from automatic and it is not enough to merely sum the Δ Gs of two supposedly coupled reactions and show their combined thermodynamic viability. An exergonic reaction will not drive an endergonic one unless ‘forced’ to do so by being tied to it mechanistically via an organized “engine” of “Free Energy Conversion” (FEC). Here we discuss the thermodynamics of FEC and advance proposals regarding the nature and roles of the FEC devices that could, in principle, have arisen spontaneously in the alkaline hydrothermal context and have forced the onset of a protometabolism. The key challenge is to divine what these initial engines of life were in physicochemical terms and as part of that, what structures provided the first “turnstile-like” mechanisms needed to couple the partner processes in free energy conversion; in particular to couple the dissipation of geochemically given gradients to, say, the reduction of CO₂ to formate and the generation of a pyrophosphate disequilibrium. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.► A model for the origin of life is discussed in thermodynamic and geochemical terms. ► Its geochemical basis is the alkaline vent, serpentinization, Hadean ocean model. ► Its thermodynamic approach is framed in terms of non-equilibrium thermodynamics. ► It emphasizes processes of free energy conversion and their mechanistic requirements. ► Living systems are seen as a network of disequilibria linked in driver–driven pairs.

Keywords: Alkaline hydrothermal vent; Origin of life; Chemiosmosis; Serpentinization; Free energy conversion; Non-equilibrium thermodynamics

On the universal core of bioenergetics by Barbara Schoepp-Cothenet; Robert van Lis; Ariane Atteia; Frauke Baymann; Line Capowiez; Anne-Lise Ducluzeau; Simon Duval; Felix ten Brink; Michael J. Russell; Wolfgang Nitschke (pp. 79-93).

Living cells are able to harvest energy by coupling exergonic electron transfer between reducing and oxidising substrates to the generation of chemiosmotic potential. Whereas a wide variety of redox substrates is exploited by prokaryotes resulting in very diverse layouts of electron transfer chains, the ensemble of molecular architectures of enzymes and redox cofactors employed to construct these systems is stunningly small and uniform. An overview of prominent types of electron transfer chains and of their characteristic electrochemical parameters is presented. We propose that basic thermodynamic considerations are able to rationalise the global molecular make-up and functioning of these chemiosmotic systems. Arguments from palaeogeochemistry and molecular phylogeny are employed to discuss the evolutionary history leading from putative energy metabolisms in early life to the chemiosmotic diversity of extant organisms. Following the Occam's razor principle, we only considered for this purpose origin of life scenarios which are contiguous with extant life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.► Diversity of electrochemical regimes explored by bioenergetic chains ► Availability of redox substrates through 4billion years of life ► Quinones and methanophenazines, crucial elements of almost all bioenergetic chains ► Limited set of protein building blocks used by life to construct all the enzymes ► Phylogeny as a tool for the elucidation of the bioenergetic evolutionary history

Keywords: Chemiosmosis; 2nd law of thermodynamics; Electron transfer; Evolution; Quinone; Origin of life

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na⁺ translocating ferredoxin oxidation by Wolfgang Buckel; Rudolf K. Thauer (pp. 94-113).

The review describes four flavin-containing cytoplasmatic multienzyme complexes from anaerobic bacteria and archaea that catalyze the reduction of the low potential ferredoxin by electron donors with higher potentials, such as NAD(P)H or H₂ at ≤100kPa. These endergonic reactions are driven by concomitant oxidation of the same donor with higher potential acceptors such as crotonyl-CoA, NAD⁺ or heterodisulfide (CoM-S-S-CoB). The process called flavin-based electron bifurcation (FBEB) can be regarded as a third mode of energy conservation in addition to substrate level phosphorylation (SLP) and electron transport phosphorylation (ETP). FBEB has been detected in the clostridial butyryl-CoA dehydrogenase/electron transferring flavoprotein complex (BcdA-EtfBC), the multisubunit [FeFe]hydrogenase from Thermotoga maritima (HydABC) and from acetogenic bacteria, the [NiFe]hydrogenase/heterodisulfide reductase (MvhADG–HdrABC) from methanogenic archaea, and the transhydrogenase (NfnAB) from many Gram positive and Gram negative bacteria and from anaerobic archaea.The Bcd/EtfBC complex that catalyzes electron bifurcation from NADH to the low potential ferredoxin and to the high potential crotonyl-CoA has already been studied in some detail. The bifurcating protein most likely is EtfBC, which in each subunit (βγ) contains one FAD. In analogy to the bifurcating complex III of the mitochondrial respiratory chain and with the help of the structure of the human ETF, we propose a conformational change by which γ-FADH⁻ in EtfBC approaches β-FAD to enable the bifurcating one-electron transfer. The ferredoxin reduced in one of the four electron bifurcating reactions can regenerate H₂ or NADPH, reduce CO₂ in acetogenic bacteria and methanogenic archaea, or is converted to ΔμH⁺/Na⁺ by the membrane-associated enzyme complexes Rnf and Ech, whereby NADH and H₂ are recycled, respectively. The mainly bacterial Rnf complexes couple ferredoxin oxidation by NAD⁺ with proton/sodium ion translocation and the more diverse energy converting [NiFe] hydrogenases (Ech) do the same, whereby NAD⁺ is replaced by H⁺. Many organisms also use Rnf and Ech in the reverse direction to reduce ferredoxin driven by ΔμH⁺/Na⁺. Finally examples are shown, in which the four bifurcating multienzyme complexes alone or together with Rnf and Ech are integrated into energy metabolisms of nine anaerobes. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.Display Omitted► Bifurcation enables high potential donors to reduce low potential ferredoxin. ► Four enzyme complexes from anaerobes catalyze flavin-based electron bifurcation. ► The membrane complexes Rnf and Ech generate ΔμH⁺/Na⁺ with reduced ferredoxin. ► Electron bifurcation, Rnf and Ech make anaerobes to efficient energy converters.

Keywords: Flavin-based electron bifurcation (FBEB); Flavin semiquinone; Etf-Butyryl-CoA Dehydrogenase Complex; [FeFe] and [FeNi]hydrogenases; NADH:NADPH Transhydrogenase; Heterodisulfide Reductase Complex

Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations by Jörg Simon; Martin G. Klotz (pp. 114-135).

Nitrogen is an essential element of life that needs to be assimilated in its most reduced form, ammonium. On the other hand, nitrogen exists in a multitude of oxidation states and, consequently, nitrogen compounds (NCs) serve as electron donor and/or acceptors in many catabolic pathways including various forms of microbial respiration that contribute to the global biogeochemical nitrogen cycle. Some of these NCs are also known as reactive nitrogen species able to cause nitrosative stress because of their high redox reactivity. The best understood processes of the nitrogen cycle are denitrification and ammonification (both beginning with nitrate reduction to nitrite), nitrification (aerobic oxidation of ammonium and nitrite) and anaerobic ammonium oxidation (anammox). This review presents examples of the diverse architecture, either elucidated or anticipated, and the high degree of modularity of the corresponding respiratory electron transport processes found in Bacteria and Archaea, and relates these to their respective bioenergetic mechanisms of proton motive force generation. In contrast to the multiplicity of enzymes that catalyze NC transformations, the number of proteins or protein modules involved in connecting electron transport to and from these enzymes with the quinone/quinol pool is comparatively small. These quinone/quinol-reactive protein modules consist of cytochromes b and c and iron-sulfur proteins. Conclusions are drawn towards the evolutionary relationships of bioenergetic systems involved in NC transformation and deduced aspects of the evolution of the biogeochemical nitrogen cycle are presented. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.► Review on bioenergetic systems of bacterial and archaeal nitrogen compound transformations ► Discussion of evolutionary consequences drawn from the design of respiratory chains ► Model on the evolution of the global nitrogen cycle based on microbial energy metabolism

Keywords: Abbreviations; Amo; ammonium monooxygenase; Ca.; Candidatus; Cu-MMO; copper-dependent membrane monooxygenase family; DMSO; dimethyl sulfoxide; ETC; electron transport chain; Fe/S; iron-sulfur center; GOE; Great Oxygenation Event; Hao; hydroxylamine oxidoreductase; HCO; heme-copper oxidase family; Hzo; hydrazine oxidoreductase; Hzs; hydrazine synthase; Hyd; hydrogenase; Fdh; formate dehydrogenase; MCC; multiheme cytochrome; c; family; Mo-; bis; -MGD; molybdenum; bis; molybdopterin guanine dinucleotide; MK/MKH; ₂; menaquinone/menaquinol; N; nitrogen; Nap; periplasmic nitrate reductase; Nar; membrane-bound nitrate reductase; NC; nitrogen compound; NirK; copper nitrite reductase; NirS; cytochrome; cd; ₁; nitrite reductase; Nod; nitric oxide dismutase; Nor; nitric oxide reductase; Nos; nitrous oxide reductase; Nrf; cytochrome; c; nitrite reductase; Nxr; nitrite oxidoreductase; pMmo; particulate methane monooxygenase; pmf; proton motive force; Q/QH; ₂; quinone/quinol (unspecified); QRP; quinone/quinol-reactive protein; rET; reverse electron transport; Tat; twin arginine translocation; TMAO; trimethylamine; N; -oxide; UQ/UQH; ₂; ubiquinone/ubiquinolAnammox; Biogeochemical nitrogen cycle; Denitrification; Nitrification; Quinone/quinol-reactive protein module; Respiratory nitrate and nitrite ammonification

Denitrification and aerobic respiration, hybrid electron transport chains and co-evolution by Jianwei Chen; Marc Strous (pp. 136-144).

This paper explores the bioenergetics and potential co-evolution of denitrification and aerobic respiration. The advantages and disadvantages of combining these two pathways in a single, hybrid respiratory chain are discussed and the experimental evidence for the co-respiration of nitrate and oxygen is critically reviewed. A scenario for the co-evolution of the two pathways is presented. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.► The bioenergetics and potential co-evolution of denitrification and aerobic respiration are explored. ► The advantages and disadvantages of combining the two pathways in a single, hybrid respiratory chain are discussed. ► The experiment evidence for co-respiration of nitrate and oxygen is critically reviewed. ► A scenario for the co-evolution of the two pathways is presented.

Keywords: Abbreviations; Complex I; NADH dehydrogenase; Complex III; bc; ₁; complex; Complex IV; terminal oxidase; FMN; flavin-mono-nucleotide; ISP; iron sulfur protein; Mo-; bis; MGD; molybdenum; bis; molybdopterin guanine dinucleotide; Nap; periplasmic nitrate reductase; Nar; membrane bound nitrate reductase; Nir; nitrite reductase; Nod; nitric oxide dismutase; Nor; nitric oxide reductase; Nos; nitrous oxide reductase; Nrf; nitrite:ammonia oxidoreductase; Paz; pseudoazurin; Q; quinol; TAT; twin-arginine translocationDenitrification; Aerobic denitrification; Nitric oxide dismutation; Respiratory chain

Unifying concepts in anaerobic respiration: Insights from dissimilatory sulfur metabolism by Fabian Grein; Ana Raquel Ramos; Sofia S. Venceslau; Inês A.C. Pereira (pp. 145-160).

Behind the versatile nature of prokaryotic energy metabolism is a set of redox proteins having a highly modular character. It has become increasingly recognized that a limited number of redox modules or building blocks appear grouped in different arrangements, giving rise to different proteins and functionalities. This modularity most likely reveals a common and ancient origin for these redox modules, and is obviously reflected in similar energy conservation mechanisms. The dissimilation of sulfur compounds was probably one of the earliest biological strategies used by primitive organisms to obtain energy. Here, we review some of the redox proteins involved in dissimilatory sulfur metabolism, focusing on sulfate reducing organisms, and highlight links between these proteins and others involved in different processes of anaerobic respiration. Noteworthy are links to the complex iron–sulfur molybdoenzyme family, and heterodisulfide reductases of methanogenic archaea. We discuss how chemiosmotic and electron bifurcation/confurcation may be involved in energy conservation during sulfate reduction, and how introduction of an additional module, multiheme cytochromes c, opens an alternative bioenergetic strategy that seems to increase metabolic versatility. Finally, we highlight new families of heterodisulfide reductase-related proteins from non-methanogenic organisms, which indicate a widespread distribution for these protein modules and may indicate a more general involvement of thiol/disulfide conversions in energy metabolism. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.Display Omitted► Dissimilation of sulfur compounds is an ancient metabolism. ► We present proteins involved in dissimilatory sulfur metabolism. ► Their modular character and links to other respiratory systems are discussed. ► Unique complexes show links to CISM family and heterodisulfide reductases. ► Electron bifurcation linked to chemiosmotic mechanisms are proposed.

Keywords: Abbreviations; SRO; Sulfate reducing organisms; SOB; Sulfur oxidizing bacteria; LUCA; Last universal common ancestor; CISM; Complex iron–sulfur molybdoenzymes; TpI; c; ₃; Type I cytochrome; c; ₃; TpII; c; ₃; Type II cytochrome; c; ₃Anaerobic respiration; Dissimilatory sulfur metabolism; Sulfate reducing bacteria; Sulfur oxidizing bacteria; Redox module; Respiratory membrane complex

Insight into the evolution of the iron oxidation pathways by Marianne Ilbert; Violaine Bonnefoy (pp. 161-175).

Iron is a ubiquitous element in the universe. Ferrous iron (Fe(II)) was abundant in the primordial ocean until the oxygenation of the Earth's atmosphere led to its widespread oxidation and precipitation. This change of iron bioavailability likely put selective pressure on the evolution of life. This element is essential to most extant life forms and is an important cofactor in many redox-active proteins involved in a number of vital pathways. In addition, iron plays a central role in many environments as an energy source for some microorganisms. This review is focused on Fe(II) oxidation. The fact that the ability to oxidize Fe(II) is widely distributed in Bacteria and Archaea and in a number of quite different biotopes suggests that the dissimilatory Fe(II) oxidation is an ancient energy metabolism. Based on what is known today about Fe(II) oxidation pathways, we propose that they arose independently more than once in evolution and evolved convergently. The iron paleochemistry, the phylogeny, the physiology of the iron oxidizers, and the nature of the cofactors of the redox proteins involved in these pathways suggest a possible scenario for the timescale in which each type of Fe(II) oxidation pathways evolved. The nitrate dependent anoxic iron oxidizers are likely the most ancient iron oxidizers. We suggest that the phototrophic anoxic iron oxidizers arose in surface waters after the Archaea/ Bacteria-split but before the Great Oxidation Event. The neutrophilic oxic iron oxidizers possibly appeared in microaerobic marine environments prior to the Great Oxidation Event while the acidophilic ones emerged likely after the advent of atmospheric O₂. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.► Primordial ocean rich in ferrous iron ► Ferrous iron: an energy source for microorganisms ► Different strategies developed by microorganisms to oxidize ferrous iron ► Ferrous iron oxidation pathways evolution: more than one independent events ► Ferrous iron oxidation pathways: convergent evolution

Keywords: Ferrous iron; Paleogeochemistry; Iron oxidizing microorganisms; Evolution

Arsenics as bioenergetic substrates by Robert van Lis; Wolfgang Nitschke; Simon Duval; Barbara Schoepp-Cothenet (pp. 176-188).

Although at low concentrations, arsenic commonly occurs naturally as a local geological constituent. Whereas both arsenate and arsenite are strongly toxic to life, a number of prokaryotes use these compounds as electron acceptors or donors, respectively, for bioenergetic purposes via respiratory arsenate reductase, arsenite oxidase and alternative arsenite oxidase. The recent burst in discovered arsenite oxidizing and arsenate respiring microbes suggests the arsenic bioenergetic metabolisms to be anything but exotic. The first goal of the present review is to bring to light the widespread distribution and diversity of these metabolizing pathways. The second goal is to present an evolutionary analysis of these diverse energetic pathways. Taking into account not only the available data on the arsenic metabolizing enzymes and their phylogenetical relatives but also the palaeogeochemical records, we propose a crucial role of arsenite oxidation via arsenite oxidase in primordial life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.Display Omitted► Structural and functional presentation of arsenite oxidase and arsenate reductase ► Genetic organization of arsenite oxidase and arsenate reductase ► Diversity of pathways involving arsenic bioenergetic enzymes ► Evolutionary aspects of arsenic metabolisms

Keywords: Arsenic metabolism; Denitrification; Photosynthesis; O; ₂; respiration; Quinone; Evolution

Microbial metabolism of oxochlorates: A bioenergetic perspective by Thomas Nilsson; Maria Rova; Smedja Backlund Anna Smedja Bäcklund (pp. 189-197).

The microbial metabolism of oxochlorates is part of the biogeochemical cycle of chlorine. Organisms capable of growth using perchlorate or chlorate as respiratory electron acceptors are also interesting for applications in biotreatment of oxochlorate-containing effluents or bioremediation of contaminated areas. In this review, we discuss the reactions of oxochlorate respiration, the corresponding enzymes, and the relation to respiratory electron transport that can contribute to a proton gradient across the cell membrane. Enzymes specific for oxochlorate respiration are oxochlorate reductases and chlorite dismutase. The former belong to DMSO reductase family of molybdenum-containing enzymes. The heme protein chlorite dismutase, which decomposes chlorite into chloride and molecular oxygen, is only distantly related to other proteins with known functions. Pathways for electron transport may be different in perchlorate and chlorate reducers, but appear in both cases to be similar to pathways found in other respiratory systems. This article is part of a Special Issue entitled: Evolutionary aspects bioenergetic systems.► Oxochlorate respiration is widespread in nature and of interest for applications. ► (per)chlorate/chlorate reductase and chlorite dismutase are key enzymes. ► Also included are a microaerophilic oxidase and electron transport components. ► Different pathways for electron transport are used. ► The components have counterparts in other bioenergetic systems.

Keywords: Abbreviations; DMSO; dimethyl sulfoxide; E; _m,7; midpoint potential at pH 7Perchlorate reductase; Chlorate reductase; Chlorite dismutase; Respiration; Cytochrome; Electron transport

A missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases by Bruno C. Marreiros; Ana P. Batista; Afonso M.S. Duarte; Manuela M. Pereira (pp. 198-209).

Complex I of respiratory chains is an energy transducing enzyme present in most bacteria, mitochondria and chloroplasts. It catalyzes the oxidation of NADH and the reduction of quinones, coupled to cation translocation across the membrane. The complex has a modular structure composed of several proteins most of which are identified in other complexes. Close relations between complex I and group 4 membrane-bound [NiFe] hydrogenases and some subunits of multiple resistance to pH (Mrp) Na⁺/H⁺ antiporters have been observed before and the suggestion that complex I arose from the association of a soluble nicotinamide adenine dinucleotide (NAD⁺) reducing hydrogenase with a Mrp-like antiporter has been put forward. In this article we performed a thorough taxonomic profile of prokaryotic group 4 membrane-bound [NiFe] hydrogenases, complexes I and complex I-like enzymes. In addition we have investigated the different gene clustering organizations of such complexes. Our data show the presence of complexes related to hydrogenases but which do not contain the binding site of the catalytic centre. These complexes, named before as Ehr (energy-convertinghydrogenasesrelated complexes) are a missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases. Based on our observations we put forward a different perspective for the relation between complex I and related complexes. In addition we discuss the evolutionary, functional and mechanistic implications of this new perspective. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.► We performed a taxonomic profile of prokaryotic complex I and related enzymes. ► We investigated the different gene clustering organizations of such complexes. ► We identified complexes related to hydrogenases without the catalytic centre (Ehr). ► Ehr complexes are a missing link between complex I and hydrogenases. ► We propose a new perspective for the relation of complex I and related complexes.

Keywords: Abbreviations; DUF; domain of unknown function; Ech; energy-converting hydrogenase; Eha; energy-converting hydrogenase A; Ehr; energy-converting hydrogenase related complex; FHL-1; formate hydrogen lyase 1; Fpo; F; ₄₂₀; H; ₂; :phenazine oxidoreductase; Mbh; membrane‐bound hydrogenase; Mbx; membrane‐bound hydrogenase related complex; Mrp; multiple resistance to pH; Nuo; NADH:quinone oxidoreductaseComplex I; NADH:quinone oxidoreductase; Group 4 membrane‐bound hydrogenase; Ehr; Mrp Na; ⁺; /H; ⁺; antiporter; NuoH structure

Anaerobic energy metabolism in unicellular photosynthetic eukaryotes by Ariane Atteia; Robert van Lis; Aloysius G.M. Tielens; William F. Martin (pp. 210-223).

Anaerobic metabolic pathways allow unicellular organisms to tolerate or colonize anoxic environments. Over the past ten years, genome sequencing projects have brought a new light on the extent of anaerobic metabolism in eukaryotes. A surprising development has been that free-living unicellular algae capable of photoautotrophic lifestyle are, in terms of their enzymatic repertoire, among the best equipped eukaryotes known when it comes to anaerobic energy metabolism. Some of these algae are marine organisms, common in the oceans, others are more typically soil inhabitants. All these species are important from the ecological (O₂/CO₂ budget), biotechnological, and evolutionary perspectives. In the unicellular algae surveyed here, mixed-acid type fermentations are widespread while anaerobic respiration, which is more typical of eukaryotic heterotrophs, appears to be rare. The presence of a core anaerobic metabolism among the algae provides insights into its evolutionary origin, which traces to the eukaryote common ancestor. The predicted fermentative enzymes often exhibit an amino acid extension at the N-terminus, suggesting that these proteins might be compartmentalized in the cell, likely in the chloroplast or the mitochondrion. The green algae Chlamydomonas reinhardtii and Chlorella NC64 have the most extended set of fermentative enzymes reported so far. Among the eukaryotes with secondary plastids, the diatom Thalassiosira pseudonana has the most pronounced anaerobic capabilities as yet. From the standpoints of genomic, transcriptomic, and biochemical studies, anaerobic energy metabolism in C. reinhardtii remains the best characterized among photosynthetic protists. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.► Many eukaryotic algae can generate ATP anaerobically via mixed acid fermentations. ► Algae use the same enzymes as heterotrophic eukaryotes for anaerobic energy metabolism. ► Enzymes of algal fermentations were present in the algal and eukaryote common ancestor. ► The H₂-producing fermentations of Chlamydomonas are the best studied system to date. ► Anaerobic respirations in algae occur, for example nitrate, but have not been well-characterized.

Keywords: Abbreviations; ACS; acetate CoA synthetase; ACK; acetate kinase; ADHE; aldehyde/alcohol dehydrogenase; ASCT; acetate:succinate CoA-transferase; ATP; adenosine 5′ triphosphate; PTA; phosphotransacetylase; PFL; pyruvate formate-lyase; PFL-AE; pyruvate formate-lyase activating enzyme; PFO; pyruvate:ferredoxin oxidoreductase; SLP; substrate level phosphorylation Chlamydomonas; Photosynthetic alga; Metabolism; Fermentative enzyme; Compartmentalization; Evolution

Loss, replacement and gain of proteins at the origin of the mitochondria by Martijn A. Huynen; Isabel Duarte; Radek Szklarczyk (pp. 224-231).

We review what has been inferred about the changes at the level of the proteome that accompanied the evolution of the mitochondrion from an alphaproteobacterium. We regard these changes from an alphaproteobacterial perspective: which proteins were lost during mitochondrial evolution? And, of the proteins that were lost, which ones have been replaced by other, non-orthologous proteins with a similar function? Combining literature-supported replacements with quantitative analyses of mitochondrial proteomics data we infer that most of the loss and replacements that separate current day mitochondria in mammals from alphaproteobacteria took place before the radiation of the eukaryotes. Recent analyses show that also the acquisition of new proteins to the large protein complexes of the oxidative phosphorylation and the mitochondrial ribosome occurred mainly before the divergence of the eukaryotes. These results indicate a significant number of pivotal evolutionary events between the acquisition of the endosymbiont and the radiation of the eukaryotes and therewith support an early acquisition of mitochondria in eukaryotic evolution. Technically, advancements in the reconstruction of the evolutionary trajectories of loss, replacement and gain of mitochondrial proteins depend on using profile-based homology detection methods for sequence analysis. We highlight the mitochondrial Holliday junction resolvase endonuclease, for which such methods have detected new "family members" and in which function differentiation is accompanied by the loss of catalytic residues for the original enzymatic function and the gain of a protein domain for the new function. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.► Analysis of the loss of alphaproteobacterial proteins from mitochondria ► Overview of non-orthologous protein replacement in mitochondrial evolution ► Tracing the gain of supernumerary subunits in mitochondrial complex evolution ► Analysis of the evolution of the mitochondrial Holliday junction resolvase family

Keywords: Alphaproteobacteria; Mitochondrial proteome; Non-orthologous gene displacement; Holliday junction resolvase; Endosymbiosis

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BBA - Bioenergetics (v.1827, #2)