The emergence of ribozymes synthesizing membrane components in RNA-based protocells

A significant problem of the origin of life is the emergence of cellular self-replication. In the context of the “RNA world”, a crucial concern is how the RNA-based protocells could achieve the ability to produce their own membrane. Here we show, with the aid of a computer simulation, that for these protocells, there would be “immediately” a selection pressure for the emergence of a ribozyme synthesizing membrane components. The ribozyme would promote the enlargement of cellular space and favor the incoming (by permeation) of RNA's precursors, thus benefit the replication of inner RNA, including itself. Via growth and division, protocells containing the ribozyme would achieve superiority and spread in the system, and meanwhile the ribozyme would spread in the system. The present work is inspiring because it suggests that the transition from molecular self-replication to cellular self-replication might have occurred naturally (and necessarily) in the origin of life, leading to the emergence of Darwinian evolution at the cellular level.     

The "protocell": a mathematical model of self-maintenance

The concepts of self-generation, autonomous boundary and self-maintenance are explained briefly. The "protocell" is presented as a model of self-maintenance which is based on simple physical mechanisms of diffusion and reaction. The time evolution of the surface of the protocell is taken into account explicitly in the form of a Stefan condition giving rise to a non-linear feedback of the surface motion to the reaction and diffusion processes inside the protocell. The spatio-temporal dynamics are investigated, particularly in the neighbourhood of the stationary states, showing a self-maintaining behaviour under a certain range of nutritional conditions. Under another set of conditions we find an instability leading to a division process so that the population of protocells becomes self-maintaining instead of the single individual. The presented formulation of the protocell model is crucially improved compared with a previous version which required boundary conditions at infinity. The previous version was not strictly self-maintaining since dynamics outside the cell were essential for its behaviour.     

The origins of cellular life

All life on earth can be naturally classified into cellular life forms and virus-like selfish elements, the latter being fully dependent on the former for their reproduction. Cells are reproducers that not only replicate their genome but also reproduce the cellular organization that depends on semipermeable, energy-transforming membranes and cannot be recovered from the genome alone, under the famous dictum of Rudolf Virchow, Omnis cellula e cellula. In contrast, simple selfish elements are replicators that can complete their life cycles within the host cell starting from genomic RNA or DNA alone. The origin of the cellular organization is the central and perhaps the hardest problem of evolutionary biology. I argue that the origin of cells can be understood only in conjunction with the origin and evolution of selfish genetic elements. A scenario of precellular evolution is presented that involves cohesion of the genomes of the emerging cellular life forms from primordial pools of small genetic elements that eventually segregated into hosts and parasites. I further present a model of the coevolution of primordial membranes and membrane proteins, discuss protocellular and non-cellular models of early evolution, and examine the habitats on the primordial earth that could have been conducive to precellular evolution and the origin of cells.     

Less can be more: RNA-adapters may enhance coding capacity of replicators

It is still not clear how prebiotic replicators evolved towards the complexity found in present day organisms. Within the most realistic scenario for prebiotic evolution, known as the RNA world hypothesis, such complexity has arisen from replicators consisting solely of RNA. Within contemporary life, remarkably many RNAs are involved in modifying other RNAs. In hindsight, such RNA-RNA modification might have helped in alleviating the limits of complexity posed by the information threshold for RNA-only replicators. Here we study the possible role of such self-modification in early evolution, by modeling the evolution of protocells as evolving replicators, which have the opportunity to incorporate these mechanisms as a molecular tool. Evolution is studied towards a set of 25 arbitrary 'functional' structures, while avoiding all other (misfolded) structures, which are considered to be toxic and increase the death-rate of a protocell. The modeled protocells contain a genotype of different RNA-sequences while their phenotype is the ensemble of secondary structures they can potentially produce from these RNA-sequences. One of the secondary structures explicitly codes for a simple sequence-modification tool. This 'RNA-adapter' can block certain positions on other RNA-sequences through antisense base-pairing. The altered sequence can produce an alternative secondary structure, which may or may not be functional. We show that the modifying potential of interacting RNA-sequences enables these protocells to evolve high fitness under high mutation rates. Moreover, our model shows that because of toxicity of misfolded molecules, redundant coding impedes the evolution of self-modification machinery, in effect restraining the evolvability of coding structures. Hence, high mutation rates can actually promote the evolution of complex coding structures by reducing redundant coding. Protocells can successfully use RNA-adapters to modify their genotype-phenotype mapping in order to enhance the coding capacity of their genome and fit more information on smaller sized genomes.     

Self-maintenance and self-reproduction in an abstract cell model

Living cells must maintain their membranes by active metabolism. The membrane is not static but a dynamic structure that has evolved along with its internal reactions. When we reflect on the emergence and evolution of primitive cells, we should not forget the mutual dependency between membranes and metabolic cycles inside the cell. In this paper, we present a simple abstract model of the self-maintaining cell. A metabolic cycle will produce a self-assembling membrane that will enclose the metabolic cycle. We show that a self-maintaining cell has the potential to reproduce itself spontaneously. Further, we have demonstrated two different ways of cellular reproduction depending on the mobility of chemicals. In the first case, a cell releases autocatalytic chemicals that create new cells outside the mother cell. In the second case, a cell grows larger and divides itself into daughter cells by creating a new internal dividing membrane.     

Domain protolife

We propose the Thermal Protein First Paradigm (protocell theory) that affirms that first life was cellular. The first cells emerged from molecular (chemical) evolution as protocells (heated amino acids self-order in copolymerization reactions to form thermal proteins which self-organize when in contact with water to form protocells). Metaprotocells are specialized protocells capable of synthesizing ATP (light energy conversion to chemical energy), polypeptides, and polynucleotides. Aggregations of protocells in thermal protein matrices form distinctive morphologies (protocellular networks). Prokaryotic cells emerged from metaprotocells. We classify protocells and metaprotocells as members of the Domain Protolife. We revised the cell theory to include protolife.     

How did bacterial ancestors reproduce? Lessons from L‐form cells and giant lipid vesicles

In possible scenarios on the origin of life, protocells represent the precursors of the first living cells. To study such hypothetical protocells, giant vesicles are being widely used as a simple model. Lipid vesicles can undergo complex morphological changes enabling self‐reproduction such as growth, fission, and extra‐ and intravesicular budding. These properties of vesicular systems may in some way reflect the mechanism of reproduction used by protocells. Moreover, remarkable similarities exist between the morphological changes observed in giant vesicles and bacterial L‐form cells, which represent bacteria that have lost their rigid cell wall, but retain the ability to reproduce. L‐forms feature a dismantled cellular structure and are unable to carry out classical binary fission. We propose that the striking similarities in morphological transitions of L‐forms and giant lipid vesicles may provide insights into primitive reproductive mechanisms and contribute to a better understanding of the origin and evolution of mechanisms of cell reproduction. Editor's suggested further reading in BioEssays Synthesizing artificial cells from giant unilamellar vesicles: State‐of‐the art in the development of microfluidic technology Abstract     

The ribotype theory on the origin of life

The ribotype is defined as the ribonucleoprotein system of any cell. The theory substitutes the genotype-phenotype duality with the trinity genotype-ribotype-phenotype, and proposes that life on earth originated with the ancestors of today's ribotypes.The first three chapters describe separate models on precellular evolution, the evolution of protocells and the nature of the cell respectively, and the unity of the theory comes from the fact that they form a consistent and interdependent whole.The core of the theory is the ribotype hypothesis, of which two formulations are given. The restricted version is based on a link between ribotypes and ribosome biogenesis, and provides an explanation for the difference between 70S and 80S ribosomes. The general version describes a link between ribotypes and cell-types and explains why prokaryotes have 70S ribosomes, eukaryotes 80S ribosomes and endosymbionts a type of ribosomes similar to the bacterial ones.If the creation hypothesis, panspermia and spontaneous generation are set aside, all alternative models of the origin of life belong to two schemes which are referred to as the genotype and the phenotype theories. It is shown that these theories rely on some discontinuity between past and present biological principles because of the need to break their inherent chicken-and-egg paradoxes, while the ribotype theory does not. Its hypotheses, free and arbitrary as they are or appear to be, have been built exclusively on properties and processes for which solid evidence exists, and the continuity between past and present biological laws is assumed as a corollary. Finally, it is shown that falsification tests are possible, and some of them are expected in the relatively near future.     

Self-sequencing of amino acids and origins of polyfunctional protocells

The primal role of the origins of proteins in molecular evolution is discussed. On the basis of this premise, the significance of the experimentally established self-sequencing of amino acids under simulated geological conditions is explained as due to the fact that the products are highly nonrandom and accordingly contain many kinds of information. When such thermal proteins are aggregated into laboratory protocells, an action that occurs readily, the resultant protocells also contain many kinds of information. Residue-by-residue order, enzymic activities, and lipid quality accordingly occur within each preparation of proteinoid (thermal protein).In this paper are reviewed briefly the phenomenon of self-sequencing of amino acids, its relationship to evolutionary processes, other significance of such self-ordering, and the experimental evidence for original polyfunctional protocells.     

Growth, Survivorship and Reproduction of Daphnia middendorffiana in Several Arctic Lakes and Ponds

The growth, survivorship and reproduction of Arctic region Daphniamiddendorffiana was investigated in several lakes and pondson the tundra in northern Alaska and additionally in a laboratorystudy. Growth rate equations, reproduction rates and survivorshipunder natural conditions were determined. The natural environmentsdiffered in the available resources; investigations were madein undisturbed oligotrophic lakes, lakes undergoing nutrientmanipulations, lakes recovering from nutrient manipulation,and a small human-created pond. The lakes also differed in thepresence or absence of fish. The results indicated that resourceavailability affected the growth, survivorship and reproductionof D. middendorffiana. The lake with the highest resources producedthe greatest reproduction and growth. The environments withthe lowest resources had the least reproduction. Secondly, resourcelevel was observed to influence life history choices. Underlow resource conditions D. middendorffiana produced ephippiaat first reproduction rather than neonates. Third, the resultsalso indicated that refuge from predation significantly affectsthe distribution of D. middendorffiana. Lakes that contain fishdo not support significant populations of D. middendorffiana,although the growth and survivorship studies indicate they coulddo well in those environments.     

The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions,and opportunism in the design of metabolic pathways during evolution

The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into asingle-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.     

Clonal plants as cooperative systems: Benefits in heterogeneous environments

All natural environments are spatially and temporally heterogeneous. Consequently, their ability to provide essential resources for the growth of plants is variable. Modular plant species produce repeated basic structures which, in the case of clonal species, are called ramets. Ramets belonging to the same clone are distributed throughout the environment in space and time, and therefore they may be located in sites which differ in resource-providing quality. The connections between ramets may allow resources to be shared, enabling the clone to behave as a cooperative system. As a result of such physiological integration, ramets can survive in conditions where there is lethal shortage of a resource because they are connected to, and supported by, ramets located in conditions where there is ample supply of the same resource. Physiological integration between connected ramets presents opportunities for heterogeneous environments to be exploited to an extent that is only just becoming apparent. As heterogeneity is ubiquitous in natural environments, it may be expected that plants, as relatively immobile organisms, will have evolved the capacity to cope with it by making appropriate localized morphological and/or physiological plastic responses. Recent studies suggest that such responses not only enable clonal species to cope with environmental heterogeneity, but that under some circumstances they can benefit more from environments which are heterogeneous rather than homogeneous, even when both types of environment contain the same amount of resources. Studies on Glechoma hederacea (Lamiaceae) that illustrate this phenomenon are described.     

Contrasting Responses of Saproxylic Insects to Focal Habitat Resources: The Example of Longhorn Beetles and Hoverflies in Belgian Deciduous Forests

Although both saproxylic longhorn beetles and hoverflies benefit from the presence of woody substrates for reproduction, they differ in their requirements for floral resources and for microbiotopes of overmature and senescent trees. This led us to expect contrasting responses between the two species groups in relation to these essential resources. We examined this prediction in 22 mature oak- and beech-dominated stands of southern Belgium by relating their species assemblages to local vegetation structure and composition, altitude and landscape composition. Stands were organised in pairs as a function of their overall dead wood supply. Free-hanging window traps, stump emergence traps and Malaise traps produced 30 longhorn beetle species (1637 individuals) and 106 hoverfly species (3020 individuals). Paired-comparisons controlling for annual variation in captures showed that, unlike saproxylic hoverflies, stands with dead wood hosted more species and individuals of longhorn beetles. Accordingly, the two species groups were found to be independent on ordination axes, responding to different sets of environmental conditions. While stands dominated by oaks with a high snag volume were highly favoured by longhorn beetles, saproxylic and threatened syrphids were limited to open-stands with large trees and a well-developed, species rich herb layer providing the floral resources required for their reproduction. Our results suggest that, when defining criteria to identify or restore important habitats for saproxylic insect conservation, variables related to different aspects of dead wood supply should not be the only criteria taken into account.     

The Origin and Evolution of Metabolic Pathways: Why and How did Primordial Cells Construct Metabolic Routes?

The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present on the primordial Earth imposed an important selective pressure, favoring those primordial heterotrophic cells that became able to synthesize those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria, and Eukarya reveal that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the emergence of new metabolic abilities. Among these gene elongations, gene and operon duplications played a crucial role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence, giving rise to new genes coding for new metabolic abilities. Concerning the mechanisms of pathway assembly, both the analysis of completely sequenced genomes and directed evolution experiments strongly support the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis, suggests that other different hypothesis, i.e., the retrograde hypothesis, may account for the evolution of some steps within metabolic pathways.     

Generic Darwinian selection in catalytic protocell assemblies

To satisfy the minimal requirements for life, an information carrying molecular structure must be able to convert resources into building blocks and also be able to adapt to or modify its environment to enhance its own proliferation. Furthermore, new copies of itself must have variable fitness such that evolution is possible. In practical terms, a minimal protocell should be characterized by a strong coupling between its metabolism and genetic subsystem, which is made possible by the container. There is still no general agreement on how such a complex system might have been naturally selected for in a prebiotic environment. However, the historical details are not important for our investigations as they are related to assembling and evolution of protocells in the laboratory. Here, we study three different minimal protocell models of increasing complexity, all of them incorporating the coupling between a 'genetic template', a container and, eventually, a toy metabolism. We show that for any local growth law associated with template self-replication, the overall temporal evolution of all protocell's components follows an exponential growth (efficient or uninhibited autocatalysis). Thus, such a system attains exponential growth through coordinated catalytic growth of its component subsystems, independent of the replication efficiency of the involved subsystems. As exponential growth implies the survival of the fittest in a competitive environment, these results suggest that protocell assemblies could be efficient vehicles in terms of evolving through Darwinian selection.     

Effects of burial in sand and water supply regime on seedling emergence of six species

BACKGROUND AND AIMS: Air seeding has long been regarded as a quick and successful measure for vegetation rehabilitation in China. However, seedling emergence of often-used species including Agriophyllum squarrosum, Artemisia sphaerocephala, Artemisia ordosica, Hedysarum fruticosum, Caragana korshinskii and Medicago sativa is low. Experiments were conducted under controlled conditions to study the effects of sowing depth and water supply on seedling emergence, in order to understand the requirements for increasing seedling emergence. METHODS: Seeds were exposed to different environments of burial and water supply regimes in PVC pots (7 cm in diameter and 11 cm in height) under the same light intensity and alternating temperature regimes in a growth chamber. KEY RESULTS: Seedlings of three species (Agriophyllum squarrosum, Artemisia sphaerocephala, Artemisia ordosica) with relatively light seeds emerged well at a 0.5 cm sowing depth under a 7.5 and 10 mm water supply regime. However, few seedlings of these species emerged when the sowing depth was over 1 cm or when water supply was 5 mm. Seedlings of Caragana korshinskii, Hedysarum fruticosum and Medicago sativa emerged from sowing depths of 0.5-4 cm, 0.5-3 cm, and 0.5-4 cm, respectively, under both 7.5 and 10 mm water supply regimes. Under a 5 mm water supply regime, seedlings of these species also emerged at over 1 cm sowing depth. Seeds of all six species sown on the surface of sand did not germinate, and seedlings did not emerge when they were sown at depths greater than 6 cm. CONCLUSIONS: Based on these experiments, a 0.5 cm sowing depth resulted in the highest seedling emergence and it is concluded that this is the optimal sowing depth for seedling emergence of all six species.     

The evolution of phenotypic plasticity in spatially structured environments: implications of intraspecific competition, plasticity costs and environmental characteristics

We model the evolution of reaction norms focusing on three aspects: frequency-dependent selection arising from resource competition, maintenance and production costs of phenotypic plasticity, and three characteristics of environmental heterogeneity (frequency of environments, their intrinsic carrying capacity and the sensitivity to phenotypic maladaptation in these environments). We show that (i) reaction norms evolve so as to trade adaptation for acquiring resources against cost avoidance; (ii) maintenance costs cause reaction norms to better adapt to frequent rather than to infrequent environments, whereas production costs do not; and (iii) evolved reaction norms confer better adaptation to environments with low rather than with high intrinsic carrying capacity. The two previous findings contradict earlier theoretical results and originate from two previously unexplored features that are included in our model. First, production costs of phenotypic plasticity are only incurred when a given phenotype is actually produced. Therefore, they are proportional to the frequency of environments, and these frequencies thus affect the selection pressure to avoid costs just as much as the selection pressure to improve adaptation. This prevents the frequency of environments from affecting the evolving reaction norm. Secondly, our model describes the evolution of plasticity for a phenotype determining an individual's capability to acquire resources, and thus its realized carrying capacity. When individuals are distributed randomly across environments, they cannot avoid experiencing environments with intrinsically low carrying capacity. As selection pressures arising from the need to improve adaptation are stronger under such extreme conditions than under mild ones, better adaptation to environments with low rather than with high intrinsic carrying capacity results.     

From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.     

Steps Towards the Formation of A Protocell: The Possible Role of Short Peptides

The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.     

Life history and the evolution of family living in birds

The reason why some bird species live in family groups is an important question of evolutionary biology that remains unanswered. Families arise when young delay the onset of independent reproduction and remain with their parents beyond independence. Explanations for why individuals forgo independent reproduction have hitherto focused on dispersal constraints, such as the absence of high-quality breeding openings. However, while constraints successfully explain within-population dispersal decisions, they fail as an ultimate explanation for variation in family formation across species. Most family-living species are long-lived and recent life-history studies demonstrated that a delayed onset of reproduction can be adaptive in long-lived species. Hence, delayed dispersal and reproduction might be an adaptive life-history decision rather than 'the best of a bad job'. Here, we attempt to provide a predictive framework for the evolution of families by integrating life-history theory into family formation theory. We suggest that longevity favours a delayed onset of reproduction and gives parents the opportunity of a prolonged investment in offspring, an option which is not available for short-lived species. Yet, parents should only prolong their investment in offspring if this increases offspring survival and outweighs the fitness cost that parents incur, which is only possible under ecological conditions, such as a predictable access to resources. We therefore propose that both life-history and ecological factors play a role in determining the evolution of family living across species, yet we suggest different mechanisms than those proposed by previous models.