PERSPECT IVE

HFSP Journal

The origin of modern terrestrial life

1

Patrick Forterre and Simonetta Gribaldo

Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris et Universit Paris-Sud, CNRS, UMR 8621,
91405, Crsay-Cedex, France
2
Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
(Received 22 June 2007; accepted 22 June 2007; published online 25 July 2007; corrected 11 March 2008 )

The study of the origin of life covers many areas of expertise and requires the
input of various scientific communities. In recent years, this research field has
often been viewed as part of a broader agenda under the name of exobiology
or astrobiology. In this review, we have somewhat narrowed this agenda,
focusing on the origin of modern terrestrial life. The adjective modern here
means that we did not speculate on different forms of life that could have
possibly appeared on our planet, but instead focus on the existing forms cells
and viruses. We try to briefly present the state of the art about alternative
hypotheses discussing not only the origin of life per se, but also how life
evolved to produce the modern biosphere through a succession of steps that
we would like to characterize as much as possible. [DOI: 10.2976/1.2759103]

CORRESPONDENCE
P. Forterre: forterre@pasteur.fr
S. Gribaldo: simo@pasteur.fr

Traditionally, two approaches have

been employed to understand how terrestrial life originated (Fig. 1). The
bottom-up approach, exemplified by
Millers experiment, attempts to reconstruct the conditions of the primitive
Earth in order to imagine how the
main components of living organisms
came into being. This is the realm of
astro- physics, geophysics and
chemists. The top-down approach is
favored by biolo- gists, who try
finding in modern organ- isms the
relics of their ancestors in or- der to
reconstruct
ancient
metabolic
pathways and molecular processes.
Neither of these two approaches can
be successful alone, and the final goal
of any origin-of-life program should
be to bring together all these lines of
re- search to build up a coherent
scenario leading from inorganic
chemistry to Darwinian evolution. In
that sense, the quest of our origin is
intrinsically inter- disciplinary and
should
bring
together
various
expertises to deal with the same
issues.
Despite the difficulty of the topic,
great advances have been made during

the last decade in understanding the

origin of modern life. A major issue

that remains to be
solved is the origin
of
RNA, since this is
where the bottomup and top-down
approaches meet.
We definitely know,
from the resolution
of the ribosome
structure,
that
modern
proteins
were invented by
156

RNA (Steitz and Moore, 2003). This

means that, once upon a time, RNA
was the master of life, covering both
the genetic and catalytic properties
today per- formed by DNA and
proteins, respec- tively. However, the
formation
of
a
bona
fide
ribonucleotide has so far never been
successfully achieved
in
the
laboratory, and the formation of oligoribonucleotides from monomers is
extremely difficult to achieve. In this
review, keeping in mind that the

origin of RNA is the central issue, we

will briefly review the state of the art
and the recent controversies in the
fields, and we will try to identify the
most promising areas of research for
the next decade.
THE BUILDING UP OF A
HABITABLE PLANET
The formation of the Earth

Plausible mechanisms for the formation of the solar system have now been

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PERSPECTIVE

Figure 1. Schematic of bottom-up and top-down approaches. Major events discussed in the text are highlighted.

formulated, especially explaining the accretion mechanism

that could have led to the formation of a terrestrial-like
planet (Montmerle et al., 2006). The formation of Earth is
quite precisely dated at 4 56 Ga ago, based on the dating of
a particular type of meteorites called ordinary chondrites.
The accretion mechanism was probably rapid (about
100 Myr), leading in a first time to a very hot planet with a
magma ocean. The formation of oceans and continents took
place probably more rapidly than previously thought (between 4.5 and 4.4 Ga) (Hawkesworth and Kemp, 2006).
This is inferred from the study of the oldest rock, a 4.4 Ga
old zircon from Australia that gives evidence for an
interaction between water and rock at temperatures below
100 C (Wilde et al., 2001). An atmosphere would also
have formed quite early from volatile elements (such as
nitrogen) contrib- uted by extraterrestrial material on the
surface of the Earth. Astrophysics has taught us that life is
not alien to the uni- verse, since its fundamental fabric
organic chemistryis a ubiquitous component of the
interstellar space. Complex or- ganic molecules, as well as
silicates, hydrocarbons, and vari- ous forms of ice have
been found in extrasolar clouds (Bern- stein, 2006).
Therefore, as temperature decreased, organics, either
produced on Earth or coming from meteorites or miHFSP Journal Vol. 1, September 2007

crometeorites (cosmic dust), could have started accumulating on the surface. For some authors, the conditions for the

15
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HFSP
Journal

emergence of life (liquid water, continental crust, atmosphere) were already in place at 4.4 4.3 Ga. However,
the habitability of the early Earth was seriously
compromised by multiple giant impacts. In particular,
around 3.9 Ga the Earth was subjected to an impressive
episode of bombard- ment, called the late heavy
bombardment (LHB) (Cohen et al., 2000).
The Late Heavy Bombardment

The craters observed on the surface of the Moon and

other planets whose surface was not remodeled by
erosion, sedi- mentation, and plate tectonics (Mars,
Venus) testify for the diameter of the giant meteorites

158

(more than 100 km and up to 5000 km) that hit the Earths
surface during the LHB [for a recent review, see (Claeys
and Morbidelli, 2006)]. This dra- matic event could have
been triggered by the migration of giant planets that took
place after the dissipation of the gas- eous circumsolar
nebula (Gomes et al., 2005). The LBH may have lasted
from 20 to 200 million years, with a frequency of impact
that is highly debated (from one each 10,000 years to one
every 20 years). Models predict that such impacts would
have almost completely resurfaced our planet, leading to
evaporation of the oceans, melting of the crust down to at
least 1000 ms, and loss of the atmosphere. It might be significant that the oldest terrestrial continental crust (Isua,

The origin of modern terrestrial life | P. Forterre and S. Gribaldo

Greenland) dates exactly to the end of the LHB, at 3.8 Ga.

In our opinion, it is unlikely that any forms of life, if
already present, would have survived the devastating
impacts of the LHB. If this view is correct, it implies that
the path to mod- ern life would have (re)started after 3.9
3.8 Ga. The pres- ence of sedimentary rocks testifies that
oceans had already reformed by that time. However,
putative isotopic traces of life found in these rocks are now
believed to be artifactual (see below), consistent with the
idea that modern life might have indeed originated after the
LHB.

Primitive atmosphere and oceans

It has been accepted for a long time that the atmosphere of

the early Archaean was anoxic and probably weakly reducing, and dominated by oxidative species such as CO2, N2,
CO, and H2O, with small amounts of H 2, that would have
escaped rapidly to the outer space (Kasting, 1993).
Reduced gases supplied by volcanic outgassing, such as
CH4 and NH3, would have been destroyed by UV
(photodissociation), and may have subsisted only locally
around hydrothermal vents. However, a recent theoretical
model has estimated that the hydrogen escape rates were
lower than previously as- sumed in the early archaean
atmosphere, suggesting that hy- drogen may have been
abundant (Tian et al., 2005). This would be good news for
models in which life originated at the surface of our planet,
since a reducing atmosphere would have favored
traditional prebiotic chemistry. However, these recent
estimations have already been criticized (Catling, 2006),
and the debate is ongoing. It was noticed early on that the
early Earth was in danger of freezing due to the low
luminosity of the Sun, which was about 30% less than it is
today (the faint young Sun paradox) (Sagan and Chyba,
1997). Several authors have suggested that high CO2
concentrations (or a mixture of CO 2 and CH4) in the early
atmosphere were required to prevent (via a greenhouse effect) Earth from freezing (Pavlov et al., 2000). Indeed, the
presence of 3.5 Ga old sedimentary rocks excludes a
global- scale glaciation of the planet at least by that time.
The study of organic carbon isotopes indicates that oxygen
concentra- tions became significant (but still very low) only
at 2.7 Ga and then started to rise steadily (up to 1% of the
present level) from 2.4 Ga, what is called the great
oxidation Event (GOE) (Holland, 2006). Interestingly, this
period coincides with two possible snowball Earth episodes
around 2.9 and
2.4 Ga, which is assumed to have been triggered by the accumulation of biologically produced oxygen (and consequently the removal of methane and its greenhouse effect)
following the emergence of oxygenic photosynthesis
(Farqu- har et al., 2000; Holland, 2006; Kasting and Ono,
2006). The isotopic fractionation of elements such as sulfur
in archaean deposits points to an anoxic ocean during the

whole archaean period and beyond, up to 1.8 Gyr. The

oceans would have then gone through a euxinic phase
(hydrogen-sulfide rich) and
finally
become
fully
oxygenated around 0.75 Gyr

(Kump, 2005). Oxygen and silicon isotope data from archaean cherts indicate that ancient oceans may have been
warmer than today, with temperatures as high as 70 C
around 3.3 Ga (Knauth, 1998; Robert and Chaussidon,
2006). However, the interpretation of isotopic data
remains controversial since this would imply that
archaean hot and acidic rainwater would have produced
intense weathering that is not observed in the
paleoweathering record. Further- more, a hot ocean is
difficult to reconcile with a first global glaciation that
could have occurred at 2.9 and 2.4 Ga [for a critical
review of these data, see (Kasting and Howard, 2006)].

The fossil record

The first and now popular descriptions of life traces in the

Archaean regard layered structures very similar to
present- day stromatolites from a 3.4 Ga old Australian
Apex chert. These structures contain putative microfossils
presenting morphological characteristics resembling
present-day fila- mentous bacteria [for a review see
(Schopf, 2006)]. How- ever, their biologic nature remains
hotly debated. For in- stance, it was shown that many of
these structures are produced abiogenically in the
laboratory under particular conditions [reviewed in
(Brasier et al., 2006)]. Organic mat- ter has been detected
in these structures by in situ laser Ra- man spectroscopy
(Schopf, 2006), although abiogenic struc- tures also can
absorb organic inclusions that give the typical Raman

spectrum of a microfossil (Brasier et al., 2006). The earliest

stromatolite formations of unambiguous biological origin
thus remain for the time being those from around
2.6 Ga (Schopf, 2006). The question of the biogenic or
abio- genic nature of earlier Archaean microfossils will
have to await future methodological developments [for
recent re- views see (Lopez-Garcia et al., 2006; Westall,
2005)].
The isotopic composition of different elements is affected by biological processes and can thus indicate the
pres- ence of particular metabolisms. Isotopic signatures of
differ- ent elements (carbon, sulfur, nitrogen, and more
recently iron) have therefore been extensively studied to
search for life signatures in ancient rocks and to identify
specific an- cient metabolisms (Tice and Lowe, 2004)
(Ueno et al., 2006). In particular, the carbon isotope values
from apatites in Isua banded iron formations (3.8 Ga) have
often been con- sidered to be the earliest signatures of life
on Earth (Mojzsis et al., 1996). However, all the data
obtained remain vigor- ously debated (Fedo and
Whitehouse, 2002; Mojzsis and Harrison, 2002). Some
authors have argued, in particular, that some results are
indeed compatible with an abiotic ori- gin of isotopic
composition from hydrothermal activity [for an extensive
critical and well-balanced review on this topic, see Lollar
and McCollom (2006)].
Finally, molecular fossils (kerogens) derived from the
transformation of lipids have also been used to tentatively
determine the age for the emergence of various life forms.

However, it is very difficult to extract kerogens from Archaean rocks, and not all lipids are equally resistant. For
ex- ample, lipids from archaea are very fragile and have not
been found in rocks older than 1.8 Ga (Summons et al.,
1988). The older biomarker record regards the presence of
hopanes, lipids that today are distinctive of cyanobacteria,
in 2.7 Ga old rocks from Australia (Brocks et al., 1999).
The presence of eukaryotic-type steranes in the same
ancient rocks (Brocks et al., 1999) is more controversial
since some bacte- ria can produce sterols as well (Pearson
et al., 2003; Tippelt et al., 1998), although not of the
complexity of those found by Brocks et al. (Summons et
al., 2006).
In conclusion, the fact that the oldest traces of life that
are not controversial are only those from 2.6 Ga (Schopf,
2006) leaves open a wide window for the origin of modern
life be- tween 3.9 (end of the LHB) and 2.7 Ga. The quest
for traces of life in this time interval is a rapidly expanding
research field. New drilling projects have now started in
order to ob- tain novel samples of archaean rocks. Isotopic
and chemical techniques are being improved to detect the
presence of or- ganic matter with less ambiguity, and new
in situ techniques start to be applied to the analysis of
putative microfossils. Novel and more performing
techniques of lipid extraction will hopefully push back the
limit of detection of biomarkers to the early Archaean. In
parallel, theoretical models for the early Earth will surely
benefit from a better description of known metabolisms
(see below) and metabolic consortia, and their current
distribution in a wide range of environmen- tal settings.
THE ORIGIN AND EARLY EVOLUTION OF LIFE
Heterotrophic versus autotrophic theories

In the traditional prebiotic soup scenario, organic molecules would have first accumulated in the ocean or in
smaller water bodies on the early Earth, either delivered by
extraterrestrial sources (micrometeorites, dust) and/or produced by Millers type experiments (especially if the
early atmosphere was hydrogen rich, see above) (Bada and
Lazcano, 2003). The first living systems would have then
emerged from the gradual complexification of the prebiotic
broth. The authors supporting this heterotrophic theory
of- ten argue that prebiotic chemistry is the prolongation on
our planet of the cosmic chemistry, whose products (e.g.,
amino acids) indeed overlap with the building blocks of
life. For them, the possibility to easily produce in prebiotic
conditions simple amino acids, purines, sugars, fatty acids,
and other small organic molecules essential to modern life
is too strik- ing to be fortuitous (de Duve, 2003).
Proponents of the pre- biotic soup scenario (especially the
Bada and Miller school) have in general argued in favor of
a slow (gradual accumula- tion) and cold origin of life
(essential to the long-term stabil- ity of organic matter).

As an alternative to the heterotrophic theory, 20 years ago

Wachtershauser proposed an autotrophic origin of life, in

which an energy flux provided by chemical reactions at

liquidsolid interfaces was used for carbon fixation
(Wacht- ershauser, 1988) (Wachtershauser, 2006). A
related model was proposed later on by Russell and Hall
(1997). In this view, gradual accumulation and
complexification of organic matter occurred either on
mineral surfaces (i.e., a two- dimensional life) or in
networks of mineral pores. Instead of linking cosmic
chemistry with biochemistry, the proponents of an
autotrophic origin of life try to link biochemistry with
geochemistry. Wachterhauser specifically suggested that a
primitive metabolism evolved at the surface of pyrite
miner- als from the reduction of carbon dioxide using
hydrogen sul- fide (H2S) over ferrous sulfide (FeS) as the
reducing agent
[pioneer metabolism theory (Wachtershauser, 1988)
(Wachtershauser, 2006) and references therein]. The
nega- tively charged organic molecules synthesized by
this reac- tion would have been stabilized by binding to
the positively charged pyrite surface, thus forming a twodimensional net- work. The number and diversity of these
molecules would have thus grown autocatalytically in situ
by carbon fixation, leading to the self-organization of
cyclic chemical reactions, producing more and more
elaborated products. Russell and Hall (1997) suggested
that carbon fixation first occurred in- side mineral threedimensional networks formed by the pre- cipitation of
iron monosulfide from the mixing of sulfide- rich
hydrothermal fluid and the iron-containing water of an
acidic ocean, the system being energetically driven by a

natu- rally occurring geochemical pH gradient. The authors

of au- totrophic scenarios have been strongly influenced by
the dis- covery of hydrothermal vents and
hyperthermophiles in the late 1970s and early 1980s. In
contrast to the proponents of the heterotrophic origin, they
usually favor a hot origin of life, the initial reaction being
driven by a geothermal energy source. In their models, the
stability of organic molecules is no more an issue, since
these would have been short lived. On the contrary, high
temperature is supposed to have in- creased the rate of
reactions at the surface of the minerals or inside mineral
structures.
Although the autotrophic models for the origin of life
are in theory experimentally realizable in toto (Huber and
Wachtershauser, 2006), experimental programs designed to
test these theories have succeeded up to now in producing
only simple organic molecules (from C2 to C4).
Furthermore, none of these reactions has been shown to be
autocatalytic, a crucial requirement to start real chemical
evolution (Orgel,
2000). The controversy between the proponents of heterotrophic and autotrophic theories thus remains lively (de
Duve and Miller, 1991) (Bada et al., 2007). However, there
is now a general agreement on the idea that minerals (especially clays) may have catalyzed prebiotic reactions and
that metal sulfides have been an important source of
electrons for the reduction of organic compounds (Bada
and Lazcano, 2002). In particular, proponents of the
heterotrophic theory now often agree that reactions
occurring in a hydrothermal

and/or in a volcanic setting may have enriched the prebiotic

arsenal of organic molecules, or else suggest that the first
or- ganics useful for life were concentrated at mineralwater in- terfaces and/or into porous minerals. Volcanic
activity might have been especially important for the
production of phos- phoric compounds that are essential for
life (Yamagata et al., 1991) (Schwartz, 2006). Indeed, the
first source of phosphate may have been polyphosphates,
which are found in volcanic condensates and hydrothermal
vents produced by volcanic activity (Yamagata et al., 1991).
In order to reconcile the re- quirements of volcanic activity
with an environment favor- ing molecular stability, it is
tempting to suggest that life originated in an Iceland-like
setting mixing ice and fire, in which a geothermal gradient
could provide a stable and con- tinuous energy source over
long periods, whereas a cold en- vironment could provide
stability for the accumulation of or- ganic molecules.
Both heterotrophic and autotrophic theories are faced
with the problem of ending up with a robust protometabolism that could provide the energy and monomers to
establish the RNA world (de Duve, 2003). In a first step, it
is important to consider how to transfer the energy acquired
either from the outside (heterotrophic theory) or from the
reactions in hydrothermal fluids (autotrophic theory) for
further elabora- tion of the system inside protocells. Ferry
and House (2006) recently proposed an interesting model
in which the energy obtained from a geothermal energy
flux is coupled to the for- mation of phosphorylated
compounds. This model combines both features of the
autotrophic and heterotrophic theories since the mechanism
of energy conservation resembles those of modern
heterotrophs that metabolize reduced organic compounds
for the synthesis of adenosine triphosphate (ATP) by
substrate-level phosphorylation. A major question is indeed
whether the protometabolism can be inferred from the
metabolism of modern cells. The proponents of the heterotrophic scenario have often considered that the first organic molecules were produced by reactions completely independent from modern metabolism. In particular, Orgel
argued that the metabolisms of the RNA world would have
been completely erased by the emergence of a new metabolism based on proteinenzymes (Orgel, 2003). On the contrary, the proponents of the autotrophic theory tend to directly
link
the
protometabolism
to
modern
(hyperthermophilic) proteins via the coevolution of RNA
and peptides. In fact, as suggested by de Duve (2003) a metabolism entirely sustained by RNA catalysts can also be
linked to the modern one, if one reasons in terms of
Darwin- ian evolution (de Duve, 2003) by assuming that a
protein en- zyme could have initially only replaced the
function of an existing ribozyme (i.e., transformation of a
given substrate into a given product). Similarly, if
ribozymes themselves re- placed the function of more
160

ancient catalysts, the metabolism of the RNA cells could

have been built upon the more ancient

The origin of modern terrestrial life | P. Forterre and S. Gribaldo

protometabolism, especially if the RNA world itself originated in the framework of Darwinian evolution between
competing protocells.

On the way to proto-cells

Some authors have suggested that Darwinian evolution

could have already occurred prior to the existence of
cellular enti- ties, through the competition of isolated
supramolecular as- semblies concentrated on mineral
surfaces or inside mineral pores (Wachtershauser, 2006)
(Russell and Hall, 1997). However, compelling theoretical
and experimental argu- ments suggest that cell formation
occurred early in life evo- lution [see for instance (de
Duve, 2003; Deamer et al., 2006) (Muller, 2006) (LopezGarcia et al., 2006; Forterre, 2005)]. The formation of
protocells was probably essential for the evolution of
RNA replicators (see below) and the establish- ment of
any sustained energy-driven protometabolism by (i)
keeping together RNA replicators and their corresponding
genomic RNAs (i.e., only catalysts enclosed by
membranes can benefit from their own reaction), (ii)
excluding poten- tially competing external parasitic
RNAs, and (iii) prevent- ing the dilution of molecules and
macromolecules. Further- more, a protometabolism able
to synthesize nucleotides for RNA production would have
also been able to produce simple (amphiphilic) molecules
that are rather easy to syn- thesize prebiotically and could
have been abundant on early Earth [see (Muller, 2006)

HFSP Journal Vol. 1, September 2007

and references therein]. Lipid vesicles can be produced

quite easily in vitro from fatty acids or even better from
fatty acid glycerol ester. These vesicles have the ability to
undergo several cycles of growth and di- vision (Hanczyc
et al., 2003). Mineral surfaces, such as montmorillonite,
also stimulate the formation of lipid vesicles (Hanczyc et
al., 2007). Interestingly, mineral cata- lysts are trapped
inside vesicles during this process, suggest- ing that
interactions between fatty acids and minerals on early Earth
may have resulted in the enclosure of diverse ar- rays of
mineral particles with catalytic properties.
Most interestingly, Szostak and co-workers have
recently shown that vesicles encapsulating RNA grow
preferentially by lipid capture at the expense of empty
vesicles (Chen et al., 2004; Chen and Szostak, 2004) (Fig.
2). This is explained by the higher osmotic pressure inside
RNA-containing vesicles due to the counterions screening
the negative charges of RNA. This osmotic pressure is
counterbalanced by mem- brane tension, driving the uptake
of fatty acids. At an early stage, this mechanism could have
favored vesicles contain- ing charged molecules, such as
ribose phosphate and/or polyphosphate, over those
containing neutral molecules. Later on, the encapsulation
of RNA replicators would have induced a primitive form of
competition between the first RNA cells, since those
containing more efficient replicators would have grown
faster (Chen et al., 2004) (Fig. 2). In these scenarios,
natural selection between competing protocells in the
absence of genetic systems could have been originally

161

Figure
2.
Competition
between
vesicles in the early RNA world
adapted
from
Chen
2006.
Lipid vesicles containing mineral catalysts
(hexagons) and able to incorporate ribose
(R) and polyphosphate (PP) grow by capturing lipids from vesicles containing
amino acids (AA) only. The growth of
vesicles induces a proton gradient (H+)
that is used to facilitate the transport of
various compounds, followed by the synthesis of small RNA oligomers (crosses).
After division, vesicles containing RNA
replicators (red crosses) grow at the expense of those containing RNA without
self-replicating activity (blue crosses).
These grow further using additional RNA
(green barrel) to facilitate the transport of
small polar molecules.

driven by the physicochemical features of early systems.

Fi- nally, vesicle membrane growth generates a
transmembrane pH gradient (Chen and Szostak, 2004),
suggesting that some universal features of the living world
could have their origin in fundamental physicochemical
features. The perspective now would be to use such
vesicles (with various mixtures of putative catalysts,
minerals, peptides, or ribozymes) to test if they could favor
to set up some form of protometabolism.
Origin of ribonucleotides

ATP and other NTPs, including many modified bases which

were not included later on in RNA, probably originated
first as energy conveyors in the protometabolism and as
coen- zymes of peptide catalysts before the origin of RNA
itself (de Duve, 2003). Unfortunately, despite recent
progress (see be- low) a single consecutive and convincing
prebiotic process has not yet been experimentally
demonstrated for their origin [for recent reviews, see
(Joyce, 2002; Muller, 2006; Orgel, 2004) and references
therein]. The main problem is the for- mation of ribose and
nucleosides. Many sugars with four to six carbons can be
produced at alkaline pH by the so-called formose reaction
from formaldehyde and catalytic amounts of
glycoaldehyde, two simple precursors that are present in
interstellar space and were probably on early Earth as well.
However, the products of the formose reaction are unstable,
and ribose accounts for only a minor portion. Moreover, attempts to combine ribose with bases and/or phosphate in
pre- biotic conditions also produces complex mixtures of
nonspe- cific products, generating many parasitic
molecules that compete with the normal building blocks
of a nucleotide in the assembly reaction. These
observations have led many au- thors to conclude that
ribose was not a prebiotic compound, but was invented
by organisms living in a pre-RNA world, where the

scaffold of the genetic material was not ribose but simple

sugars [threofuranose nucleic acids (TNA)] or amino acids
[peptide nucleic acids (PNA)] [for

reviews see (Joyce, 2002; Orgel, 2004; Eschenmoser,

1999)]. However, these compounds are also difficult to
produce by prebiotic chemistry and lack some of the
interesting proper- ties of RNA. In particular, PNA lacks
the charged groups that allow RNA to favor the growth of
RNA-containing vesicles versus RNA free vesicles in
Szostaks experiments, whereas TNA lacks an activated
oxygen (such as the ribose 2'OH), essential for ribozyme
activity.
Whereas the formation of ribose has never been
experi- mentally investigated in the framework of
autotrophic theo- ries, much effort has been done by
proponents of the het- erotrophic theory to increase the
yields and specificity of the formose reaction. It was
shown recently that several com- pounds( Pb++),
cyanamide, or borate preferentially com- plex and
stabilize aldopentose and/or especially ribose with respect
to other sugars (Ricardo et al., 2004; Springsteen and
Joyce, 2004; Zubay and Mui, 2001). The complex formed
between ribose and boron is especially interesting since

bo- rate occupies the 2' and 3' position of the ribose thus
leaving the 5' position available for reactions such as
phosphoryla- tion (Li et al., 2005). Borate minerals were
probably present in the interstellar space and on early
Earth. It was also sug- gested that ribose, together with
purine bases, could have been synthesized in hydrothermal
environments on the sea floor (favoring the formose
reaction) that could be enriched in borate (Holm et al.,
2006). Another recent finding that could be of great
importance is that ribose permeates both fatty acid and
phospholipid membranes more rapidly than other
aldopentoses (Sacerdote and Szostak, 2005). The formation of nucleosides (ribose+base) is also very difficult to
achieve in any prebiotic condition. Interestingly, the use of
phosphorylated ribose instead of ribose facilitates the association between the base and the sugar, suggesting that
phos- phoribose might have been a major prebiotic
intermediate [(Orgel, 2004) and references therein]. Future
effort should thus be concentrated on the search for
catalysts (including

mixtures of minerals, peptides, and amino acids) that could

produce ribonucleotides (and activated ribonucleotides
such as NTP) from phosphorylated ribose and various
bases, pos- sibly inside lipid vesicles.

several laboratories using modern enzymes to produce

libraries of random RNA oligomers. Large artifi- cial
ribozymes selected in vitro can catalyze a wide range of

Origin of ribozymes

The polymerization of ribonucleotides in prebiotic conditions has only been achieved using nucleotide monophosphate activated by various amine compounds and using
RNA primers. It has been shown that clays
(montmorillonite) cata- lyze the condensation of such
activated substrates to form RNA oligomers up to 40 50
nucleotides long [for recent re- views see (Muller, 2006)
(Ferris, 2006) (Huang and Ferris, 2003)]. Importantly, the
mineral catalysts increase the ratio of 3' to 5' over 2' to 5'
phosphodiester bonds. A major prob- lem for the
establishment of a robust RNA world is the insta- bility of
RNA due to the reactive oxygen in 2' of the ribose
(Forterre et al., 1995; Lazcano and Miller, 1996). RNA can
be stabilized by a high concentration of monovalent salts
(Hethke et al., 1999) (Tehei et al., 2002), but most
ribozymes absolutely require millimolar concentrations of
divalent salts (Woodson, 2005) which, in contrast, strongly
increase RNA degradation at high temperatures (Ginoza et
al., 1964). To solve this problem, Vlassov and co-workers
have suggested that RNA occurred first in cold
environments, where synthe- sis would have been favored
over degradation, an RNA world on ice hypothesis
(Vlassov et al., 2005). They re- ported that polymerization
of nucleotides, ligation of small RNAs, and other critical
prebiotic chemical reactions are in- deed stimulated by
freezing [(Vlassov et al., 2004) and ref- erences therein].
Interestingly, a 3 ' 5 ' linkage between nucleotides is the
major or even the only product formed un- der freezing
conditions. Freezing probably accelerates some chemical
reactions in aqueous solution because of the orga- nization
of frozen water and the concentration of reactants. In the
RNA world on ice scenario, early ribozymes might have
survived transport to more warm and wet environments by
virtue of their synthetic power outpacing degradation
(Vlassov et al., 2004).
The next problem is the production of polymers of
suffi- cient length to harbor catalytic activity (minimal
ribozymes). The smallest known ribozyme is a 7mer
olinucleotide that can cleave itself at 37 C [for reviews,
see (Muller, 2006; Vlassov et al., 2005)]. A mini-RNA
ligase of 29 nucleotides has also been obtained by in vitro
selection (see below) (Landweber and Pokrovskaya, 1999).
This shows that small ribozymes may support simple
reactions of cleavage and li- gation of other small RNAs.
The production of large RNAs by successive ligation of
small RNAs would have opened the way to the emergence
of true ribozymes. The repertoire of catalytic activities
accessible to RNA has been systemati- cally explored in

16
2

The origin of modern terrestrial life | P. Forterre and S. Gribaldo

reactions such as RNA polymerization, aminoacylation of

transfer RNA, and peptide bond formation [for reviews
see (Brosius, 2005; Joyce, 2002; McGinness and Joyce,
2003; Muller, 2006)]. It has even been recently shown
that RNA can be used to transport tryptophan across a
membrane vesicle (Janas et al., 2004). A major goal of
these approaches is to produce an RNA polymerase able
to synthesize itself by carrying its own template [for
reviews see (Muller, 2006; Or- gel, 2004)]. However,
whereas the most active RNA poly- merase ribozyme
(RPR) is 189 nucleotides long, it can only replicate a 14
nucleotide long template (Johnston et al., 2001). The next
objectives are to increase the processivity of present RPRs
and to introduce a helicase activity (an essen- tial
component of all modern polymerases). Future work will
probably focus on the possibility of combining various
RNA modules with different activities to produce a truly
efficient RPR. There is no a priori obstacle to this, and
workers in the field argue that powerful evolutionary
search procedures us- ing high throughput methodology
should allow reaching the goal in the next decade (Muller,
2006).

Emergence of the protein-RNA world

At some point, one has to assume that an efficient polymerase was not only able to replicate itself, but also to
repli- cate templates producing catalysts (either ribozymes
or pep- tides) useful for the metabolism of the RNA cell

HFSP Journal Vol. 1, September 2007

[for reviews and hypotheses on this period see (Jeffares et

al., 1998; Poole et al., 1998)]. It is likely that many
different types of ribozyme-catalyzed peptide synthesis
arose, but that only one survived, leading to the modern
translation apparatus with tRNA and ribosomes. Many
authors have suggested that protein synthesis first appeared
as a by-product of RNA rep- lication and was later on
selected based on the expanding chaperone and catalytic
activities of longer and longer pep- tides (see below). For
instance, by analogy with modern RNA viruses that contain
tRNA-like structures at their 3' end used to initiate the
replication of viral genomes, Maizels and Weiner (Maizels
and Weiner, 1994) suggested that the amino-acid module of
tRNA with its CCA end first origi- nated as a tag for
genomic RNA replication (functioning both as a telomer
and as a marker for RNA to be replicated). All modern
tRNAs are monophyletic, i.e., they originated from a single
ancestral molecule that would have appeared in a particular
RNA-cell lineage. They are made of two mod- ules, the
amino-acid binding module and the module carry- ing the
anticodon. The amino-acid binding module probably
originated first and was later on duplicated to produce the
anticodon module (Maizels and Weiner, 1994). From the
imagination of scientists, a great variety of scenarios have
been proposed to explain the origin of the translation machinery (Schimmel and Henderson, 1994) (Poole et al.,
1998) (Copley et al., 2005) (Taylor, 2006) (Szathmary,
1999) (Wolf and Koonin, 2007). A detailed presentation of
these models is beyond the scope of this review. It is
usually as-

16
3

sumed that the primitive genetic code was simpler (for instance with a two-nucleotide codon and less amino acids)
and expanded in the course of evolution. Two main theories
have been proposed, suggesting either that codon choice
was initiated by specific interaction between amino acids
and an- ticodons (stereochemical theories) or that codon
choice was set up parallel with the evolution of the amino
acid biosyn- thetic pathways (historical theories) [for
reviews see (Di Giulio, 2005; Ellington et al., 2000; Wong,
2005; Yarus et al., 2005) (Knight and Landweber, 2000)].
In any case, the modern genetic code is probably not a
frozen accident, but seems to be optimized to minimize
the deleterious conse- quences of mutations (Vogel, 1998)
[for review see (Freeland et al., 2003)]. This indicates that
the tendency to increase faithful translation was the major
selection pressure that di- rected the evolution of the
genetic code, as suggested early on by Woese (1965).
Goldenfeld and co-workers have re- cently shown from in
silico stimulation that an optimal code might have become
universal in the frame of a communal evolution pervaded
by intense horizontal gene transfer of coding sequences and
coding system components among co- evolving
communities with different codes (Vetsigian et al., 2006). If
correct, this suggests that mechanisms of gene transfer
were operational very early, allowing genetic ex- change
between RNA-protein cells. Theories about the ori- gin of
the genetic code should now also accommodate struc- tural
data obtained for modern amino-acyl tRNA synthetases
and ribosomes. For instance, from comparative structural
analysis, it has been suggested that all modern amino-acyl
tRNA synthetases evolved from two proteins whose initial
role was to chaperone the tRNA (Ribas de Pouplana and
Schimmel, 2001).
The first proteins were indeed probably short
chaperone- like proteins that stabilized ribozymes and
increased their catalytic activities. They would also have
facilitated the transport of molecules (including nucleic
acids) through the membranes of the RNA cells, (Jay and
Gilbert, 1987). Longer genes and proteins may have
originated by RNA re- combination producing proteins of
increasing size via a mul- tistep combinatorial mechanism
under the control of natural selection (de Duve, 2003).
Starting from a small number of proteins of small size
(corresponding to modern folds), this mechanism would
have allowed the extensive exploration of the space
sequence at each size level size. This period ended up with
the establishment of all modern protein superfami- lies by
the various combinations of protein folds. Recent advances in comparative and structural genomics have provided fascinating insights on this process [see for instance
many recent papers by the group of Koonin (Iyer et al.,
2003) (Iyer et al., 2004)]. Complex protein enzymes, such
as large RNA polymerases, ribonucleotide reductases, and

thymydy- late synthases, all required for the origin of DNA,

likely only originated at the end of this process.

In the above scenario it is already very clear that DNA

probably originated much later than RNA, i.e., in the
ribo- nucleoprotein world (also called the second age of
the RNA world (Forterre, 2005)]. Indeed, it has been
convincingly ar- gued that the reduction of ribose is too
complex in terms of chemistry to be catalyzed by a
ribozyme (Freeland et al., 1999). One can safely assume
that the first DNA molecules still contained uracil,
because deoxythymidine triphosphate (dTMP) is
produced in modern organisms by a modification
(methylation) of deoxyuridine triphosphate (dUMP), a
reac- tion catalyzed by thymydylate synthase.
Interestingly, recent work has uncovered the existence of
two nonhomologous thymydylate synthases, ThyA and
ThyX, suggesting that modern DNA with thymidine may
have been invented twice, and possibly independently
(Myllykallio et al., 2002).
It is usually assumed that DNA replaced RNA because
it is more stable and can be replicated more faithfully
(Lazcano et al., 1988; Poole et al., 2001). As a
consequence, DNA ge- nomes would have become larger,
allowing the evolution of complex cells. However, this
cannot explain the selection of the first organisms with
DNA because genome stability and fidelity was probably
not a major problem for fast-replicating RNA cells with
small genomes, and the first DNA cells could not have
anticipated that their descendents would benefit from a
larger genome. One of us has thus suggested that DNA
first originated in viruses as a modified form of RNA to

protect the viral genetic material against defense mechanisms of the infected cell (a direct selection pressure) (Forterre, 2002). Cellular RNA genomes would have then been
transformed later on into DNA genomes following the recruitment by RNA cells of viral enzymes to produce and
rep- licate DNA, or by the takeover of RNA cells by DNA
viruses living in a carrier state (Forterre, 2005).
The introduction of viruses in the early evolutionary
sce- nario implies that viruses themselves originated at an
early stage in life evolution. The concept of an ancient viral
world was indeed first proposed by scientists who
suggested that RNA viruses are relics of the RNA world
[see, for instance (Maizels and Weiner, 1994)], and that
retroviruses, with their RNADNA cycles, could give
evidence for the transition from the RNA to the DNA
world. This concept is now sup- ported by the existence of
viruses harboring homologous capsid proteins that infect
cells from different domains (Ar- chaea, Bacteria, Eukarya)
(Akita et al., 2007; Bamford et al., 2005) suggesting that
capsid proteins originated prior to the last universal
common ancestor (LUCA). Several models have thus been
recently proposed to explain the origin of vi- ruses in the
RNA world (Forterre, 2006). Interestingly, the concept of
an ancient viral world implies that both modern RNA and
DNA viruses might have preserved ancient mo- lecular
features from the pre-LUCA era. The study of viruses
(especially the extensive exploration of their diversity)
should thus be a major area for research on early life evolution in the next decade.

THE ORIGIN OF MODERN CELLS

The last universal common ancestor

A major goal of the top-down approaches in the origin-oflife field is to reconstruct the common ancestor of all extant
organisms to reach an intermediary stage between the
origin of life and the present biosphere. The basic principle
of cell division and membrane heredity (Cavalier-Smith,
2001) im- plies that all modern cells derive from a single
cell. This his- torical entity was called the cenancestor (for
common ances- tor in Greek), the progenote, or the LUCA.
This last term has the advantage to be both neutral (unlike
the term progenote, which suggests a very primitive
organism) and precise. It clearly states that LUCA should
not be confused with the first cell, but was the product of a
long period of evolution. Being the last means that LUCA
was preceded by a long suc- cession of older ancestors.
In this framework, a plethora of cellular lineages that have
left no descendants today may have existed before LUCA.
It is important to consider that many of these were probably
still present at the time of LUCA, and some have probably
even coexisted for some time with its descendants, possibly
contributing via horizon- tal gene transfer to some traits
present in modern lineages (Fig. 3).
A consensus on the nature of LUCA is far from reached.
For some authors LUCA was a very simple organism, even
possibly acellular (Woese, 1998) (Russell and Martin,
2004),

Figure 3. LUCA was the last bottleneck in a long series of ancestors to the three present-day cellular domains: Archaea,
Bacteria, and Eukarya. Extinct lineages may have coexisted for
some time with the descendants of LUCA, and transferred some
features to them (yellow arrows). The emergence of a universal
code in an earlier bottleneck organism may have been favored by

preferential transfer between organisms sharing the same genetic

code.

whereas others consider that LUCA was a modern-type

bac- terium (Cavalier-Smith, 2002) or even a primitive
Eucaryote with a nucleus (Fuerst, 2005). Thanks to the
advances of comparative genomics, some aspects of these
hypotheses can now be tested. The identification of a set
of genes present in Archaea, Bacteria, and Eukarya has
led to the definition of a minimal gene content for LUCA
(Delaye et al., 2005; Harris et al., 2003; Koonin, 2003).
As expected from the universal- ity of the genetic code,
the minimal protein set includes a core of ribosomal
proteins, tRNA synthetases, and transla- tion factors (for
both initiation and elongation) indicating that the
translation apparatus was already well established in
LUCA. Importantly, the minimal set includes the components of machineries that are intimately associated with
the membrane, such as the signal recognition particle
(SRP) and the Sec systeminvolved in protein secretion
and the complex ATP synthasesthat function with a
transmem- brane proton gradient. These observations
clearly indicate that LUCA was a cellular organism with a
membrane rather similar to that of modern organisms
(Jekely, 2006; Pereto et al., 2004). It remains to be
explained why modern lipids are so different in Archaea
compared to the classical lipids found in Bacteria and
Eukaryotes (including an opposite po- larity) [for
discussion see (Pereto et al., 2004) (Xu and Glansdorff,
2002)]. Future experimental work should focus on the
study of vesicles made of the two types of lipids and to
the expression in bacteria of enzymes involved in the archaeal lipid pathway and vice versa.

Another controversial idea is that modern hyperthermophiles (i.e., organisms having an optimal growth
temperature above 80 C) could be the direct descendants
of a heat- loving LUCA. Hyperthermophiles indeed appear
as early di- verging lineages in the rRNA universal tree and
have rela- tively short branches (Stetter, 2006). However,
this position might be due to the high guaninecytosine
content of their rRNAs, which could have reduced their rate
of evolution (leading to shorter branches and artifactual
grouping) (Fort- erre, 1996). Several attempts have been
made to determine putative compositional biases in the
rRNA, tRNA, or pro- teins from LUCA in order to
determine the temperature at which these molecules were
functional [see, for instance (Galtier et al., 1999) (Di
Giulio, 2003)]. However, these ap- proaches led to
contradictory results and are hampered by the difficulty of
reconstructing ancient phylogenies and un- certainties
concerning the root of the tree of life (see below). In our
opinion, a mesophilic LUCA fits better with the observation that hyperthermophiles are sophisticated organisms
that have evolved specific mechanisms to thrive at very
high temperatures [for a review see (Forterre and Philippe,
1999a; Xu and Glansdorff, 2002)]. In particular,
phylogenomics analyses indeed suggest that reverse gyrase,
an atypical DNA topoisomerase present in all
hyperthermophiles, was absent in LUCA (BrochierArmanet and Forterre, 2006; Forterre et al., 2000) whereas
hot-temperature-adapted lipids are not

homologous in Archaea and Bacteria, suggesting a secondary adaptation that occurred independently in each of these
domains (Forterre and Philippe, 1999a; Xu and Glansdorff,
2002).
The minimal set of universal proteins includes a surprisingly small number of proteins that function in DNA
replica- tion, lacking in particular a DNA replicase, a
primase, and a helicase. This is not due to unrecognized
homology since the proteins performing these functions in
Bacteria on one side, and ArcheaEukaryotes on the other,
belong to different pro- tein superfamilies (Bailey et al.,
2006; Leipe et al., 1999). To explain this observation,
Koonin and colleagues have sug- gested that LUCA had an
RNA genome, but used DNA as a replication intermediate
(much like a retrovirus) (Leipe et al., 1999). Alternatively,
if LUCA had a DNA genome, the ancestral system might
have been replaced in one lineage (probably in Bacteria) by
a new system of viral origin (Fort- erre, 1999). Finally, if
LUCA still had a bona fide RNA ge- nome, Forterre
suggested that the few universal proteins in- volved in
DNA metabolism were independently introduced by DNA
viruses in the three cellular domains (Forterre, 2006). The
idea that LUCA still had a RNA genome has been recently
boosted by the discovery of mechanisms for the re- pair of
RNA damages and for enhancing the fidelity of RNA
transcription and replication. These findings have suggested
that RNAprotein cells may have reached a level of
sophisti- cation much more important than previously
thought (Fort- erre, 2005; Poole and Logan, 2005).
Most authors assume that LUCA was identical to the
last common ancestor of Archaea and Bacteria, either
because it is commonly believed that the tree of life is
rooted between the ArchaeaEukaryotes on one side and
Bacteria on the other, or because of models where
Eukaryotes originated from some kind of association
between Archaea and Bacteria (Lopez-Garcia and Moreira,
1999; Martin and Muller, 1998; Rivera and Lake, 2004;
Wachtershauser, 2006). However, the root of the bacterial
tree and the origin of Eukaryotes remain highly
controversial (Forterre and Philippe, 1999b; Gribaldo and
Philippe, 2002), (Poole and Penny, 2007). If the root turned
out to be in the eucaryotic branch (Philippe and Fort- erre,
1999), several features now exclusively present in Eukaryotes could already have been present in LUCA,
whereas features common to Archaea and Bacteria might
have origi- nated in a common lineage to these two
domains. At the mo- ment, there is no definitive argument
to conclude if the archaealeukaryal or even the unique
eucaryotic features (e.g., the spliceosome and spliceosomal
introns) are ances- tral or derived. The same can be said for
the features that are common to Bacteria and Archaea, such
as the superoperons encoding ribosomal proteins. In any
case, many puzzling ob- servations that are difficult to fit in
a single coherent scenario remain to be explained. The

question of the topology of the universal tree of life is

intimately linked to the problem of the origin of the three
domains. The main questions to be solved

are (i) why three canonical versions of the ribosome (or

other universal traits) exist and (ii) how they are now so
different from each other, but so similar inside each
domain (Woese, 1987). Many contradictory scenarios
have been proposed and are still actively debated (LopezGarcia and Moreira, 1999; Martin and Muller, 1998;
Martin and Russell, 2003; Rivera and Lake, 2004; Woese,
2002) (Cavalier-Smith, 2002) (Forterre, 2006). Much
more work has to be done in comparative biochemistry
and molecular biology to test vari- ous evolutionary
scenarios for all possible molecular ma- chines present in
modern organisms. In particular, it will be critical to
analyze in depth the history of all universal mo- lecular
machines (especially the translation apparatus).

sup- ported the early emergence of life, and the particular

path of evolution of the matter that produced life on our
planet could be at least partly revealed by studying modern
cells. A major bottleneck for further advances is that
scientists working in the various origin of life fields are
often isolated from each other either by the borders of their
disciplines or by their own theoretical preferences.
Research on the origin of life will thus surely benefit from
interdisciplinary projects gathering all relevant disciplines
to dive into our most distant past.

PERSPECTIVES

REFERENCES

Although dramatic progress has been made these last

20 years concerning all aspects of research on the origin
of life, there are still critical gaps, especially in the RNA
world theory, and no experimental evidence for a
consensus sce- nario. We still do not know how life
originated on our planet, and we will possibly never know,
since we address here a historical problem for which
critical records may have com- pletely disappeared.
Furthermore, although the study of the origin of life is a
popular subject, the number of laboratories truly working
on the subject is extremely small. On the other hand,
considering recent trends, we should be able in the near
future to understand the physicochemical principles that

ACKNOWLEDGMENTS

Work in our laboratory on DNA replication was funded by a

HFSP grant.

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