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PR8 Nastanek Genov, Genomov in LUCA PR8_Nastanek genov, genomov in LUCA Origin and early evolution of life Early evolution of life on Earth. Life originated from prebiotic chemistry. First stages of cellular evolution may have included replicative polymers other than DNA and RNA; the RNA world refers to a time when the RNA molecule acted as the hereditary as well as catalytic molecule of cells; eventually, RNA chemistry originated proteins (a relic from these days is the RNA-mediated synthesis of proteins in extant ribosomes); it is thought that cells capable of synthesizing proteins were selected for having superior catalytic molecules; finally, protein chemistry-originated DNA and cells with DNA genomes were selected for having a more stable hereditary molecule; the last universal common ancestor or cenancestor was very likely similar to extant cells in their metabolic and hereditary capacities. Timeline of the events leading to the origin and early evolution of life. LCA, last common ancestor. The path from prebiotic chemistry to the RNA world is likely to have involved template-directed RNA replication. Replicating genome in protocell A simple protocell model based on a replicating vesicle for compartmentalization, and a replicating genome to encode heritable information. A complex environment provides lipids, nucleotides capable of equilibrating across the membrane bilayer, and sources of energy (left), which leads to subsequent replication of the genetic material and growth of the protocell (middle), and finally protocellular division through physical and chemical processes (right). The model behind “RNA world”, where an RNA replicase and a self-replicating membrane-bound vesicle combine to form a protocell. Inside the vesicle, the RNA RNA-dependent RNA polymerase (RdRP), (RDR), or RNA replicase, is replicase functions, and might add a function to improve the an enzyme that catalyzes the replication of RNA from an RNA template. production of the vesicle wall through a ribozyme. At this point, the RNA replicase and the vesicle are functioning together, and the protocell has become a living cell, capable of nutrition, growth, reproduction and evolution. Proposed prebiotic scenario. Monomers first concatenate into compositionally biased short oligomers. When the oligomers are long enough to act as templates, template-directed ligation produces relatively long, compositionally diverse sequences. These sequences can fold into stable structures, some of which may be catalytically active, leading to the RNA world. Energy, genes and evolution RNA svet/RNA world The RNA World Hypothesis Two properties of RNA that would have allowed it to play a role in the origin of life The RNA world hypothesis proposes that a world filled with RNA-based life predates current DNA-based organisms. RNA has two key properties that would have allowed it to function in this manner: 1. RNA can self-replicate -RNA is able to store information in a sequence of four nucleotides (similar to DNA) -Short sequences of RNA have been able to duplicate other molecules of RNA accurately 2. RNA can act as a catalyst -Modern cells use RNA catalysts (called ribozymes) to remove introns from mRNA and help synthesise new RNA molecules -In ribosomes, rRNA is found in the catalytic site and plays a role in peptide bond formation RNA is the only molecule capable of both these properties but has since been superceded: -DNA, through its greater chemical stability (double helical structure) has taken over as the data storage form -Protein, through its greater variability (20 amino acids as opposed to 4 nucleotides) has taken over as the catalytic form. A popular model for the development of the genetic system. The RNA world hypothesis proposes that the first genetic system involved informational RNA molecules that encoded the synthesis of modestly functional RNA molecules. Protein translation developed during this period leading to the RNA-protein world. Finally, protein enzymes produced deoxyribonucleotides through ribonucleotide reduction. The availability of deoxyribonucleotides led to the establishment of the DNA genome and the modern genetic system. Biochemical epochs in the RNA world. Early nucleic-acid or non-nucleic-acid replicators gave rise to faster and more faithful mononucleotide or polynucleotide polymerases. As foodstuffs for replicators were exhausted, an evolutionary advantage would have accrued to organisms that evolved the ability to generate new building blocks (for instance, using the thiouridine synthetase identified by Unrau and Bartel). At this stage, ribozymes would have possessed the chemical sophistication to modify nucleotide or oligonucleotide precursors. Modified nucleotides could have improved all extant catalysts and fostered the evolution of more sophisticated catalysts, such as ribosomal RNA. The advent of neither cells nor energy metabolism is explicitly indicated, as either innovation would have yielded an evolutionary advantage irrespective of when it occurred. A logic tree for the origin of life. A series of questions surrounding the chemistry and precursors required for life’s origin on Earth or Mars. The inset is a modification of PDB 3R1L, a ligase ribozyme that has been further developed into a polymerase. Evolution of an RNA population in a network of inorganic compartments. Open arrows show thermoconvection, and horizontal filled arrows show thermophoresis. Compartment 1, accumulation of mononucleotides; compartment 2, accumulation of abiogenically synthesized RNA molecules; compartment 3, exploration of the RNA sequence space by ligation and recombination of RNA molecules; and compartment 4, emergence of the RNA world. The putative ribozyme replicase is denoted by a ‘‘globular’’ RNA molecule, possibly emerging by the ligation–recombination process. The stack of compartments depicts a contemporaneous, three- dimensional network. However, within the compartments, putative successive stages of evolution are shown, in the direction from the inside (near the vent) to the outside of the network. The RNA world hypothesis proposes that RNA molecules, which both catalyze some reactions and Aminoacylating Urzymes Challenge the RNA carry genetic information, evolved before proteins. However, researchers have yet to find ribozymes in World Hypothesis living organisms that support this hypothesis. In this Paper of the Week, Charles W. Carter, Jr., and colleagues at the University of North Carolina at Chapel Hill and the University of Vermont argue that peptides and RNA cooperated to develop the genetic code. They demonstrate that Urzymes, which are molecules derived from conserved portions of Class I and Class II aminoacyl-tRNA synthetases, accelerate tRNA aminoacylation by ∼106-fold over the uncatalyzed peptide synthesis rate. This excess catalytic proficiency indicates that Urzymes were highly evolved and so probably had even more primitive peptide ancestors. The investigators say that by searching for the evolutionary origins of modern aminoacyl-tRNA synthetases, “we demonstrate key steps for a simpler and hence more probable peptide·RNA development of rapid coding systems matching amino acids with anticodon trinucleotides.” These data have very significant implications for the experimental study of the origin of protein synthesis. Izvor in evolucija proteinov in proteomov Possible evolutionary process of the origin of amino acid homochirality. The "RNA world" is believed to an early form of life. The elongation of small RNA molecules would have eventually led to "symmetry violation," and a D-ribose-based RNA world would have been established. Because of this, L- amino acids would have been selectively aminoacylated to primordial tRNA (minihelix). This in turn would have led to the synthesis of homochiral (L) natural proteins, and the minihelices would have evolved to L-shaped tRNAs by the addition of another domain. Schematic representation of cellular functions represented by the ancestral set of superfamilies. The cellular and/or functional locations of the superfamilies domains are represented by numbers. CATH identifications and functional description of all ancestral superfamilies are given in Supplementary Table 3 following the same numbering code. Protein fold expansion plotted as a function of ancestry. Fold expansion is calculated as the cumulative fraction of folds less than or equal to a given ancestry value. Ancestry values for fold architectures were derived from the phylogenetic tree of all folds by Wang et al. [26] and are equal to the number of nodes from a given fold to the root of the phylogenetic tree divided by the number of nodes from the most recent fold to the root of the tree. Fold expansion can be considered a proxy for sophistication while ancestry value can be considered a proxy for evolutionary time. For reference, the same analysis is performed on canonical TCA cycle enzymes, immune system proteins, and the whole proteome. The first fold of a ribonucleotide reductase catalytic domain appears at 19% ancestry, while the first fold found in only one taxonomic domain of life appears at 40% ancestry. We use these values to approximate ranges in ancestry value that correspond to the RNA- protein world, the era of the Last Universal Common Ancestor (LUCA), and the era of modern biology. These results reveal a rapid expansion of translation protein architectures before the divergence of LUCA and even before the establishment of the DNA genome. The rise of the urancestor. A geological timeline defined by a molecular clock of domain structure at
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