Monte Carlo simulation of early molecular evolution in the RNA World

The origin of life remains a highly speculative field, mainly due to the shortage of our knowledge on prebiotic chemistry and basic understanding on the essence of life. In this context, computer simulation is expected to play an important role. For instance, the scenario concerning the genesis of the widely accepted RNA World remains blurry, though we have gathered some circumstantial evidence and fragmented knowledge on several supposed stages, including formation of polynucleotides from a prebiotic nucleotide pool, emergence of RNA replicases (RNA molecules catalyzing their own replication), and evolution of RNA replicases. It is highly valuable to simulate the stages as a continuous process to evaluate the plausibility of the supposition and study the rules involved. Here we construct a computer simulation on the process using Monte Carlo method. It demonstrates that primordial RNA replicases may appear and spread in a nucleotide pool provided they could recognize their own sequence and their complements as catalytic targets, and then may evolve to more efficient RNA replicases. Apart from its indication on the genesis of the RNA World, the vivid simulation of emergence of the “first replicative molecules” and their subsequent evolution is impressive and may help to get insight into “how could self-replication and Darwinian evolution, two key features of life, emerge in a non-life background?” thus improve our understanding of “what is life” when studying origins of life.     

An Integrated Case Study for Evaluating the Impacts of an Oil Refinery Effluent on Aquatic Biota in the Delaware River: Integration and Analysis of Study Components

A series of statistical and graphical techniques incorporating a “weight of evidence” approach were used to interpret results from an integrated Triad case study designed to determine potential environmental impacts to aquatic biota in the Delaware River that may be linked to PAHs found in Motiva's oil refinery effluent. Sediment concentrations of various metals, PCBs and LMW PAHs exceeding both ERL and ERM sediment quality guidelines (SQGs) were reported in the study area. However, most chemical contaminants did not exceed their respective SQGs. Results from a long-term sediment coring study indicated that there was no evidence of significant historical PAH contamination of sediments related to Motiva's exceedences. PAHs comprising the Motiva “fingerprint” were found in the surficial sediments at four near-field sites but non-Motiva PAH concentrations (background) were shown to be significantly higher at other far-field sites (non-Motiva influence). Chronic sediment toxicity appears to have significant relationships to the patterns of most PAH isomers, certain PCB isomers, and certain metals. However, sediment toxicity does not appear to be related to the PAH isomers that are characteristic of Motiva's effluent nor to the near-field sites. Impacted benthic communities were reported in the study area, primarily at one near-field and two far-field sites. However, there were no apparent relationships between benthic community health and sediment contaminants. The status of benthic communities does not appear to be related to PAHs derived from the Motiva effluent. The “weight of evidence” analysis developed from a systematic and comprehensive series of statistical and graphical assessments indicates that, although the study area displayed some degree of sediment contamination, chronic sediment toxicity, and benthic health impacts, these environmental effects generally could not be related to Motiva's exceedences.     

Sequence and significance of dopamine metabolism in the rat brain

This commentary is a critical evaluation of research on the significance of dopamine (DA) metabolism in the striatum of the rat. The possible sequence of DA metabolism is discussed. Special reference was given to a possible differentiation between “intra-neuronal” and “extra-neuronal” formation of DA. In addition a possible relation between drug-induced changes in DA metabolite levels to processes as release and metabolism of the transmitters, was investigated. It is concluded that our understanding of DA metabolism is still far from clear. The only consistent finding at the present time is the fact that decreased DA release is reflected by decreased 3-MT levels. It is emphasized that one should investigate complete changes in the “fingerprint” of changes of DA metabolism rather than to rely on one or two metabolites, when the influence of a drug on dopaminergic transmission is to be established.     

The isochore patterns of mammalian genomes and their phylogenetic implications

The compositional distributions of high molecular weight DNA fragments from 20 species belonging to 9 out of the 17 eutherian orders were investigated by analytical CsCl density gradient centrifugation and by preparative fractionation in Cs₂SO₄/BAMD density gradients followed by analysis of the fractions in CsCl. These compositional distributions reflect those of the isochores making up the corresponding genomes. A “general distribution” was found in species belonging to eight mammalian orders. A “myomorph distribution” was found in Myomorpha, but not in the other rodent infraorders Sciuromorpha and Histricomorpha, which share the general distribution. Two other distributions were found in a megachiropteran (but not in microchiropteran, which, again, shares the general distribution) and in pangolin (a species from the only genus of the order Pholidota), respectively. The main difference between the general distribution and all other distributions is that the former contains sizable amounts (6–10%) of GC-rich isochores (detected as DNA fragments equal to, or higher than, 1.710 g/cm³ in modal buoyant density), which are scarce, or absent, in the other distributions. This difference is remarkable because gene concentrations in mammalian genomes are paralleled by GC levels, the highest gene concentrations being present in the GC-richest isochores. The compositional distributions of mammalian genomes reported here shed light on mammalian phylogeny. Indeed, all orders investigated, with the exception of Pholidota, seem to share a common ancestor. The compositional patterns of the megachiropteran and of Myomorpha may be derived from the general pattern or have independent origins.     

Isolation of pyrimidine isostichs from chick erythrocyte DNA

The isolation of pyrimidine oligonucleotides (isostichs) from chick erytyrocyte DNA was accomplished on a preparative scale with the goal of providing starting material for further chemical modifications. The DNA was degraded by the method of Burton and Petersen and the isostichs were obtained via paper chromatography and ion-exchange chromatography. The various isostichs were further fractionated into base compositional isomers, the frequency of which was determined as mole percent of total pyrimidines. Although this work was not intended to be an analytical study, the large quantities of DNA used allowed the measurement of most compositional isomers with an accuracy of 5% of the listed values. The data for long oligothymidylates are less reliable. The results of the present study revealed the anticipated bias in the distribution of pyrimidine isostichs in favor of longer chain lengths as compared to that expected for a random distribution. Isostichs above chain length 10 occur in amounts approximately 7 times greater than calculated.     

Evolution of Helix Formation in the Ribosomal Internal Transcribed Spacer 2 (ITS2) and Its Significance for RNA Secondary Structures

Helices are the most common elements of RNA secondary structure. Despite intensive investigations of various types of RNAs, the evolutionary history of the formation of new helices (novel helical structures) remains largely elusive. Here, by studying the nuclear ribosomal Internal Transcribed Spacer 2 (ITS2), a fast-evolving part of the eukaryotic nuclear ribosomal operon, we identify two possible types of helix formation: one type is “dichotomous helix formation”—transition from one large helix to two smaller helices by invagination of the apical part of a helix, which significantly changes the shape of the original secondary structure but does not increase its complexity (i.e., the total length of the RNA). An alternative type is “lateral helix formation”—origin of an extra helical region by the extension of a bulge loop or a spacer in a multi-helix loop of the original helix, which does not disrupt the pre-existing structure but increases RNA size. Moreover, we present examples from the RNA sequence literature indicating that both types of helix formation may have implications for RNA evolution beyond ITS2.     

The genome of Uukuniemi virus consists of three unique RNA segments

The three RNA species isolated from virions of Uukuniemi virus, a proposed member of the newly defined Bunyaviridae family, have been characterized by analysis of ³²P-labeled ribonuclease T1 oligonucleotides separated on two-dimensional polyacrylamide gels. Each RNA species contains unique oligonucleotides not present in the two others, indicating that the genome of this virus is segmented. Each segment appears to contain a unique primary sequence with little or no overlapping among the segments. The complexities of the RNA segments as calculated from the radioactivity in unique oligonucleotides of defined lengths are about 8000 (L RNA), 3500 (M) and 1900 (S) nucleotides. Since these values are similar to the molecular weights determined by other methods, each size class of RNA corresponds to a single molecular species. The presence of a 5′ terminal pppAp … structure in each RNA segment confirms indications from electron microscopy that the apparently circular RNA segments are not covalently closed. The absence of either a 5′ terminal “cap” or 3′ terminal poly(A) supports the concept that Uukuniemi virus is a negative strand virus.     

Aspects of late triassic palynology. 3. Palynology of latest triassic and earliest jurassic deposits of the northern limestone alps in Austria and southern Germany,with special reference to a palynological characterization of the Rhaetian stage in Europe

The present paper provides a palynological analysis of samples from the “Kössener Schichten”, “Schattwalder Schichten” and the ammonoid (Psiloceras planorbe)-bearing beds of the “Fleckenmergel/Fleckenkalk” found in the vicinity of Salzburg (Austria and adjacent part of Germany).It is shown that the compositional development of latest Triassic—earliest Jurassic palynological assemblages from Alpine sequences matches the situation in the Germanic realm. A characteristic phase in this development is interpreted in terms of the Rhaetipollis germanicus Assemblage Zone. It is considered that this zone could well be regarded as a palynological characterization of the Rhaetian Stage in Europe and North America.Although palynology does not support the Rhaetian concept based on the occurrence of the species Choristoceras marshi exclusively, the traditional ammonoid-based Triassic—Jurassic boundary can be palynologically recognized.     

On the mutability of the yeast mitochondrial genome.

A mechanism is proposed to explain how a mutation in a single molecule of mitochondrial DNA (mitDNA) can come to affect all the other mitDNA molecules of a yeast cell. It is suggested that an initial mutation may be “amplified” by a process which is, in fact, intended to ensure the identity of the cell's complement of mitDNA molecules. It is postulated that this process involves a small number of “reference” copies of mitDNA to which all other (“derived”) copies are compared and corrected once per cell cycle. Asymmetric gene conversion is proposed as the correction mechanism and the means of “amplifying” mutations. The model is shown to be compatible with current data on spontaneous and induced mitochondrial mutation in Saccharomyces cerevisiae.     

Amplification as a Rectification Mechanism for the Redundant rRNA Genes

IN eukaryotic cells multiple copies of ribosomal RNA (rRNA) genes are clustered in one or a few nucleolar organizers per haploid genome. These “redundant” or “reiterated” genes have all been shown to be, within the limits of available experimental techniques, identical within a given organism and species, producing homogeneous populations of rRNA molecules. On the other hand, rRNAs from organisms of different taxonomic position display evidence of considerable evolutionary change from the point of view of size, base sequence (revealed by RNA-DNA hybridization) and base composition^1,2.     

Evolution and Taxonomy of Positive-Strand RNA Viruses: Implications of Comparative Analysis of Amino Acid Sequences

Abstract

Despite the rapid mutational change that is typical of positive-strand RNA viruses, enzymes mediating the replication and expression of virus genomes contain arrays of conserved sequence motifs. Proteins with such motifs include RNA-dependent RNA polymerase, putative RNA helicase, chymotrypsin-like and papain-like proteases, and methyltransferases. The genes for these proteins form partially conserved modules in large subsets of viruses. A concept of the virus genome as a relatively evolutionarily stable “core” of housekeeping genes accompanied by a much more flexible “shell” consisting mostly of genes coding for virion components and various accessory proteins is discussed. Shuffling of the “shell” genes including genome reorganization and recombination between remote groups of viruses is considered to be one of the major factors of virus evolution.

Multiple alignments for the conserved viral proteins were constructed and used to generate the respective phylogenetic trees. Based primarily on the tentative phylogeny for the RNA-dependent RNA polymerase, which is the only universally conserved protein of positive-strand RNA viruses, three large classes of viruses, each consisting of distinct smaller divisions, were delineated. A strong correlation was observed between this grouping and the tentative phylogenies for the other conserved proteins as well as the arrangement of genes encoding these proteins in the virus genome. A comparable correlation with the polymerase phylogeny was not found for genes encoding virion components or for genome expression strategies. It is surmised that several types of arrangement of the “shell” genes as well as basic mechanisms of expression could have evolved independently in different evolutionary lineages.

The grouping revealed by phylogenetic analysis may provide the basis for revision of virus classification, and phylogenetic taxonomy of positive-strand RNA viruses is outlined. Some of the phylogenetically derived divisions of positive-strand RNA viruses also include double-stranded RNA viruses, indicating that in certain cases the type of genome nucleic acid may not be a reliable taxonomic criterion for viruses.

Hypothetical evolutionary scenarios for positive-strand RNA viruses are proposed. It is hypothesized that all positive-strand RNA viruses and some related double-stranded RNA viruses could have evolved from a common ancestor virus that contained genes for RNA-dependent RNA polymerase, a chymotrypsin-related protease that also functioned as the capsid protein, and possibly an RNA helicase.     

Can tumorigenesis result from in vivo “transfection” of a normal cell with DNA escaped from disintegrating nontransformed cells?

In this paper I present a hypothetical step on the route to turmorigenesis which may be common to many of the tumorogenic events taking place in vivo. According to this hypothesis portions of DNA from normal nontransformed dying cells may escape degradation, “transfect” other cells and under appropriate conditions also induce transformation. When various high risk factors for carcinogenesis are examined this hypothesis may easily fit into each of them. In addition, recent reports of experimental “transfection” indirectly support this hypothesis. It could now be argued that aging, ionizing radiation, immunosuppressive drugs, genetic errors, defects in DNA repair, immunodeficiency states, chronic infections and chronic inflammatory diseases may all increase the availability of free DNA or the readiness of cells to accommodate “transfection” DNA, or both. Thus the risk of cancer associated with these situations may be explained by increased chance for “transfection” with DNA.It is suggested that the minimal requirements for cell transformation consist of a certain sequence of DNA which does not have to be integrated into the nucleus at once, it may instead accumulate piece by piece so that the first “transfection” of a cell may occur long before transformation takes place. If the “transfecting” DNA sequence does not fulfil the minimal requirements for maintaining a state of repetitive uncontrolled mitosis, then this cell may wait silently or remain a benign tumor until “boosted” with an ultimate complementary DNA sequence to develop into a fully fledged cancer.     

Phylogenetic Origin of the Chloroplast*†

SYNOPSIS. The 16S ribosomal RNA of the chloroplast of Euglena gracilis strain Z has been characterized in terms of its 2-dimensional electrophoretic “fingerprint” (T1 ribonuclease). Over 100 spots were resolved on the “fingerprint” and each spot was characterized as to which RNA oligonucleotide fragment(s) it contained. When compared to similar analyses of prokaryotic 16S rRNAs and eukaryotic cytoplasmic 18S rRNAs, the chloroplast 16S rRNA was a typically prokaryotic RNA, but bore little if any relationship to eukaryotic 18S rRNAs. Therefore, the cistrons for chloroplast 16S rRNA are related to the equivalent prokaryotic cistrons, but, apparently, are not related to the equivalent eukaryotic cistrons. Among the organisms available for comparison, the Euglena chloroplast 16S rRNA appears most closely related to the 16S rRNA of the eukaryote, Porphyridium cruentum (a red alga), and at least distantly related to the 16S rRNAs of the blue-green algae and perhaps also to the bacilli.     

Secondary structure in heterogeneous nuclear RNA: involvement of regions from repeated DNA sites

Heterogeneous nuclear RNA was found to contain regions of secondary structure based on a relative resistance to nuclease treatment compared with mRNA or poliovirus RNA and a shift in density toward double-stranded RNA early in the course of nuclease digestion. The regions involved in this secondary structure are enriched for RNA segments transcribed from repeated sites in the DNA. Thus, to maximize hybridization to repetitive sites heterogeneous nuclear RNA molecules must be both denatured and fragmented. Some of the self-complementary regions in heterogeneous nuclear RNA are released by alkali denaturation and fragmentation below 1500 nucleotides but maximum release is not achieved until fragmentation below 500 nucleotides. These results indicate that these self-complementary regions (“loops” plus “stems”) are mainly below 500 nucleotides in length.