Bioenergetic Aspects of Halophilism

Examinination of microbial diversity in environments of increasing salt concentrations indicates that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis for H₂ + CO₂ or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. Occurrence of the different metabolic types is correlated with the free-energy change associated with the dissimilatory reactions. Life at high salt concentrations is energetically expensive. Most bacteria and also the methanogenic archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. All halophilic microorganisms expend large amounts of energy to maintain steep gradients of NA⁺ and K⁺ concentrations across their cytoplasmic membrane. The energetic cost of salt adaptation probably dictates what types of metabolism can support life at the highest salt concentrations. Use of KCl as an intracellular solute, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic-compatible solutes. This may explain why the anaerobic halophilic fermentative bacteria (order Haloanaerobiales) use this strategy and also why halophilic homoacetogenic bacteria that produce acetate from H₂ + CO₂ exist whereas methanogens that use the same substrates in a reaction with a similar free-energy yield do not.     

Bioenergetic Constraints on Primate Abundance

Explaining variation in primate population densities is central to understanding primate ecology, evolution, and conservation. Yet no researchers to date have successfully explained variation in primate population density across dietary class and phylogeny. Most previous work has focused on measures of food availability, as access to food energy likely constrains the number of individuals supported in a given area. However, energy output may provide a measure of energy constraints on population density that does not require detailed data on food availability for a given taxon. Across mammals, many studies have shown that population densities generally scale with body mass^−0.75. Because individual energy expenditures scale with body mass^0.75, population energy use (the product of population density and individual energy use) does not change with body mass, which suggests the existence of energy constraints on population density across body sizes, i.e., taxa are limited to a given amount of energy use, constraining larger taxa to lower densities. We examined population energy use and individual energy expenditure in primates and tested this energy equivalence across body mass. We also used a residual analysis to remove the effects of body mass on primate population densities and energy expenditures using basal metabolic rates (BMR; kcal/d) as a proxy for total daily energy expenditure. After taking into account phylogeny, population energy use did not significantly correlate with body mass. Larger primates, which use more energy per day, live at lower population densities than smaller primates. In addition, we found a significant negative correlation between residuals of BMR from body mass and residuals of population density from body mass after taking phylogeny into account. Thus, energy costs constrain population density across a diverse sample of primates at a given body mass, and primate species that have relatively low BMRs exist at relatively high densities. A better understanding of the determinants of primate energy costs across geography and phylogeny will ultimately help us explain and predict primate population densities.     

Bioenergetic aspects of halophilism.

Examination of microbial diversity in environments of increasing salt concentrations indicates that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis for H2 + CO2 or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. Occurrence of the different metabolic types is correlated with the free-energy change associated with the dissimilatory reactions. Life at high salt concentrations is energetically expensive. Most bacteria and also the methanogenic Archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. All halophilic microorganisms expend large amounts of energy to maintain steep gradients of NA+ and K+ concentrations across their cytoplasmic membrane. The energetic cost of salt adaptation probably dictates what types of metabolism can support life at the highest salt concentrations. Use of KCl as an intracellular solute, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic-compatible solutes. This may explain why the anaerobic halophilic fermentative bacteria (order Haloanaerobiales) use this strategy and also why halophilic homoacetogenic bacteria that produce acetate from H2 + CO2 exist whereas methanogens that use the same substrates in a reaction with a similar free-energy yield do not.     

Bioenergetic strategy of a xylem-feeder

To understand the efficiency of energy flow through an organism living in a nutrient poor environment, the bioenergetics of a xylem-feeding beetle Aredolpona rubra was investigated. The larvae of different ages were kept at a constant high, constant low and seasonally variable temperature or in agar plates and agar + nitrogen plates. Bioenergetic parameters were measured during the course of 1 year. The results showed (i) a very strong influence of food moisture on the bioenergetic parameters of A. rubra, (ii) the influence of temperature depends on whether it is fluctuating or constant, (iii) opposite mechanisms regulate growth in a shortage of water and at a suboptimal temperature: in the former case, consumption does not change while the metabolic rate decreases, and at a suboptimal temperature the metabolic rate is dictated by temperature and the consumption rate is altered and (iv) a nitrogen-rich diet results in a decreased metabolic rate, suggesting the existence of energetically costly adaptations to low quality wood as a food source. The study results have broad implications for environmental influences on insect life histories.     

Bioenergetic profiling of zebrafish embryonic development

Many debilitating conditions are linked to bioenergetic defects. Developing screens to probe the genetic and/or chemical basis for such links has proved intractable. Furthermore, there is a need for a physiologically relevant assay of bioenergetics in whole organisms, especially for early stages in life where perturbations could increase disease susceptibility with aging. Thus, we asked whether we could screen bioenergetics and mitochondrial function in the developing zebrafish embryo. We present a multiplexed method to assay bioenergetics in zebrafish embryos from the blastula period (3 hours post-fertilization, hpf) through to hatching (48 hpf). In proof of principle experiments, we measured respiration and acid extrusion of developing zebrafish embryos. We quantified respiratory coupling to various bioenergetic functions by using specific pharmacological inhibitors of bioenergetic pathways. We demonstrate that changes in the coupling to ATP turnover and proton leak are correlated with developmental stage. The multiwell format of this assay enables the user to screen for the effects of drugs and environmental agents on bioenergetics in the zebrafish embryo with high sensitivity and reproducibility.     

Bioenergetic challenges of microbial iron metabolisms

Before cyanobacteria invented oxygenic photosynthesis and O(2) and H(2)O began to cycle between respiration and photosynthesis, redox cycles between other elements were used to sustain microbial metabolism on a global scale. Today these cycles continue to occur in more specialized niches. In this review we focus on the bioenergetic aspects of one of these cycles - the iron cycle - because iron presents unique and fascinating challenges for cells that use it for energy. Although iron is an important nutrient for nearly all life forms, we restrict our discussion to energy-yielding pathways that use ferrous iron [Fe(II)] as an electron donor or ferric iron [Fe(III)] as an electron acceptor. We briefly review general concepts in bioenergetics, focusing on what is known about the mechanisms of electron transfer in Fe(II)-oxidizing and Fe(III)-reducing bacteria, and highlight aspects of their bioenergetic pathways that are poorly understood.     

Bioenergetic role of mitochondrial fusion and fission

Mitochondria are highly dynamic organelles. Frequent cycles of fusion and fission adapt the morphology of the mitochondrial compartment to the metabolic needs of the cell. Mitochondrial fusion is particularly important in respiratory active cells. It allows the spreading of metabolites, enzymes, and mitochondrial gene products throughout the entire mitochondrial compartment. This serves to optimize mitochondrial function and counteracts the accumulation of mitochondrial mutations during aging. Fragmented mitochondria are frequently found in resting cells, and mitochondrial fission plays an important role in the removal of damaged organelles by autophagy. Thus, mitochondrial fusion and fission both contribute to maintenance of mitochondrial function and optimize bioenergetic capacity. Multiple signalling pathways regulate the machinery of mitochondrial dynamics to adapt the shape of the mitochondrial compartment to the metabolic conditions of the cell. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).     

Bioenergetic consequences of protein overexpression in Saccharomyces cerevisiae

Summary Some bioenergetic consequences of overexpression of plasmid-encoded homologous (phosphoglycerate kinase), and heterologous (prochymosin), protein in S. cerevisiae strains grown in chemostat culture have been investigated. Both overexpressing strains were found to exhibit similar fermentation patterns despite a 10-fold difference in product expression levels. Biomass yields were lower than those for a control strain, and the onset of oxido-fermentative metabolism occurred at a lower dilution rate. A marked rise in cellular ATP content with increasing dilution rate during oxidative growth was observed in the strain overexpressing yeast phosphoglycerate kinase (PGK); this at present cannot be adequately explained. The inorganic phosphate content of the overexpressing strains was higher than that of the control and the phosphorylation potential of the prochymosin expressing strain was up to 10-fold lower than both the control and PGK overexpressing strains. It is proposed that expression of heterologous prochymosin imposes a greater energy drain on the host than overexpression of homologous PGK. This energetic drain may be a limiting factor in heterologous gene expression.     

神经退化性疾病生物能量代谢和氧化应激研究进展

衰老是导致几种常见的神经系统退化性疾病的主要危险因素,包括帕金森氏病（Ｐａｒｋｉｎｓｏｎ’ｓ ｄｉｓｅａｓｅ ＰＤ）,肌萎缩性侧索硬化（Ａｍｙｏｔｒｏｐｈｉｃ ｌａｔｅｒａｌ ｓｃｌｅｒｏｓｉｓ,ＡＬＳ）,早老性痴呆（Ａｌｚｈｅｉｍｅｒ’ｓ ｄｉｓｅａｓｅ ＡＤ）和亨廷顿氏病（Ｈｕｎｔｉｎｇｔｏｎ’ｓ ｄｉｓｅａｓｅ ＨＤ）。最近研究表明,神经退化性疾病涉及到线粒体缺陷,氧化应激等因素。在脑和其它组织中,老化可导致线粒体功能的损伤和氧化损伤的增强。ＰＤ病人中,已发现线粒体复合酶体Ⅰ活性降低,氧化损伤增加和抗氧化系统活性的改变。在几例家族性ＡＬＳ病人中,也发现Ｃｕ、Ｚｎ超氧化物歧化酶（Ｃｕ,Ｚｎ ＳＯＤ）基因的突变,导致Ｃｕ、Ｚｎ超氧化物歧化酶活性减低;散发的ＡＬＳ病人氧化损伤增高。在ＨＤ病人中已发现能量代谢异常     

Bioenergetic Constraints on the Evolution of Complex Life

All morphologically complex life on Earth, beyond the level of cyanobacteria, is eukaryotic. All eukaryotes share a common ancestor that was already a complex cell. Despite their biochemical virtuosity, prokaryotes show little tendency to evolve eukaryotic traits or large genomes. Here I argue that prokaryotes are constrained by their membrane bioenergetics, for fundamental reasons relating to the origin of life. Eukaryotes arose in a rare endosymbiosis between two prokaryotes, which broke the energetic constraints on prokaryotes and gave rise to mitochondria. Loss of almost all mitochondrial genes produced an extreme genomic asymmetry, in which tiny mitochondrial genomes support, energetically, a massive nuclear genome, giving eukaryotes three to five orders of magnitude more energy per gene than prokaryotes. The requirement for endosymbiosis radically altered selection on eukaryotes, potentially explaining the evolution of unique traits, including the nucleus, sex, two sexes, speciation, and aging.Evolutionary theory has enormous explanatory power and is understood in detail at the molecular genetic level, yet it cannot easily predict even the past. The history of life on Earth is troubling. Life apparently arose very early, perhaps 4 billion years ago, but then remained essentially bacterial for probably some 2–3 billion years. Bacteria and archaea explored almost every conceivable metabolic niche and still dominate in terms of biomass. Yet, in morphological diversity and genomic complexity, bacteria barely begin to compare with eukaryotes, even at the level of cells, let alone multicellular plants and animals. Eukaryotes are monophyletic and share a common ancestor that by definition arose only once, probably between 1.5 and 2 billion years ago, although the dates are poorly constrained (Knoll et al. 2006; Parfrey et al. 2011). The eukaryotic common ancestor already had a nucleus, nuclear pore complexes, introns and exons, straight chromosomes, mitosis and meiotic sex, a dynamic cytoskeleton, an endoplasmic reticulum, and mitochondria, making it difficult to trace the evolution of these traits from a prokaryotic state (Koonin 2010). The “eukaryotic niche”—limited metabolic diversity but enormous morphological complexity—was never invaded by prokaryotes. In short, life arose early, stagnated in morphological complexity for several billion years, and then rather abruptly gave rise to a single group—the eukaryotes—which explored the morphological realm of life in ways never seen in bacteria or archaea.Consider the possibility of life evolving on other planets. Would it follow a similar trajectory? If not, why not? Evolutionary theory gives little insight. The perplexing history of life on Earth conceals a paradox relating to natural selection. If basal eukaryotic traits such as the nucleus, meiotic sex, and phagocytosis arose by selection, starting with a prokaryotic ancestor, and each step offered some small advantage over the last, then why don’t the same traits arise repeatedly in prokaryotes too? Prokaryotes made many a start. There are examples of bacteria or archaea with nucleus-like structures (Lindsay et al. 2001), recombination (Smith et al. 1993), linear chromosomes (Bentley et al. 2002), internal membranes (Pinevich 1997), multiple replicons (Robinson and Bell 2007), giant size (Schulz and Jorgensen 2001), extreme polyploidy (Mendell et al. 2008), a dynamic cytoskeleton (Vats and Rothfield 2009), predation (Davidov and Jurkevitch 2009), parasitism (Moran 2007), introns and exons (Simon and Zimmerly 2008), intercellular signaling (Waters and Bassler 2005), endocytosis-like processes (Lonhienne et al. 2010), and even endosymbionts (Wujek 1979; von Dohlen et al. 2001). Yet, for each of these traits, bacteria and archaea stopped well short of the baroque complexity of eukaryotes. Compare this with the evolution of eyes. From a simple, light-sensitive spot in an early metazoan, morphologically disparate eyes arose on scores of occasions (Vopalensky and Kozmic 2009). This is exactly what evolutionary theory predicts. Each step offers an advantage in its own ecological setting, so morphologically different eyes arise on multiple occasions. Why is this not the case for traits such as the nucleus, meiotic sex, and phagocytosis? To suggest that lateral gene transfer (LGT) or bacterial conjugation is equivalent to meiotic sex will not do: Neither involves a systematic and reciprocal exchange of alleles across the entire genome.The simplest explanation is a bottleneck. The “big bang” radiation of major eukaryotic supergroups, combined with the apparent absence of surviving evolutionary intermediates between prokaryotes and the last eukaryotic common ancestor, does indeed hint at a bottleneck at the origin of eukaryotes. There is no shortage of environmental possibilities, from snowball glaciations to rising atmospheric oxygen. The most widely held explanation contends that when oxygen levels rose after the great oxidation event, some proto-eukaryotic cells acquired mitochondria, which protected them against oxygen toxicity (Andersson and Kurland 1999) and enabled them to exploit oxygen as a terminal electron acceptor in respiration (Sagan 1967), giving the first eukaryotes an enormous competitive advantage. They swiftly occupied new niches made available by oxygen, outcompeting to extinction any other prokaryotes that tried subsequently to invade this niche (de Duve 2007; Gross and Bhattacharya 2010). But this is an evolutionary “just-so story” and has no evidence to support it. The idea that mitochondria might protect against oxygen toxicity is nonsense: The single-electron donors of respiratory chains are among the most potent free-radical generators known. And what was to stop facultatively aerobic bacteria—from which the mitochondria evolved, hence already present—from occupying the aerobic niche first?In fact, the limited evidence available suggests that oxygen had little to do with it (Müller et al. 2012; van der Giezen and Lenton 2012). A large, diverse group of morphologically simple protists dubbed archezoa are the key here. The archezoa appear to lack mitochondria; and three decades ago, looked to branch deeply in the eukaryotic tree. Cavalier-Smith postulated that some archezoa might be primitively amitochondriate: surviving evolutionary intermediates between prokaryotes and eukaryotes (Cavalier-Smith 1987, 1989). But 20 years of careful molecular biology and phylogenetics have shown that all known archezoa possess specialized organelles that derive from mitochondria, namely hydrogenosomes or mitosomes (Keeling 1998; Embley and Martin 2006; van der Giezen 2009; Archibald 2011). The archezoa are obviously not real evolutionary intermediates, and radical developments in phylogenomics have transformed the eukaryotic tree to a “big-bang” radiation with no early branching archezoa (Koonin 2010). The archezoa remain significant not because they are genuine evolutionary intermediates, but because they are true ecological intermediates. Critically, they were not outcompeted to extinction by more sophisticated aerobic eukaryotes. On the contrary, they lost their capacity for aerobic respiration and depend instead on anaerobic fermentations, yet remain, morphologically, more complex than bacteria or archaea.The fact that the archezoa are a phylogenetically disparate group that arose on multiple occasions is equally significant. The “intermediate” niche is viable and was invaded many times, without the new arrivals being outcompeted to extinction by existing cells, or vice versa. Yet each time the invader was an anaerobic eukaryote, which adapted by reductive evolution to the niche—not bacteria or archaea evolving slightly greater complexity. What is the likelihood of this bias? Given at least 20 independent origins of archezoa (van der Giezen 2009; Müller et al. 2012), the probability of these ecological intermediates arising each time from the eukaryotes rather than prokaryotes is less than one in a million. It is far more parsimonious to assume that there was something about the structure of eukaryotes that facilitated their invasion of this intermediate niche; and, conversely, something about the structure of prokaryotes that tended to preclude their evolution of greater morphological complexity. But this quite reasonable statement is loaded because it implies that prokaryotes existed for nearly 4 billion years, and throughout that time showed no tendency to evolve greater morphological complexity. In stark contrast, eukaryotes arose just once, a seemingly improbable event.Here I argue that the constraint on prokaryotes was bioenergetic. There was, indeed, a bottleneck at the origin of eukaryotes, but it was biological (restrictive), not environmental (selective). It related to the physical structure of prokaryotic cells: Both bacteria and archaea respire across their plasma membrane. I make three key points, which arguably apply to life elsewhere in the universe, and are therefore proposed as biological principles that could guide our understanding of life generally: (1) chemiosmotic coupling is as universal as the genetic code, for fundamental reasons relating to the origin of life; (2) prokaryotes are constrained by chemiosmotic coupling across their plasma membrane, but eukaryotes escaped this constraint through a rare and stochastic endosymbiosis between two prokaryotes, giving them orders of magnitude more energy per gene; and (3) this endosymbiosis, in turn, produced a unique genomic asymmetry, transforming the selection pressures acting on eukaryotes and driving the evolution of unique eukaryotic traits.     

Bioenergetic aspects of apoptosis, necrosis and mitoptosis

In this review I summarize interrelations between bioenergetic processes and such programmed death phenomena as cell suicide (apoptosis and necrosis) and mitochondrial suicide (mitoptosis). The following conclusions are made. (I) ATP and rather often mitochondrial hyperpolarization (i.e. an increase in membrane potential, ΔΨ) are required for certain steps of apoptosis and necrosis. (II) Apoptosis, even if it is accompanied by ΔΨ and [ATP] increases at its early stage, finally results in a ΔΨ collapse and ATP decrease. (III) Moderate (about three-fold) lowering of [ATP] for short and long periods of time induces apoptosis and necrosis, respectively. In some types of apoptosis and necrosis, the cell death is mediated by a ΔΨ-dependent overproduction of ROS by the initial (Complex I) and the middle (Complex III) spans of the respiratory chain. ROS initiate mitoptosis which is postulated to rid the intracellular population of mitochondria from those that are ROS overproducing. Massive mitoptosis can result in cell death due to release to cytosol of the cell death proteins normally hidden in the mitochondrial intermembrane space.     

Multi-targeted Effect of Nicotinamide Mononucleotide on Brain Bioenergetic Metabolism

Neurochemical Research - Dysfunctions in NAD+ metabolism are associated with neurodegenerative diseases, acute brain injury, diabetes, and aging. Loss of NAD+ levels results in impairment of...     

Bioenergetic examination of the heterotrophic nitrifier-denitrifier Thiosphaera pantotropha

The heterotrophic nitrifying-denitrifying bacterium Thiosphaera pantotropha is remarkable as it nitrifies and denitrifies simultaneously. With respect to nitrogenous compounds, whether nitrification or denitrification results in energy conservation is of interest. Proton translocation studies were performed to determine if energy was conserved by the bacterium during heterotrophic nitrification and denitrification. Hydrazine (N₂H _inf5 ^sup+ ) was employed as the heterotrophic nitrification substrate while nitrate, nitrite and nitrous oxide were used as denitrification substrates. Analysis of the data indicate that the bacterium does not conserve energy when hydrazine was the substrate. Conversely, energy was conserved when either nitrate, nitrite or nitrous oxide functioned as the oxidants during denitrification-dependent proton translocation experiments. Thiosphaera pantotropha thus is similar to other heterotrophic nitrifiers-denitrifiers in that it conserves energy while denitrifying but has not been observed to do so when heterotrophically nitrifying.     

Liposomal and Mitochondrial Cytochrome Oxidase Display Similar Bioenergetic Properties

Abstract

Cytochrome c oxidase, the terminal electron acceptor of the respiratory chain of mitochondria, is an integral membrane protein. The bioenergetic properties of cytochrome oxidase can be studied only when the macromolecule is inserted in a phospholipid bilayer, either in situ or after reconstitution into liposomal membranes. Reintegration of purified cytochrome oxidase in liposomes allows quantitative tests of mechanistic hypothesis concerning the functional properties of the enzyme. Small unilamellar vesicles are prepared by sonication of purified soybean asolectin, and reconstitution of cytochrome oxidase in the bilayer is carried out according to the cholate/dialysis procedure. The proteoliposomes are shown to mimick the mitochondrial state of the enzyme in so far as liposomal cytochrome oxidase : a) displays the same vectorial orientation, the cytochrome c binding site being externally exposed, b) pumps protons in the physiological inside/outside direction, and c) is functionally controlled by the transmembrane electrochemical gradient, i.e. displays respiratory control.     

Bioenergetic processes in guard cells related to stomatal function

The energy required for ion uptake in guard cells is provided by two important bioenergetic processes, namely respiration and photosynthesis. The blue light-sensitive plasma membrane redox system is considered as the third bioenergetic phenomenon, since it uses blue light to create a proton gradient across the membrane. The unique features of respiration and photosynthesis in guard cells and their role in stomatal function are emphasized. Evidence for and against the blue light-sensitive components on plasma membrane (ATPase/distinct redox chain) and the photoreceptors (flavins, carotenoids, pterins) in guard cells are presented. The information on ion channels and their response to various kinds of secondary messengers including G-proteins, phosphoinositides, diacylglycerol, calcium, cAMP and protein kinases are reviewed. A model is presented indicating the possible mechanism of perception and transduction by guard cells of external signals and their interaction with different bioenergetic components.