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PR8_Nastanek genov, genomov in LUCA

Origin and early of 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 (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, chemistry-originated DNA and cells with DNA 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 in

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 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, 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, 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 . 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 is explicitly indicated, as either innovation would have yielded an evolutionary advantage irrespective of when it occurred.

A logic 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 . 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 . 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 of domain structure at FSF level is used to date the FSF repertoires of the urancestral sets. Oxygen levels are indicated as percentage of present day atmospheric levels (PAL) [70]. Colored circles indicate FSF used for clock calibration. Black and red arrowheads labeled a and b indicate major and second transitions in ribosomal evolution, respectively [18], and lines indicate the appearance of FSFs associated with ribosomal proteins (table 2). Arrows show the discovery of crucial FSFs linked to membrane glycerol ester and ether lipid chemistries and sn1,2 and sn2,3 lineages. Time is given in billions of years (Ga). FSF= fold superfamily

Timeline of architectural landmarks in the early evolution of the protein world. a) Landmark discoveries are identified with arrows in a timeline derived from a phylogenomic analysis of FF architectures (FL420). The metabolic origin of molecular functions linked to translation is indicated with dashed black lines. The emergence of ribonucleotide reductase enzymes responsible for producing the deoxyribonucleotide components necessary for DNA-linked functions at ndFF=0.245 is used as reference to show the late arrival of DNA, prior to proteins and RNA. See Table S2 for a more extended description of architectures and timelines. Zadnji skupni prednik vseh organizmov// Last universal common ancestor (LUCA=cenancestor)

Reconstructing the cenancestor. a) as suggested by the 16S rRNA molecule; b) traits present in the cenancestor can be inferred by looking at homologous genes among the three cellular domains , , and Eukarya. How to derive minimal -sets by genome comparison Genomes 1 and 2 are arbitrary designations for two compared genomes — for example, those of Haemophilus influenzae and Mycoplasma genitalium. 'C' indicates the conserved (shared) portion of genes. The non-orthologous gene displacement (NOGD) cases are arbitrarily put into the smaller genome. COGs, clusters of orthologous groups of proteins.

Birth and legacy of the Last Universal Common Ancestor (LUCA). A large, evolving and promiscuous community stretches in time from the origins to the immediate precursors of the three Domains. (A) The "sprouting tuber" analogy, illustrated by Juan Miro's "Potato"; (B) Progression from the inorganic to self-replicating entities via a qualitative jump to complexity by catalytic closure, and further to cells with a DNA genome. The diagram illustrates the proposition that viruses originate from a cellular precursor and that viruses are responsible for the RNA-DNA transition in Bacteria on one side and Archaea/Eukarya on the other.

Complement of enzymes involved in the biosynthesis of phospholipid components in the cenancestor, and their evolution during the archaea–bacteria split. This complement of enzymes is inferred by phylogenomic analysis of complete genome sequences of contemporary . The cenancestor would have been able to synthesize heterochiral phospholipid membranes with a mix of sn- glycerol-1-phosphate (G1P) (blue) and sn-glycerol-3- phosphate (G3P) (orange) produced from dihydroxyacetone phosphate (DHAP), bound to isoprenoid and fatty acid lateral chains and to polar head radicals. We propose that the first cells were surrounded by amphiphilic vesicles that were synthesized abiotically and that the cenancestor already possessed a sophisticated enzymatic machinery for lipid biosynthesis. The divergence of bacteria and archaea from the cenancestor was paralleled by the specialization of their membranes. Bacteria use G3P that is bound via an ester link to fatty acids which are synthesized in an efficient way owing to the acyl-carrier protein. By contrast, archaea use G1P that is bound via an ether link to isoprenoids. GP, glycerol phosphate; MVA, mevalonate; FAS, fatty acid synthesis. Tree of Life (TOL) or web/network of life

Net or web of life

This net, or web, of life is characteristic of the earliest stages of evolution when all organisms were single cells and the distinction between and prokaryotes was barely discernible. Once the main groups rose out of the web, they evolved pretty much as you light expect by binary events. This gives rise to a traditional tree-like pattern. (a) A summary of the new root of the tree of life and (b) for the ring of life. The relevant four taxa representing known prokaryotic diversity are the double-membrane prokaryotes (D), the (F), the Actinobacteria (A) and the archaebacteria (R). The eukaryotes (K) are present in the ring of life (b), and the Bacilli (B) and the Clostridia (C) form a paraphyletic grouping within the ring. Eukaryotes arose from prokaryotes, hence the root in the tree of life resides among the prokaryotic domains. The position of the root is still debated, although pinpointing it would aid our understanding of the early evolution of life. Because prokaryote evolution was long viewed as a tree- like process of bifurcations, efforts to identify the most ancient microbial lineage split have traditionally focused on positioning a root on a phylogenetic tree constructed from one or several genes. Such studies have delivered widely conflicting results on the position of the root, this being mainly due to methodological problems inherent to deep gene phylogeny and the workings of lateral gene transfer among prokaryotes over evolutionary time. Here, we report the position of the root determined with The deepest divide in the living world is that between whole genome data using network-based procedures that take into account archaebacteria and eubacteria, as earlier studies both gene presence or absence and the level of sequence similarity among indicated (Gogarten et al. 1989; Iwabe et al. 1989) and all individual gene families that are shared across genomes. On the basis of 562,321 protein-coding gene families distributed across 191 genomes, we as is compatible with much recent genome data (Koonin find that the deepest divide in the prokaryotic world is interdomain, 2009). Like approaches (Pisani et al. 2007), that is, separating the archaebacteria from the eubacteria. This result our method takes the signal of all genes—including resonates with some older views but conflicts with the results of most those that have undergone LGT—into account rather studies over the last decade that have addressed the issue. In particular, than demanding that gene families harboring LGT several studies have suggested that the molecular distinctness of archaebacteria is not evidence for their antiquity relative to eubacteria but events first be identified and purged from the data. In instead stems from some kind of inherently elevated rate of archaebacterial contrast to supertree and supermatrix methods, however, sequence change. Here, we specifically test for such a rate elevation across our procedure is independent of individual all prokaryotic lineages through the analysis of all possible quartets among phylogenetic trees and utilizes an approach entailing eight genes duplicated in all prokaryotes, hence the last common ancestor phylogenetic networks to the study of evolutionary thereof. The results show that neither the archaebacteria as a group nor the eubacteria as a group harbor evidence for elevated evolutionary rates in the genome comparisons. sampled genes, either in the recent evolutionary past or in their common ancestor. The interdomain prokaryotic position of the root is thus not attributable to lineage-specific rate variation. Great prokaryotic (archaebacterial-eubacterial) divide: the deepest divide in the prokaryotic world is interdomain, that is, separating the archaebacteria from the eubacteria.

The principal forces of evolution in prokaryotes and their effects on archaeal and bacterial genomes. The horizontal line shows archaeal and bacterial genome size on a logarithmic scale (in megabase pairs) and the approximate corresponding number of genes (in parentheses). On this axis, some values that are important in the context of comparative genomics are roughly mapped: the two peaks of genome size distribution; ‘Van Nimwegen Limit’ (VNL) determined by the ‘cellular bureaucracy’ burden; the minimal genome size of free-living archaea and bacteria (MFL); the minimal genome size inferred by genome comparison [MG]; the smallest (C.r., C. rudii); and the largest (S.c., S. cellulosum) known bacterial genome size. The effects of the main forces of prokaryotic genome evolution are denoted by triangles that are positioned, roughly, over the ranges of genome size for which the corresponding effects are thought to be most pronounced. Diagram illustrating the dynamics of HGT in . Horizontal lines and arrows show HGT donors and recipients. Information about HGT in the ancestor of red and green plants is based on ref. 31,32. Nastanek eukariontskih genomov in celic – EUKARIOGENEZA (Eukaryogenesis, the origin of the nucleus, cytoskeleton, and mitochondria) The chimeric nature of genome in extant eukaryotes (center image,i) is consistent with a fusion of an archaeon and a bacterium at the time of the origin of eukaryotes coupled with subsequent aberrant lateral transfers of genes from food items. (a) An archaeon and a proteobacterium that are potential symbiotic partners in the origin of eukaryotes. (b) Eukaryogenesis, the origin of the nucleus, cytoskeleton, and mitochondria through as yet unknown mechanisms and events. (c) Last eukaryotic common ancestor (LECA) with nucleus, mitochondria, and chimeric genome (i.e., purple portions of chromosome). (d–h) Repeated engulfment of food and incorporation of genes into the host nucleus. (i) Modern whose chimeric genome is the product of panels a–h. The proposed chain of causes and events in eukaryogenesis – the pivotal roles of mitochondrial endosymbiosis and intron invasion. Arrows indicate proposed causal relationships (selective forces). Models for eukaryote origins that are, in principle, testable with genome data.

(A-D) Models that propose the origin of a nucleus-bearing but amitochondriate cell first, followed by the acquisition of mitochondria in a eukaryotic host.

(E-G) Models that propose the origin of mitochondria in a prokaryotic host, followed by the acquisition of eukaryotic-specific features. The relevant microbial players in each model are labelled.

Archaebacterial and eubacterial lipid membranes are indicated in red and blue, respectively. Models explaining the bacterial-like nature of phospholipid membranes in eukaryotes. Different views of the evolutionary relationships among the three domains of life are depicted as simplified phylogenetic trees. The cenancestor (green) is placed at the root of the trees. Orange branches correspond to organisms with bacterial- like phospholipids, and blue branches correspond to organisms with archaeal-like phospholipids. Red stars indicate transitions from one type of phospholipid (archaeal or bacterial) to the other. Insets in the hydrogen and syntrophy hypotheses provide details about lipid evolution after the chimeric origin of eukaryotes by a symbiosis between archaea and bacteria. a | The classical three-domain model from Woese. b | The classical pre-cell-like model from Kandler. c | The Neomura model from Cavalier-Smith. d | The hydrogen hypothesis as detailed by Martin and Koonin. e | The syntrophy hypothesis as detailed by López- García and Moreira. A, Archaea; B, Bacteria; E, Eukarya. Functional evolution of nuclear structure. Proposed incremental transition from FECA (no nuclear structure) to LECA (nucleus). The first eukaryotic common ancestor (FECA) is proposed to have lacked nuclear structure. Partitioning of the duplicated genome (yellow/orange) is proposed to be mediated by the polymerization of protein(s) related to bacterial par “motors” (blue; e.g., actin; ATPase; tubulin; DNA-binding coiled-coil protein), bound to centromere proteins (red squares). Over significant time, the FECA is proposed to have given rise to the last eukaryotic common ancestor (LECA), a cell with fully functional NPCs (not depicted) and endomembranes (Neumann et al., 2010) and, we suggest, a nucleoskeleton that included components involved in genome partitioning. After the LECA, further evolution of nuclear structure followed different pathways as seen in the six living eukaryotic supergroups (Hampl et al., 2009). The endomembrane system: establishment, elaboration, and sculpting across evolutionary time. Top: cellular configuration of intracellular membrane architectural features. Second from top: molecular machineries that are associated with the endomembrane system, and predicted points of origin in eukaryotic evolution. Third from top: diagrams of cellular architectures to illustrate the origins of phagocytosis, internal membranes, and endosymbiotic organelles, and how these relate to the origins of cellular systems and the first (FECA) and last (LECA) eukaryotic common ancestors. The suggested sequence of events, although being the one that we favor, is not the only possible order; it is still unresolved at which points the nucleus, flagellum, mitochondria, phagocytosis, and endocytosis developed. Bottom: category of cell, using a generalized terminology. Last and ‘first’ common ancestors. (A) A scheme of the procedure used to derive the gene sets in the last and ‘first’ common ancestors of eukaryotes. (B) The gene sets of ‘first common ancestors’ of eukaryotes, archaea and bacteria derived from the gene repertoires of the respective last common ancestors and identification of ancestral duplications. Abbreviations: A, archaea; B, bacteria; E, eukaryotes; LECA, last eukaryotic common ancestor; FECA, first eukaryotic common ancestor; LACA, last archaeal common ancestor; FACA, first archaeal common ancestor; LBCA, last bacterial common ancestor; FBCA, first bacterial common ancestor; LUCA, last universal common ancestor. Coulson plot demonstrating presence and absence (or loss) of IFT subunits in 52 eukaryotic genomes. Complexes are divided into IFT-A and -B and BBSome (rows), and taxa are displayed as columns. Super groups are color-coded for clarity, and phylogenetic relationships are shown at the top schematically. The presence of a cilium is also shown in the top row (black). A brief early history of spliceosomal introns. The scheme shows the inferred sequence of events from the primordial pool of genetic elements to the origin of spliceosomal introns from group II introns invading the host genome upon mitochondrial endosymbiosis. Origin of nucleus–cytosol compartmentalization in the wake of mitochondrial origin. Blue arrows indicate symbiont-to-host gene transfer. The arrows marked with crosses symbolize the ill fate of most progeny that suffered intron invasion and other -triggered disturbances, resulting in a population bottleneck among progeny from a singular endosymbiotic event. Archaebacterial and eubacterial features are indicated in red and blue, respectively.

However, these legitimate concerns notwithstanding, there seems to be some emerging clarity with respect to the nature of the archaeal ancestor of eukaryotes. The two key observations are the apparent deep phylogenetic affinity of the Evolutionary scenario for the origin of the protoeukaryote from a complex core of the eukaryotic information-processing machinery with archaeal ancestor. M, Mitochondria; N, nucleus. the archaeal TACK superphylum and the dispersal of the eukaryome components across Archaea. The combination of these findings implies a highly complex archaeal ancestor of eukaryotes that possessed certain signature eukaryotic features, such as the cytoskeleton and the Ub system, while remaining a typical archaeon in terms of overall cellular organization and genome structure. The presence of a well- developed cytoskeleton could facilitate the engulfment of Bacteria, creating the conditions for the evolution of endosymbiosis. The complexity of the archaeal ancestor was apparently fixed in the emerging eukaryotes thanks to endosymbiosis. In contrast, the proto-eukaryotic features were differentially lost in archaeal lineages in the course of reductive evolution, resulting in the currently observed dispersed eukaryome. Given the dispersed eukaryome, extensive sampling of the archaeal diversity by genome sequencing is essential to advance our understanding of eukaryogenesis. The model of the evolution of all extant life forms (top) from a virus- like primordial state (bottom).

The tree of life and major steps in cell evolution. Archaebacteria are sisters to eukaryotes and, contrary to widespread assumptions, the youngest bacterial phylum. This tree topology, coupled with extensive losses of posibacterial properties by the ancestral archaebacterium, explains (without lateral gene transfer) how eukaryotes possess a unique combination of properties now seen in archaebacteria, posibacteria and α-proteobacteria. Eukaryote origins in three stages indicated by asterisks probably immediately followed divergence of archaebacteria and eukaryote precursors from the ancestral neomuran. This ancestor arose from a stem actinobacterial posibacterium by a quantum evolutionary shake-up of bacterial organization - the neomuran revolution: surface N-linked glycoproteins replaced murein; ribosomes evolved the signal recognition particle's translational arrest domain; histones replaced DNA gyrase, radically changing DNA replication, repair, and transcription enzymes. The eukaryote depicted is a hypothetical early stage after the origin of nucleus, , cilium, and microtubular skeleton but before distinct anterior and posterior cilia and centriolar and ciliary transformation (anterior cilium young, posterior old) evolved (probably in the cenancestral eukaryote). Chromista was recently expanded to include not only the original groups Heterokonta, Cryptista and Haptophyta, but also Alveolata, Rhizaria and Heliozoa, making the name chromalveolates now unnecessary. Excavata now exclude Euglenozoa and comprise just three phyla: the ancestrally aerobic Percolozoa and Loukozoa and the ancestrally anaerobic Metamonada (e.g. Giardia, Trichomonas), which evolved from an aerobic Malawimonas-related loukozoan. Sterols and phosphatidylinositol (PI) probably evolved in the ancestral stem actinobacterium but the ancestral hyperthermophilic archaebacterium lost them when isoprenoid ethers replaced acyl ester lipids.