Population Biology of the First Replicators: On the Origin of the Genotype, Phenotype and Organism

Prebiotic synthesis of short length macromolecules from precursormolecules results in a dynamic of spontaneous creation, whichallows for growth from zero density. At this prereplicator stagein the evolution of life there is no life history, since thebirth and death processes are intimately coupled through thephysical chemistry of a single reaction. With the emergenceof nonenzymatic, template-directed replication, the birth anddeath processes could diverge for the first time, since selectioncould act differently on the birth and death rates of the replicatingmolecule. Thus, with replication, natural selection and life-historyevolution began. The genotype, or nucleotide sequence, of thereplicating molecule gave rise to several phenotypic properties,the most important of which was its three-dimensional structurewhich in turn affected the birth and death processes. However,at this stage of nonenzymatic template replication, the phenotypewas the physical structure of the genotype, nothing more: Forthe divergence of the phenotype from the genotype it was necessaryfor the replicator to produce a protein. It is shown here thatthe evolution of enzyme production is facilitated by the existenceof population structure in the distribution of the macromoleculesassociated with replication. Initially, this structure was createdpassively by the localization of the macromolecules in rockcrevices, suspended water droplets, etc. Ultimately, the replicatoralong with its proteins were localized in a protocellular structureand this became the first organism. Thus, initially, the organismwas one extreme of the population structure of the macromoleculesassociated with life. The organism was the culmination of theencapsulation phase of evolution which proceeded through initialphases of passive localization.     

Rate Variation as a Function of Gene Origin in Plastid-Derived Genes of Peridinin-Containing Dinoflagellates

Peridinin-pigmented dinoflagellates contain secondary plastids that seem to have undergone more nearly complete plastid genome reduction than other eukaryotes. Many typically plastid-encoded genes appear to have been transferred to the nucleus, with a few remaining genes found on minicircles. To understand better the evolution of the dinoflagellate plastid, four categories of plastid-associated genes in dinoflagellates were defined based on their history of transfer and evaluated for rate of sequence evolution, including minicircle genes (presumably plastid-encoded), genes probably transferred from the plastid to the nucleus (plastid-transferred), and genes that were likely acquired directly from the nucleus of the previous plastid host (nuclear-transferred). The fourth category, lateral-transferred genes, are plastid-associated genes that do not appear to have a cyanobacterial origin. The evolutionary rates of these gene categories were compared using relative rate tests and likelihood ratio tests. For comparison with other secondary plastid-containing organisms, rates were calculated for the homologous sequences from the haptophyte Emiliania huxleyi. The evolutionary rate of minicircle and plastid-transferred genes in the dinoflagellate was strikingly higher than that of nuclear-transferred and lateral-transferred genes and, also, substantially higher than that of all plastid-associated genes in the haptophyte. Plastid-transferred genes in the dinoflagellate had an accelerated rate of evolution that was variable but, in most cases, not as extreme as the minicircle genes. Furthermore, the nuclear-transferred and lateral-transferred genes showed rates of evolution that are similar to those of other taxa. Thus, nucleus-to-nucleus transferred genes have a more typical rate of sequence evolution, while those whose history was wholly or partially within the dinoflagellate plastid genome have a markedly accelerated rate of evolution. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Debashish Battacharya]     

Protein-mediated Selective Enclosure of Early Replicators Inside of Membranous Vesicles: First Step Towards Cell Membranes

Containment in cell membranes is essential for all contemporary life, and apparently even the earliest life forms had to be somehow contained. It has been postulated that random enclosure of replicating molecules inside of spontaneously assembled vesicles would have formed the initial cellular ancestors. However, completely random re-formation or division of such primitive vesicles would have abolished the heritability of their contents, nullifying any selective advantage to them. We propose that the containment of the early replicators in membranous vesicles was adopted only after the invention of genetically encoded proteins, and that selective enclosure of target molecules was mediated by specific proteins. A similar containment process is still utilised by various RNA- and retroviruses to isolate their replication complexes from the host’s intracellular environment. Such selective encapsulation would have protected the replicators against competitor and parasitic sequences, and provided a strong positive selection within the replicator communities.     

Plasmid Conjugation from Proteobacteria as Evidence for the Origin of Xenologous Genes in Cyanobacteria

Comparative genomics have shown that 5% of Synechococcus elongatus PCC 7942 genes are of probable proteobacterial origin. To investigate the role of interphylum conjugation in cyanobacterial gene acquisition, we tested the ability of a set of prototype proteobacterial conjugative plasmids (RP4, pKM101, R388, R64, and F) to transfer DNA from Escherichia coli to S. elongatus. A series of BioBrick-compatible, mobilizable shuttle vectors was developed. These vectors were based on the putative origin of replication of the Synechococcus resident plasmid pANL. Not only broad-host-range plasmids, such as RP4 and R388, but also narrower-host-range plasmids, such as pKM101, all encoding MPF_T-type IV secretion systems, were able to transfer plasmid DNA from E. coli to S. elongatus by conjugation. Neither MPF_F nor MPF_I could be used as interphylum DNA delivery agents. Reciprocally, pANL-derived cointegrates could be introduced in E. coli by electroporation, where they conferred a functional phenotype. These results suggest the existence of potentially ample channels of gene flow between proteobacteria and cyanobacteria and point to MPF_T-based interphylum conjugation as a potential mechanism to explain the proteobacterial origin of a majority of S. elongatus xenologous genes.     

Origin of Bacteriochlorophyll a and the Early Diversification of Photosynthesis

Photosynthesis originated in the domain Bacteria billions of years ago; however, the identity of the last common ancestor to all phototrophic bacteria remains undetermined and speculative. Here I present the evolution of BchF or 3-vinyl-bacteriochlorophyll hydratase, an enzyme exclusively found in bacteria capable of synthetizing bacteriochlorophyll a. I show that BchF exists in two forms originating from an early divergence, one found in the phylum Chlorobi, including its paralogue BchV, and a second form that was ancestral to the enzyme found in the remaining anoxygenic phototrophic bacteria. The phylogeny of BchF is consistent with bacteriochlorophyll a evolving in an ancestral phototrophic bacterium that lived before the radiation event that gave rise to the phylum Chloroflexi, Chlorobi, Acidobacteria, Proteobacteria, and Gemmatimonadetes, but only after the divergence of Type I and Type II reaction centers. Consequently, it is suggested that the lack of phototrophy in many groups of extant bacteria is a derived trait.     

Bacterial Origin and Community Composition in the Barley Phytosphere as a Function of Habitat and Presowing Conditions

An understanding of the factors influencing colonization of the rhizosphere is essential for improved establishment of biocontrol agents. The aim of this study was to determine the origin and composition of bacterial communities in the developing barley (Hordeum vulgare) phytosphere, using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified from extracted DNA. Discrete community compositions were identified in the endorhizosphere, rhizoplane, and rhizosphere soil of plants grown in an agricultural soil for up to 36 days. Cluster analysis revealed that DGGE profiles of the rhizoplane more closely resembled those in the soil than the profiles found in the root tissue or on the seed, suggesting that rhizoplane bacteria primarily originated from the surrounding soil. No change in bacterial community composition was observed in relation to plant age. Pregermination of the seeds for up to 6 days improved the survival of seed-associated bacteria on roots grown in soil, but only in the upper, nongrowing part of the rhizoplane. The potential occurrence of skewed PCR amplification was examined, and only minor cases of PCR bias for mixtures of two different DNA samples were observed, even when one of the samples contained plant DNA. The results demonstrate the application of culture-independent, molecular techniques in assessment of rhizosphere bacterial populations and the importance of the indigenous soil population in colonization of the rhizosphere.     

6. Chasing the enzymes of secondary metabolism: Plant cell cultures as a pot of gold

The development of plant cell cultures for the study of the biosynthesis of secondary metabolises in the 1970s revolutionized the field. It became possible to identify, characterize and ultimately, in specific cases, to purify the biocatalysts involved in the individual transformations. The precise knowledge of the biosynthetic pathways provided by the identification of these enzymes, of the stereo- and substrate- specificity of lhe reactions they catalyse and of the sequence of these reactions in situ opened new fields for study in plant sciences. We now have detailed knowledge of light and elicitor regulation of flavonoid genes, of the molecular mode of action of certain herbicides, and are beginning to form an understanding of the regulation of alkaloid biosynthesis. It is without question that plant cell cultures have become a central, indispensable vehicle in secondary metabolic research.     

The Location of Viability Genes within a Testcross Framework

The maximum likelihood method is applied to the problem of estimating the positions and effects of viability genes. Whenever testcross linkage data indicate the presence of differential viability, it is hypothesized that there exists one viability gene between each marker. Estimation is possible only for two-point data since the number of independent expectation expressions is less than the number of parameters for three or more markers. It is pointed out that within the two-point testcross system, it is impossible to distinguish between pleiotropic effects of the marker genes and the effect of a middle viability gene, if existent. The methods outlined will be useful in their application to experiments specifically designed to locate induced viability genes.     

On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses

In genetic language a peculiar arrangement of biological information is provided by overlapping genes in which the same region of DNA can code for functionally unrelated messages. In this work, the informational content of overlapping genes belonging to prokaryotic and eukaryotic viruses was analyzed. Using information theory indices, we identified in the regions of overlap a first pattern, exhibiting a more uniform base composition and more severe constraints in base ordering with respect to the nonoverlapping regions. This pattern was found to be peculiar to coliphage, avian hepatitis B virus, human lentivirus, and plant luteovirus families. A second pattern, characterized by the occurrence of similar compositional constraints in both types of coding regions, was found to be limited to plant tymoviruses. At the level of codon usage, a low degree of correlation between overlapping and nonoverlapping coding regions characterized the first pattern, whereas a close link was found in tymoviruses, indicating a fine adaptation of the overlapping frame to the original codon choice of the virus. As a result of codon usage correlation analysis, deductions concerning the origin and evolution of several overlapping frames were also proposed. Comparison of amino acid composition revealed an increased frequency of amino acid residues with a high level of degeneracy (arginine, leucine, and serine) in the proteins encoded by overlapping genes; this peculiar feature of overlapping genes can be viewed as a way with which they may expand their coding ability and gain new, specialized functions. Received: 28 October 1996 / Accepted: 29 January 1997     

Chasing the urmetazoon: Striking a blow for quality data?

The ever-lingering question: “What did the urmetazoan look like?” has not lost its charm, appeal or elusiveness for one and a half centuries. A solid amount of organismal data give what some feel is a clear answer (e.g. Placozoa are at the base of the metazoan tree of life (ToL)), but a diversity of modern molecular data gives almost as many answers as there are exemplars, and even the largest molecular data sets could not solve the question and sometimes even suggest obvious zoological nonsense. Since the problems involved in this phylogenetic conundrum encompass a wide array of analytical freedom and uncertainty it seems questionable whether a further increase in molecular data (quantity) can solve this classical deep phylogeny problem. This review thus strikes a blow for evaluating quality data (including morphological, molecule morphologies, gene arrangement, and gene loss versus gene gain data) in an appropriate manner.     

昆虫病毒gp37/fusolin基因研究进展

昆虫病毒gp37fusolin基因属病毒复制非必需基因,其编码的蛋白能形成一种纺锤形包涵体(spindlebodies,SBs),该包涵体内不含有病毒粒子。Fusolin蛋白形成的SBs与纯化的Fusolin蛋白均能提高靶昆虫对杆状病毒的敏感性,推测GP37蛋白也具有类似的功能。对gp37fusolin基因的深入研究,有可能开发出新型病毒增效剂 。