life
Review
A Self-Assembled Aggregate Composed of a Fatty
Acid Membrane and the Building Blocks of
Biological Polymers Provides a First Step in the
Emergence of Protocells
Roy A. Black 1, * and Matthew C. Blosser 2
1
2
*
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; [email protected]
Correspondence: [email protected]; Tel.: +1-206-713-4603
Academic Editor: David Deamer
Received: 30 June 2016; Accepted: 9 August 2016; Published: 11 August 2016
Abstract: We propose that the first step in the origin of cellular life on Earth was the self-assembly of
fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme
provides explanations for the selection and concentration of the prebiotic components of cells;
the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the
co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale
for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly
of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to
and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well. We then
explain how the conformational constraints and altered chemical environment due to binding of the
components to the membrane could facilitate the formation of nucleosides, oligonucleotides and
peptides. We conclude by discussing how the resulting oligomers, even if short and random,
could have increased vesicle stability and growth more than their building blocks did, and how
competition among these vesicles could have led to longer polymers with complex functions.
Keywords: origin of life; prebiotic; self-assembly; amphiphiles; fatty acid; vesicle; nucleoside; peptide;
oligonucleotide; membrane
1. Introduction
How did prebiotic molecules on the early Earth assemble into machinery (proteins) and stores of
information (RNA) surrounded by a membrane? How each of these structures assembled and how
they became co-localized remain unclear. All three structures are composed of simple building blocks
that can be generated by abiotic processes [1]. Therefore any explanation for the origin of cells requires
solving two problems: (1) how were the building blocks selected and concentrated as required for
the formation of the three structures; and (2) how did the membranes, RNA, and protein become
associated with each other?
We have proposed that interactions among the building blocks of the three structures, prior to the
formation of RNA or proteins, can answer both of these questions [2]. The heart of our proposal is that
the building blocks self-assembled into an aggregate with RNA and protein components bound to
a fatty acid membrane, and that this aggregate stabilized the membrane and facilitated the formation
of the two polymers. In more detail, we hypothesize:
Life 2016, 6, 33; doi:10.3390/life6030033
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Life 2016, 6, 33
a.
b.
c.
d.
e.
f.
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Fatty acids self-assembled in water to form a membrane.
Components of RNA and protein were selected and concentrated via binding to self-assembled
fatty acid membranes.
These bound building blocks stabilized fatty acid membranes against salt-induced flocculation
and increased the rate of vesicle formation.
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Membranes that were more stable bound more building blocks, leading to
a. Fatty acidssystem.
self-assembled in water to form a membrane.
an auto-amplifying
b. Components of RNA and protein were selected and concentrated via binding to self-assembled
The resulting aggregate facilitated the formation of nucleosides, oligonucleotides and peptides,
fatty acid membranes.
both because
ofbound
the building
selection
concentration
of building
blocks flocculation
and because of the
c. These
blocksand
stabilized
fatty acid membranes
against salt-induced
and increased
the rate
of vesicle
formation.
conformational
constraints
and
altered
chemical environment due to binding.
d. Membranes that were more stable bound more building blocks, leading to an auto-amplifying
The oligomers,
initially composed of random sequences, stabilized membranes and induced
system.
membrane
growth
more
effectively
than
theirof nucleosides,
unjoinedoligonucleotides
componentsanddid,
leading to the
e. The
resulting
aggregate
facilitated the
formation
peptides,
both
because
of
the
selection
and
concentration
of
building
blocks
and
because
of
the
accumulation of oligonucleotides and peptides prior to the evolution of their complex
functions
conformational constraints and altered chemical environment due to binding.
in metabolism
and
information
transfer.
f. The oligomers, initially composed of random sequences, stabilized membranes and induced
membrane growth more effectively than their unjoined components did, leading to the
This model (Figure
1, filled
arrows) offers
a simple
explanation
forofthe
and concentration
accumulation
of oligonucleotides
and peptides
prior
to the evolution
theirselection
complex functions
in metabolismof
and
information
transfer.
of the prebiotic components
cells;
the stabilization
and growth of early membranes; the formation of
This model
(Figure 1, any
filledother
arrows)
offers awe
simple
explanation
for the
selection and
the two biopolymers;
and—unlike
scheme
are aware
of—the
occurrence
of membranes,
concentration of the prebiotic components of cells; the stabilization and growth of early membranes;
RNA and protein in a single unit. Indeed, we view this co-localization as a clue to the origin of cells,
the formation of the two biopolymers; and—unlike any other scheme we are aware of—the
rather than asoccurrence
the result
of a random
that in
followed
theIndeed,
formation
ofthis
these
three structures.
In our
of membranes,
RNAevent
and protein
a single unit.
we view
co-localization
as
a
clue
to
the
origin
of
cells,
rather
than
as
the
result
of
a
random
event
that
followed
the
formation
of
scenario, membranes, protein and RNA emerge together because the prebiotic building blocks for all
these three structures. In our scenario, membranes, protein and RNA emerge together because the
three self-assemble into a stable aggregate.
prebiotic building blocks for all three self-assemble into a stable aggregate.
Figure 1. Proposed scheme for origin of protocells. Conventional (open arrows) and proposed (filled
Figure 1. Proposed
scheme
for origin of protocells. Conventional (open arrows) and proposed
arrows) paths
to a protocell.
(filled arrows) paths to a protocell.
This scheme relates to other perspectives on prebiotic chemistry in several ways. It is consistent
with the suggestion that RNA was not the first informational polymer but rather evolved from an
earlier relates
structureto
with
different
components.on
This
suggestionchemistry
stems from in
the several
observation
that the
This scheme
other
perspectives
prebiotic
ways.
It is consistent
sugar, bases and inorganic linker of RNA are remarkably well-suited to the structural requirements
with the suggestion
that
RNA
was
not
the
first
informational
polymer
but
rather
evolved from
of a self-coding polymer [3,4]. Our scheme would apply equally well to building blocks of any
an earlier structure
with
different
components.
This
suggestion
stems
from
the
observation
that the
evolutionary predecessor of RNA, as long as these building blocks, too, co-aggregate with fatty acids.
The
scenario
is
broader
in
some
respects
than
other
proposals
that
the
membrane
was
the
sugar, bases and inorganic linker of RNA are remarkably well-suited to the structural requirements
starting point or played an active role in the emergence of cells [5–7]. Objections to these proposals
of a self-coding polymer [3,4]. Our scheme would apply equally well to building blocks of any
evolutionary predecessor of RNA, as long as these building blocks, too, co-aggregate with fatty acids.
The scenario is broader in some respects than other proposals that the membrane was the starting
point or played an active role in the emergence of cells [5–7]. Objections to these proposals have
included the lack of a compelling explanation for how RNA and proteins became associated with
Life 2016, 6, 33
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the membranes, although some progress in this regard has recently been made. Szostak’s group
broke new ground by showing that certain mineral surfaces stimulate membrane formation as well
as increase the polymerization of nucleotides [8,9], but this work did not address how nucleotides
arose or how proteins were incorporated into protocells. Ruiz-Mirazo [10] and Sutherland [11] have
recently advanced the case for a systems chemistry approach to the origin of protocells to replace
the more typical approach of explaining one structure at a time. However, neither of these papers
offer a mechanism to explain the association of amphiphiles with bases, sugars and amino acids.
Deamer and colleagues moved the field forward by showing that a phospholipid matrix can organize
and polymerize mononucleotides [12,13] (with caveats discussed below), and they have described
how functional systems could emerge in hydrothermal pools from hydration-dehydration cycling of
vesicles encapsulating polymers [14].
A key feature of our scenario, unlike the previous membrane-centered proposals, is the focus on
how the components of all three essential protocell structures were brought together. Affinities among
the components in aqueous solution would complement their concentration in evaporating pools.
In addition, differential affinities provide a plausible explanation for the selection of monomers found
in biopolymers, and our scheme highlights the catalytic potential of a fatty acid membrane associated
with RNA and protein building blocks. We propose that such a membrane could catalyze nucleoside
synthesis and facilitate the condensation reactions required for the formation of both peptides and
oligonucleotides; for example, nucleoside formation in this scheme would have resulted from the
joining of ribose and bases bound to a vesicle surface, rather than from reactions between compounds
smaller than bases and sugars as proposed by Sutherland. By identifying an integral role for fatty
acid membranes in the selection, concentration and oligomerization of the building blocks of RNA
and proteins, we strengthen the argument that the pathway to cells began with the self-assembly
of amphiphiles.
The rest of this review is organized as follows. In Section 2, we describe the characteristics
of the building blocks of RNA and protein that would enable them to spontaneously bind to fatty
acid membranes. For each component, we then review the current evidence that such binding does
occur (scenario elements a and b) and that membranes that bind the building blocks are more stable
than membranes composed solely of amphiphiles (scenario elements c and d). We also discuss the
potential for additive or synergistic interactions among building blocks. In Section 3, we discuss how
the binding of RNA and protein building blocks to fatty acid membranes could help explain both
the synthesis of nucleosides and the formation of short oligomers of nucleotides and of amino acids
(scenario element e). This section is more speculative than the previous one, and we suggest how to
pursue these ideas experimentally. In Section 4, we discuss, still more speculatively, how our scheme
could also explain the accumulation of longer oligonucleotides and peptides prior to evolution of their
complex biological functions (scenario element f). At this point, the scenario merges with later stages
in protocell evolution suggested by Szostak (e.g., [15]) and Damer and Deamer [14].
As is the case with most proposed prebiotic chemistry scenarios, this scheme may inadequately
account for the complexity of the early Earth environment. The impossibility of reproducing the full
range of compounds and conditions means that some reactions that proceed in laboratory settings
would not proceed in early-Earth conditions, and vice versa. Nonetheless, the more aspects of the
scheme that we validate experimentally, the stronger the case will be that it describes one possible route
to protocells. Other routes, including those that do not involve lipids at an early stage, are reviewed
in [5,6].
2. Formation and Stabilization of a Self-Assembled Aggregate of Prebiotic Building Blocks
2.1. Amphiphiles
Amphiphiles are molecules with a hydrophilic “head” group and a hydrophobic “tail”. In water,
amphiphiles can spontaneously aggregate into small clusters called micelles or larger structures called
Life 2016, 6, 33
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vesicles (Figure 2). Vesicles are cell-like compartments, composed of an aqueous core separated from
the
environment
by a by
bilayer
of amphiphiles.
Multilamellar
vesicles
have
from
the environment
a bilayer
of amphiphiles.
Multilamellar
vesicles
haveone
oneorormore
moreadditional
additional
bilayers
bilayers inside.
inside.
Figure 2. Self-assembly of a simple amphiphile. Fatty acids self-assemble into micelles and into bilayer
Figure 2. Self-assembly of a simple amphiphile. Fatty acids self-assemble into micelles and into bilayer
structures called vesicles that resemble cell membranes. Provided by Sarah L. Keller.
structures called vesicles that resemble cell membranes. Provided by Sarah L. Keller.
The first membranes were probably composed of simple amphiphiles such as fatty acids, which
Theoffirst
membraneschain
were(the
probably
simple
amphiphiles
as fatty
consist
a hydrocarbon
“tail”) composed
of various of
lengths
with
a terminal such
carboxyl
groupacids,
(the
which
consist
of
a
hydrocarbon
chain
(the
“tail”)
of
various
lengths
with
a
terminal
carboxyl
group
“head” group) (Figure 2) [16,17]. Fatty acids as short as eight carbons spontaneously form vesicles in
(the
“head”
group)
(Figure
2) [16,17].
Fatty acids
as short
eight reactions
carbons spontaneously
vesicles
water
at neutral
pH
[18]. These
molecules
are made
by as
abiotic
likely to haveform
occurred
on
in
water
at
neutral
pH
[18].
These
molecules
are
made
by
abiotic
reactions
likely
to
have
occurred
on
the ancient Earth [17,19], and are found in meteorites [20]. Fatty acid vesicles grow by incorporating
the
Earthfatty
[17,19],
and
are the
found
in meteorites
[20]. Fatty
acidThus
vesicles
grow by
incorporating
freeancient
or micellar
acids
from
surrounding
solution
[8,21,22].
prebiotic
fatty
acids could
free
or
micellar
fatty
acids
from
the
surrounding
solution
[8,21,22].
Thus
prebiotic
fatty
acids could
have self-assembled into cell-like compartments with the capacity for growth.
have One
self-assembled
into cell-like
capacity
for growth.
concern regarding
an compartments
early role for with
fatty the
acids
in protocell
membranes has been that
One
concern
regarding
an
early
role
for
fatty
acids
in
protocell
membranes
hasrelatively
been thathigh
the
the short-chain species that probably predominated [23] form vesicles
only at
short-chain
species
that
probably
predominated
[23]
form
vesicles
only
at
relatively
high
concentrations.
concentrations. This concern is reduced by the recent finding that small percentages of long-chain
This
is reduced
by the recent
finding
thatformation
small percentages
of long-chain
fatty acideither
species
fattyconcern
acid species
substantially
increase
vesicle
[24]. Moreover,
concentrations
at
substantially
increase
vesicle
formation
[24].
Moreover,
concentrations
either
at
surfaces
or in
surfaces or in evaporating pools would have been much higher than in the prebiotic ocean
as
evaporating
would have
been much
thanused
in the
ocean
as a whole
a whole [14].pools
Experimentally,
decanoic
acid ishigher
generally
as aprebiotic
prototypical
prebiotic
fatty [14].
acid
Experimentally,
decanoic
is generally
as a[25]
prototypical
fatty
acid
because
is long
because it is long
enoughacid
to form
vesiclesused
readily
and shortprebiotic
enough to
have
been
foundit in
high
enough
to form
abundance
[20].vesicles readily [25] and short enough to have been found in high abundance [20].
Two
Two additional
additional problems
problems have
have weakened
weakened the
the case
case for
for an
an early
early role
role of
of fatty
fatty acid
acid vesicles
vesicles in
in the
the
emergence
of
protocells:
First,
they
flocculate
in
the
presence
of
low
concentrations
of
divalent
ions
or
emergence of protocells: First, they flocculate in the presence of low concentrations of divalent ions
moderate
(~0.3
M)
concentrations
of
NaCl
[26].
Long-chain
alcohols
and
glycerol
monoesters
stabilize
or moderate (~0.3 M) concentrations of NaCl [26]. Long-chain alcohols and glycerol monoesters
vesicles
these
conditions
[18,27,28], [18,27,28],
but the prebiotic
availability
of these compounds
is uncertain.
stabilizeunder
vesicles
under
these conditions
but the
prebiotic availability
of these compounds
A
fresh
water
origin
for
protocells
has
been
proposed
as
another
solution
[14].
Second,
as noted
in
is uncertain. A fresh water origin for protocells has been proposed as another solution [14].
Second,
Section
1,
other
proposals
emphasizing
a
primary
role
for
fatty
acids
have
lacked
a
compelling
as noted in Section 1, other proposals emphasizing a primary role for fatty acids have lacked a
explanation
for how RNAfor
and
proteins
associated
with
prebiotic with
membranes.
Our
proposed
compelling explanation
how
RNA became
and proteins
became
associated
prebiotic
membranes.
scenario,
in
which
the
building
blocks
of
RNA
and
protein
spontaneously
bound
to
and
stabilized
Our proposed scenario, in which the building blocks of RNA and protein spontaneously bound to and
fatty
acid aggregates
and subsequently
oligomerized,
solves both of
theseboth
problems.
Theproblems.
remainderThe
of
stabilized
fatty acid aggregates
and subsequently
oligomerized,
solves
of these
Section
2
presents
the
rationale
and
evidence
for
the
association
of
RNA
and
protein
building
blocks
remainder of Section 2 presents the rationale and evidence for the association of RNA and protein
with
fattyblocks
acid membranes.
In both
this sectionInand
Section
3, the focus
on associations
with
building
with fatty acid
membranes.
both
this section
and is
Section
3, the focus
is the
on
surfaces
of
fatty
acid
aggregates,
whether
unilamellar
vesicles,
micelles
or
multilamellar
structures
associations with the surfaces of fatty acid aggregates, whether unilamellar vesicles, micelles as
or
indicated,
rather
than on entrapment
of rather
solutesthan
in the
spaceofinside
vesicles.
multilamellar
structures
as indicated,
onaqueous
entrapment
solutes
in the aqueous space
inside vesicles.
2.2. Bases
RNA is composed of a ribose-phosphate backbone with one of four nitrogenous heterocyclic bases
2.2. Bases
attached to each ribose (Figure 3). In this section we present the rationale and evidence for the binding
RNA is composed of a ribose-phosphate backbone with one of four nitrogenous heterocyclic
of bases to fatty acid surfaces, and in Section 2.3 we address the binding of ribose.
bases attached to each ribose (Figure 3). In this section we present the rationale and evidence for the
The nucleobases (the bases found in RNA and DNA) have been identified in meteorites [29]
binding of bases to fatty acid surfaces, and in Section 2.3 we address the binding of ribose.
and/or are generated by plausibly prebiotic reactions [1]. Their structural features suggest how these
The nucleobases (the bases found in RNA and DNA) have been identified in meteorites [29]
bases might interact with a lipid bilayer. They share structural characteristics of planarity and of both
and/or are generated by plausibly prebiotic reactions [1]. Their structural features suggest how these
bases might interact with a lipid bilayer. They share structural characteristics of planarity and of
both hydrophobicity and hydrophilicity. Planarity could enable the insertion of bases into a lipid
Life 2016, 6, 33
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hydrophobicity and hydrophilicity. Planarity could enable the insertion of bases into a lipid bilayer
without
excessiveexcessive
disruptiondisruption
of the packing
of the
hydrocarbon
The simultaneous
bilayer without
of the
packing
of the tails.
hydrocarbon
tails. Thehydrophobicity
simultaneous
bilayer without excessive disruption of the packing of the hydrocarbon tails. The simultaneous
and
hydrophilicity
the bases [30] would
themwould
to interact
with
bothtothe
headgroups
and the
hydrophobicity
andofhydrophilicity
of the enable
bases [30]
enable
them
interact
with both
hydrophobicity and hydrophilicity of the bases [30] would enable them to interact with both the
hydrocarbon
corethe
of ahydrocarbon
fatty acid membrane.
headgroups and
core of a fatty acid membrane.
headgroups and the hydrocarbon core of a fatty acid membrane.
Figure 3.
3. Structure
of
RNA.
The
organic
building
blocks of
of RNA
RNA are
are the
the sugar
sugar (ribose)
(ribose) and
and four
four bases
bases
Figure
Structure of
of RNA.
RNA. The
The organic
organic building
building blocks
blocks
Figure
3. Structure
of RNA
are the
sugar (ribose)
and four
bases
(adenine,
guanine,
uracil
and
cytosine).
(adenine, guanine,
guanine, uracil
(adenine,
uracil and
and cytosine).
cytosine).
To test
whether
nucleobases
dodoinin
fact interact
with
fatty acidacid
membranes,
we employed
three
test whether
whethernucleobases
nucleobasesdo
interact
with
membranes,
we employed
To test
in factfact
interact
with
fattyfatty
acid membranes,
we employed
three
independent
assays
[2].
Our
most
compelling
result
was
that
nucleobases
are
retained
with
decanoic
three independent
assays
[2]. Our
most compelling
result
was that are
nucleobases
are decanoic
retained
independent
assays [2].
Our most
compelling
result was that
nucleobases
retained with
acid
micelles
in
a
filtration-based
assay.
In
this
assay,
unbound
compounds
pass
through
a
filter
that
withmicelles
decanoic
micelles in aassay.
filtration-based
assay.
In this
assay, unbound
compounds
acid
inacid
a filtration-based
In this assay,
unbound
compounds
pass through
a filterpass
that
retains
the
micelles
and
micelle-bound
components.
The
nucleobases
were
generally
retained
to
throughthe
a filter
that and
retains
the micellescomponents.
and micelle-bound
components.
nucleobases
were
retains
micelles
micelle-bound
The nucleobases
wereThe
generally
retained
to
a
greater
extent
than
related
bases
that
are
not
incorporated
into
RNA
(Figure
4).
In
a
second
assay,
retained
to arelated
greaterbases
extent
than
bases that are
not
incorporated
(Figure
4).
agenerally
greater extent
than
that
arerelated
not incorporated
into
RNA
(Figure 4).into
In aRNA
second
assay,
weafound
that
adenine
dialyzes
more slowly
in the presence
ofthe
decanoic
acid
vesicles thanvesicles
in the
In
secondthat
assay,
we found
that adenine
dialyzes
slowly inof
presenceacid
of decanoic
we
found
adenine
dialyzes
more slowly
in more
the presence
decanoic
vesicles acid
than in the
presence
of acetic acid,
which is too
short to form
vesicles.
In the thirdInassay,
we found
that
including
than
in the
of acetic
short
to form
the third
assay, that
we found
that
presence
ofpresence
acetic acid,
whichacid,
is toowhich
shortistotoo
form
vesicles.
Invesicles.
the third assay,
we found
including
adenine
in
the
aqueous
solution
below
a
monolayer
of
stearic
acid
in
a
Langmuir
trough
altered
the
including
in thesolution
aqueous
solution
below a monolayer
of stearic
acid in atrough
Langmuir
trough
adenine
inadenine
the aqueous
below
a monolayer
of stearic acid
in a Langmuir
altered
the
surface the
pressure
of the monolayer,
even though
adenine
alone
is not surface
active.
altered
surface
of the monolayer,
even
though
adenine
is not
surface active.
surface
pressure
of pressure
the monolayer,
even though
adenine
alone
is notalone
surface
active.
Figure 4. Decanoic acid micelles selectively bind heterocyclic nitrogenous bases. The solution to which
Figure
4.
acid
micelles
selectively bind
heterocyclic
nitrogenous
bases.
The solution
to which
Figure
4.Decanoic
Decanoic
acid
micelles
bind
heterocyclic
nitrogenous
bases.
solution
to
bases were
added contained
180selectively
mM decanoic
acid,
pH 8.25.
Reproduced
fromThe
reference
[2].
bases
were
added
contained
180
mM
decanoic
acid,
pH
8.25.
Reproduced
from
reference
[2].
which
bases
were
added
contained
180
mM
decanoic
acid,
pH
8.25.
Reproduced
from
Reference
[2].
Scatchard analysis of additional data for adenine suggests two modes of binding, one with a Kd of
Scatchard
binding, one
one with
with aa K
Kd of
Scatchard analysis
analysis of
of additional
additional data
data for
for adenine
adenine suggests
suggests two
two modes
modes of
of binding,
d of
about 11 µM and one with much lower affinity [2].
about
11
µM
and
one
with
much
lower
affinity
[2].
about 11 µM and one with much lower affinity [2].
Thus nucleobases bind to fatty acid membranes as proposed in element b of our scenario.
Thus nucleobases bind to fatty acid membranes as proposed in element b of our scenario.
Thus also
nucleobases
bind
to fattyas
acid
membranes
proposed
of our scenario.
Do they
stabilize
vesicles
proposed
in as
element
c? in
Aselement
noted babove,
NaCl atDo
0.3they
M
Do they also stabilize vesicles as proposed in element c? As noted above, NaCl at 0.3 M
also
stabilize
vesicles
as
proposed
in
element
c?
As
noted
above,
NaCl
at
0.3
M
flocculates
decanoic
acid
flocculates decanoic acid vesicles [2,26]. We found that adenine virtually eliminates this flocculation
flocculates decanoic acid vesicles [2,26]. We found that adenine virtually eliminates this flocculation
(at ≥32 °C) [2]. Other bases also reduce flocculation, and the magnitudes of the inhibitory effects
(at ≥32 °C) [2]. Other bases also reduce flocculation, and the magnitudes of the inhibitory effects
correlate with the extent to which the bases bind decanoic acid aggregates in the filtration assay [2].
correlate with the extent to which the bases bind decanoic acid aggregates in the filtration assay [2].
Elements b and c of our scenario therefore hold true for nucleobases.
Elements b and c of our scenario therefore hold true for nucleobases.
Life 2016, 6, 33
6 of 15
Another possible interplay between fatty acid vesicles and bases, which we have not6 ofyet
15
explored, is formation of Watson-Crick pairs within the membrane or between the lamellae of
multilamellar vesicles. Neither bases nor nucleosides (e.g., adenosine and uridine) pair in aqueous
vesicles [2,26].
adenine
virtually
eliminates
flocculation
(atnonaqueous
ě32 ˝ C) [2]. media
Other bases
solution
[3,30],We
butfound
base that
pairing
between
monomers
hasthis
been
detected in
[31].
also
reduce
flocculation,
and
the
magnitudes
of
the
inhibitory
effects
correlate
with
the
extent
to
which
Interactions with a fatty acid bilayer (or bilayers in the case of a multilamellar vesicle) could confine
the bases
decanoic
acidallowing
aggregates
inpairs
the filtration
Elements
and c of vesicles,
our scenario
and
align bind
the bases,
thereby
base
to form. assay
If such[2].
base
pairingbstabilizes
this
therefore holdwould
true for
nucleobases.
phenomenon
help
explain how bases that are capable of pairing were selected by protocells.
Another possible interplay between fatty acid vesicles and bases, which we have not yet explored,
2.3.
Sugars of Watson-Crick pairs within the membrane or between the lamellae of multilamellar
is formation
vesicles. Neither bases nor nucleosides (e.g., adenosine and uridine) pair in aqueous solution [3,30],
Ribose and related sugars were probably available prebiotically. These compounds are
but base pairing between monomers has been detected in nonaqueous media [31]. Interactions with
generated by the formose reaction, which starts with simple prebiotic compounds [32]. The products
a fatty acid bilayer (or bilayers in the case of a multilamellar vesicle) could confine and align the bases,
tend to react with each other rather than remaining in solution and ribose is not typically a major
thereby allowing base pairs to form. If such base pairing stabilizes vesicles, this phenomenon would
product. However, interaction with borate preserves the products, particularly ribose [32,33].
help explain how bases that are capable of pairing were selected by protocells.
Alternately, ribose may have been delivered to the prebiotic Earth via interstellar ice grains. A recent
study
demonstrated that sugars including ribose form when analogs of interstellar ice are irradiated,
2.3. Sugars
apparently through a formose-type reaction [34].
Ribose
and relatedfeature
sugarsofwere
probably
available prebiotically.
These compounds
are of
generated
A
distinguishing
sugars
is an abundance
of hydroxyl groups.
The aldehyde
a linear
by
the
formose
reaction,
which
starts
with
simple
prebiotic
compounds
[32].
The
products
tend
react
aldose and one of the hydroxyl groups can react to generate a ring with a new hydroxyl to
group,
with
each
other
rather
than
remaining
in
solution
and
ribose
is
not
typically
a
major
product.
However,
at the “anomeric” carbon, that increases the conformational complexity since it can point up or
interaction
with borate
preserves(Figure
the products,
particularly
ribose
[32,33]. Alternately,
down
(in Haworth
projections)
5). We speculate
that
the hydroxyl
groups of aribose
sugarmay
can
have
been
delivered
to
the
prebiotic
Earth
via
interstellar
ice
grains.
A
recent
study
demonstrated
hydrogen-bond with the carboxyl head groups of a fatty acid vesicle, and if so, it is likely that some
that sugars including
ribose groups
form when
analogs of interstellar
ice arethan
irradiated,
through
configurations
of hydroxyl
hydrogen-bond
more strongly
others.apparently
These interactions
a formose-type
reaction
[34].
could
stabilize the
vesicle,
as proposed in element c of our scheme. Consistent with this idea, glycerol
A
distinguishing
feature
of sugars
is an
abundance
of hydroxyl
The aldehyde
of the
a linear
esterified with a fatty acid stabilizes
fatty
acid
vesicles, possibly
duegroups.
to interactions
between
two
aldose
and
one
of
the
hydroxyl
groups
can
react
to
generate
a
ring
with
a
new
hydroxyl
group,
free hydroxyls of the glycerol and the carboxyl headgroups of the fatty acids [27,28,35].
at the
carbon, that
increases
the conformational
complexity
since
it can point
up or
To“anomeric”
determine whether
sugars
do stabilize
fatty acid vesicles,
we tested
whether
they inhibit
down
(in
Haworth
projections)
(Figure
5).
We
speculate
that
the
hydroxyl
groups
of
a
sugar
can
salt-induced flocculation as described in Section 2.2. We found that a number of sugars do inhibit
hydrogen-bond
with the carboxyl
head groups
fatty acid
vesicle,
andglucose
if so, it is
likely
that
some
flocculation
of decanoic
acid vesicles.
Ribose ofisamore
effective
than
and
even
xylose,
configurations
of
hydroxyl
groups
hydrogen-bond
more
strongly
than
others.
These
interactions
a diastereomer of ribose (Figure 5). The difference in efficacy between closely related sugars suggests
couldthe
stabilize
the of
vesicle,
as proposed
of ourthan
scheme.
with
idea,
that
inhibition
flocculation
is due in
to element
binding crather
merelyConsistent
to an effect
on this
the bulk
glycerol esterified
with a fatty
stabilizes
fattybeacid
vesicles,
dueminor
to interactions
between
properties
of the solution;
theacid
latter
would not
expected
topossibly
vary with
differences
in the
the
two
free
hydroxyls
of
the
glycerol
and
the
carboxyl
headgroups
of
the
fatty
acids
[27,28,35].
sugars’ structures.
Life 2016, 6, 33
Figure 5. Interaction between sugars and fatty acid vesicles. The green arrow indicates the anomeric
Figure 5. Interaction between sugars and fatty acid vesicles. The green arrow indicates the anomeric
carbon. The pyranose rather than furanose forms and α rather than β anomers are shown to
carbon. The pyranose rather than furanose forms and α rather than β anomers are shown to emphasize
emphasize the potential for hydrogen bonding with a surface. The addition of ribose to a solution of
the potential for hydrogen bonding with a surface. The addition of ribose to a solution of decanoic acid
decanoic acid vesicles inhibits salt-induced flocculation of vesicles more effectively than addition of
vesicles inhibits salt-induced flocculation of vesicles more effectively than addition of glucose or xylose.
glucose
or were
xylose.
The tosugars
were
added to80solutions
containing
80 mM
mMbicine/pH
decanoic acid/100
The sugars
added
solutions
containing
mM decanoic
acid/100
7.9; NaCl mM
was
bicine/pH
7.9;
NaCl
was
added
to
300
mM.
Graph
reproduced
from
reference
[2];
structures
provided
added to 300 mM. Graph reproduced from Reference [2]; structures provided by Sarah L. Keller.
by Sarah L. Keller.
To determine whether sugars do stabilize fatty acid vesicles, we tested whether they inhibit
salt-induced flocculation as described in Section 2.2. We found that a number of sugars do inhibit
Life 2016, 6, 33
7 of 15
flocculation of decanoic acid vesicles. Ribose is more effective than glucose and even xylose,
a diastereomer of ribose (Figure 5). The difference in efficacy between closely related sugars suggests
that the inhibition of flocculation is due to binding rather than merely to an effect on the bulk properties
Life
6, 33
7 of 15
of 2016,
the solution;
the latter would not be expected to vary with minor differences in the sugars’ structures.
2.4.
2.4.Amino
AminoAcids
Acidsand
andDipeptides
Dipeptides
Ten
Tenamino
aminoacids
acids(glycine,
(glycine,alanine,
alanine,valine,
valine,leucine,
leucine,isoleucine,
isoleucine,proline,
proline,serine,
serine,threonine,
threonine,aspartate
aspartate
and
andeven
even
some
dipeptides
(Figure
6) are generally
considered
to prebiotically
have been
and glutamate)
glutamate) and
some
dipeptides
(Figure
6) are generally
considered
to have been
prebiotically
available
The designation
is various
based onlines
various
lines of evidence
available [36,37].
The[36,37].
designation
of prebioticofisprebiotic
based on
of evidence
including
including
identification
in meteorites
and under
synthesis
underprebiotic
plausiblyconditions
prebiotic conditions
as the
identification
in meteorites
and synthesis
plausibly
such as the such
Miller-Urey
Miller-Urey
sparking experiments
sparking experiments
[1,38,39]. [1,38,39].
Figure 6. Two amino acids (top) join via a peptide bond (bottom). Proteins are long, linear polymers
Figure 6. Two amino acids (top) join via a peptide bond (bottom). Proteins are long, linear polymers
of amino acids.
of amino acids
Aminoacids
acidsand
anddipeptides
dipeptidescould
couldinteract
interactwith
withaafatty
fattyacid
acidmembrane
membraneininatatleast
leastfive
fiveways:
ways:
Amino
(1)
amine
groups
could
hydrogen
bond
with
fatty
acid
carboxyl
groups;
(2)
if
protonated,
amines
could
(1) amine
could hydrogen bond with fatty acid carboxyl groups; (2) if protonated, amines
bond bond
electrostatically
to the to
carboxyl
groups;groups;
(3) the carboxyl
group ofgroup
the amino
or dipeptide
could
electrostatically
the carboxyl
(3) the carboxyl
of theacid
amino
acid or
could hydrogen
bond withbond
a fattywith
acidacarboxyl
group;
(4) the
hydrophobic
sidechain (R1sidechain
and R2 in
dipeptide
could hydrogen
fatty acid
carboxyl
group;
(4) the hydrophobic
Figure
amino
as leucine
could
interactcould
with the
hydrocarbon
of the membrane;
(R
1 and 6)
R2 of
inan
Figure
6) acid
of ansuch
amino
acid such
as leucine
interact
with the core
hydrocarbon
core of
andmembrane;
(5) the hydrophilic
of an amino
acid like
serine
or threonine
with the
fatty
the
and (5) sidechain
the hydrophilic
sidechain
of an
amino
acid like could
serineinteract
or threonine
could
acid
carboxyl
groups.
interact with the fatty acid carboxyl groups.
Severalstudies
studiessuggest
suggestthe
theplausibility
plausibilityofofsuch
suchinteractions.
interactions.Decylamine,
Decylamine,composed
composedofofan
anamine
amine
Several
groupattached
attachedtotoaachain
chainofoften
tencarbons,
carbons,stabilizes
stabilizesdecanoic
decanoicacid
acidvesicles
vesiclesatatboth
bothhigh
highand
andlow
lowpH,
pH,
group
suggesting that the
whether
or not
interacts
with thewith
fattythe
acidfatty
carboxyl
[40].
suggesting
theamine,
amine,
whether
or protonated,
not protonated,
interacts
acidgroups
carboxyl
A hydroxyl
attached
to a chain
of ten
stabilizes
decanoic
acid vesicles
[18].
groups
[40]. group
A hydroxyl
group
attached
to carbons
a chain dramatically
of ten carbons
dramatically
stabilizes
decanoic
As noted
in [18].
Section
2.3, theinfree
hydroxyl
groups
of a glycerol
monoester
increase
vesicleincrease
stability.
acid
vesicles
As noted
Section
2.3, the
free hydroxyl
groups
of a glycerol
monoester
Finally,stability.
lysine (albeit
notlysine
a prebiotic
acid) associates
withassociates
palmitic acid
form a foam
[41].
vesicle
Finally,
(albeitamino
not a prebiotic
amino acid)
withtopalmitic
acid to
form
our knowledge, there are no published studies of whether single amino acids or unmodified,
a foamTo[41].
prebiotic
interact
with
acid bilayers.
studies
didamino
showacids
interaction
between
To ourdipeptides
knowledge,
there are
no fatty
published
studies of Two
whether
single
or unmodified,
fatty acid
vesiclesinteract
and dipeptides
thatbilayers.
included
a studies
nonprebiotic
amino
acid (phenylalanine
or
prebiotic
dipeptides
with fatty acid
Two
did show
interaction
between fatty acid
O-methyltyrosine)
and
that
had the
ends blocked
by acid
acetylation
of the or
amine
and amidation
of
vesicles
and dipeptides
that
included
a nonprebiotic
amino
(phenylalanine
O-methyltyrosine)
and
the had
carboxyl
group
[42,43],byand
the interaction
nonprebiotic
amphipathic
peptides group
with oleic
acid
that
the ends
blocked
acetylation
of the of
amine
and amidation
of the carboxyl
[42,43],
vesicles
been reported
[44]. Other studies
have demonstrated
interactions
between
phospholipid
and
the has
interaction
of nonprebiotic
amphipathic
peptides with
oleic acid
vesicles
has been
membranes
not have
considered
prebiotic)
and hydrophobic
againmembranes
containing
reported
[44].(which
Other are
studies
demonstrated
interactions
between peptides,
phospholipid
a nonprebiotic
acid and
blockedand
endshydrophobic
[45,46]. Separately,
Pohorille
modeledalonger
peptides
(which
are not amino
considered
prebiotic)
peptides,
againhas
containing
nonprebiotic
interacting
withblocked
phospholipid
membranes
[47]. Pohorille has modeled longer peptides interacting
amino
acid and
ends [45,46].
Separately,
These studies,membranes
along with[47].
the analysis of possible modes of interaction and the studies with
with phospholipid
compounds
related along
to amino
acids,
prebiotic
amino acids
can
These studies,
with
the support
analysisour
of proposal
possible that
modes
of interaction
andand
the dipeptides
studies with
interact withrelated
a fattytoacid
bilayer.
In support
additionour
to such
directthat
interactions,
association
compounds
amino
acids,
proposal
prebiotic amino
acidswith
and nucleobases
dipeptides
or sugars
would
of ways
in whichassociation
amino acidswith
and
can
interactbound
with to
a the
fattymembrane
acid bilayer.
In increase
addition the
to number
such direct
interactions,
nucleobases or sugars bound to the membrane would increase the number of ways in which amino
acids and dipeptides could bind to a vesicle. To investigate whether unmodified prebiotic amino
acids and dipeptides do in fact bind to and stabilize fatty acid aggregates, we propose employing the
same methods used to demonstrate interactions with nucleobases and sugars.
Life 2016, 6, 33
8 of 15
dipeptides could bind to a vesicle. To investigate whether unmodified prebiotic amino acids and
dipeptides do in fact bind to and stabilize fatty acid aggregates, we propose employing the same
methods used to demonstrate interactions with nucleobases and sugars.
2.5. Simultaneous Binding of Multiple RNA and Protein Building Blocks to Fatty Acid Membranes
Just as bound bases and sugars could increase amino acid and dipeptide binding, the inverse
is also possible, and indeed a key feature of our scenario is that more than one type of molecular
building block binds to a fatty acid membrane at a time. In support of this proposition, we found
that the inhibition of salt-induced flocculation of decanoic acid when both adenine and ribose are
present is greater than the inhibitory effects of either alone, and consistent with the sum of their
independent inhibitory effects. This finding suggests that the two compounds do bind to fatty acid
vesicles simultaneously [2].
3. Formation of Oligomers
Section 2 addressed how the building blocks of fatty acid membranes, RNA, and protein might
have become co-localized in a stable aggregate. In this section, we discuss how this co-localization
could have facilitated the formation of the two biological polymers (element e of our scheme).
Several challenges arise in explaining the abiotic formation of RNA and protein. Association of
their building blocks with a fatty acid membrane helps overcome all of these challenges. (i) How
building blocks were concentrated sufficiently to react with each other is plausibly solved by their
binding to a membrane. Even low energy binding of reactants to a soft interface is sufficient to increase
reaction rates, as demonstrated in emulsified water droplets [48]; the authors of this study note that
“the process is based on an interfacial reaction-diffusion mechanism that is expected to be quite general”;
(ii) Indiscriminate incorporation of all possible prebiotic bases, sugars and amino acids into polymers
would have impeded the formation of reproducible, functional sequences. The selective binding of
building blocks to a fatty acid membrane would eliminate this problem; (iii) Even with sufficient
concentrations of a limited number of reactants, polymerization would have required catalysts to
bring the reactants together and to constrain their conformations in ways that favored the formation
of specific covalent bonds. Both the hydrophobic core and hydrophilic surface of an amphiphilic
bilayer plausibly fulfill these functions. In addition, membranes could incorporate components such
as dipeptides (as discussed in Section 2.4) which could have contributed to the catalytic activity of the
bilayer. In support of this idea, plausibly prebiotic dipeptides catalyze at least two reactions important
for protocells, the stereospecific synthesis of sugars [49] and the aminoacylation of an RNA [50];
(iv) Finally, the formation of both phosphodiester and peptide bonds requires the generation of
a water molecule, and the reactions are not thermodynamically favored in an aqueous environment.
Amphiphilic bilayers and multilamellar structures provide an environment with reduced water activity,
which may lessen this barrier [51].
Most of these potential roles of membranes have been noted by others in various contexts [52].
Several experiments, which will be discussed in Sections 3.1 and 3.2, have indeed found that
membranes can increase the formation of oligonucleotides from mononucleotides and of peptides
from activated amino acids. However, in these experiments neither the monomers nor, in most cases,
the amphiphiles employed were plausibly prebiotic. Below we describe in more detail the status of
efforts to produce the two biological polymers by plausibly prebiotic mechanisms, and the critical role
a bilayer composed of prebiotic amphiphiles and prebiotic building blocks of RNA and protein could
have played.
3.1. RNA
The first step in explaining the origin of RNA is understanding the formation of nucleosides
(Figure 7), and much work has been devoted to possible abiotic mechanisms. Since the bases
and ribose are confirmed or likely prebiotic compounds, as discussed in Section 2, the simplest
Life 2016, 6, 33
9 of 15
explanation for the formation of nucleosides is that a reaction occurred between preformed bases
and preformed ribose. However, the requisite glycosidic bond forms inefficiently under all prebiotic
Life 2016, 6, 33
conditions tested over the past 40 years [53–55]. Recent efforts have succeeded in synthesizing
pyrimidine [56] and purine [57] nucleosides by starting with compounds smaller than bases and sugars,
questionedalthough
[58]. Nonbiological
nucleosides
are easier
to synthesize
and they[58].
offer
the prebiotic plausibility
of the sequences
of reactions
employed[59–62],
has been questioned
Nonbiological
nucleosides are easier
synthesize
[59–62],
and
they offer a molecules.
further solution if there is
solution if there
is an evolutionary
pathtofrom
them
to the
biological
an evolutionary path from them to the biological molecules.
9 of 15
a further
Figureof
7. One
units
from which
which RNA
is built.
is the nucleoside
composed
of adeninecomposed of
Figure 7. One
fourof four
units
from
RNA
is Adenosine
built. Adenosine
is the
nucleoside
and ribose. The glycosidic bond is circled.
adenine and ribose. The glycosidic bond is circled.
Our scheme focusses on the possibility of formation of the glycosidic bond by a reaction between
Our scheme
focusses on
of formation
the glycosidic
bond
by abecause
reaction between
a membrane-bound
basethe
andpossibility
membrane-bound
ribose. This of
possibility
is of particular
interest
it would help base
to explain
selection of the bases and
sugar inThis
RNA and
the co-localization
of RNA
a membrane-bound
andthemembrane-bound
ribose.
possibility
is of particular
interest
with
membranes.
As
reviewed
by
Sutherland
in
detail
[54],
there
are
several
reasons
why
formation
because it would help to explain the selection of the bases and sugar in RNA and the co-localization
of the glycosidic bond is difficult. Taking adenine and ribose as example reactants, the tautomers
of RNA with
membranes.
Asthat
reviewed
by Sutherland
inminor.
detailMoreover,
[54], there
severalofreasons why
of the
two compounds
favor the reaction
are relatively
whileare
protonation
formation the
of the
glycosidic
is makes
difficult.
Taking
adenine
and
ribose
as example
reactants, the
anomeric
hydroxylbond
of ribose
it a better
leaving
group, the
acidic
conditions
required for
the adeninethat
less nucleophilic.
suggest that
observed binding
of adenine
tautomers its
ofprotonation
the two make
compounds
favor theWereaction
aretherelatively
minor.
Moreover, while
and ribose to fatty acid vesicles [2] could solve these problems by inducing favorable conformations;
protonationtheofreactants
the anomeric
hydroxyl of ribose makes it a better leaving group, the acidic conditions
could bind either to apposing surfaces in a multilamellar vesicle or to the same membrane
required for
its protonation
the adenine
less nucleophilic.
We suggest
observed
binding
surface.
Interaction ofmake
the adenine
and/or ribose
with other components
such as that
aminothe
acids
and
dipeptides
could
also
affect
the
frequency
of
the
required
tautomers.
To
test
for
glycosidic
bond
of adenine and ribose to fatty acid vesicles [2] could solve these problems by inducing favorable
formation in the presence of fatty acid vesicles, we propose incubating a mixture of adenine, ribose and
conformations;
the reactants could bind either to apposing surfaces in a multilamellar vesicle or to
decanoic acid over a range of temperatures, pHs and salt concentrations, with or without dehydration.
the same membrane
surface.
Interaction
of the adenine
and/or
ribose
with
other
components
such as
Explaining
the prebiotic
polymerization
of nucleosides
to form
RNA
is as
challenging
as
explaining
the generation
of nucleosides
[3,4,55,58,63].
After nucleosides
formed, thetautomers.
next step is To test for
amino acids
and dipeptides
could
also affect
the frequency
of thearerequired
the
addition
of
phosphate
as
a
linker;
phosphate
may
have
been
derived
prebiotically
from
the mineral a mixture of
glycosidic bond formation in the presence of fatty acid vesicles, we propose incubating
schreibersite [64]. In order to polymerize with regiospecificity, the resulting nucleotides must be
adenine, ribose
and decanoic acid over a range of temperatures, pHs and salt concentrations, with or
oriented properly [63]. Certain mineral surfaces apparently fulfill the need for orientation, but virtually
without dehydration.
all studies to date in this area have employed artificially activated (i.e., not prebiotically plausible)
nucleotides
A more promising
approach employs
repeated drying
rehydration
Explaining
the[65].
prebiotic
polymerization
of nucleosides
toand
form
RNA ofisa solution
as challenging as
of nucleotide monophosphates with phospholipids [12,62] or salts [66]. Strikingly, drying adenosine
explaining monophosphate
the generation
of nucleosides [3,4,55,58,63]. After nucleosides are formed, the next step is
in the presence of a multilamellar phospholipid matrix organizes the monomers
the addition
of phosphate
as athatlinker;
may have[67];
been
derived
prebiotically
from the
between
lamellae in a way
appearsphosphate
to facilitate polymerization
a caveat
to this finding
is that
the combination
of low
pH andto
high
temperaturewith
employed
can lead to loss of
some
bases from
the
mineral schreibersite
[64].
In order
polymerize
regiospecificity,
the
resulting
nucleotides
must
phosphate-ribose backbone [68].
be oriented properly [63]. Certain mineral surfaces apparently fulfill the need for orientation, but
We hypothesize that the orientation of nucleotides required for polymerization could also occur
virtually allonstudies
area
have the
employed
(i.e., due
nottoprebiotically
the surfaceto
of date
a fatty in
acidthis
vesicle
or between
lamellae ofartificially
a multilamellaractivated
fatty acid vesicle,
interactions of hydroxyl
the sugar with
the headgroups
of fatty
acids. Such
interactions
plausible) nucleotides
[65]. A groups
more on
promising
approach
employs
repeated
drying
and rehydration
of a solution of nucleotide monophosphates with phospholipids [12,62] or salts [66]. Strikingly,
drying adenosine monophosphate in the presence of a multilamellar phospholipid matrix organizes
the monomers between lamellae in a way that appears to facilitate polymerization [67]; a caveat to
this finding is that the combination of low pH and high temperature employed can lead to loss of
Life 2016, 6, 33
10 of 15
and/or the presence of plausible prebiotic catalysts such as amino acids and dipeptides may eliminate
the need for low pH. We also suggest that once a polymer formed in this way, it would be positioned to
serve as a template for a complementary strand. This suggestion is plausible because when nucleosides
covalently attached to fatty acids form a monolayer at an air-water interface, they are capable of base
pairing with nucleosides in the aqueous phase [69,70]. Thus aggregation with fatty acids provides
sufficient structural scaffolding to align free nucleosides. Whether free nucleosides and/or nucleotides
bind directly to fatty acid aggregates could be investigated by the methods used to demonstrate
binding by nucleobases. To test for the polymerization of mononucleotides in our proposed system,
we suggest using methods similar to those employed in the studies with phospholipids [12,68].
3.2. Proteins
Proteins are chains of amino acids joined by peptide bonds. These bonds result from
a condensation reaction between amine and carboxyl groups (Figure 6). Peptide bonds form under
putative prebiotic conditions ranging from dry heat to cold eutectic solutions [38,71–74]. An alternative
pathway toward proteins involves depsipeptides, which form more easily than peptides [75].
Our proposal that binding of amino acids to a bilayer facilitates peptide bond formation is
supported by work with nonprebiotic systems. Several studies have shown that phospholipid
membranes increase peptide bond formation between nonprebiotic amino acids [45,46,76].
A conceptually related study demonstrated peptide bond formation at an air-water interface,
with an esterified form of the amino acid [77]. More relevant to our proposal, Adamala and Szostak
showed that an oleic acid membrane increases the Ser-His-catalyzed formation of a peptide from
amidated leucine and esterified acetyl-phenylalanine. They speculate that the reactants may “partition
to the membrane, which allows the reaction to occur at the solvent-lipid bilayer interface, or even
within the bilayer, and thereby minimize ester hydrolysis”. They also note that “membrane localization
of [the amino acid substrates] may . . . decrease the pKa of the N-terminal amino group, and so
enhance its reactivity by increasing the fraction of nucleophilic deprotonated amine” [42]. In another
study with a fatty acid system, Murillo-Sanchez et al. present evidence for acid-base catalysis of
peptide formation between amidated leucine and an activated tyrosine-like compound [43]. Finally,
Furuuchi et al. reported that decanoic acid vesicles increase synthesis of di- and triglycine from glycine
in high-pressure chambers at temperatures above 100 ˝ C [78].
These studies, together with the general consideration of the catalytic potential of membranes
found at the beginning of Section 3, support our hypothesis that prebiotic lipid vesicles can facilitate
peptide bond formation between unmodified prebiotic amino acids. To test this hypothesis, we propose
incubating such amino acids with decanoic acid over a range of temperatures, pHs and salt
concentrations, with or without dehydration.
4. From an Assemblage of the Components to an Evolving Protocell
How did assemblies composed of a membrane, nucleobases, sugars, amino acids, and short
oligomers become evolving protocells? A major step in the pathway to protocells would have been
the emergence of polymers sufficiently long to carry out such functions as replication, acquisition of
additional building blocks, and cell division. In the final element of our scheme, we propose that this
step could have been accomplished as follows:
A
B
C
Some short oligomers catalyzed condensation (i.e., covalent linkage) between building blocks to
form new oligomers, including at least some copies of itself.
The presence of oligomers increased the stability, growth or division of vesicles to a greater extent
than monomers.
Vesicles bearing catalytic oligomers would have a higher overall concentration of oligomers,
and would accumulate fatty acid and biopolymer building blocks at the expense of vesicles that
lack catalytic oligomers.
Life 2016, 6, 33
D
11 of 15
If the condensation mechanism joined short oligomers as well as single building blocks,
longer oligomers would accumulate (assuming the reaction was faster than hydrolysis).
Several lines of experimental evidence support the first three points above, and point D follows
logically. With respect to point A, the demonstrated ability of dipeptides to catalyze organic reactions
is discussed in Section 3. In support of point B, Szostak and colleagues have shown the following:
(i) Oligonucleotides are retained within fatty acid vesicles and can osmotically stress them such
that they grow at the expense of unstressed vesicles [15]; (ii) An acetylated, amidated hydrophobic
dipeptide (acetyl-phenylalanine-leucine-amide) that inserts into the bilayer can increase vesicle growth
at the expense of vesicles lacking this peptide [42]; (iii) Oxidized di-cysteine induces pearling of
filaments in multilamellar vesicles, giving rise to daughter vesicles [79,80]; (iv) An enzyme that
catalyzes formation of a certain fatty acid derivative inside fatty acid vesicles can thereby stabilize
the vesicles against Mg2+ [81]. Regarding point C, the Ser-His dipeptide catalyzes formation of the
dipeptide acetyl-phenylalanine-leucine-amide, just mentioned, that increases vesicle growth [42].
The extent to which a dipeptide that catalyzed condensation between two amino acids would have
to prefer synthesis of itself in order to propagate is beyond the scope of this review; a sophisticated
treatment of the analogous problem for a self-replicating RNA has been published by Higgs and
colleagues [82].
Once polymers accumulated that were sufficiently long to carry out complex functions such as
replication, acquisition of additional building blocks, and cell division, then Darwinian evolution could
begin. As others have argued [37], the first polymers with evolved complex functions must have been
RNAs or molecular predecessors of RNA that could propagate by template-directed replication, and the
coding of protein sequences by RNA was presumably a later development. A distinct implication
of our scheme, stemming from its emphasis on the potential of even random peptides to increase
vesicle stability and growth, is the following: RNAs that facilitated the production even of noncoded
peptides would have conferred a selectable advantage on protocells. One way an RNA could increase
peptide production is to activate amino acids by acylation. The subsequent evolution of RNAs that
aligned their activated amino acid with other, similarly activated amino acids by base-pairing at
a distal site with a “guide” RNA could have led to coded protein synthesis. As described by Damer
and Deamer [14], the emergence of such activating and template RNAs in a small number of fatty acid
vesicles (or possibly only one) is conceivable given the vast number of vesicles that can form in even
a small volume of water.
5. Conclusions
The concept of a self-assembled fatty acid membrane binding the building blocks of RNA
and protein helps answer two fundamental questions regarding the origin of protocells: how the
components of the polymers were selected and concentrated, and why the polymers emerged together
in a membranous package. Experimental evidence shows that nucleobases and sugars bind to and
stabilize fatty acid membranes, and that there are sound reasons to predict that amino acids and
dipeptides do so as well. These associations of the building blocks with a fatty acid bilayer could have
overcome barriers to abiotic formation of oligonucleotides and peptides, which in turn led to more
competitive vesicles and ultimately to the package of two polymers and a membrane that took over
the world.
Acknowledgments: We thank Sarah L. Keller for her extensive contributions to our research and to this
manuscript, including editorial advice, organization of the references and Figures 1, 2 and 5. Some of the
experiments described in this review were supported by National Science Foundation MCB1402059 and by
funding from the University of Washington MolES Faculty Partnership Program. M.C.B. was supported by
National Institutes of Health NRSA 1F32GM115236.
Conflicts of Interest: The authors declare no conflict of interest.
Life 2016, 6, 33
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