BBA - Bioenergetics (v.1504, #1)

Understanding the control of mitochondrial energy metabolism is central to knowing how mitochondria function within cells. Metabolic control analysis is the best approach available for studying the control of mitochondrial energy metabolism. Here I outline how metabolic control analysis has been used to help understand mitochondrial regulation, damage and pharmacology.
Keywords: Metabolic control analysis; Mitochondrial energy metabolism; Mitochondrial dysfunction;

The classical concept of ATP-demand control of energy metabolism in skeletal muscle has to be modified on the basis of studies showing the influence of additional controlling parameters (reducing equivalent supply, oxygen availability, proton leak, diffusion restrictions and the creatine kinase system) and on the basis of applications of metabolic control analysis showing very clearly multistep control. This concept of multistep control allows to quantify the individual influence of any parameter on mitochondrial oxidative phosphorylation and is extremely helpful to analyze the metabolic consequences of enzyme deficiencies in skeletal muscle occurring in mitochondrial myopathies.
Keywords: Mitochondrial oxidative phosphorylation; Skeletal muscle; Flux control; Metabolic control analysis; Metabolic threshold;

What do mitochondrial diseases teach us about normal mitochondrial functions... that we already knew: threshold expression of mitochondrial defects by Jean-Pierre Mazat; Rodrigue Rossignol; Monique Malgat; Christophe Rocher; Benjamin Faustin; Thierry Letellier (20-30).
This paper shows how metabolic control analysis (MCA) can help to explain two important features of mitochondrial diseases: (i) the existence of a threshold in the expression of the complex deficiencies on the respiratory flux or on ATP synthesis, i.e. the fact that it is necessary to have a large complex deficiency in order to observe a substantial decrease in these fluxes; (ii) the tissue specificity, i.e. the fact that all tissues are not affected, even if the complex deficiency is present in all of them. We also show the limits of MCA, particularly when considering the in vivo situation. However, MCA offers a new way to consider mitochondrial diseases. The fact that fluxes only slightly change, when a complex is affected, is done at the expense of great changes in intermediate metabolite concentrations; intermediate metabolites situated upstream from the deficient complex are more reduced, leading to a greater generation of free radicals. This could bring an explanation for the diseases observed in conditions where the mitochondrial rate of ATP synthesis is only slightly affected.
Keywords: Inborn error of metabolism; Mitochondria; Oxidative phosphorylation; Mitochondrial diseases; Metabolic control analysis;

The theoretical studies on the regulation of oxidative phosphorylation that were performed with the aid of kinetic models of this process are overviewed. A definition of the regulation of the flux through a metabolic pathway is proposed and opposed to the control exerted by particular enzymes over this flux. Different kinetic models of oxidative phosphorylation proposed in the literature are presented, of which only the model proposed by myself and co-workers was extensively used in theoretical studies on the regulation and compensation in the oxidative phosphorylation system. These theoretical studies have led to the following conclusions: (1) in isolated mitochondria, an increase in the activity of an artificial ATP-using system stimulates mitochondria mainly via changes in [ADP], while changes in [ATP] and [Pi] play only a minor role; (2) in non-excitable tissues (e.g. liver), hormones (acting via some cytosolic factor(s)) activate directly both ATP usage and at least some enzymes of the ATP-producing block; (3) in excitable tissues (e.g. skeletal muscle), neural signals stimulate (via some cytosolic factor(s)) in parallel all the steps of oxidative phosphorylation together with ATP usage and substrate dehydrogenation; (4) the decrease in the flux through cytochrome oxidase caused by a decrease in oxygen concentration is, at least partially, compensated by a decrease in Δp and increase in the reduction level of cytochrome c. A theoretical prediction is formulated that there should exist and be observable a universal cytosolic factor/regulatory mechanism which directly activates (at least in excitable tissues) all complexes of oxidative phosphorylation during an increased energy demand.
Keywords: Regulation of metabolism; Oxidative phosphorylation; Mitochondrion; Energy demand; Computer model; Theoretical prediction;

Nitric oxide (NO) and its derivatives inhibit mitochondrial respiration by a variety of means. Nanomolar concentrations of NO immediately, specifically and reversibly inhibit cytochrome oxidase in competition with oxygen, in isolated cytochrome oxidase, mitochondria, nerve terminals, cultured cells and tissues. Higher concentrations of NO and its derivatives (peroxynitrite, nitrogen dioxide or nitrosothiols) can cause irreversible inhibition of the respiratory chain, uncoupling, permeability transition, and/or cell death. Isolated mitochondria, cultured cells, isolated tissues and animals in vivo display respiratory inhibition by endogenously produced NO from constitutive isoforms of NO synthase (NOS), which may be largely mediated by NO inhibition of cytochrome oxidase. Cultured cells expressing the inducible isoform of NOS (iNOS) can acutely and reversibly inhibit their own cellular respiration and that of co-incubated cells due to NO inhibition of cytochrome oxidase, but after longer-term incubation result in irreversible inhibition of cellular respiration due to NO or its derivatives. Thus the NO inhibition of cytochrome oxidase may be involved in the physiological and/or pathological regulation of respiration rate, and its affinity for oxygen.
Keywords: Nitric oxide; Mitochondrion; Cytochrome oxidase; Respiration; Oxygen consumption;

Control of plant mitochondrial respiration by Charles Affourtit; Klaas Krab; Anthony L. Moore (58-69).
Plant mitochondria are characterised by the presence of both phosphorylating (cytochrome) and non-phosphorylating (alternative) respiratory pathways, the relative activities of which directly affect the efficiency of mitochondrial energy conservation. Different approaches to study the regulation of the partitioning of reducing equivalents between these routes are critically reviewed. Furthermore, an updated view is provided regarding the understanding of plant mitochondrial respiration in terms of metabolic control. We emphasise the extent to which kinetic modelling and ‘top-down’ metabolic control analysis improve the insight in phenomena related to plant mitochondrial respiration. This is illustrated with an example regarding the affinity of the plant alternative oxidase for oxygen.
Keywords: Plant mitochondrion; Respiration; Alternative oxidase; Ubiquinone-pool; Kinetic modelling; Metabolic control analysis;

Brown fat is a thermogenic organ that allows newborns and small mammals to maintain a stable body temperature when exposed to cold. The heat generation capacity is based on the uncoupling of respiration from ATP synthesis mediated by the uncoupling protein UCP1. The first studies on the properties of these mitochondria revealed that fatty acid removal was an absolute prerequisite for respiratory control. Thus fatty acids, that are substrate for oxidation, were proposed as regulators of respiration. However, their ability to uncouple all types of mitochondria and the demonstration that several mitochondrial carriers catalyze the translocation of the fatty acid anion have made them unlikely candidates for a specific role in brown fat. Nevertheless, data strongly argue for a physiological function. First, fatty acids mimic the noradrenaline effects on adipocytes. Second, there exists a precise correlation between fatty acid sensitivity and the levels of UCP1. Finally, fatty acids increase the conductance by facilitating proton translocation, a mechanism that is distinct from the fatty acid uncoupling mediated by other mitochondrial carriers. The regulation of UCP1 and UCP2 by retinoids and the lack of effects of fatty acids on UCP2 or UCP3 are starting to set differences among the new uncoupling proteins.
Keywords: Uncoupling protein; UCP1; UCP2; Fatty acid; Retinoid; Thermogenesis; Mitochondrion;

UCP1: the only protein able to mediate adaptive non-shivering thermogenesis and metabolic inefficiency by Jan Nedergaard; Valeria Golozoubova; Anita Matthias; Abolfazl Asadi; Anders Jacobsson; Barbara Cannon (82-106).
The uniqueness of UCP1 (as compared to UCP2/UCP3) is evident from expression analysis and ablation studies. UCP1 expression is positively correlated with metabolic inefficiency, being increased by cold acclimation (in adults or perinatally) and overfeeding, and reduced in fasting and genetic obesity. Such a simple relationship is not observable for UCP2/UCP3. Studies with UCP1-ablated animals substantiate the unique role of UCP1: the phenomenon of adaptive adrenergic non-shivering thermogenesis in the intact animal is fully dependent on the presence of UCP1, and so is any kind of cold acclimation-recruited non-shivering thermogenesis; thus UCP2/UCP3 (or any other proteins or metabolic processes) cannot substitute for UCP1 physiologically, irrespective of their demonstrated ability to show uncoupling in reconstituted systems or when ectopically expressed. Norepinephrine-induced thermogenesis in brown-fat cells is absolutely dependent on UCP1, as is the uncoupled state and the recoupling by purine nucleotides in isolated brown-fat mitochondria. Although very high UCP2/UCP3 mRNA levels are observed in brown adipose tissue of UCP1-ablated mice, there is no indication that the isolated brown-fat mitochondria are uncoupled; thus, high expression of UCP2/UCP3 does not necessarily confer to the mitochondria of a tissue a propensity for being innately uncoupled. Whereas the thermogenic effect of fatty acids in brown-fat cells is fully UCP1-dependent, this is not the case in brown-fat mitochondria; this adds complexity to the issues concerning the mechanisms of UCP1 function and the pathway from β3-adrenoceptor stimulation to UCP1 activation and thermogenesis. In addition to amino acid sequences conserved in all UCPs as part of the tripartite structure, all UCPs contain certain residues associated with nucleotide binding. However, conserved amongst all UCP1s so far sequenced, and without parallel in all UCP2/UCP3, are two sequences: 144SHLHGIKP and the C-terminal sequence RQTVDC(A/T)T; these sequences may therefore be essential for the unique thermogenic function of UCP1. The level of UCP1 in the organism is basically regulated at the transcriptional level (physiologically probably mainly through the β3-adrenoceptor/CREB pathway), with influences from UCP1 mRNA stability and from the delay caused by translation. It is concluded that UCP1 is unique amongst the uncoupling proteins and is the only protein able to mediate adaptive non-shivering thermogenesis and the ensuing metabolic inefficiency.
Keywords: Uncoupling proteins; Mitochondria; Brown adipose tissue; Fatty acids; Non-shivering thermogenesis;

Homologues of the uncoupling protein from brown adipose tissue (UCP1): UCP2, UCP3, BMCP1 and UCP4 by Frédéric Bouillaud; Elodie Couplan; Claire Pecqueur; Daniel Ricquier (107-119).
Keywords: Mitochondrion; Uncoupling protein; Energy expenditure; Recombinant expression; Membrane protein; Proton transport;

In mitochondria ATP synthesis is not perfectly coupled to oxygen consumption due to proton leak across the mitochondrial inner membrane. Quantitative studies have shown that proton leak contributes to ∼25% of the resting oxygen consumption of mammals. Proton leak plays a role in accounting for differences in basal metabolic rate. Thyroid studies, body mass studies, phylogenic studies and obesity studies have all shown that increased mass-specific metabolic rate is linked to increased mitochondrial proton leak. The mechanism of the proton leak is unclear. Evidence suggests that proton leak occurs by a non-specific diffusion process across the mitochondrial inner membrane. However, the high degree of sequence homology of the recently cloned uncoupling proteins UCP 2 and UCP 3 to brown adipose tissue UCP 1, and their extensive tissue distribution, suggest that these novel uncoupling proteins play a role in proton leak. Early indications from reconstitution experiments and several in vitro expression studies suggest that the novel uncoupling proteins uncouple mitochondria. Furthermore, mice overexpressing UCP 3 certainly show a phenotype consistent with increased metabolism. The evidence for a role for these novel UCPs in mitochondrial proton leak is reviewed.
Keywords: Mitochondrion; Oxidative phosphorylation; Proton leak; Uncoupling protein(s); Oxygen consumption; Basal metabolic rate;

Uncoupling proteins: the issues from a biochemist point of view by Martin Klingenberg; Karim S Echtay (128-143).
The functional characteristics of uncoupling proteins (UCP) are reviewed, with the main focus on the results with isolated and reconstituted proteins. UCP1 from brown adipose tissue, the paradigm of the UCP subfamily, is treated in more detail. The issues addressed are the role and mechanism of fatty acids, the nucleotide binding, the regulation by pH and the identification by mutagenesis of residues involved in these functions. The transport and regulatory functions of UCP2 and 3 are reviewed in comparison to UCP1. The inconsistencies of a proposed nucleotide insensitive H+ transport by these UCPs as concluded from the expression in yeast and Escherichia coli are elucidated. In both expression system UCP 2 and 3 are not in or cannot be converted to a functionally native state and thus also for these UCPs a nucleotide regulated H + transport is postulated.
Keywords: Uncoupling protein; H+ transport; Cl transport; Fatty acid; Nucleotide binding; Site-directed mutagenesis; Thermogenesis; Brown adipose tissue;

Mitochondrial proton leak and the uncoupling protein 1 homologues by J.A Stuart; S Cadenas; M.B Jekabsons; D Roussel; M.D Brand (144-158).
Mitochondrial proton leak is the largest single contributor to the standard metabolic rate (SMR) of a rat, accounting for about 20% of SMR. Yet the mechanisms by which proton leak occurs are incompletely understood. The available evidence suggests that both phospholipids and proteins in the mitochondrial inner membrane are important determinants of proton conductance. The uncoupling protein 1 homologues (e.g. UCP2, UCP3) may play a role in mediating proton leak, but it is unlikely they account for all of the observed proton conductance. Experimental data regarding the functions of these proteins include important ambiguities and contradictions which must be addressed before their function can be confirmed. The physiological role of the proton leak, and of the uncoupling protein 1 homologues, remains similarly unclear.
Keywords: Mitochondrion; Proton conductance; Basal metabolic rate; Respiration; UCP1; UCP2; UCP3; BMCP1; Fatty acid; Brown adipose tissue; Thermogenesis; Zebrafish; Carp;

Mitochondrial efficiency: lessons learned from transgenic mice by Mary-Ellen Harper; Jean Himms-Hagen (159-172).
Metabolic research has, like most areas of research in the life sciences, been affected dramatically by the application of transgenic technologies. Within the specific area of bioenergetics it has been thought that transgenic approaches in mice would provide definitive proof for some longstanding metabolic theories and assumptions. Here we review a number of transgenic approaches that have been used in mice to address theories of mitochondrial efficiency. The focus is largely on genes that affect the coupling of energy substrate oxidation to ATP synthesis, and thus, mice in which the uncoupling protein (Ucp) genes are modified are discussed extensively. Transgenic approaches have indeed provided proof-of-concept in some instances, but in many other instances they have yielded results that are in contrast to initial hypotheses. Many studies have also shown that genetic background can affect phenotypic outcomes, and that the upregulated expression of genes that are related to the modified gene often complicates the interpretation of findings.
Keywords: Uncoupling protein; Oxidative phosphorylation; Thermogenesis; Brown adipose tissue; Energy expenditure; Mouse; Obesity;