The origin of replicators and reproducers

Replicators are fundamental to the origin of life and evolvability. Their survival depends on the accuracy of replication and the efficiency of growth relative to spontaneous decay. Infrabiological systems are built of two coupled autocatalytic systems, in contrast to minimal living systems that must comprise at least a metabolic subsystem, a hereditary subsystem and a boundary, serving respective functions. Some scenarios prefer to unite all these functions into one primordial system, as illustrated in the lipid world scenario, which is considered as a didactic example in detail. Experimentally produced chemical replicators grow parabolically owing to product inhibition. A selection consequence is survival of everybody. The chromatographized replicator model predicts that such replicators spreading on surfaces can be selected for higher replication rate because double strands are washed away slower than single strands from the surface. Analysis of real ribozymes suggests that the error threshold of replication is less severe by about one order of magnitude than thought previously. Surface-bound dynamics is predicted to play a crucial role also for exponential replicators: unlinked genes belonging to the same genome do not displace each other by competition, and efficient and accurate replicases can spread. The most efficient form of such useful population structure is encapsulation by reproducing vesicles. The stochastic corrector model shows how such a bag of genes can survive, and what the role of chromosome formation and intragenic recombination could be. Prebiotic and early evolution cannot be understood without the models of dynamics.     

Group selection of early replicators and the origin of life

A major problem of the origin of life has been that of information integration. As Eigen (1971) has shown, a mutant distribution of RNAs replicating without the aid of a replicase cannot integrate sufficient information for the functioning of a higher-level unit utilizing several types of encoded enzymes. He proposed the hypercycle model to bridge this gap in prebiology. It can be shown by a nonlinear game model, incorporating mutation of a hypercycle, that the selection properties of hypercycles make them inefficient information integrators as they cannot compete favourably with all kinds of less efficient information carriers or mutationally coupled hypercycles. The stochastic corrector model is presented as an alternative resolution of Eigen's paradox. It assumes that replicative templates are competing within replicative compartments, whose selective values depend on the internal template composition via a catalytic acid in replication and "metabolism". The dynamics of template replication are analyzed by numerical simulation of master equations. Due to the stochasticity in replication and compartment fission the best compartment types recur. An Eigen equation at the compartment level is set up and calculated. Even selfish template mutants cannot destroy the system though they make it less efficient. The genetic information of templates is evaluated at both levels, and the higher (compartment) level successfully constrains the lower (template) one. Compartmentation together with stochastic effects is sufficient to integrate information dispersed in competitive replicators. Compartment selection is considered to be group selection of replicators. Implications for the origin of life are discussed.     

A replicator was not involved in the origin of life

The fact that stem cells do not express gap junctions while most differentiated cells do suggests that gap junctions serve a vital function in the maintenance of the differentiated state. This would require that connexin genes be expressed even in conditions where cap-mediated translation is impaired. It is hypothesized that IRES elements in the 5'-UTRs of the mRNAs of most connexins are required for this purpose.     

Selection advantage of metabolic over non-metabolic replicators: A kinetic analysis

A kinetic analysis and simulation of the replication reactions of two competing replicators—one non-metabolic (thermodynamic), the other metabolic, are presented. Our analysis indicates that in a rich resource environment the non-metabolic replicator is likely to be kinetically selected for over the metabolic replicator. However, in the more typical resource-poor environment it will be the metabolic replicator that is the kinetically more stable entity, and the one that will be kinetically selected for. Accordingly, a causal relationship between the emergence of a simple replicator and the emergence of a metabolic system is indicated. The results lend further support for the “replication first” school of thought in the origin of life problem by providing a mechanistic basis for the emergence of a metabolism, once a simple non-metabolic replicating system has itself been established. The study reaffirms our view that the roots of Darwinian theory may be found within standard chemical kinetic theory.     

G4 motifs affect origin positioning and efficiency in two vertebrate replicators

DNA replication ensures the accurate duplication of the genome at each cell cycle. It begins at specific sites called replication origins. Genome‐wide studies in vertebrates have recently identified a consensus G‐rich motif potentially able to form G‐quadruplexes (G4) in most replication origins. However, there is no experimental evidence to demonstrate that G4 are actually required for replication initiation. We show here, with two model origins, that G4 motifs are required for replication initiation. Two G4 motifs cooperate in one of our model origins. The other contains only one critical G4, and its orientation determines the precise position of the replication start site. Point mutations affecting the stability of this G4 in vitro also impair origin function. Finally, this G4 is not sufficient for origin activity and must cooperate with a 200‐bp cis‐regulatory element. In conclusion, our study strongly supports the predicted essential role of G4 in replication initiation.     

Interspecific hybridization in Daphnia: distinction and origin of hybrid matrilines

Three coexisting Daphnia species belonging to the D. longispina group (D. galeata, D. hyalina, and D. cucullata) form species-hybrid complexes by producing interspecific hybrids in several lakes in Germany and The Netherlands. To evaluate the genetic consequences of interspecific hybridization, I studied the patterns of mitochondrial DNA (mtDNA) sequence variation. The directionality of interspecific hybridization and divergence of hybrids from parental species was tested, using the DNA sequences of a segment of mtDNA. Via the polymerase chain reaction, it was possible to investigate single animals and even single resting eggs. A species-specific marker was established, using restriction patterns of amplified cytochrome b segments. mtDNA genotypes of hybrids revealed unidirectional mitochondrial gene flow for two hybrids, which were investigated by using multiple clones. No evidence for introgression of mtDNA was found. On the basis of a phylogenetic analysis, the species exhibit considerable distinctness, whereas differences between clones within species and between hybrids and maternal species tend to be very low. These results indicate a recent origin of hybrids and suggest that the radiation of the D. longispina group occurred > 5 Mya.      

Evolution,explanation, and the fact/value distinction

Though modern non-cognitivists in ethics characteristically believe that values are irreducible to facts, they nevertheless believe that values are determined by facts, viz., those specified in functionalist, explanatory theories of the evolutionary origin of morality. The present paper probes the consistency of this position. The conventionalist theories of Hume and Harman are examined, and are seen not to establish a tight determinative reduction of values to facts. This result is illustrated by reference to recent theories of the sociobiological mechanisms involved in moral evolution. Though explanatory theories have linguistic implications,exaggerated in Harman's linguistic form of social relativism, there is also failure to establish the semantic reductionism which non-cognitivists reject under the rubric of ethical naturalism. It is concluded that explanatory forms of naturalism, the best of which is a functionalist-utilitarian account, are compatible with the fact/value distinction.     

Species, languages, and the horizontal/vertical distinction

In addition to the distinction between species as a category and speciesas a taxon, the word species is ambiguous in a very different butequally important way, namely the temporal distinction between horizontal andvertical species. Although often found in the relevant literature, thisdistinction has thus far remained vague and undefined. In this paper the use ofthe distinction is explored, an attempt is made to clarify and define it, andthen the relation between the two dimensions and the implications of thatrelation are examined. Using Darwin's analogy of language evolution forspeciesevolution, and by appealing to a major change in the conception of languagebetween 19th- and 20th-century linguistics, it is argued that the horizontaldimension has priority (pragmatic, epistemological, logical, and ontological)over the vertical dimension. This has immense ramifications for the modernspecies problem. Fundamentally, it favors horizontal species concepts oververtical ones. In so doing it places species realism on a much more securefoundation and largely undercuts species pluralism. In addition it raises aserious problem for the increasingly popular family of phylogenetic speciesconcepts, which generally suffer from a dimensionality confusion. However,thereis a recent trend within this family that attempts to restore the priority ofthe horizontal dimension. It is concluded that this trend should be affirmedandthat the species-as-individuals view should be abandoned.     

On the origin of DNA genomes: evolution of the division of labor between template and catalyst in model replicator systems

The division of labor between template and catalyst is a fundamental property of all living systems: DNA stores genetic information whereas proteins function as catalysts. The RNA world hypothesis, however, posits that, at the earlier stages of evolution, RNA acted as both template and catalyst. Why would such division of labor evolve in the RNA world? We investigated the evolution of DNA-like molecules, i.e. molecules that can function only as template, in minimal computational models of RNA replicator systems. In the models, RNA can function as both template-directed polymerase and template, whereas DNA can function only as template. Two classes of models were explored. In the surface models, replicators are attached to surfaces with finite diffusion. In the compartment models, replicators are compartmentalized by vesicle-like boundaries. Both models displayed the evolution of DNA and the ensuing division of labor between templates and catalysts. In the surface model, DNA provides the advantage of greater resistance against parasitic templates. However, this advantage is at least partially offset by the disadvantage of slower multiplication due to the increased complexity of the replication cycle. In the compartment model, DNA can significantly delay the intra-compartment evolution of RNA towards catalytic deterioration. These results are explained in terms of the trade-off between template and catalyst that is inherent in RNA-only replication cycles: DNA releases RNA from this trade-off by making it unnecessary for RNA to serve as template and so rendering the system more resistant against evolving parasitism. Our analysis of these simple models suggests that the lack of catalytic activity in DNA by itself can generate a sufficient selective advantage for RNA replicator systems to produce DNA. Given the widespread notion that DNA evolved owing to its superior chemical properties as a template, this study offers a novel insight into the evolutionary origin of DNA.     

Binding of AlF-C, an Orc1-binding transcriptional regulator, enhances replicator activity of the rat aldolase B origin

A region encompassing the rat aldolase B gene (aldB) promoter acts as a chromosomal origin of DNA replication (origin) in rat aldolase B-nonexpressing hepatoma cells. To examine replicator function of the aldB origin, we constructed recombinant mouse cell lines in which the rat aldB origin and the mutant derivatives were inserted into the same position at the mouse chromosome 8 by cre-mediated recombination. Nascent strand abundance assays revealed that the rat origin acts as a replicator at the ectopic mouse locus. Mutation of site C in the rat origin, which binds an Orc1-binding protein AlF-C in vitro, resulted in a significant reduction of the replicator activity in the mouse cells. Chromatin immunoprecipitation (ChIP) assays indicated that the reduction of replicator activity was paralleled with the reduced binding of AlF-C and Orc1, suggesting that sequence-specific binding of AlF-C to the ectopic rat origin leads to enhanced replicator activity in cooperation with Orc1. Involvement of AlF-C in replication in vivo was further examined for the aldB origin at its original rat locus and for a different rat origin identified in the present study, which contained an AlF-C-binding site. ChIP assays revealed that both replication origins bind AlF-C and Orc1. We think that the results presented here may represent one mode of origin recognition in mammalian cells.     

The replicator of the Epstein-Barr virus latent cycle origin of DNA replication, oriP, is composed of multiple functional elements

Replication of the Epstein-Barr virus genome initiates at one of several sites in latently infected, dividing cells. One of these replication origins is close to the viral DNA maintenance element, and, together, this replication origin and the maintenance element are referred to as oriP. The replicator of oriP contains four binding sites for Epstein-Barr virus nuclear antigen 1 (EBNA-1), the sole viral protein required for the replication and maintenance of oriP plasmids. We showed previously that these EBNA-1 sites function in pairs and that mutational inactivation of one pair does not eliminate replicator function. In this study we characterized the contribution of each EBNA-1 site within the replicator and flanking sequences through the use of an internally controlled replication assay. We present evidence that shows that all four EBNA-1 sites are required for an oriP plasmid to be replicated in every cell cycle. Results from these experiments also show that the paired EBNA-1 binding sites are not functionally equivalent and that the low affinity of sites 2 and 3 compared to that of sites 1 and 4 is not essential for replicator function. Our results suggest that a host cell protein(s) binds sequences flanking the EBNA-1 sites and that interactions between EBNA-1 and this protein(s) are critical for replicator function. Finally, we present evidence that shows that the minimal replicator of oriP consists of EBNA-1 sites 3 and 4 and two copies of a 14-bp repeat that is present in inverse orientation flanking these EBNA-1 sites. EBNA-1 sites 1 and 2, together with an element(s) within nucleotides 9138 to 9516, are ancillary elements required for full replicator activity.     

Root nodule development: origin, function and regulation of nodulin genes

The symbiotic root nodule, an organ formed on leguminous plants, is a product of successful interactions between the host plant and the soil bacteria, Rhizobium spp. Plant hormones play an important role in the genesis of this organ. The hormonal balance appears to be modulated by the signals produced by bacteria. Many host genes induced during nodule organogenesis and the symbiotic state have been identified and characterized from several legumes. These genes encode nodule-specific proteins (nodulins) which perform diverse functions in root nodule development and metabolism. Formation of a subcellular compartment housing the bacteria is essential to sustain the symbiotic state, and several nodulins are involved in maintaining the integrity and function of this compartment. The bacteroid enclosed in the perbacteroid membrane behaves as an 'organelle,'completely dependent on the host for all its requirements for carbon, nitrogen and other essential elements. Thus it seems likely that the nodulins in the peribacteroid membrane perform specific transport functions. While the function of a few other nodulins is known (e.g. nodulin-100, nodulin-35), a group of uncharacterized nodulins exists in soybean root nodules. These nodulins share structural similarities and seem to have been derived from a common ancestor. Induction of nodulin genes occurs prior to and independent of nitrogen fixation, and thus is a prelude to symbiosis. Although some of the early nodulin genes are induced prior to or during infection, induction of late nodulins requires endocytotic release of bacteria.     

Sequence requirements for function of the Drosophila chorion gene locus ACE3 replicator and ori-beta origin elements

The developmentally regulated amplification of the Drosophila third chromosome chorion gene locus requires multiple chromosomal elements. Amplification control element third chromosome (ACE3) appears to function as a replicator, in that it is required in cis for the activity of nearby DNA replication origin(s). Ori-beta is the major origin in the locus, and is a sequence-specific element that is sufficient for high-level amplification in combination with ACE3. Sequence requirements for amplification were examined using a transgenic construct that was buffered from chromosomal position effects by flanking insulator elements. The parent construct supported 18- to 20-fold amplification, and contained the 320 bp ACE3, the approximately 1.2 kb S18 chorion gene and the 840 bp ori-beta. Deletion mapping of ACE3 revealed that an evolutionarily conserved 142 bp core sequence functions in amplification in this context. Several deletions had quantitative effects, suggesting that multiple, partially redundant elements comprise ACE3. S. cerevisiae ARS1 origin sequences could not substitute for ori-beta, thereby confirming the sequence specificity of ori-beta. Deletion mapping of ori-beta identified two required components: a 140 bp 5' element and a 226 bp A/T-rich 3' element called the beta-region that has significant homology to ACE3. Antibody to the origin recognition complex subunit 2 (ORC2) recognizes large foci that localize to the endogenous chorion gene loci and to active transgenic constructs at the beginning of amplification. Mutations in Orc2 itself, or the amplification trans regulator satin eliminated the ORC2 foci. By contrast, with a null mutation of chiffon (dbf4-like) that eliminates amplification, diffuse ORC2 staining was still present, but failed to localize into foci. The data suggest a novel function for the Dbf4-like chiffon protein in ORC localization. Chromosomal position effects that eliminated amplification of transgenic constructs also eliminated foci formation. However, use of the buffered vector allowed amplification of transgenic constructs to occur in the absence of detectable foci formation. Taken together, the data suggest a model in which ACE3 and ori-beta nucleate the formation of a ORC2-containing chromatin structure that spreads along the chromosome in a mechanism dependent upon chiffon.