Possible origin of a membrane in the subsurface of the Earth

A location for the origin of life on Earth could have been an oil/water interface in the warm, subsurface environment of the Earth. The physico-chemical conditions of the subsurface would include elevated, but eventually cooling temperatures, anaerobic conditions, and protection from intense surface radiation. This type of subsurface oil/water environment may have been ideal for the assembly of the first simple membrane(s), where no enzyme catalysis was needed. Once a stable, simple, continuous closed membrane was formed, one central component of the first cell(s) would have been present; a semi-permeable open system that allowed the passage of both matter and energy in and out of the cell. Such an open system could also acquire novel functions, whereas a closed system would be unable to evolve.     

Evolution of proton pumping ATPases: Rooting the tree of life

Proton pumping ATPases are found in all groups of present day organisms. The F-ATPases of eubacteria, mitochondria and chloroplasts also function as ATP synthases, i.e., they catalyze the final step that transforms the energy available from reduction/oxidation reactions (e.g., in photosynthesis) into ATP, the usual energy currency of modern cells. The primary structure of these ATPases/ATP synthases was found to be much more conserved between different groups of bacteria than other parts of the photosynthetic machinery, e.g., reaction center proteins and redox carrier complexes.These F-ATPases and the vacuolar type ATPase, which is found on many of the endomembranes of eukaryotic cells, were shown to be homologous to each other; i.e., these two groups of ATPases evolved from the same enzyme present in the common ancestor. (The term eubacteria is used here to denote the phylogenetic group containing all bacteria except the archaebacteria.) Sequences obtained for the plasmamembrane ATPase of various archaebacteria revealed that this ATPase is much more similar to the eukaryotic than to the eubacterial counterpart. The eukaryotic cell of higher organisms evolved from a symbiosis between eubacteria (that evolved into mitochondria and chloroplasts) and a host organism. Using the vacuolar type ATPase as a molecular marker for the cytoplasmic component of the eukaryotic cell reveals that this host organism was a close relative of the archaebacteria.A unique feature of the evolution of the ATPases is the presence of a non-catalytic subunit that is paralogous to the catalytic subunit, i.e., the two types of subunits evolved from a common ancestral gene. Since the gene duplication that gave rise to these two types of subunits had already occurred in the last common ancestor of all living organisms, this non-catalytic subunit can be used to root the tree of life by means of an outgroup; that is, the location of the last common ancestor of the major domains of living organisms (archaebacteria, eubacteria and eukaryotes) can be located in the tree of life without assuming constant or equal rates of change in the different branches.A correlation between structure and function of ATPases has been established for present day organisms. Implications resulting from this correlation for biochemical pathways, especially photosynthesis, that were operative in the last common ancestor and preceding life forms are discussed.     

Experimental silicification of the extremophilic Archaea Pyrococcus abyssi and Methanocaldococcus jannaschii: applications in the search for evidence of life in early Earth and extraterrestrial rocks

Hydrothermal activity was common on the early Earth and associated micro‐organisms would most likely have included thermophilic to hyperthermophilic species. 3.5–3.3 billion‐year‐old, hydrothermally influenced rocks contain silicified microbial mats and colonies that must have been bathed in warm to hot hydrothermal emanations. Could they represent thermophilic or hyperthermophilic micro‐organisms and if so, how were they preserved? We present the results of an experiment to silicify anaerobic, hyperthermophilic micro‐organisms from the Archaea Domain Pyrococcus abyssi and Methanocaldococcus jannaschii, that could have lived on the early Earth. The micro‐organisms were placed in a silica‐saturated medium for periods up to 1 year. Pyrococcus abyssi cells were fossilized but the M. jannaschii cells lysed naturally after the exponential growth phase, apart from a few cells and cell remains, and were not silicified although their extracellular polymeric substances were. In this first simulated fossilization of archaeal strains, our results suggest that differences between species have a strong influence on the potential for different micro‐organisms to be preserved by fossilization and that those found in the fossil record represent probably only a part of the original diversity. Our results have important consequences for biosignatures in hydrothermal or hydrothermally influenced deposits on Earth, as well as on early Mars, as environmental conditions were similar on the young terrestrial planets and traces of early Martian life may have been similarly preserved as silicified microfossils.     

What are toxins to microbes? (the role of toxins in bacterial ecology)

The author attempts to answer two questions: whether the toxins, in particular the toxins having their specificity connected with enzymatic activity, are needed for microbial cell physiology and their significance for bacteria that are not the obligate parasites for warm blooded animals. The analysis of literary data supposes the toxins to be essential cellular metabolites since many of them participate in energy acquiring. Besides that a number of toxins is shown to be relevant to microbial life and to affect the micropredators, especially the monocellular organisms feeding the microbes. In connection with the above mentioned, special attention is paid to extrachromosomal location of many toxins genes relating them to bacteriocins. The possibility is not excluded that in the future the new toxins might come to be found having the enzymatic activities.     

Thermal Energy and the Origin of Life

Life has evolved on Earth with electromagnetic radiation (light), fermentable organic molecules, and oxidizable chemicals as sources of energy. Biological use of thermal energy has not been observed although heat, and the thermal gradients required to convert it into free energy, are ubiquitous and were even more abundant at the time of the origin of life on Earth. Nevertheless, Earth-organisms sense thermal energy, and in suitable environments may have gained the capability to use it as energy source. It has been proposed that the first organisms obtained their energy by a first protein named pF₁ that worked on a thermal variation of the binding change mechanism of today's ATP sythase enzyme. Organisms using thermosynthesis may still live where light or chemical energy sources are not available. Possible suitable examples are subsurface environments on Earth and in the outer Solar System, in particular the subsurface oceans of the icy satellites of Jupiter and Saturn.     

Germ plasm in Caenorhabditis elegans, Drosophila and Xenopus

Special cytoplasm, called germ plasm, that is essential for the differentiation of germ cells is localized in a particular region of Caenorhabditis elegans, Drosophila and Xenopus eggs. The mode of founder cell formation of germline, the origin and behavior of the germline granules, and the molecules localized in germline cells are compared in these organisms. The common characteristics of the organisms are mainly as follows. First, the founder cells of germline are established before the intiation of gastrulation. Second, the germline granules or their derivatives are always present in germline cells or germ cells throughout the life cycle in embryos, larvae, and adults. Lastly, among the proteins localized in the germ plasm, only Vasa protein or its homolog is detected in the germline cells or germ cells throughout the life cycle. As the protein of vasa homolog has been reported to be also localized in the germline-specific structure or nuage in some of the organisms without the germ plasm, the possibility that the mechanism for differentiation of primordial germ cells is basically common in all organisms with or without the germ plasm is discussed.     

Deciphering the hunting strategy of a bacterial wolfpack

Myxococcus xanthus is a common soil bacterium with an intricate multicellular lifestyle that continues to challenge the way in which we conceptualize the capabilities of prokaryotic organisms. Myxococcus xanthus is the preferred laboratory representative from the Myxobacteria , a family of organisms distinguished by their ability to form highly structured biofilms that include tentacle-like packs of surface-gliding cell groups, synchronized rippling waves of oscillating cells and massive spore-filled aggregates that protrude upwards from the substratum to form fruiting bodies. But most of the Myxobacteria are also predators that thrive on the degradation of macromolecules released through the lysis of other microbial cells. The aim of this review is to examine our understanding of the predatory life cycle of M. xanthus . We will examine the multicellular structures formed during contact with prey, and the molecular mechanisms utilized by M. xanthus to detect and destroy prey cells. We will also examine our understanding of microbial predator–prey relationships and the prospects for how bacterial predation mechanisms can be exploited to generate new antimicrobial technologies.     

Development of lamellar bodies and subsurface cisterns in pyramidal cells and neuroblasts of hamster cerebral cortex.

In pyramidal cells of hamster frontal cortex lamellar bodies and subsurface cisterns sequentially occurred during development from newborn to three months of age. Neither of these two specializations of the rough endoplasmic reticulum was seen in neurons of the newborn. The first specialization that we observed was the subsurface cistern, which appeared at five days and showed a significant increase both in frequency and in length throughout development. The lamellar body was first seen at ten days of age. This specialization showed a peaking of frequency, length, and number of cisterns per body at 15 days, which subsequently decreased gradually to 3-month-old levels. The occurrence of lamellar body-subsurface cistern complexes increased with age. We suggest that the lamellar body may be an ER specialization that is involved in an increased and/or stage-specific protein synthesis in the young prior to the final maturation of the usual neuronal protein synthetic organelles, and that in the 3-month-old neurons, the lamellar body may be involved in modifying, storing or transporting metabolites received from the neuropil components via the subsurface cisterns. The subsurface cistern, on the other hand, by virtue of its location subjacent to the neuronal plasma membrane and of its increased frequency from birth to maturation, may be involved in the exchange of metabolites and nonsynaptic forms of communication at all ages.     

Biostructural theory of the living systems

Eugen Macovschi is among the few scientists who tried, and partly succeeded, to explain the differences between "dead" and "living" in biological sciences. He discovered and characterized the so-called biostructure of the living bodies and worked out a biostructural theory, which is the first supramolecular conception in biology. Nevertheless, complex biological systems are currently considered only from the molecular point of view, although they may be regarded as specific phenomena on highly structured bodies within the four-dimensional Universe. According to Macovschi, the biostructure provides organisms with life properties and controls their life processes and chemical changes. Nevertheless, plant cells or bacterial ones differ much from the animal or human cells. In fact, there are various biostructures which are related with cell properties. Hence, this theory creates confusions and cannot be easily used to explain all the properties of the biosystems. Consequently, it is our goal to highlight the principles, advantages, limitations, and applications of the biostructural theory, which might support new ideas and theories in modern life sciences.     

Death's toolbox: examining the molecular components of bacterial programmed cell death

Programmed cell death (PCD) is a genetically determined process of cellular suicide that is activated in response to cellular stress or damage, as well as in response to the developmental signals in multicellular organisms. Although historically studied in eukaryotes, it has been proposed that PCD also functions in prokaryotes, either during the developmental life cycle of certain bacteria or to remove damaged cells from a population in response to a wide variety of stresses. This review will examine several putative examples of bacterial PCD and summarize what is known about the molecular components of these systems.     

Self-assembly of the first cells in a hydrophobic environment with hydrogen as the energy source.

Two fundamental questions in biology are how and where the first cell(s) self-assembled under anoxic conditions on the Earth. The possibility is explored that life first self-assembled in a hydrophobic environment in the subsurface protected from radiation with ubiquitous hydrogen as the likely universal energy source.     

Perspective: Researching the transition from non-living to the first microorganisms: Methods and experiments are major challenges

Methods to research the origin of microbial life are limited. However, microorganisms were the first organisms on the Earth capable of cell growth and division, and interactions with their environment, other microbial cells, and eventually with diverse eukaryotic organisms. The origin of microbial life and the supporting scientific evidence are both an enigma and a scientific priority. Numerous hypotheses have been proposed, scenarios imagined, speculations presented in papers, insights shared, and assumptions made without supporting experimentation, which have led to limited progress in understanding the origin of microbial life. The use of the human imagination to envision the origin of life events, without supporting experimentation, observation and independently replicated experiments required for science, is a significant constraint. The challenge remains how to better understand the origin of microbial life using observations and experimental methods as opposed to speculation, assumptions, scenarios, envisioning events and un-testable hypotheses. This is not an easy challenge as experimental design and plausible hypothesis testing are difficult. Since past approaches have been inconclusive in providing evidence for the origin of microbial life mechanisms and the manner in which genetic instructions was encoded into DNA/RNA, it is reasonable and logical to propose that progress will be made when testable, plausible hypotheses and methods are used in the origin of microbial life research, and the experimental observations are, or are not reproduced in independent laboratories. These perspectives will be discussed in this article as well as the possibility that a pre-biotic film preceded a microbial biofilm as a possible micro-location for the origin of microbial cells capable of growth and division.     

Actin-Based Motility of Intracellular Microbial Pathogens

A diverse group of intracellular microorganisms, including Listeria monocytogenes, Shigella spp., Rickettsia spp., and vaccinia virus, utilize actin-based motility to move within and spread between mammalian host cells. These organisms have in common a pathogenic life cycle that involves a stage within the cytoplasm of mammalian host cells. Within the cytoplasm of host cells, these organisms activate components of the cellular actin assembly machinery to induce the formation of actin tails on the microbial surface. The assembly of these actin tails provides force that propels the organisms through the cell cytoplasm to the cell periphery or into adjacent cells. Each of these organisms utilizes preexisting mammalian pathways of actin rearrangement to induce its own actin-based motility. Particularly remarkable is that while all of these microbes use the same or overlapping pathways, each intercepts the pathway at a different step. In addition, the microbial molecules involved are each distinctly different from the others. Taken together, these observations suggest that each of these microbes separately and convergently evolved a mechanism to utilize the cellular actin assembly machinery. The current understanding of the molecular mechanisms of microbial actin-based motility is the subject of this review.     

PERSPECTIVE: THE EVOLUTIONARY BIOLOGY OF AGING,SEXUAL REPRODUCTION,AND DNA REPAIR

Three recent books on the evolutionary biology of aging and sexual reproduction are reviewed, with particular attention focused on the provocative suggestion by Bernstein and Bernstein (1991) that senescence and genetic recombination are related epiphenomena stemming from the universal challenge to life posed by DNA damages and the need for damage repair. Embellishments to these theories on aging and sex are presented that consider two relevant topics neglected or underemphasized in the previous treatments. The first concerns discussion of cytoplasmic genomes (such as mtDNA), which are transmitted asexually and therefore do not abide by the recombinational rules of nuclear genomes; the second considers the varying degrees of cellular and molecular autonomy which distinguish unicellular from multicellular organisms, germ cells from somatic cells, and sexual from asexual genomes. Building on the Bernsteins' suggestions, two routes to immortality for cell lineages appear to be available to life: an asexual strategy (exemplified by some bacteria), whereby cell proliferation outpaces the accumulation of DNA damages, thereby circumventing Muller's ratchet; and a sexual strategy (exemplified by germlines in multicellular organisms), whereby recombinational repair of DNA damages in conjunction with cell proliferation and gametic selection counter the accumulation of nuclear DNA damages. If true, then elements of both the recombinational strategy (nuclear DNA) and replacement strategy (cytoplasmic DNA) may operate simultaneously in the germ-cell lineages of higher organisms, producing at least some gametes that are purged of the DNA damages accumulated during the lifetime of the somatic parent. For multicellular organisms, production of functionally autonomous and genetically screened gametic cells is a necessary and sufficient condition for the continuance of life.     

Actin-based motility of intracellular microbial pathogens.

A diverse group of intracellular microorganisms, including Listeria monocytogenes, Shigella spp., Rickettsia spp., and vaccinia virus, utilize actin-based motility to move within and spread between mammalian host cells. These organisms have in common a pathogenic life cycle that involves a stage within the cytoplasm of mammalian host cells. Within the cytoplasm of host cells, these organisms activate components of the cellular actin assembly machinery to induce the formation of actin tails on the microbial surface. The assembly of these actin tails provides force that propels the organisms through the cell cytoplasm to the cell periphery or into adjacent cells. Each of these organisms utilizes preexisting mammalian pathways of actin rearrangement to induce its own actin-based motility. Particularly remarkable is that while all of these microbes use the same or overlapping pathways, each intercepts the pathway at a different step. In addition, the microbial molecules involved are each distinctly different from the others. Taken together, these observations suggest that each of these microbes separately and convergently evolved a mechanism to utilize the cellular actin assembly machinery. The current understanding of the molecular mechanisms of microbial actin-based motility is the subject of this review.     

The second cell membrane: the basal lamina and the tissue cell theory of metazoa.

We suggest that the basal lamina is essentially a second plasma or cell membrane appearing at the next higher level of biological organization; that together with associated cell monolayers it creates a tissue level membrane which is used to form multicellular cells and that collections of these provide the essential structure of metazoa. Thus when the histological structure of multicellular organisms is viewed in a topologically simplified form such organisms appear to be sets of multicellular cells (m-cells) formed by a unit tissue membrane built around the basal lamina. Not only are m-cells in this way structurally isomorphous (homeomorphic) to unit or classical biological cells (u-cells) but the two cellular levels are also functionally isomorphous. This suggests a “General Principle of Hierarchical Isomorphism or Iteration”, i.e. that multicellular evolution recapitulates unicellular evolution. This principle of structural and functional isomorphic mappability of unicellular onto multicellular organisms then governs the organization of matter all the way from molecules to man. Just as cytoplasm precipitates the bimolecular plasma membrane to form u-cells for the purpose of achieving reaction sequestration, in turn, these u-cells precipitate a common basal lamina to form m-cells, the histologist's acini, to produce sequestered “tissue plasms”. Thus, the “generalized acinus” with its basal laminar complex seem to constitute a second level (multicellular) cell and cell membrane, respectively.Four operators, ultimately under genetic control, can generate both u and m-cells from planar configurations of their respective unit membranes therewith providing the essential structure of all cells, tissues, organs and organisms. These are the ply, permeability vector, topological and stratificational operators. They are collected into a set of “organ formulae”. Both the plasma membrane and the basal lamina act as covering membranes and, again, as membranes for subcells so that a complete multicellular organism is a tetrahierarchical cell in which the molecule is the element of the first two cellular domains and the cell is the element of the last two. The analysis identifies a new transport organ group which together with the classical endocrine and exocrine groups comprises nearly the whole of the soft tissue organs. In a major reduction, all these organs are continuously (topologically) transformable into each and into hollow spheres, cells or acini thus greatly simplifying the histology of metazoa. Given this emphasis on cellularization it would seem that life, i.e. the autonomous chemoservo, results from the cooperation of cellularization and replication operations on the catalyzation process. Through cellularization, the lipid bilayer and basal laminar membranes provide the essential catalytic reaction sequestration demanded by chemical reaction theory while through complementary base pairing the DNA double helix provides the essential memory which stores the patterns of the variations of the sequestered reactions.     

Studies on rickettsia-like organism disease of the tropical marine pearl oyster I: the fine structure and morphogenesis of pinctada maxima pathogen rickettsia-like organism

The present paper reports for the first time the discovery of a rickettsia-like organism (RLO) in the cultured tropical marine pearl oyster Pinctada maxima with mass mortality in the Hainan Province of China. This organism parasitizes the cytoplasm of host cells and forms intracytoplasmic eosinophilic inclusions. These organisms are extremely pleiomorphic in shape and average 967 x 551 nm in size, as measured in cross sections of transmission electron micrographs. The organisms exhibit clearly recognizable ultrastructural characteristics of prokaryotic bacteria-like cells, including two trilaminar membranes, an increasing electron-dense periplasmic ribosome zone, and a thread-like DNA nucleoidal structure. In addition to the above prokaryotic characteristics, the following unique biological characteristics were confirmed by TEM: (i) These organisms are usually located in host cells in two ways, namely, free in the cell cytoplasm and involved within membrane-limited phagolysosomes; (ii) The organisms exist in two morphological cell types, namely a small cell variant (SCV) and a large cell variant (LCV). The most important morphological difference between two cell types is that the SCV is obviously ribosome-rich in the periphery of the body, which makes SCV more electron-dense in the cytoplasm and narrower in the central nucleoid area than the LCV; (iii) Two propagative modes of the organisms, transverse binary fission and budding, are observed in cytoplasm and phagolysosomes of host cells under TEM, in which the budding is more often seen in phagolysosomes. These characteristics indicate that the organism is a separate species in the family Rickettsiaceae and should be classified into the genus Rickettsia. On the basis of the existence of the two propagative modes and two cell types, and intracellular location, we propose a developmental cycle for this organism which includes a vegetative differentiation stage to develop LCV by transverse binary fisson and a budding differentiation stage to develop resistant SCV. Copyright 1999 Academic Press.     

Organism size promotes the evolution of specialized cells in multicellular digital organisms

Specialized cells are the essence of complex multicellular life. Fossils allow us to study the modification of specialized, multicellular features such as jaws, scales, and muscular appendages. But it is still unclear what organismal properties contributed to the transition from undifferentiated organisms, which contain only a single cell type, to multicellular organisms with specialized cells. Using digital organisms I studied this transition. My simulations show that the transition to specialized cells happens faster in organism composed of many cells than in organisms composed of few cells. Large organisms suffer less from temporarily unsuccessful evolutionary experiments with individual cells, allowing them to evolve specialized cells via evolutionary trajectories that are unavailable to smaller organisms. This demonstrates that the evolution of simple multicellular organisms which are composed of many functionally identical cells accelerates the evolution of more complex organisms with specialized cells.     

“Unidentified” Mobile Protozoans from the Blood of Carp and Some Unsolved Problems of Myxosporean Life Cycles1

Heavy infections with enigmatic mobile organisms have recently been found in the blood of carp (Cyprinus carpio) in Central Europe. The organisms measure up to 15 μm, are variable in shape, and exhibit an unceasing twitching or dancing movement. Their developmental cycle starts with a primary cell enclosing a secondary cell. The former grows while the latter produces inside itself by a series of binary fissions and internal cleavages up to eight secondary cells, each of which encloses an inner (tertiary) cell of its own. In addition, up to four tiny cells with compact nuclei (“residual bodies”) also result from divisions of the secondary cells. Primary cells containing the products of the division of secondary cells finally disintegrate, releasing the secondary cells, which in their turn become new primary cells and repeat the cycle all over again. The structure and behavior of these organisms were so incompatible with existing ideas on myxosporean development that their myxosporean affinity was at first unrecognized. The final proof of their identity–appearance of myxosporean spores in sterile, experimentally infected hosts–is still to be presented. The interpretation of the myxosporean features of their life cycle (i.e., [1] the pericyte nature of the primary cell, [2] proliferation by disintegration of the pseudoplasmodial primary cell, [3] no rigidly fixed pattern in vegetative development), their ultrastructure (i.e., [1] characteristic bundles of microtubules and numerous free ribosomes in secondary cells, [2] lack of centrioles, [3] membranes enclosing the secondary cells within the primary cells), and facts on their epizootiology (i.e., [1] no success at transmission via leeches, [2] the occurrence of these organisms along with Sphaerospora renicola Dykova and Lom) suggest that they are stages of S. renicola from the kidney of carp. Similar mobile organisms were found in the blood of fry of two other fishes (Gobio gobi and Tinca tinca) which are also hosts for a Sphaerospora that infects the kidney. This suggests that these organisms represent an early phase in the developmental cycle in the genus Sphaerospora. The existence of cells enveloped one within the other (secondary and tertiary cells) in the developmental cycle, a characteristic myxosporean feature itself, is an intriguing parallel to similarly enclosed cells in sporogenesis of Paramyxea (Ascetospora).     

FLUID SHEAR-STIMULATED DINOFLAGELLATE BIOLUMINESCENCE

Bioluminescence studies provide insight into the properties of water motion that are stimulatory to flow-sensitive organisms such as dinoflagellates, the most common sources of near-surface oceanic bioluminescence. Previous laboratory studies employing steady flows have characterized the luminescent response of dinoflagellates in terms of shear stress. In the present study, computational and experimental approaches were used to investigate the contributions of shear and acceleration to cells responding in a laminar converging flow field, where regions of high acceleration and shear are spatially separated. Flow-stimulated flashes by the dinoflagellates Lingulodinium polyedrum and Ceratocorys horrida were used as a near-instantaneous monitor of cell response. By combining video analysis of flash trajectories with computational methods, the location of each stimulated cell was determined and flow parameters at that location were calculated. Based on several criteria, shear stress was considered the flow parameter most stimulatory to cells. For both dinoflagellates species and for all flow rates, essentially all cells responded downstream near the wall where shear stress levels were maximal, and levels of acceleration and extensional stress were as much as two orders of magnitude less than locations away from the wall. Minimum shear stress levels at the cell positions were consistent with response thresholds based on previous studies. Bioluminescence is an excellent tool for examining how organisms respond to flow at the small temporal and spatial scales relevant to planktonic organisms.