Biochemical and thermodynamic analyses of energy conversion in extremophiles

A variety of extreme environments, characterized by extreme values of various physicochemical parameters (temperature, pressure, salinity, pH, and so on), are found on Earth. Organisms that favorably live in such extreme environments are called extremophiles. All living organisms, including extremophiles, must acquire energy to maintain cellular homeostasis, including extremophiles. For energy conversion in harsh environments, thermodynamically useful reactions and stable biomolecules are essential. In this review, I briefly summarize recent studies of extreme environments and extremophiles living in these environments and describe energy conversion processes in various extremophiles based on my previous research. Furthermore, I discuss the correlation between the biological system of electrotrophy, a third biological energy acquisition system, and the mechanism underlying microbiologically influenced corrosion. These insights into energy conversion in extremophiles may improve our understanding of the “limits of life”.

Abbreviations: PPi: pyrophosphate; PPase: pyrophosphatase; ITC: isothermal titration microcalorimetry; SVNTase: Shewanella violacea 5?-nucleotidase; SANTase: Shewanella amazonensis 5?-nucleotidase     

Bananas as an energy source during exercise: a metabolomics approach

This study compared the acute effect of ingesting bananas (BAN) versus a 6% carbohydrate drink (CHO) on 75-km cycling performance and post-exercise inflammation, oxidative stress, and innate immune function using traditional and metabolomics-based profiling. Trained cyclists (N?=?14) completed two 75-km cycling time trials (randomized, crossover) while ingesting BAN or CHO (0.2 g/kg carbohydrate every 15 min). Pre-, post-, and 1-h-post-exercise blood samples were analyzed for glucose, granulocyte (GR) and monocyte (MO) phagocytosis (PHAG) and oxidative burst activity, nine cytokines, F?-isoprostanes, ferric reducing ability of plasma (FRAP), and metabolic profiles using gas chromatography-mass spectrometry. Blood glucose levels and performance did not differ between BAN and CHO (2.41±0.22, 2.36±0.19 h, P?=?0.258). F?-isoprostanes, FRAP, IL-10, IL-2, IL-6, IL-8, TNFα, GR-PHAG, and MO-PHAG increased with exercise, with no trial differences except for higher levels during BAN for IL-10, IL-8, and FRAP (interaction effects, P?=?0.003, 0.004, and 0.012). Of 103 metabolites detected, 56 had exercise time effects, and only one (dopamine) had a pattern of change that differed between BAN and CHO. Plots from the PLS-DA model visualized a distinct separation in global metabolic scores between time points [R2Y(cum)?=?0.869, Q2(cum)?=?0.766]. Of the top 15 metabolites, five were related to liver glutathione production, eight to carbohydrate, lipid, and amino acid metabolism, and two were tricarboxylic acid cycle intermediates. BAN and CHO ingestion during 75-km cycling resulted in similar performance, blood glucose, inflammation, oxidative stress, and innate immune levels. Aside from higher dopamine in BAN, shifts in metabolites following BAN and CHO 75-km cycling time trials indicated a similar pattern of heightened production of glutathione and utilization of fuel substrates in several pathways.     

Microbial fuel cells as an alternative energy source: current status

Microbial fuel cell (MFC) technology is an emerging area for alternative renewable energy generation and it offers additional opportunities for environmental bioremediation. Recent scientific studies have focused on MFC reactor design as well as reactor operations to increase energy output. The advancement in alternative MFC models and their performance in recent years reflect the interests of scientific community to exploit this technology for wider practical applications and environmental benefit. This is reflected in the diversity of the substrates available for use in MFCs at an economically viable level. This review provides an overview of the commonly used MFC designs and materials along with the basic operating parameters that have been developed in recent years. Still, many limitations and challenges exist for MFC development that needs to be further addressed to make them economically feasible for general use. These include continued improvements in fuel cell design and efficiency as well scale-up with economically practical applications tailored to local needs.     

Ecological succession as an energy dispersal process

Ecological succession is described by the 2nd law of thermodynamics. According to the universal law of the maximal energy dispersal, an ecosystem evolves toward a stationary state in its surroundings by consuming free energy via diverse mechanisms. Species are the mechanisms that conduct energy down along gradients between repositories of energy which consist of populations at various thermodynamic levels. The salient characteristics of succession, growing biomass production, increasing species richness and shifting distributions of species are found as consequences of the universal quest to diminish energy density differences in least time. The analysis reveals that during succession the ecosystem's energy transduction network, i.e., the food web organizes increasingly more effective in the free energy reduction by acquiring new, more effective and abandoning old, less effective species of energy transduction. The number of species does not necessarily peak at the climax state that corresponds to the maximum-entropy partition of species maximizing consumption of free energy. According to the theory of evolution by natural selection founded on statistical physics of open systems, ecological succession is one among many other evolutionary processes.     

Inorganic pyrophosphate as an energy source for ruminal bacteria

The ability of the predominant ruminal flora to utilize inorganic pyrophosphate as an energy source was examined. Rumen contents from steers fed diets containing pyrophosphate from 0%–0.13% of the diet dry matter were serially diluted and inoculated into (a) basal medium, no carbohydrates (BM); (b) basal medium plus pyrophosphate (0.05%) (BP); (c) basal medium plus carbohydrates (CM); and (d) basal medium plus carbohydrates plus pyrophosphate (0.05%) (CP). Growth was measured as increase in optical density. Addition of pyrophosphate to the CM medium reduced the maximum optical density by 36% and 98% in tubes inoculated with 10^–1 and 10^–3 dilutions of rumen contents, repectively. No growth occurred in pyrophosphate-containing media at dilutions higher than 10^–3. In vitro enrichment of bacteria growing on pyrophosphate did not increase the growth yield. These result indicate that the predominant ruminal bacteria do not utilize pyrophosphate as an energy source.     

Biomass production and alcoholic fermentation performance of Saccharomyces cerevisiae as a function of nitrogen source

Nitrogen limitation is one of the most common causes for stuck or sluggish fermentation. A broad range of values have been reported as the minimum nitrogen concentration necessary for the completion of alcoholic fermentation. We have analyzed the minimum nitrogen concentration required to yield the maximum biomass (nitrogen reference value) using a microwell plate reader to monitor fermentation with different nitrogen sources and sugar concentrations. The biomass yield was dependent on the amount of available nitrogen, the nature of nitrogen source, and the sugar concentration in the medium. Nevertheless, achieving the maximum biomass was not sufficient to ensure the completion of the alcoholic fermentation, because the fermentation of 280?g?sugar?L(-1) stuck, regardless of the nature and concentration of nitrogen source. However, a mixture of five amino acids (Leu, Ile, Val, Phe and Thr) as the nitrogen source allowed for maximum sugar consumption. Analysis of cell vitality by impedance showed a significant improvement in the vitality for cells fermenting using this amino acid combination.     

Polyphosphates as an energy source for growth of Saccharomyces cerevisiae

Cells of the yeast Saccharomyces cerevisiae with a low content of polyphosphates (polyP) are characterized by disturbance of growth in medium with 0.5% glucose. The parent strain with polyP level reduced by phosphate starvation had a longer lag phase. The growth rate of strains with genetically determined low content of polyP due to their enhanced hydrolysis (CRN/pMB1_PPN1 Sc is a superproducer of exopolyphosphatase PPN1) or reduced synthesis (the BY4741 vma2Δ mutant with impaired vacuolar membrane energization) was lower in the exponential phase. The growth of cells with high content of polyP was accompanied by polyP consumption. In cells of strains with low content of polyP, CRN/pMB1_PPN1 Sc and BY4741 vma2Δ, their consumption was insignificant. These findings provide more evidence indicating the use of polyP as an extra energy source for maintaining high growth rate.     

Microwave heating as an energy source for the predrying of herbage samples

Summary Preliminary experiments have shown that a commercial microwave cooking range can give a very rapid low-temperature drying of herbage samples. Its throughput can compete with hot-air ovens used for laboratory drying. The capital cost of the equipment will resrict its use to samples for chemical or biochemical analysis. The samples obtained are similar to freeze-dried samples.     

Membrane phospholipids as an energy source in the operation of the visual cycle

Biology depends on the coupling of the free energy of hydrolysis of phosphate esters, such as ATP, to drive processes which would otherwise be thermodynamically unfavorable. Carboxyl esters are like phosphate esters in their ability to hydrolyze with substantial negative free energies, enabling them to participate in group transfer processes as well. In particular, membrane phospholipids constitute an enormous store of potential energy that could be used to fuel energetically unfavorable processes. One such process involves the biosynthesis of 11-cis-retinal, the chromophore of rhodopsin, from all-trans-retinol (vitamin A). The difference in free energy between an all-trans retinoid and its corresponding 11-cis retinoid is approximately 4 kcal/mol. This energy is provided for in a minimally two-step process involving membrane phospholipids as the energy source. First, all-trans-retinol is esterified in the retinal pigment epithelium by lecithin retinol acyl transferase (LRAT) to produce an all-trans-retinyl ester. Second, this ester is transformed into 11-cis-retinol by an isomerohydrolase in a process that couples the negative free energy of hydrolysis of the acyl ester to the formation of the strained 11-cis-retinol.     

Efficiency of energy conversion in model biological pumps: Optimization by linear nonequilibrium thermodynamic relations

Experimental investigations showed linear relations between flows and forces in some biological energy converters operating far from equilibrium. This observation cannot be understood on the basis of conventional nonequilibrium thermodynamics. Therefore, the efficiencies of a linear and a nonlinear mode of operation of an energy converter (a hypothetical redox-driven H⁺ pump) were compared. This comparison revealed that at physiological values of the forces and degrees of coupling (1) the force ratio permitting optimal efficiency was much higher in the linear than in the nonlinear mode and (2) the linear mode of operation was at least 10⁶-times more efficient that the nonlinear one. These observations suggest that the experimentally observed linear relations between flows and forces, particularly in the case of oxidative phosphorylation, may be due to a feedback regulation maintaining linear thermodynamic relations far from equilibrium. This regulation may have come about as the consequence of an evolutionary drive towards higher efficiency.     

Distillers grains as an energy source and effect of drying on protein availability

The use of distillers byproducts as energy sources would expand the market for these byproducts. Drying of these byproducts may produce changes that affect the nutritional value. A series of experiments was conducted to evaluate distillers byproducts as an energy source for finishing cattle and to compare wet vs. dried byproducts. The energy value of wet distillers byproducts was 132 to 174% the value of dry rolled corn for finishing cattle when the byproducts were fed as 40% of the diet dry matter. Distillers dried grains plus solubles were 130% the energy value of corn. Acid detergent insoluble nitrogen level of the dried grains did not affect feeding value. Distillers dried grains plus solubles were equal in protein value to wet byproducts when fed to growing calves. Acid detergent insoluble nitrogen level did not affect protein utilization of dried distillers byproducts.     

Plant and animal wastes composting: Effects of the N source on process performance

The aim of this work was to evaluate the impact of different N-rich animal wastes on the composting of ligno-cellulosic wastes by a range of classical and novel methods, with particular emphasis on microbial community composition.     

Ecosystem engineering as an energy transfer process: a simple agent-based model

Ecosystem engineers are defined as organisms who modulate the availability of resources for themselves and other organisms by physically changing the environment. Ecosystem engineering is a well-recognised ecological interaction, but there is a limited number of general models due to the recent development of the field. Agent-based models are often used to study how organisms respond to changing environments and are suitable for modelling ecosystem engineering. To our knowledge, agent-based methodology has not yet been used to model ecosystem engineering. In this paper, we develop a simple agent-based population dynamics model of ecosystem engineering as an energy transfer process. We apply energy budget approach to conceptually explain how ecosystem engineers transfer energy to the environment and define various types of energy transfers relative to their effects on the engineers and other organisms. We simulate environments with various levels of resource abundance and compare the results of the model without ecosystem engineering agents to the model with ecosystem engineering agents. We find that in environments with higher levels of resources, the presence of ecosystem engineers increases the average carrying capacity and the strength of population fluctuations, while in environments with lower levels of resources, ecosystem engineering mitigates fluctuations, increases average carrying capacity and makes environments more resilient. Finally, we discuss about the further application of agent-based modelling for the theoretical and experimental development of the ecosystem engineering concept.     

Fluctuations in repressor control: thermodynamic constraints on stochastic focusing

The influence of fluctuations in molecule numbers on genetic control circuits has received considerable attention. The consensus has been that such fluctuations will make regulation less precise. In contrast, it has more recently been shown that signal fluctuations can sharpen the response in a regulated process by the principle of stochastic focusing (SF) (, Proc. Natl. Acad. Sci. USA. 97:7148-7153). In many cases, the larger the fluctuations are, the sharper is the response. Here we investigate how fluctuations in repressor or corepressor numbers can improve the control of gene expression. Because SF is found to be constrained by detailed balance, this requires that the control loops contain driven processes out of equilibrium. Some simple and realistic out-of-equilibrium steps that will break detailed balance and make room for SF in such systems are discussed. We conclude that when the active repressors are controlled by corepressor molecules that display large ("coherent") number fluctuations or when corepressors can be irreversibly removed directly from promoter-bound repressors, the response in gene activity can become significantly sharper than without intrinsic noise. A simple experimental design to establish the possibility of SF for repressor control is suggested.     

The chloroplast Tat pathway utilizes the transmembrane electric potential as an energy source

The thylakoid membrane, located inside the chloroplast, requires proteins transported across it for plastid biogenesis and functional photosynthetic electron transport. The chloroplast Tat translocator found on thylakoids transports proteins from the plastid stroma to the thylakoid lumen. Previous studies have shown that the chloroplast Tat pathway is independent of NTP hydrolysis as an energy source and instead depends on the thylakoid transmembrane proton gradient to power protein translocation. Because of its localization on the same membrane as the proton motive force-dependent F(0)F(1) ATPase, we believed that the chloroplast Tat pathway also made use of the thylakoid electric potential for transporting substrates. By adjusting the rate of photosynthetic proton pumping and by utilizing ionophores, we show that the chloroplast Tat pathway can also utilize the transmembrane electric potential for protein transport. Our findings indicate that the chloroplast Tat pathway is likely dependent on the total protonmotive force (PMF) as an energy source. As a protonmotive-dependent device, certain predictions can be made about structural features expected to be found in the Tat translocon, specifically, the presence of a proton well, a device in the membrane that converts electrical potential into chemical potential.     

Review: microbial mechanisms of accessing insoluble Fe(III) as an energy source

Of all the terminal electron acceptors, Fe(III) is the most naturally abundant in many subsurface environments. Fe(III)-reducing microorganisms are phylogenetically diverse and have been isolated from a variety of sources. Unlike most electron acceptors, Fe(III) has a very low solubility and is usually present as insoluble oxides at neutral pH. The mechanisms by which microorganisms access and reduce insoluble Fe(III) are poorly understood. Initially, it was considered that microorganisms could only reduce insoluble Fe(III) through direct contact with the oxide. However, recent studies indicate that extracellular electron shuttling or Fe(III)-chelating compounds may alleviate the need for cell–oxide contact. These include microbially secreted compounds or exogenous electron shuttling agents, mainly from humic substances. Electron shuttling via humic substances is likely a significant process for Fe(III) reduction in subsurface environments. This paper reviews the various mechanisms by which Fe(III) reduction may be occurring in pure culture and in soils and sediments.     

The three-state model for the elementary process of energy conversion in muscle

A three-state model for the elementary process of energy conversion in striated muscle is analysed; in two of the three states, the crossbridge is attached to an actin site, while the third is a detached state. This model accounts for the mechanical properties of steady shortening and lengthening processes as well as those of isometric and isotonic transient processes in a quantitative way. Moreover, qualitative agreement is obtained for the total energy liberation from muscle. Biochemical properties are also computed for transient processes. Comparisons are made with other models with “three states”.