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.

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

replicase functions, and might add a function to improve the

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.

RNA-dependent RNA polymerase (RdRP), (RDR), or RNA replicase, is

an enzyme that catalyzes the replication of RNA from an RNA template.

Replicating genome in protocell

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 HypothesisTwo properties of RNA that would have

allowed it to play a role in the origin of lifeThe 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.

Aminoacylating Urzymes Challenge the RNA

World Hypothesis

The RNA world hypothesis proposes that RNA

molecules, which both catalyze some reactions and

carry genetic information, evolved before proteins.

However, researchers have yet to find ribozymes in

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 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) Tree of life 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 Bacteria, Archaea, and Eukarya.

How to derive minimal gene-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

species. 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

This net, or web, of life is

characteristic of the earliest stages

of evolution when all organisms

were single cells and the distinction

between eukaryotes and prokaryotes

was barely discernible. Once the

main groups rose out of the web,

they evolved pretty much as you

light expect by binary speciation

events. This gives rise to a

traditional tree-like pattern.

Net or web of life

(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 firmicutes (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.

The deepest divide in the living world is that between

archaebacteria and eubacteria, as earlier studies

indicated (Gogarten et al. 1989; Iwabe et al. 1989) and

as is compatible with much recent genome data (Koonin

2009). Like supertree approaches (Pisani et al. 2007),

our method takes the signal of all genes—including

those that have undergone LGT—into account rather

than demanding that gene families harboring LGT

events first be identified and purged from the data. In

contrast to supertree and supermatrix methods, however,

our procedure is independent of individual

phylogenetic trees and utilizes an approach entailing

phylogenetic networks to the study of evolutionary

genome comparisons.

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 lineage 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

whole genome data using network-based procedures that take into account

both gene presence or absence and the level of sequence similarity among

all individual gene families that are shared across genomes. On the basis of

562,321 protein-coding gene families distributed across 191 genomes, we

find that the deepest divide in the prokaryotic world is interdomain,

that is, separating the archaebacteria from the eubacteria. This result

resonates with some older views but conflicts with the results of most

studies over the last decade that have addressed the issue. In particular,

several studies have suggested that the molecular distinctness of

archaebacteria is not evidence for their antiquity relative to eubacteria but

instead stems from some kind of inherently elevated rate of archaebacterial

sequence change. Here, we specifically test for such a rate elevation across

all prokaryotic lineages through the analysis of all possible quartets among

eight genes duplicated in all prokaryotes, hence the last common ancestor

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

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 plants. Horizontal lines and

arrows show HGT donors and

recipients. Information about HGT in

the ancestor of red algae 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 eukaryote 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 endosymbiont-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

core of the eukaryotic information-processing machinery with

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.

Evolutionary scenario for the origin of the protoeukaryote from a complex

archaeal ancestor. M, Mitochondria; N, nucleus.

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, mitochondrion, 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).

Kingdom 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.