Evolution was chemically constrained

The objective of this paper is to present a systems view of the major features of biological evolution based upon changes in internal chemistry and uses of cellular space, both of which it will be stated were dependent on the changing chemical environment. The account concerns the major developments from prokaryotes to eukaryotes, to multi-cellular organisms, to animals with nervous systems and a brain, and finally to human beings and their uses of chemical elements in space outside themselves. It will be stated that the changes were in an inevitable progression, and were not just due to blind chance, so that "random searching" by a coded system to give species had a fixed overall route. The chemical sequence is from a reducing to an ever-increasingly oxidizing environment, while organisms retained reduced chemicals. The process was furthered recently by human beings who have also increased the range of reduced products trapped on Earth in novel forms. All the developments are brought about from the nature of the chemicals which organisms accumulate using the environment and its changes. The relationship to the manner in which particular species (gene sequences) were coincidentally changed, the molecular view of evolution, is left for additional examination.There is a further issue in that the changes of the chemistry of the environment developed largely at equilibrium due to the relatively fast reactions there of the available inorganic chemicals. Inside cells, some of these same chemicals also came to equilibrium within compounds. All such equilibria reduced the variance (degrees of freedom) of the total environmental/biological system and its possible development. However, the more sophisticated organic chemistry, almost totally inside cells until humans evolved, is kinetically controlled and limited by the demands of cellular reduction necessary to produce essential chemicals and by the availability of certain elements and energy. Hence the variability of reductive cellular organic chemistry and its limitations in cells have to be considered separately. While as a whole they drive the oxidation of the environment, they also allow speciation within the major changes of organisms. Human beings have introduced recently new, virtually irreversible, inorganic and organic chemistry in the environment, much of it new modes of irreversible storage of reduced chemicals, and this is, we state, the last possible step of chemical evolution. We must attempt to evaluate its effect on organisms generally.It must be clear that all the changes and the original life forms are dependent upon energy as well as material capture and flow. We shall have to consider in which forms energy was available over the period of evolution, how it was usefully transformed, and the ways in which its sources changed.     

Copper proteomes, phylogenetics and evolution

This paper is a continuation of our study of the connection between the changing environment and the changing use of particular elements in organisms in the course of their combined evolution (Decaria, Bertini and Williams, Metallomics, 2010, 2, 706). Here we treat the changes in copper proteins in historically the same increasingly oxidising environmental conditions. The study is a bioinformatic analysis of the types and the numbers of copper domains of proteins from 435 DNA sequences of a wide range of organisms available in NCBI, using the method developed by Andreini, Bertini and Rosato in Accounts of Chemical Research 2009, 42, 1471. The copper domains of greatest interest are found predominantly in copper chaperones, homeostatic proteins and redox enzymes mainly used outside the cytoplasm which are in themselves somewhat diverse. The multiplicity of these proteins is strongly marked. The contrasting use of the iron and heme iron proteins in oxidations, mostly in the cytoplasm, is compared with them and with activity of zinc fingers during evolution. It is shown that evolution is a coordinated development of the chemistry of elements with use of novel and multiple copies of their proteins as their availability rises in the environment.     

The ins and outs of bacterial iron metabolism

Iron is a critical nutrient for the growth and survival of most bacterial species. Accordingly, much attention has been paid to the mechanisms by which host organisms sequester iron from invading bacteria and how bacteria acquire iron from their environment. However, under oxidative stress conditions such as those encountered within phagocytic cells during the host immune response, iron is released from proteins and can act as a catalyst for Fenton chemistry to produce cytotoxic reactive oxygen species. The transitory efflux of free intracellular iron may be beneficial to bacteria under such conditions. The recent discovery of putative iron efflux transporters in Salmonella enterica serovar Typhimurium is discussed in the context of cellular iron homeostasis.     

Zinc proteomes, phylogenetics and evolution

Evolution has not been studied in detail with reference to the changing environment. This requires a study of the inorganic chemistry of organisms, especially metalloproteins. The evolution of organisms has been analysed many times previously using comparative studies, fossils, and molecular sequences of proteins, DNA and 16s rRNA (Zhang and Gladyshev, Chem. Rev., 2009, 109, 4828). These methods have led to the confirmation of Darwin's original proposal that evolution followed from natural selection in a changing environment often pictured as a tree. In all cases, the main tree in its upper later reaches has been well studied but its lower earlier parts are not so well defined. To approach this topic we have treated evolution as due to the intimate combination of the effect of chemical changes in the environment and in the organisms (Williams and da Silva, The Chemistry of Evolution, 2006, Elsevier). The best chemicals to examine are inorganic ions as they are common to both. As a more detailed example of the chemical study of organisms we report in this paper a bioinformatic approach to the characterization of the zinc proteomes. We deduce them from the 821 totally sequenced DNA of organisms available on NCBI, exploiting a published method developed by one of us (Andreini, Bertini and Rosato, Acc. Chem. Res., 2009, 42, 1471). Comparing the derived zinc-finger-containing proteins and zinc hydrolytic enzymes in organisms of different complexity there is a correlation in their changes during evolution related to environmental change.     

Recent achievements on siderophore production and application

Iron is the most abundant chemical element on Earth but its most common oxidation state is Fe(III) which presents a very low solubility under physiological conditions. During evolution, micro-organisms have developed sound strategies to acquire iron from both the environment and superior organisms, including direct uptake of iron ions from exogenous iron/heme sources and the synthesis of specialized Fe(III) chelators called siderophores. The present review paper aims at presenting and discussing the latest achievements in siderophore isolation and production, as well as novel applications of these molecules in therapies against iron-related diseases and in vaccines, and their application as antimicrobial agents and biosensors.     

My past and a future role for inorganic biochemistry

The first part of this paper describes how my interest in bioinorganic chemistry was stimulated more than sixty years ago and how it has developed. The second part concerns a view of the future of the subject as an essential integral part of systems studies including organisms. After describing the essentials of any irreversible system, explaining how it is inevitably linked to its environment for material and energy, I analyse the roles of inorganic ions in this interactive unity to show the way the accidental oxidation of the environment by organisms has led to an inevitable progression of chemotypes in evolution. What is required in the future is detailed knowledge of the analytical content of the different compartmental structures of organisms, their division between free and bound forms, and the timing of their appearance. Historically this information needs to be related to both environmental and gene changes.     

Mitochondrial adaptations to utilize hydrogen sulfide for energy and signaling

Sulfur is a versatile molecule with oxidation states ranging from -2 to +6. From the beginning, sulfur has been inexorably entwined with the evolution of organisms. Reduced sulfur, prevalent in the prebiotic Earth and supplied from interstellar sources, was an integral component of early life as it could provide energy through oxidization, even in a weakly oxidizing environment, and it spontaneously reacted with iron to form iron-sulfur clusters that became the earliest biological catalysts and structural components of cells. The ability to cycle sulfur between reduced and oxidized states may have been key in the great endosymbiotic event that incorporated a sulfide-oxidizing α-protobacteria into a host sulfide-reducing Archea, resulting in the eukaryotic cell. As eukaryotes slowly adapted from a sulfidic and anoxic (euxinic) world to one that was highly oxidizing, numerous mechanisms developed to deal with increasing oxidants; namely, oxygen, and decreasing sulfide. Because there is rarely any reduced sulfur in the present-day environment, sulfur was historically ignored by biologists, except for an occasional report of sulfide toxicity. Twenty-five years ago, it became evident that the organisms in sulfide-rich environments could synthesize ATP from sulfide, 10?years later came the realization that animals might use sulfide as a signaling molecule, and only within the last 4?years did it become apparent that even mammals could derive energy from sulfide generated in the gastrointestinal tract. It has also become evident that, even in the present-day oxic environment, cells can exploit the redox chemistry of sulfide, most notably as a physiological transducer of oxygen availability. This review will examine how the legacy of sulfide metabolism has shaped natural selection and how some of these ancient biochemical pathways are still employed by modern-day eukaryotes.     

Systems biology of evolution: the involvement of metal ions

This article outlines a novel way of looking at the relevance of metal ions in organisms to the whole of life as part of an ecosystem bringing together the environment and cellular life. It does so by examining the evolution of the environment due to the “waste”, mainly oxygen, from cell metabolism which back reacts with the cells themselves. The oxygen generates a progressive change in the metal ions in the environment. The resultant change is buffered by ferrous iron and sulfide and is therefore slow so that there is a gradual adaptation of life to utilisation of elements in a time sequence. In order to appreciate this, systems (biological) evolution, it is necessary to describe the very nature of a thermodynamic flow system of which life is an example.     

Life, the environment and our ecosystem

This article is dedicated to Ed Stiefel who not only contributed with distinction to the development of biological inorganic chemistry with a special interest in molybdenum and its chemistry but had begun the long task of increasing our awareness of the difficulties mankind faces arising from damage to the environment. Here, I take up this theme in an effort to illustrate the nature of today's problems by putting them in the perspective of the whole of evolution of our ecosystem. The central theme is that evolution of organisms has always had to come to terms with the systematic development of the environment. In the past, environmental changes have been slow so that adaptation through genetic adjustment has had time to follow. In the last two hundred years change has become fast and the adaptive process rests not with genes but with mankind's physical-chemical control.     

Old Iron, Young Copper: from Mars to Venus

Iron and copper are metals which play an important role in the living world. From a brief consideration of their chemistry and biochemistry we conclude that the early chemistry of life used water soluble ferrous iron while copper was in the water-insoluble Cu(I) state as highly insoluble sulphides. The advent of oxygen was a catastrophic event for most living organisms, and can be considered to be the first general irreversible pollution of the earth. In contrast to the oxidation of iron and its loss of bioavailability as insoluble Fe(III), the oxidation of insoluble Cu(I) led to soluble Cu(II). A new iron biochemistry became possible after the advent of oxygen, with the development of chelators of Fe(III), which rendered iron once again accessible, and with the control of the potential toxicity of iron by its storage in a water soluble, non-toxic, bio-available storage protein (ferritin). Biology also discovered that whereas enzymes involved in anaerobic metabolism were designed to operate in the lower portion of the redox spectrum, the arrival of dioxygen created the need for a new redox active metal which could attain higher redox potentials. Copper, now bioavailable, was ideally suited to exploit the oxidizing power of dioxygen. The arrival of copper also coincided with the development of multicellular organisms which had extracellular cross-linked matrices capable of resisting attack by oxygen free radicals. After the initial `iron age' subsequent evolution moved, not towards a `copper age', but rather to an `iron-copper' age. In the second part of the review, this symbiosis of iron and copper is examined in yeast. We then briefly consider iron and copper metabolism in mammals, before looking at iron-copper interactions in mammals, particularly man, and conclude with the reflection that, as in Greek and Roman mythology, a better understanding of the potentially positive interactions between Mars (iron) and Venus (copper) can only be to the advantage of our species.     

Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs

Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and E(h) of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to Hydrogenobaculum spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of Hydrogenobaculum spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature.     

Effects of Abiotic Factors on the Phylogenetic Diversity of Bacterial Communities in Acidic Thermal Springs

Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and E_h of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to Hydrogenobaculum spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of Hydrogenobaculum spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature.     

Chemistry and biology of eukaryotic iron metabolism

With rare exceptions, virtually all studied organisms from Archaea to man are dependent on iron for survival. Despite the ubiquitous distribution and abundance of iron in the biosphere, iron-dependent life must contend with the paradoxical hazards of iron deficiency and iron overload, each with its serious or fatal consequences. Homeostatic mechanisms regulating the absorption, transport, storage and mobilization of cellular iron are therefore of critical importance in iron metabolism, and a rich biology and chemistry underlie all of these mechanisms. A coherent understanding of that biology and chemistry is now rapidly emerging. In this review we will emphasize discoveries of the past decade, which have brought a revolution to the understanding of the molecular events in iron metabolism. Of central importance has been the discovery of new proteins carrying out functions previously suspected but not understood or, more interestingly, unsuspected and surprising. Parallel discoveries have delineated regulatory mechanisms controlling the expression of proteins long known--the transferrin receptor and ferritin--as well as proteins new to the scene of iron metabolism and its homeostatic control. These proteins include the iron regulatory proteins (IRPs 1 and 2), a variety of ferrireductases in yeast an mammalian cells, membrane transporters (DMT1 and ferroportin 1), a multicopper ferroxidase involved in iron export from cells (hephaestin), and regulators of mitochondrial iron balance (frataxin and MFT). Experimental models, making use of organisms from yeast through the zebrafish to rodents have asserted their power in elucidating normal iron metabolism, as well as its genetic disorders and their underlying molecular defects. Iron absorption, previously poorly understood, is now a fruitful subject for research and well on its way to detailed elucidation. The long-sought hemochromatosis gene has been found, and active research is underway to determine how its aberrant functioning results in disease that is easily controlled but lethal when untreated. A surprising connection between iron metabolism and Friedreich's ataxia has been uncovered. It is no exaggeration to say that the new understanding of iron metabolism in health and disease has been explosive, and that what is past is likely to be prologue to what is ahead.     

Impact constraints on the environment for chemical evolution and the continuity of life

The Moon and the Earth were bombarded heavily by planetesimals and asteroids that were capable of interfering with chemical evolution and the origin of life. In this paper, we explore the frequency of giant terrestrial impacts able to stop prebiotic chemistry in the probable regions of chemical evolution. The limited time available between impacts disruptive to prebiotic chemistry at the time of the oldest evidence of life suggests the need for a rapid process for chemical evolution of life. The classical hypothesis for the origin of life through the slow accumulation of prebiotic reactants in the primordial soup in the entire ocean may not be consistent with constraints imposed by the impact history of Earth. On the other hand, rapid chemical evolution in cloud systems and lakes or other shallow evaporating water bodies would have been possible because reactants could have been concentrated and polymerized rapidly in this environment. Thus, life probably could have originated near the surface between frequent surface sterilizing impacts. There may not have been continuity of life depending on sunlight because there is evidence that life, existing as early as 3.8 Gyr ago, may have been destroyed by giant impacts. The first such organisms on Earth where probably not the ancestors of present life.     

Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play

Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems. Eco-evolutionary feedbacks require that populations alter their environment (niche construction) and that those changes in the environment feed back to influence the subsequent evolution of the population. There is strong evidence that organisms influence their environment through predation, nutrient excretion and habitat modification, and that populations evolve in response to changes in their environment at time-scales congruent with ecological change (contemporary evolution). Here, we outline how the niche construction and contemporary evolution interact to alter the direction of evolution and the structure and function of communities and ecosystems. We then present five empirical systems that highlight important characteristics of eco-evolutionary feedbacks: rotifer–algae chemostats; alewife–zooplankton interactions in lakes; guppy life-history evolution and nutrient cycling in streams; avian seed predators and plants; and tree leaf chemistry and soil processes. The alewife–zooplankton system provides the most complete evidence for eco-evolutionary feedbacks, but other systems highlight the potential for eco-evolutionary feedbacks in a wide variety of natural systems.     

What is wrong with aluminium? The J.D. Birchall Memorial Lecture

Aluminium chemistry has features in common with two other groups of elements: (1) divalent magnesium and calcium, and (2) trivalent chromium and iron. The essential differences between the first group and aluminium are explored and it is shown that the much higher acidity of aluminium makes it such a powerful competitor for oxygen-donor ligands, opposite functions of both magnesium and calcium, in cells that its presence is damaging. By way of contrast aluminium is a weaker acid than ferric ions but it is more available. It was necessary for iron to be utilised in the presence of aluminium so special methods had to be devised to distinguish between them. In essence aluminium has always, throughout evolution, been a threat to the biological chemistry of all these three elements. We shall examine this chemistry and then explore the relationship of calcium and aluminium under acid rain conditions.     

Iron toxicity in neurodegeneration

Iron is an essential element for life on earth, participating in a plethora of cellular processes where one-electron transfer reactions are required. Its essentiality, coupled to its scarcity in aqueous oxidative environments, has compelled living organisms to develop mechanisms that ensure an adequate iron supply, at times with disregard to long-term deleterious effects derived from iron accumulation. However, iron is an intrinsic producer of reactive oxygen species, and increased levels of iron promote neurotoxicity because of hydroxyl radical formation, which results in glutathione consumption, protein aggregation, lipid peroxidation and nucleic acid modification. Neurons from brain areas sensitive to degeneration accumulate iron with age and thus are subjected to an ever increasing oxidative stress with the accompanying cellular damage. The ability of these neurons to survive depends on the adaptive mechanisms developed to cope with the increasing oxidative load. Here, we describe the chemical and thermodynamic peculiarities of iron chemistry in living matter, review the components of iron homeostasis in neurons and elaborate on the mechanisms by which iron homeostasis is lost in Parkinson's disease, Alzheimer's disease and other diseases in which iron accumulation has been demonstrated.     

鱼腥蓝细菌PCC7120铁吸收机制

铁离子是鱼腥蓝细菌PCC7120进行呼吸作用、光合作用和固氮作用中相关酶的重要辅基之一,缺铁将严重影响蓝细菌的生存.富氧的生态环境中铁通常以不溶的Fe3+形式存在,不易被细胞吸收利用.低铁条件下,鱼腥蓝细菌PCC7120分泌能螯合铁离子的嗜铁素,通过外膜上相应的转运体将嗜铁素-铁复合物转运到细胞内.综述了近年来在嗜铁素的种类及其生物合成途径、铁吸收系统的组成和功能等方面的最新进展,分析了铁吸收系统的调控机制,为进一步开展鱼腥蓝细菌铁吸收机制的研究提供依据.     

Balancing acts: molecular control of mammalian iron metabolism

Iron is ubiquitous in the environment and in biology. The study of iron biology focuses on physiology and homeostasis-understanding how cells and organisms regulate their iron content, how diverse tissues orchestrate iron allocation, and how dysregulated iron homeostasis leads to common hematological, metabolic, and neurodegenerative diseases. This has provided novel insights into gene regulation and unveiled remarkable links to the immune system.