The Evolution of Bioluminescent Oxygen Consumption as an Ancient Oxygen Detoxification Mechanism

Endogenous reductants such as hydrogen sulfide and alkylthiols provided free radical scavenging systems during the early evolution of life. The development of oxygenic photosynthesis spectacularly increased oxygen levels, and ancient life forms were obliged to develop additional antioxidative systems. We develop here the hypothesis of how ``prototypical' bioluminescent reactions had a plausible role as an ancient defense against oxygen toxicity through their ``futile' consumption of oxygen. As oxygen concentrations increased, sufficient light would have been emitted from such systems for detection by primitive photosensors, and evolutionary pressures could then act upon the light emitting characteristics of such systems independently of their use as futile consumers of oxygen. Finally, an example of survival of this ancient mechanism in present-day bioluminescent bacteria (in the Euprymna scolopes–Vibrio fischeri mutualism) is discussed. Once increasing ambient oxygen levels reached sufficiently high levels, the use of ``futile' oxygen consumption became too bioenergetically costly, so that from this time the evolution of bioluminescence via this role was made impossible, and other mechanisms must be developed to account for the evolution of bioluminescence by a wide range of organisms that patently occurred after this (e.g., by insects). Received: 25 May 2000 / Accepted: 14 November 2000     

The origin of membranes

The physicochemical conditions of the environment in which life arose are discussed, along with the appearance of protocells, their membranous envelope and the subsequent appearance of plasma membranes. The hypothesis that the first cells originated in reservoirs where potassium and magnesium salts (necessary for protein synthesis and thus for the formation of a cellular membrane) dominated, is substantiated. This was followed by adaptation of these cells to an external ocean-like environment, where sodium salts were prevalent. This stage of evolution required a plasma membrane capable of providing ion asymmetry between the cell’s cytoplasm and the external environment. At this stage of evolution in the predecessors of animals, the process of removal of sodium ions and accumulation of potassium ions began functioning in the plasma membrane. The problem of multicellular organisms was solved differently by animals and plants: animals developed a system of the extracellular fluids that provided stable physicochemical conditions on the external surface of the plasma membrane. Sodium ions were the stimulus for the formation of the polar cell, where sodium channels are situated on one side of the plasma membrane, and sodium pumps on the other, allowing the development of the absorption, excretion and breathing functions. The formation of fluids of the internal environment enabled the development of homeostasis and facilitated the biological progress of the animal kingdom.     

Quantifying the ion selectivity of the Ca2+ site in photosystem II: evidence for direct involvement of Ca2+ in O2 formation.

Calcium is an essential cofactor in the oxygen-evolving complex (OEC) of photosystem II (PSII). The removal of Ca2+ or its substitution by any metal ion except Sr2+ inhibits oxygen evolution. We used steady-state enzyme kinetics to measure the rate of O2 evolution in PSII samples treated with an extensive series of mono-, di-, and trivalent metal ions in order to determine the basis for the affinity of metal ions for the Ca2+-binding site. Our results show that the Ca2+-binding site in PSII behaves very similarly to the Ca2+-binding sites in other proteins, and we discuss the implications this has for the structure of the site in PSII. Activity measurements as a function of time show that the binding site achieves equilibrium in 4 h for all of the PSII samples investigated. The binding affinities of the metal ions are modulated by the 17 and 23 kDa extrinsic polypeptides; their removal decreases the free energy of binding of the metal ions by 2.5 kcal/mol, but does not significantly change the time required to reach equilibrium. Monovalent ions are effectively excluded from the Ca2+-binding site, exhibiting no inhibition of O2 evolution. Di- and trivalent metal ions with ionic radii similar to that of Ca2+ (0.99 A) bind competitively with Ca2+ and have the highest binding affinity, while smaller metal ions bind more weakly and much larger ones do not bind competitively. This is consistent with a size-selective Ca2+-binding site that has a rigid array of coordinating ligands. Despite the large number of metal ions that competitively replace Ca2+ in the OEC, only Sr2+ is capable of partially restoring activity. Comparing the physical characteristics of the metal ions studied, we identify the pK(a) of the aqua ion as the factor that determines the functional competence of the metal ion. This suggests that Ca2+ is directly involved in the chemistry of water oxidation and is not only a structural cofactor in the OEC. We propose that the role of Ca2+ is to act as a Lewis acid, binding a substrate water molecule and tuning its reactivity.     

Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules

Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth''s atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.     

The fundamental nature of life as a chemical system: the part played by inorganic elements

In this article we show why inorganic metal elements from the environment were an essential part of the origin of living aqueous systems of chemicals in flow. Unavoidably such systems have many closely fixed parameters, related to thermodynamic binding constants, for the interaction of the essential exchangeable inorganic metal elements with both inorganic and organic non-metal materials. The binding constants give rise to fixed free metal ion concentration profiles for different metal ions and ligands in the cytoplasm of all cells closely related to the Irving-Williams series. The amounts of bound elements depend on the organic molecules present as well as these free ion concentrations. This system must have predated coding which is probably only essential for reproductive life. Later evolution in changing chemical environments became based on the development of extra cytoplasmic compartments containing quite different energised free (and bound) element contents but in feed-back communication with the central primitive cytoplasm which changed little. Hence species multiplied late in evolution in large part due to the coupling with the altered inorganic environment.     

Bringing inorganic chemistry to life with inspiration from R. J. P. Williams

Our appreciation of the scholarly ideas and thinking of Bob Williams is illustrated here by a few of the areas in which he inspired us. His journey to bring inorganic chemistry to life began with an early interest in analytical chemistry, rationalising the relative stabilities of metal coordination complexes (The Irving-Williams Series), and elucidating the organometallic redox chemistry of vitamin B₁₂. He (and Vallee) recognised that metal ions are in energised (entatic) states in proteins and enzymes, which themselves are dynamic structures of rods and springs. He played a key role in helping Rosenberg to pave the road toward the clinic for the anticancer drug cisplatin. He believed that evolution is not just dependent on DNA, but also on the metallome. Organisms and the environment are one system: does DNA code directly for all the essential elements of life?     

环境重金属污染的植物修复及基因工程在其中的应用

随着工业技术的发展,重金属在土壤和水体中的含量越来越高,重金属污染已日益成为威胁人类健康和人类生活质量的严重的社会问题和环境问题。植物修复可部分解决这一问题且正引起人们的普遍关注。但现在发现许多用于修复的超量积累植物生长缓慢、植株矮小、地上部生物量小,成了实际应用中的最大限制。利用基因工程手段改变植物对重金属吸收、转运、积累和忍耐的机制,从而提高植物对重金属的富集能力,将成为今后植物修复领域研究的一个重要方向。     

重金属结合肽（蛋白）的结构分析

金属离子与金属结合肽（蛋白）的相互作用与应用研究,一直是生物无机化学的重点和热点,也是分子间相互作用研究领域的难点。本研究利用ClustalX、BLAST等生物信息技术与方法对大量已知的重金属结合肽进行分析与数据挖掘。确定筛选获得的重金属结合肽常富含His,无Cys,无金属结合肽模式序列,进化不保守;部分氨基酸序列结构（如六肽）可在蛋白数据库中找到相似序列。序列特征主要为Zn^2＋相关的转录因子。本研究为重金属结合蛋白-重金属离子的相互作用分析简化为重金属结合肽-重金属离子的结构模拟与分析提供了重要的理论基础和研究手段。     

Symbiosis and the origin of life

The paper uses chemical kinetic arguments and illustrations by computer modelling to discuss the origin and evolution of life. Complex self-reproducing chemical systems cannot arise spontaneously, whereas simple auto-catalytic systems can, especially in an irradiated aqueous medium. Self-reproducing chemical particles of any complexity, in an appropriate environment, have a self-regulating property which permits long-term survival. However, loss of materials from the environment can lead to continuing decay which is circumvented by physical union between different kinds of self-reproducing particles. The increasing complexity produced by such unions (symbioses) is irreversible so that the chemical system evolves. It is suggested that evolution by successive symbioses brough about the change from simple, spontaneously arising, auto-catalytic particles to complex prokaryotic cells.     

Photosystem II: Its function,structure, and implications for artificial photosynthesis

Somewhere in the region of 3 billion years ago an enzyme emerged which would dramatically change the chemical composition of our planet and set in motion an unprecedented explosion in biological activity. This enzyme used solar energy to power the thermodynamically and chemically demanding reaction of water splitting. In so doing it provided biology with an unlimited supply of hydrogen equivalents needed to convert carbon dioxide into the organic molecules of life. The enzyme, which facilitates this reaction and therefore underpins virtually all life on our planet, is known as Photosystem II (PSII). It is a multisubunit enzyme embedded in the lipid environment of the thylakoid membranes of plants, algae, and cyanobacteria. Over the past 10 years, crystal structures of a 700 kDa cyanobacterial dimeric PSII complex have been reported with ever increasing improvement in resolution with the latest being at 1.9 details of its many subunits and cofactors are now well understood. The water splitting site was revealed as a cluster of four Mn ions and a Ca ion surrounded by amino acid side chains, of which seven provide ligands to the metals. The metal cluster is organized as a cubane-like structure composed of three Mn ions and the Ca²⁺ linked by oxo-bonds with the fourth Mn attached to the cubane via one of its bridging oxygens together with another oxo bridge to a Mn ion of the cubane. The overall structure of the catalytic site is providing a framework on which to develop a mechanistic scheme for the water splitting process and gives a blue print and confidence for the development of catalysts for mimicking the reaction in an artificial photo-electrochemical system to generate solar fuels.     

Cadmium and mercury cause an oxidative stress-induced endothelial dysfunction

We investigated the ability of cadmium and mercury ions to cause endothelial dysfunction in bovine pulmonary artery endothelial cell monolayers. Exposure of monolayers for 48 h to metal concentrations greater than 3–5 μM produced profound cytotoxicity (increased lactate dehydrogenase leakage), a permeability barrier failure, depletion of glutathione and ATP and almost complete inhibition of the activity of key thiol enzymes, glucose-6-phosphate dehydrogenase (G6PDH) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In contrast, metal concentrations less than 1–2 μM induced increases in glutathione and thiol-enzyme activities with minimal changes in LDH leakage, barrier function and ATP content. At shorter incubation times (24 h or less), high concentrations of cadmium caused glutathione induction rather than depletion. Thus, oxidative stress and cytotoxicity induced by lower concentrations of the metal ions stimulate compensatory responses, including increased synthesis of glutathione, which presumably preserved the activity of key thiol enzymes, however these responses were not sustainable at higher metal ion concentrations. We conclude, while high concentrations of heavy metals are cytotoxic, lower concentration induce a compensatory protective response, which may explain threshold effects in metal-ion toxicity.     

A model for the emergence of adaptive subsystems

We investigate the interaction of learning and evolution in a changing environment. A stable learning capability is regarded as an emergent adaptive system evolved by natural selection of genetic variants. We consider the evolution of an asexual population. Each genotype can have ‘fixed’ and ‘flexible’ alleles. The former express themselves as synaptic connections that remain unchanged during ontogeny and the latter as synapses that can be adjusted through a learning algorithm. Evolution is modelled using genetic algorithms and the changing environment is represented by two optimal synaptic patterns that alternate a fixed number of times during the ‘life’ of the individuals. The amplitude of the change is related to the Hamming distance between the two optimal patterns and the rate of change to the frequency with which both exchange roles. This model is an extension of that of Hinton and Nowlan in which the fitness is given by a probabilistic measure of the Hamming distance to the optimum. We find that two types of evolutionary pathways are possible depending upon how difficult (costly) it is to cope with the changes of the environment. In one case the population loses the learning ability, and the individuals inherit fixed synapses that are optimal in only one of the environmental states. In the other case a flexible subsystem emerges that allows the individuals to adapt to the changes of the environment. The model helps us to understand how an adaptive subsystem can emerge as the result of the tradeoff between the exploitation of a congenital structure and the exploration of the adaptive capabilities practised by learning.     

On the Beneficial Role of Silicon to Organisms: A Case Study on the Importance of Silicon Chemistry to Metal Accumulation in Yeast

Silicon is involved in numerous important structural and functional roles in a wide range of organisms, including diatoms, plants, and humans, but clear mechanisms have been discovered only in diatoms and sponges. Silicate availability influences metal concentrations within various cell- and tissue-types, but a mechanism has not been discovered so far. In an earlier study on Baker’s yeast Saccharomyces cerevisiae it was proposed that a chemical mechanism, rather than a biological one, is important. In the present study, the interaction of silicon with Baker’s yeast is further investigated by studying the influence of zinc and magnesium on Si accumulation both at a low and a high silicate concentration in the medium. Si accumulation fitted well with Freundlich adsorption and Si release followed depolymerization kinetics, indicating that silicate adsorbs to the surface of the cell rather than being transported over the cell membrane. Subsequently, adsorbed silicate interacts with metal ions and, therefore, alters the cell’s affinity for these ions. Since several metals are nutritional, these Si interactions can significantly change the growth and viability of organisms. In conclusion, the results show that chemistry is important in Si and metal accumulation in Baker’s yeast, and suggest that similar mechanisms should be studied in detail in other organisms to unravel essential roles of Si.     

Phytochelatin-mediated cadmium tolerance inschizosaccharomyces pombe

Summary Plants and certain fungi respond to heavy metal toxicity with the induced synthesis of metal-binding peptides known as phytochelatins (PCs). With cadmium, PCs can bind the metal to form a low molecular weight PC-Cd complex and a high molecular weight PC-Cd-S²⁻ complex. The sulfide ions enhance the stability and Cd-binding capacity of the metal chelate, and formation of this sulfide-containing complex is associated with enhanced tolerance to cadmium. Molecular analyses of two fission yeast mutants that fail to produce a wild type level of the PC-Cd-S²⁻ complex have determined that a vacuolar membrane transporter and several enzymes of the purine biosynthesis pathway are necessary in vivo for formation of the PC- Cd-S²⁻ complex. A model based on vacuolar sequestration of the PC-Cd complex by an ATP-binding cassette-type transporter and its subsequent maturation into the stable PC-Cd-S²⁻ complex via the actions of two purine biosynthetic enzymes is described. Presented in the Session-in-Depth Bioremediation through Biotechnological Means at the 1993 Congress on Cell and Tissue Culture, San Diego, CA, June 5–9, 1993.     

Comparison between <Emphasis Type="Italic">Compsopogon coeruleus</Emphasis> and <Emphasis Type="Italic">Porphyra yezoensis</Emphasis> in their O<Subscript>2</Subscript> evolution rates and phycobilisome composition

In order to investigate the possible effects of the ecological environment on photosynthetic activity and the major light harvesting complex, the oxygen evolution rates and composition of phycobilisome from marine red alga Porphyra yezoensis Ueda and freshwater red alga Compsopogon coeruleus (Balbis) Montagne, which could grow and reproduce under salinity up to 35 ppt, were studied. The results showed that the oxygen evolution rate of P. yezoensis in seawater was significantly higher than that of C. coeruleus in freshwater, and P. yezoensis tolerated inorganic ions at a relatively higher concentration than C. coeruleus. Moreover, the phycoerythrin (PE) of P. yezoensis was R-phycoerythrin containing α, β, and γ subunits comprised phycoerythrobilin and phycourobilin. In contrast, the PE from C. coeruleus consisted of α, β, and γ subunits comprised only phycoerythrobilin but not phycourobilin, suggesting that the PE from C. coeruleus was of a new type. This text was submitted by the authors in English.     

Identification of a Novel Vanadium-binding Protein by EST Analysis on the Most Vanadium-rich Ascidian, Ascidia gemmata

Ascidians are known to accumulate extremely high levels of vanadium in their blood cells (up to 350 mM). The branchial sac and the intestine are thought to be the first tissues to contact the outer environment and absorb vanadium ions. The concentration of vanadium in the branchial sac and the intestine of the most vanadium-rich ascidian Ascidia gemmata were determined to be 32.4 and 11.9 mM, respectively. Using an expressed sequence tag (EST) analysis of a cDNA library from the intestine of A. gemmata, we determined 960 ESTs and found 55 clones of metal-related gene orthologs, 6 redox-related orthologs, and 18 membrane transporter orthologs. Among them, two genes, which exhibited significant similarity to the vanadium-binding proteins of other vanadium-rich ascidian species, were designated AgVanabin1 and AgVanabin2. Immobilized metal ion affinity chromatography revealed that recombinant AgVanabin1 bound to metal ions with an increasing affinity for Cu(II) > Zn(II) > Co(II) and AgVanabin2 bound to metal ions with an increasing affinity for Cu(II) > Fe(III) > V(IV). To examine the use of AgVanabins for a metal absorption system, we constructed Escherichia coli strains that expressed AgVanabin1 or AgVanabin2 fused to maltose-binding protein and secreted into the periplasmic space. We found that the strain expressing AgVanabin2 accumulated about 13.5 times more Cu(II) ions than the control TB1 strain. Significant accumulation of vanadium was also observed in the AgVanabin2-expressing strain as seen by a 1.5-fold increase.     

How Plants Cope with Cadmium: Staking All on Metabolism and Gene Expression

Environmental pollullon is one of the major problems for human health. Toxic heavy metals are normally present as soil constituents or can also be spread out in the environment by human activity and agricultural techniques. Soil contamination by heavy metals as cadmium, highlights two main aspects: on one side they interfere with the life cycle of plants and therefore reduce crop yields, and on the other hand, once adsorbed and accumulated into the plant tissues, they enter the food chain poisoning animals and humans. Considering this point of view, understanding the mechanism by which plants handle heavy metal exposure, In particular cadmium stress, is a primary goal of plant-blotechnology research or plant breeders whose aim is to create plants that are able to recover high amounts of heavy metals, which can be used for phytoremediation, or identify crop varieties that do not accumulate toxic metal in grains or fruits. In this review we focus on the main symptoms of cadmium toxicity both on root apparatus and shoots. We elucidate the mechanisms that plants activate to prevent absorption or to detoxify toxic metal ions, such as synthesis of phytochelatins, metallothioneins and enzymes involved in stress response. Finally we consider new plant-biotechnology applications that can be applied for phytoremediation.     

The mechanism of DNA breakage by phleomycin in vitro.

Phleomycin induces DNA breakage in vitro in the presence of the sulphydryl compound dithiothreitol. The reaction appears to be free radical-mediated, and requires oxygen and metal ions. Reaction rate is limited by the concentration of oxygen, which is converted to hydrogen peroxide during DNA breakage. However there is no net change in the sulphydryl compound. The proposed reaction mechanism involves metal ion/oxygen-catalysed oxidation of dithiothreitol to its free radical form, which reacts with phleomycin, leading to formation of activated phleomycin and regeneration of free sulphydryl. Free phleomycin is converted to an inactive form, but activation of phleomycin bound to DNA leads to DNA breakage.     

植物重金属转运蛋白P1B-ATPases研究进展

P_(1B)-ATPases是在生物中广泛存在的一类可通过水解ATP跨膜运送重金属离子的蛋白,是P型ATPase家族的一个亚类。研究发现P_(1B)-ATPases在植物中主要负责重金属离子的主动转运,在植物重金属平衡调节系统中发挥重要作用。文中从P_(1B)-ATPases的结构与分类出发,介绍了P_(1B)-ATPases的作用机制,综述了目前P_(1B)-ATPases功能的研究进展,以期为未来P_(1B)-ATPases在改良作物品质以及生态环境治理的研究及应用提供参考。     

Metal ligands in micronutrient acquisition and homeostasis

Acquisition and homeostasis of micronutrients such as iron (Fe) and zinc (Zn) pose specific challenges. Poor solubility and high reactivity require controlled synthesis and supply of ligands to complex these metals extracellularly and intracellularly. Cytosolic labile pools represent only a minute fraction of the total cellular content. Several low‐molecular‐weight ligands are known in plants, including sulfur ligands (cysteine and peptides), nitrogen/oxygen ligands (S‐adenosyl‐l ‐methionine‐derived molecules and histidine), and oxygen ligands (phenolics and organic acids). Some ligands are secreted into the extracellular space and influence the phytoavailability of metal ions. A second principal function is the intracellular buffering of micronutrients as well as the facilitation of long‐distance transport in xylem and phloem. Furthermore, low‐molecular‐weight ligands are involved in the storage of metals, predominantly in vacuoles. A detailed molecular understanding is hampered by technical limitations, in particular the difficulty to detect and quantify cellular metal–ligand complexes. More, but still too little, is known about ligand synthesis and the transport across membranes, either with or without a complexed metal. Metal ligands have an immediate impact on human well‐being. Engineering metal ligand synthesis and distribution in crops has tremendous potential to improve the nutritional quality of food and to tackle major human health risks.