The evolution of prebiological self-organization: probable colloid-chemical evolution of first prokaryotic cells

This is an attempt to analyse the mechanisms of self-assembly in the course of the origin and early evolution of life on the Earth. A special attention is paid to the investigation of transient stages between the physico-chemical and biological bases of self-assembly, including experimental models and paleontological results. The theory of coacervate-in-coacervate is discussed from the point of view of evolution of first procaryotic cells. Many of the high developed structures of the contemporary cells, such as ribosomes, chromosomes, lipid membranes, some other organelles etc., are claimed to posses a rudimentary polyionic coacervate character.     

Recognition and molecular evolution in bacteria

One principal function of biological molecules in bacteria is to recognize other molecules. This allows cells to assemble for regulated enzymatic catalysis and the integration of biochemical pathways. Recognition is also an essential and a specific property in base pairing of DNA in the double helix. Therefore, recognition events must have been central to early self-assembly of primitive genetic material, genomes, cells, genetic recombination and especially in enzyme-substrate-product recognition events. Molecular recognition events are examined with an emphasis on their central role in early prokaryotic evolution.     

The origin of prokaryotic life and molecular evolution

The origin of prokaryotic life is discussed with an emphasis on the self-assembly of early life in a microscale environment where ordered cellular structures and integrated functions evolved from disorder. Early molecular evolution may have been due to both molecular chaos and evolving molecular order.     

Molecular evolution: first enzymes, gases as substrates and genetic templates.

A fundamental problem in biology is the self-assembly of the first cells capable of growth and division under anoxic conditions on the Earth. Evolution proceeded by self-assembling and self-replicating cells that reproduced their own genetic information and also changed their genetic code over time. Was it also possible that some of the first proteins were catalytic and used gases as substrates and also acted as genetic templates? This paper explores the possibility that primitive protein enzymes used gases as their substrates, and reverse translation may have been a feature in the self-assembly of the first cell(s).     

In vitro selection as a powerful tool for the applied evolution of proteins and peptides

New in vitro methods for the applied evolution of protein structure and function complement conventional cellular and phage-based methods. Strategies employing the direct physical linkage of genotype and phenotype, and the compartmental association of gene and product to select desired properties are discussed, and recent useful applications are described. Engineering of antibodies and other proteins, selection from cDNA libraries, and the creation of functional protein domains from completely random starting sequences illustrate the value of the in vitro approaches. Also discussed is an emerging new direction for in vitro display technology: the self-assembly of protein arrays.     

The evolution of calcium biochemistry

The role of calcium in evolution is best understood from a perspective based on its intrinsic value as a divalent cation able to bind and precipitate inorganic and organic anions rapidly. This binding can be useful or inhibitory. Now treatment of binding or precipitation has two different interests in biological cells. The first is thermodynamic, that is the stress is on systems biology and the second is structure, that is molecular biology. In evolution both have equal weight being connected through exchange. This paper outlines first the systems biology of the evolution of calcium functions from prokaryotes to animals with brains. The calcium ion was the only good available candidate in the environment for the functions it performs. The second section of the paper describes the evolution of the proteins which allow the messenger function. We have discussed elsewhere the structure/function relationships of the proteins. Overall the evolving and increasing involvement of calcium as possibly the major control messenger of events outside cells to action inside them is an inevitable feature of the nature of ecological, that is environmental/organism, evolution.     

Optimization of reorganization energy drives evolution of the designed Kemp eliminase KE07

Understanding enzymatic evolution is essential to engineer enzymes with improved activities or to generate enzymes with tailor-made activities. The computationally designed Kemp eliminase KE07 carries out an unnatural reaction by converting of 5-nitrobenzisoxazole to cyanophenol, but its catalytic efficiency is significantly lower than those of natural enzymes. Three series of designed Kemp eliminases (KE07, KE70, KE59) were shown to be evolvable with considerable improvement in catalytic efficiency. Here we use the KE07 enzyme as a model system to reveal those forces, which govern enzymatic evolution and elucidate the key factors for improving activity. We applied the Empirical Valence Bond (EVB) method to construct the free energy pathway of the reaction in the original KE07 design and the evolved R7 1/3H variant. We analyzed catalytic effect of residues and demonstrated that not all mutations in evolution are favorable for activity. In contrast to the small decrease in the activation barrier, in vitro evolution significantly reduced the reorganization energy. We developed an algorithm to evaluate group contributions to the reorganization energy and used this approach to screen for KE07 variants with potential for improvement. We aimed to identify those mutations that facilitate enzymatic evolution, but might not directly increase catalytic efficiency. Computational results in accord with experimental data show that all mutations, which appear during in vitro evolution were either neutral or favorable for the reorganization energy. These results underscore that distant mutations can also play role in optimizing efficiency via their contribution to the reorganization energy. Exploiting this principle could be a promising strategy for computer-aided enzyme design. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.     

TIMA Part 2. TIMA-based instructive evolution of macromolecules and organs and structures

In extending a previous paper (TIMA Part 1, Wassermann, 1982) “template induced molecular assembly” (TIMA) is being further explored. It is suggested that TIMA could first have evolved proteins without coevolution of mRNA-like systems, in the absence of tRNAs. Some of these early proteins could, by self-assembly, have built up ribosomes. Ribosomes jointly with amino acids could have served as assembly templates for the TIMA-based evolution of tRNAs. Once tRNAs had evolved, TIMA could have participated, via a modified Mekler (1967) mechanism, in the evolution of new proteins and the coevolution of corresponding mRNA-like strands. TIMA also requires gene duplications and/or random mutations of DNA, to produce partial matching by duplicated and/or randomized DNA sequences of TIMA-generated cDNA which is complementary to the mRNA-like strands. The cDNA could then become incorporated by crossover into the position of the partially matching DNA sequences of, say, duplicate genes in genomes of germ-line cells. Since one requires only partial matching between duplicate (and/or randomly generated) DNA and non-randomly, TIMA-generated cDNA, TIMA theory avoids the need to assume (as in the Baldwin effect) that complete genes were randomly evolved. While rejecting crude Lamarckism, TIMA equally avoids the assumption that genes evolved only by combined random events, gene duplications, and adaptive selection. The resulting theory explains typical pseudo-exogenous adaptations via TIMA. Darwinian selection—now in the guise of “molecular selection” (and favourable environmental adaptive selection where present)—combined with TIMA could account for Waddington's “genetic assimilation”, thereby conceding Lamarck's notion that the environment can help to model heredity (while rejecting crude Lamarckism).     

Symbiosis and the evolution of prokaryotes

It is postulated, with support from kinetic modelling, that a succession of symbioses was the major process of evolution during the early stages of life. The process became less effective with the passage of time, while evolution by the natural selection of variants became more effective. The postulate may contribute usefully to discussions on the evolution of biochemical complexity and the structure of cells.     

Symbiosis drove cellular evolution

Anthropocentric cultural bias led to conceptualizations of evolution as a tree with branches leading to a crown of vertebrates and higher plants. Gradually refined over the years it became part of common scientific culture to think of eukaryotic evolution as process by which cells, limited by surface to volume ratios and other factors, became specialized, leading to multi-cellularity and eventually to the crowned tree. Knowledge of other pathways of cellular evolution is available, but not broadly recognized. Molecular systematics, genetic analyses and ultrastructural comparisons have changed our outlook on evolution and the diversity of life. The discovery of a huge (average size 2.1 cm) unicellular, new, exceptionally complex, dinoflagellate-hosting soritid foraminiferan from the Heron-Wistori Channel, (GBR Australia) gave impetus to re-explore some old ideas on cellular evolution and place them in a contemporary context. In particular, it caused change in perspective of the evolution of the collective group known as larger foraminifera (LF). They exemplify the power by which symbiosis drove the evolution of a predisposed and malleable group of organisms. The factors that underlay foraminiferan predisposition to symbioses with algae are discussed. Each of the evolutionary lines of LF has developed, in its own way, amazing structural adaptations making them extremely complex giant cells.     

Early evolution of MHC polymorphism

There is unwarranted satisfaction with the view that MHC polymorphism evolved because there was a selective advantage in having a variety of MHC proteins to bind a variety of peptide subsets for presentation to T cells. While this may, in part, explain its maintainance, polymorphism may have evolved initially to reject foreign virus "grafts". The possession of similar membranes promotes aggregation between "like" cells, but it also promotes aggregation between the cells and viruses which retain membrane components of their previous host. The selection pressure afforded by hostile virus "grafts" would favour cells which developed polymorphic membrane components (since "like" will not aggregate with "not-like"). This polymorphism would have evolved before the appearance of multicellular organisms. Thus, the evolution of modern immune systems would have been imposed upon pre-existing polymorphic systems. A path this evolution may have taken involves the development of mechanisms for intracellular distinction between self and not-self.     

Male-driven evolution

The strength of male-driven evolution - that is, the magnitude of the sex ratio of mutation rate - has been a controversial issue, particularly in primates. While earlier studies estimated the male-to-female ratio (alpha) of mutation rate to be about 4-6 in higher primates, two recent studies claimed that alpha is only about 2 in humans. However, a more recent comparison of mutation rates between a noncoding fragment on Y and a homologous region on chromosome 3 gave an estimate of alpha = 5.3, reinstating strong male-driven evolution in hominoids. Several studies investigated variation in mutation rates among genomic regions that may not be related to sex differences and found strong evidence for such variation. The causes for regional variation in mutation rate are not clear but GC content and recombination are two possible causes. Thus, while the strong male-driven evolution in higher primates suggests that errors during DNA replication in the germ cells are the major source of mutation, the contribution of some replication-independent factors such as recombination may also be important.     

Light-dependent hydrogen evolution by Scenedesmus

Summary The effect of glucose and the uncoupler Cl-CCP upon hydrogen production was studied in adapted cells of Scenedesmus obliquus D₃. Cl-CCP at 10^-5M concentration completely inhibited the evolution of H₂ in the dark and increased the apparent rate of H₂ evolution in the light. At 10^-5M Cl-CCP, photosynthesis and photoreduction by anaerobically adapted algae were only temporarily inhibited; O₂ evolution reappeared after approximately 1 hr of illumination if CO₂ was present. Increasing the Cl-CCP concentration to 5 x 10^-5M led to a maximum rate of photohydrogen production and fully inhibited H₂ evolution, photoreduction and dark H₂ evolution. H₂ evolution was accompanied by a release of varying amounts of CO₂ in the light, as well as in the dark. Dark CO₂ production was stimulated by Cl-CCP. H₂ evolution in the light was stimulated by adding glucose to autotrophically grown cells or by growing the cells heterotrophically with glucose; starvation had an opposite effect. Adapted cells released ¹⁴CO₂ from the 3 and/or 4 position of specifically labeled glucose, indicating that degradation occurred via the Embden-Meyerhof pathway. The amount of H₂ released by autotrophically grown cells was the same either with continuous illumination or with short periods of light, followed by darkness. Scenedesmus mutant No. 11, which is unable to evolve O₂ was not inhibited in its capacity to evolve H₂ in the light. These data indicate that the evolution of H₂ in the light by adapted Scenedesmus depends upon the degradation of organic material and does not require the production of free O₂ by photosystem II.The following abbreviations are used: Cl-CCP = carbonyl cyanide m-chlorophenylhydrazone; DCMU = 3-(3,4-dichlorophenyl)-1,1-dimethylurea, DNP = 2,4-dinitrophenol.This work was supported by contract AT-(40-1)-2687 from the U.S. Atomic Energy Commission.     

The evolution of chordate neural segmentation

Amphioxus is the closest relative to vertebrates but lacks key vertebrate characters, like rhombomeres, neural crest cells, and the cartilaginous endoskeleton. This reflects major differences in the developmental patterning of neural and mesodermal structures between basal chordates and vertebrates. Here, we analyse the expression pattern of an amphioxus FoxB ortholog and an amphioxus single-minded ortholog to gain insight into the evolution of vertebrate neural segmentation. AmphiFoxB expression shows cryptic segmentation of the cerebral vesicle and hindbrain, suggesting that neuromeric segmentation of the chordate neural tube arose before the origin of the vertebrates. In the forebrain, AmphiFoxB expression combined with AmphiSim and other amphioxus gene expression patterns shows that the cerebral vesicle is divided into several distinct domains: we propose homology between these domains and the subdivided diencephalon and midbrain of vertebrates. In the Hox-expressing region of the amphioxus neural tube that is homologous to the vertebrate hindbrain, AmphiFoxB shows the presence of repeated blocks of cells along the anterior-posterior axis, each aligned with a somite. This and other data lead us to propose a model for the evolution of vertebrate rhombomeric segmentation, in which rhombomere evolution involved the transfer of mechanisms regulating neural segmentation from vertical induction by underlying segmented mesoderm to horizontal induction by graded retinoic acid signalling. A consequence of this would have been that segmentation of vertebrate head mesoderm would no longer have been required, paving the way for the evolution of the unsegmented head mesoderm seen in living vertebrates.     

Division of labour and the evolution of multicellularity

Understanding the emergence and evolution of multicellularity and cellular differentiation is a core problem in biology. We develop a quantitative model that shows that a multicellular form emerges from genetically identical unicellular ancestors when the compartmentalization of poorly compatible physiological processes into component cells of an aggregate produces a fitness advantage. This division of labour between the cells in the aggregate occurs spontaneously at the regulatory level owing to mechanisms present in unicellular ancestors and does not require any genetic predisposition for a particular role in the aggregate or any orchestrated cooperative behaviour of aggregate cells. Mathematically, aggregation implies an increase in the dimensionality of phenotype space that generates a fitness landscape with new fitness maxima, in which the unicellular states of optimized metabolism become fitness saddle points. Evolution of multicellularity is modelled as evolution of a hereditary parameter: the propensity of cells to stick together, which determines the fraction of time a cell spends in the aggregate form. Stickiness can increase evolutionarily owing to the fitness advantage generated by the division of labour between cells in an aggregate.     

The evolution of group-level pathogenic traits

A group-selection model for the evolutionary origin of phase-variation in E. coli is proposed. Populations of commensal strains of E. coli populating mammalian hosts modulate its immune defenses through population-level control of the expression of fimbriae. At any time only a proportion of the population expresses these cell-surface adhesins. Collectively they elicit a host-based nutrient release if the fimbriae expression is low. Too high levels of fimbriation would provoke an inflammatory response and thus intolerable conditions for the cells. The optimal level of fimbriation is a group property and its evolution is difficult to explain by naive individual selection scenarios. This article presents a computational model to simulate the evolution of fimbriae. The two main conclusions of this contribution are: (i) the evolution of this group property requires the population to be partitioned into weakly interacting sub-populations. (ii) Given certain scenarios evolution consistently under-performs, in the sense that it does not find the optimal level of fimbriation.     

Animal cell differentiation patterns suppress somatic evolution

Cell differentiation in multicellular organisms has the obvious function during development of creating new cell types. However, in long-lived organisms with extensive cell turnover, cell differentiation often continues after new cell types are no longer needed or produced. Here, we address the question of why this is true. It is believed that multicellular organisms could not have arisen or been evolutionarily stable without possessing mechanisms to suppress somatic selection among cells within organisms, which would otherwise disrupt organismal integrity. Here, we propose that one such mechanism is a specific pattern of ongoing cell differentiation commonly found in metazoans with cell turnover, which we call “serial differentiation.” This pattern involves a sequence of differentiation stages, starting with self-renewing somatic stem cells and proceeding through several (non–self-renewing) transient amplifying cell stages before ending with terminally differentiated cells. To test the hypothesis that serial differentiation can suppress somatic evolution, we used an agent-based computer simulation of cell population dynamics and evolution within tissues. The results indicate that, relative to other, simpler patterns, tissues organized into serial differentiation experience lower rates of detrimental cell-level evolution. Self-renewing cell populations are susceptible to somatic evolution, while those that are not self-renewing are not. We find that a mutation disrupting differentiation can create a new self-renewing cell population that is vulnerable to somatic evolution. These results are relevant not only to understanding the evolutionary origins of multicellularity, but also the causes of pathologies such as cancer and senescence in extant metazoans, including humans.     

About functional evolution of peripheral part of the auditory system

Functional evolution of the peripheral part of the auditory system is considered. The key point of the appearance of a possibility of analysis of sound waves is formation in the course of evolution of cells with protoplasmic processes (sensillae)--the hair cells--that are transformed into auditory receptors. The fundamental moment is the emergence in evolution of the specialized ionic medium (endolymph) surrounding the auditory receptors. This medium is necessary for generation of receptor potential due to mechanical deformations of the auditory receptor. The characteristic feature of functional evolution of the peripheral part of the auditory system is the many-time repetition in the course of evolution of the main devices to detect and to distinguish sounds. This indicates recapitulation in evolution not only of the central parts of the brain (including central regions of the auditory system), but also of its peripheral part.