Origins and emergent evolution of life: the colloid microsphere hypothesis revisited.

Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life's complexity to self-replication alone relies on thermodynamically untenable assumptions. Alternative, earlier hypotheses about peptide-dominated colloid self-assembly should be revived. Such macromolecular conglomerates presumably existed in a dynamic equilibrium between confluent growth in sessile films and microspheres detached in turbulent suspension. The first organic syntheses may have been driven by mineral-assisted photoactivation at terrestrial geothermal fields, allowing photo-dependent heterotrophic origins of life. Inherently endowed with rudimentary catalyst activities, mineral-associated organic microstructures can have evolved adaptively toward cooperative 'protolife' communities, in which 'protoplasmic continuity' was maintained throughout a graded series of 'proto-biofilms', 'protoorganisms' and 'protocells' toward modern life. The proneness of organic microspheres to merge back into the bulk of sessile films by spontaneous fusion can have made large populations promiscuous from the beginning, which was important for the speed of collective evolution early on. In this protein-centered scenario, the emergent coevolution of uncoded peptides, metabolic cofactors and oligoribonucleotides was primarily optimized for system-supporting catalytic capabilities arising from nonribosomal peptide synthesis and nonreplicative ribonucleotide polymerization, which in turn incorporated other reactive micromolecular organics as vitamins and cofactors into composite macromolecular colloid films and microspheres. Template-dependent replication and gene-encoded protein synthesis emerged as secondary means for further optimization of overall efficieny later on. Eventually, Darwinian speciation of cell-like lineages commenced after minimal gene sets had been bundled in transmissible genomes from multigenomic protoorganisms.

Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy.

It is commonly presumed that abiotic membranes were colonized by proteins later on. Yet, hydrophobic peptides could have formed primordial protein-dominated membranes on their own. In a metabolism-first context, "autocatalytically closed" sets of statistical peptides could organize a self-maintaining protometabolism, assisted by an unfolding set of ribotide-related cofactors. Pairwise complementary ribotide cofactors may have formed docking guides for stochastic peptide formation, before replicating RNA emerged from this subset. Tidally recurring wet-drying cycles and an early onset of photosynthetic activities are considered most likely to meet the thermodynamic requirements. Conceivably, the earliest peptide-dominated vesicles were engaged in light harvesting, together with isoprenoid-tethered pigments, rather than providing an external boundary. Early on, the bulk of prebiotic organic matter can have formed a contiguous layer covering the mineral sediment, held in place by colloidal coherence of a hydrogel matrix. This unconventional scenario assumes a late onset of cellular individualization - perhaps from within, resembling endosporogenesis.

The fission yeast heterochromatin protein Rik1 is required for telomere clustering during meiosis.

Telomeres share the ability to silence nearby transcription with heterochromatin, but the requirement of heterochromatin proteins for most telomere functions is unknown. The fission yeast Rik1 protein is required for heterochromatin formation at centromeres and the mating-type locus, as it recruits the Clr4 histone methyltransferase, whose modification of histone H3 triggers binding by Swi6, a conserved protein involved in spreading of heterochromatin. Here, we demonstrate that Rik1 and Clr4, but not Swi6, are required along with the telomere protein Taz1 for crucial chromosome movements during meiosis. However, Rik1 is dispensable for the protective roles of telomeres in preventing chromosome end-fusion. Thus, a Swi6-independent heterochromatin function distinct from that at centromeres and the mating-type locus operates at telomeres during sexual differentiation.

RecA-DNA filament topology: the overlooked alternative of an unconventional syn-syn duplex intermediate.

The helical filaments of RecA protein mediate strand exchange for homologous recombination, but the paths of the interacting DNAs have yet to be determined. Although this interaction is commonly limited to three strands, it is reasoned here that the intrinsic symmetry relationships of quadruplex topology are superior in explaining a range of observations. In particular, this topology suggests the potential of post-exchange base pairing in the unorthodox configuration of syn-syn glycosidic bonds between the nucleotide bases and the pentose rings in the sugar-phosphate backbone, which would transiently be stabilized by the external scaffolding of the RecA protein filament.

DNA replication: stalling a fork for imprinting and switching.

Mating-type switching in fission yeast has long been known to be directed by a DNA 'imprint'. This imprint has now been firmly characterized as a protected site-specific and strand-specific nick. New work also links the widely conserved Swi1-Swi3 complex to the protection of stalled replication forks in general.

Fission yeast mating-type switching: programmed damage and repair.

Mating-type switching in fission yeast follows similar rules as in budding yeast, but the underlying mechanisms are entirely different. Whilst the initiating double-strand cut in Saccharomyces cerevisiae requires recombinational repair for survival, the initial damage in Schizosaccharomyces pombe only affects a single strand, which can be sealed by gap repair in situ, whether or not it serves as an imprint for subsequent switching of mating type from an appropriate donor cassette. Recent papers have linked the transient stalling of a replication fork to the generation of a site-specific nick. This discontinuity then remains protected for a full cell cycle, until it interferes with replication in the next S-phase. It, thereby, represents a valuable model system to study the molecular safeguards to protect a replication fork at a predetermined hindrance to leading-strand extension. The versatility of this experimental system has increased further yet by the recent development of a conditional setup, where imprinting and switching can be repressed or derepressed in response to external stimuli.

A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe.

The mating-type region of the fission yeast Schizosaccharomyces pombe comprises three loci: mat1, mat2-P and mat3-M. mat1 is expressed and determines the mating type of the cell. mat2-P and mat3-M are two storage cassettes located in a 17 kb heterochromatic region with features identical to those of mammalian heterochromatin. Mutations in the swi6+, clr1+, clr2+, clr3+, clr4+ and clr6+ genes were obtained in screens for factors necessary for silencing the mat2-P-mat3-M region. swi6+ encodes a chromodomain protein, clr3+ and clr6+ histone deacetylases, and clr4+ a histone methyltransferase. Here, we describe the cloning and characterization of clr2+. The clr2+ gene encodes a 62 kDa protein with no obvious sequence homologs. Deletion of clr2+ not only affects transcriptional repression in the mating-type region, but also centromeric silencing and silencing of a PolII-transcribed gene inserted in the rDNA repeats. Using chromatin immunoprecipitation, we show that Clr2 is necessary for histone hypoacetylation in the mating-type region, suggesting that Clr2 acts upstream of histone deacetylases to promote transcriptional silencing.

Life's Order, Complexity, Organization, and Its Thermodynamic-Holistic Imperatives.

In memoriam Jeffrey S. Wicken (1942-2002)-the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken's legacy. (i) Connecting life's origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic 'charging' of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called 'microspheres' is more realistic as a kinetic transition model of primal biogenesis than 'hypercycle replication' theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic 'microspheres'. On the 'continuist vs. miraculist' schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic 'continuist' views and agenda.

Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life.

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.