Download Origins and Early Evolution of the tRNA Molecule

Review
Origins and Early Evolution of the tRNA Molecule
Koji Tamura 1,2
Received: 14 October 2015; Accepted: 26 November 2015; Published: 3 December 2015
Academic Editors: Lluís Ribas de Pouplana and Adrian Gabriel Torres
1
2
Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku,
Tokyo 125-8585, Japan; [email protected]; Tel.: +81-3-5876-1472
Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda,
Chiba 278-8510, Japan
Abstract: Modern transfer RNAs (tRNAs) are composed of ~76 nucleotides and play an important
role as “adaptor” molecules that mediate the translation of information from messenger RNAs
(mRNAs). Many studies suggest that the contemporary full-length tRNA was formed by the ligation
of half-sized hairpin-like RNAs. A minihelix (a coaxial stack of the acceptor stem on the T-stem
of tRNA) can function both in aminoacylation by aminoacyl tRNA synthetases and in peptide
bond formation on the ribosome, indicating that it may be a vestige of the ancestral tRNA. The
universal CCA-31 terminus of tRNA is also a typical characteristic of the molecule. “Why CCA?”
is the fundamental unanswered question, but several findings give a comprehensive picture of its
origin. Here, the origins and early evolution of tRNA are discussed in terms of various perspectives,
including nucleotide ligation, chiral selectivity of amino acids, genetic code evolution, and the
organization of the ribosomal peptidyl transferase center (PTC). The proto-tRNA molecules may
have evolved not only as adaptors but also as contributors to the composition of the ribosome.
Keywords: tRNA; minihelix; origin; evolution; genetic code
1. Origins of tRNA
Francis Crick once remarked that transfer RNA (tRNA) looks like nature’s attempt to make RNA
do the job of a protein [1]. tRNA, discovered by Paul Zamecnik and collaborators [2], is a literal
“adaptor” molecule [3] that mediates the translation of information from messenger RNAs (mRNAs).
tRNA was the first non-coding RNA to be discovered. Now, our knowledge of the functions of
non-coding RNAs has expanded drastically, especially in the area of microRNAs [4]. Modern tRNA
is typically composed of ~76 nucleotides with the universal CCA-31 terminus [5]. The cloverleaf
secondary structure of a tRNA molecule folds into the L-shaped three-dimensional conformation
through complex tertiary interactions, including those between the D-arm and T-arm (Figure 1). Each
arm of the L-shaped tRNA structure is composed of the acceptor stem plus T-stem/loop, and the
D-stem/loop plus anticodon stem/loop, respectively [6,7]. An amino acid is attached at the 31 -end of
the acceptor stem and a trinucleotide anticodon is located in the anticodon loop. The distance between
the ends of the two arms is about 75 Å (Figure 1).
The classic “chicken-or-egg” conundrum in molecular biology seemed to be solved by the RNA
world hypothesis [8], which was postulated following the discovery of ribozymes [9,10]. The RNA
world is believed to account for the development of primitive life on Earth. However, could tRNA
have also existed in the primitive forms of life?
Life 2015, 5, 1687–1699; doi:10.3390/life5041687
www.mdpi.com/journal/life
Life 2015, 5, 1687–1699
Life 2015, 5, page–page
Figure
Secondary(a)
(a) and
and tertiary
of of
transfer
RNA
(tRNA).
The cloverleaf
secondary
Figure
1. 1.
Secondary
tertiary(b)
(b)structures
structures
transfer
RNA
(tRNA).
The cloverleaf
secondary
structure
folds
to
the
L-shaped
tertiary
structure;
both
structures
have
corresponding
colors.
tRNA tRNA
structure folds to the L-shaped tertiary structure; both structures have corresponding colors.
has the universal single-stranded CCA-3′ terminus and a neighboring nucleotide at position 73 called
has the universal single-stranded CCA-31 terminus and a neighboring nucleotide at position 73 called
“discriminator”, which is also non-base-paired in most cases. Several positions are numbered to
“discriminator”, which is also non-base-paired in most cases. Several positions are numbered to
facilitate the discussion.
facilitate the discussion.
2. Emergence of a Self-Replicating Unit
2. Emergence of a Self-Replicating Unit
The ability to self-replicate is a crucial characteristic for defining life itself. Without coupled
self-replicators,
a limited is
amount
of information
canfor
be defining
passed on
The ability toonly
self-replicate
a crucial
characteristic
lifefrom
itself.generation
Without to
coupled
generation.
Therefore,
when
such
self-replicating
molecules
emerged,
what
was
their
maximum
self-replicators, only a limited amount of information can be passed on from generation
to generation.
size? As when
the size
of these
molecules increases,
their
complexity
and
stored
increase.
Therefore,
such
self-replicating
molecules
emerged,
what
was
theirinformation
maximumalso
size?
As the size of
The point is whether such primitive self-replicating molecules can self-replicate within the range of
these molecules increases, their complexity and stored information also increase. The point is whether
an information error threshold that is intrinsically contingent on the molecules in the system.
such primitive self-replicating molecules can self-replicate within the range of an information error
Manfred Eigen estimated the error threshold from the physical property inherent to nucleotides,
threshold
that is intrinsically
molecules
in studied
the system.
Manfred
Eigen estimated
which constitute
unmodifiedcontingent
RNA (i.e., on
A, the
U, G,
or C). He
the relation
between
the
thereplication
error threshold
physical
inherent
to nucleotides,
which
constitute
unmodified
fidelityfrom
and the
genome
sizes,property
and defined
the breakdown
of correct
replication
as “error
RNA
(i.e., A, U,[11].
G, or
Hetostudied
between
thechains
replication
fidelity andaccurate
genome sizes,
catastrophe”
In C).
order
increasethe
therelation
length of
nucleotide
while maintaining
a set
of cooperating
replicators
needs toas
appear.
“hypercycle”[11].
is composed
andreplication,
defined the
breakdown
of correct
replication
“errorThe
catastrophe”
In order of
toRNAs
increase the
and of
enzymes
that work
cooperatively
in a self-reproducing
system (Figure
the i-th RNA
length
nucleotide
chains
while maintaining
accurate replication,
a set2).ofHere,
cooperating
replicators
codes
the i-th
enzyme
Ei (i = 1, is
2, composed
..., n) and Eof
i increases the replication rate of Ii+1 in a cyclical
needs
to for
appear.
The
“hypercycle”
RNAs and enzymes that work cooperatively in a
manner, whichsystem
means (Figure
that En eventually
increases
the codes
replication
rate
ofenzyme
I1. (It does
self-reproducing
2). Here, the
i-th RNA
for the
i-th
Ei (inot
= 1,matter
2, ..., n) and
whether Ei is a ribozyme or a protein enzyme as long as it plays the cooperative role, although
Ei increases the replication rate of Ii+1 in a cyclical manner, which means that En eventually increases
Eigen may have envisaged a protein enzyme.) The cyclic behavior of the hypercycle enhances the
the replication rate of I1 . (It does not matter whether Ei is a ribozyme or a protein enzyme as long as it
stability of the system and enzymes increase the replication accuracy. Before the establishment of
plays
thehypercycle
cooperative
role, althoughsystem
Eigen may
envisaged
a protein system),
enzyme.)the
Thelength
cyclic of
behavior
such
self-replicating
(i.e., have
without
the cooperating
of the
hypercycle
enhances
the
stability
of
the
system
and
enzymes
increase
the
replication
accuracy.
nucleotide chains that could be accurately replicated under Darwinian selection was no more than
Before
of such
system
(i.e.,which
without
the cooperating
aboutthe
100establishment
nucleotides [12].
Eigenhypercycle
defined theself-replicating
single-digit quality
factors
determine
the
accuracy
of complementary
purine and
pyrimidine
pyrimidine
system),
the length
of nucleotideinstruction.
chains that Purine
could be→accurately
replicated
under→Darwinian
selection
are by
far more
frequent than[12].
any cross-type
substitutions
based on quality
the experiments
wassubstitutions
no more than
about
100 nucleotides
Eigen defined
the single-digit
factors which
with RNA-replicases.
he assumed
only one incorrect
forpyrimidine
any positionÑofpyrimidine
the
determine
the accuracy Therefore,
of complementary
instruction.
Purine Ñalternative
purine and
sequence
and
finally
concluded
that
the
properties
inherent
to
A,
U,
G,
or
C
effect
a
discrimination
substitutions are by far more frequent than any cross-type substitutions based on the experiments
of complementary from non-complementary nucleotides with a quality factor not exceeding a value
with RNA-replicases. Therefore, he assumed only one incorrect alternative for any position of the
of 0.90 to 0.99 [12]. Although the length of the chain depends on the accuracy of the primordial
sequence
and finally concluded that the properties inherent to A, U, G, or C effect a discrimination of
replication, by using the threshold value estimated under these criteria, the “error catastrophe”
complementary from non-complementary nucleotides with a quality factor not exceeding a value of
0.90 to 0.99 [12]. Although the length of the chain depends on the accuracy of the primordial replication,
by using the threshold value estimated under these
criteria, the “error catastrophe” occurs beyond
2
more than around 100 nucleotides. Notably, this size is comparable to that of the tRNA molecule [12].
1688
Life 2015, 5, page–page
Life 2015,occurs
5, 1687–1699
beyond more than around 100 nucleotides. Notably, this size is comparable to that of the
tRNA
molecule
Life
2015, 5,
page–page[12].
occurs beyond more than around 100 nucleotides. Notably, this size is comparable to that of the
tRNA molecule [12].
Figure 2. A simple model of a hypercycle. An RNA molecule (information carriers I1) not only
Figure 2. A simple model of a hypercycle. An RNA molecule (information carriers I1 ) not only instructs
instructs its own reproduction but also directs the formation of an intermediate E1, which
its own
reproduction
but also
directs
the formation
of anRNA
intermediate
E1 , whichcarrier
contributes
the
contributes
the catalytic
aid for
the reproduction
of another
molecule (information
I2). I2
catalytic
aid
for
the
reproduction
of
another
RNA
molecule
(information
carrier
I
).
I
also
has
catalytic
2
also has catalytic ability for both self-production and E2 formation, which facilitates2 I1 reproduction.
Figure 2. A simple model of a hypercycle. An RNA molecule (information carriers I1) not only
ability These
for both
self-production
and
E2 formation,
which facilitates I1 reproduction. These processes
processes
strengthen the
resistance
to mutations.
instructs its own reproduction but also directs the formation of an intermediate E1, which
strengthen the resistance to mutations.
contributes the catalytic aid for the reproduction of another RNA molecule (information carrier I2). I2
3. Features of tRNA Aminoacylation and Evolutionary Significance
also has catalytic ability for both self-production and E2 formation, which facilitates I1 reproduction.
The
top
half Aminoacylation
of
the L-shaped
tRNA
containing
the aminoacylation site is often called
3. Features
of processes
tRNA
andstructure
Evolutionary
Significance
These
strengthen
the resistance
to mutations.
a “minihelix” (a coaxial stack of the acceptor stem on the T-stem of tRNA) [13,14], and the isolated
The
top half
of
the Aminoacylation
L-shaped
tRNAand
structure
containing
aminoacylation
sitesynthetases
is often called a
function
as a substrate
for Evolutionary
aminoacylation
by the
many
aminoacyl tRNA
3.domain
Featurescan
of tRNA
Significance
“minihelix”
(a [15–17].
coaxial stack
of tRNA
the acceptor
stem onby
theanT-stem
of tRNA)occurs
[13,14],
isolated
domain
(aaRSs)
Current
aminoacylation
aaRS generally
viaand
the the
following
two
The top half of the L-shaped tRNA structure containing the aminoacylation site is often called
can function
as a reactions:
substrate for aminoacylation by many aminoacyl tRNA synthetases (aaRSs) [15–17].
consecutive
a “minihelix” (a coaxial stack of the acceptor stem on the T-stem of tRNA) [13,14], and the isolated
Current tRNA aminoacylation by aa
an+aaRS
occurs via the+ following
two consecutive(1)
reactions:
ATP +generally
aaRS → [aa−AMP]aaRS
PPi
domain can function as a substrate for aminoacylation by many aminoacyl tRNA synthetases
(aaRSs) [15–17]. Current tRNA
aminoacylation
by aa−tRNA
an aaRS generally
occurs via the following(2)
two
[aa−AMP]aaRS
+ tRNA
+ AMP`
+ aaRS
aa
` ATP ` aaRS
Ñ→
raa´AMPsaaRS
PPi
(1)
consecutive reactions:
where aminoacyl adenylate is formed as an intermediate in the form of a complex with aaRS
aa
ATP
+tRNA
aaRS
→
+ PPiis `
(1)
raa´AMPsaaRS
`the
Ñ[aa−AMP]aaRS
aa´tRNA
AMP
aaRS from adenylate
(2)
(denoted as [aa−AMP]aaRS),
and+ then
activated
aminoacyl`
group
transferred
to the 3′-end of tRNA [18]. aaRSs are classified into two groups based on the amino acid sequence
[aa−AMP]aaRS
tRNA → aa−tRNA
+ AMP
+ofaaRS
(2)
where and
aminoacyl
is
formed
an+ intermediate
in the
form
a complex
with aaRS
(denoted
catalyticadenylate
domain structure
[19].as
Within
each group, the
amino
acid
activation
domains
of aaRSs
as [aa´AMP]aaRS),
and
thenwhereas
theisactivated
aminoacyl
group
isintransferred
from
adenylate
to the
31 -end
where
aminoacyl
adenylate
formed
as
an intermediate
thepossess
form of
a complex
with
aaRS
are structurally
similar,
the anticodon-binding
domains
more
diverse
structures
(denoted
asaaRSs
[aa−AMP]aaRS),
andinteracts
then two
the activated
aminoacyl
group
is transferred
fromand
adenylate
of tRNA
are classified
into
groups
on the
amino
acid
andthe
catalytic
[20].[18].
The
minihelix
region
with
thebased
conserved
domains
of sequence
aaRSs
to
the
3′-end
of
tRNA
[18].
aaRSs
are
classified
into
two
groups
based
on
the
amino
acid
sequence
half each
interacts
withthe
theamino
non-conserved
domains
(Figure 3).
These structural
domainanticodon-containing
structure [19]. Within
group,
acid activation
domains
of aaRSs
are structurally
and
catalytic
domain
[19]. Within
each
group,
the
amino
acid
of aaRSs
features
suggest
thatstructure
the conserved
domain
of aaRSs
and
one
half
of
theactivation
L-shaped domains
tRNA
similar,
whereas
the
anticodon-binding
domains
possess
more
diverse
structures
[20].structure,
The
minihelix
a
minihelix
with
the
universal
CCA-3′,
appeared
first,
and
the
anticodon
recognition
domain
of
are
structurally
similar,
whereas
the
anticodon-binding
domains
possess
more
diverse
structures
region interacts with the conserved domains of aaRSs and the anticodon-containing half interacts
with
aaRSs
and
the
other
half
of
the
L-shaped
tRNA
structure
with
anticodon
were
added
later
[13].
[20]. The minihelix region interacts with the conserved domains of aaRSs and the
the non-conserved domains (Figure 3). These structural features suggest that the conserved domain of
anticodon-containing half interacts with the non-conserved domains (Figure 3). These structural
aaRSs and one half of the L-shaped tRNA structure, a minihelix with the universal CCA-31 , appeared first,
features suggest that the conserved domain of aaRSs and one half of the L-shaped tRNA structure,
and the
anticodon
recognition
domain
of aaRSs
and the
other
the L-shaped
tRNAdomain
structure
a minihelix
with
the universal
CCA-3′,
appeared
first,
and half
the of
anticodon
recognition
of with
anticodon
were
added
later
[13].
aaRSs and the other half of the L-shaped tRNA structure with anticodon were added later [13].
Figure 3. Evolution of aminoacyl tRNA synthetases (aaRSs) and its relation to tRNAs. The minihelix
region (half domain of tRNA with the amino acid attachment site) interacts with the conserved
domain of aaRSs for amino acid activation. The other tRNA half interacts with the non-conserved
domain of aaRSs for specific recognition of an anticodon, although there are some exceptions,
including tRNASer and tRNAAla [21].
Figure 3. Evolution of aminoacyl tRNA synthetases (aaRSs) and its relation to tRNAs. The minihelix
Figure 3. Evolution of aminoacyl tRNA synthetases (aaRSs) and its relation to tRNAs. The minihelix
region (half domain of tRNA with the amino acid attachment site) interacts with the conserved
3
region (half domain of tRNA with the amino acid attachment
site) interacts with the conserved domain
domain of aaRSs for amino acid activation. The other tRNA half interacts with the non-conserved
of aaRSs
for
amino
acid
activation.
The
other
tRNA
half
interacts
with the non-conserved domain of
domain of aaRSs for specific recognition of an anticodon, although there are some exceptions,
aaRSsincluding
for specific
recognition
of
an
anticodon,
although
there
are
some
exceptions, including tRNASer
Ser
Ala
tRNA and tRNA [21].
and tRNAAla [21].
3
Class I synthetases possess active sites with the Rossmann fold motif and consensus sequences such
as HIGH and KMSKS. In contrast, class II synthetases have active sites composed of antiparallel β-sheets
1689
Life 2015, 5, 1687–1699
Life 2015,
5, page–page
with three
motifs
[22]. Although these classes may have two distinct evolutionary origins, the tertiary
structures of aaRSs revealed that a member of each of the two classes can be docked simultaneously
Class I synthetases possess active sites with the Rossmann fold motif and consensus sequences
onto the
opposite sides of the tRNA acceptor stem, thus suggesting a possible organization of the genetic
such as HIGH and KMSKS. In contrast, class II synthetases have active sites composed of antiparallel
code [23,24].
The
amino
domains
of classes
Class Imay
and have
II aaRSs
have
been coded
by opposite
β-sheets
with
threeacid-activating
motifs [22]. Although
these
two may
distinct
evolutionary
origins,
strandsthe
of tertiary
the same
gene
[25–27].
However,
the
idea
is
somewhat
based
on
the
pre-existence
of a coding
structures of aaRSs revealed that a member of each of the two classes can be docked
onto
the opposite
sidesofofaaRSs
the tRNA
acceptor
stem, thus of
suggesting
system.simultaneously
In addition, the
proposed
ancestors
(urzymes)
are composed
still quitea apossible
large number
organization
of [27].
the genetic
code non-coded
[23,24]. The amino
domains
of ligation
Class I and
II aaRSs
of amino
acids (~46)
Therefore,
proteinacid-activating
synthesis based
on the
of short
peptides
may
have
been
coded
by
opposite
strands
of
the
same
gene
[25–27].
However,
the
idea
is
somewhat
could have existed earlier.
based on the pre-existence of a coding system. In addition, the proposed ancestors of aaRSs
(urzymes) are Primordial
composed oftRNA
still quite
a large number of amino acids (~46) [27]. Therefore,
4. Chiral-Selective
Aminoacylation
non-coded protein synthesis based on the ligation of short peptides could have existed earlier.
The free energy change in aminoacyl adenylate hydrolysis is greater than that in aminoacyl tRNA
4. Chiral-Selective
Primordial
Aminoacylation
(ester) hydrolysis
[28], which
meanstRNA
that the
activated aminoacyl group can be spontaneously transferred
1
from adenylate
to the
3 -end
of the
tRNA (the
second hydrolysis
step beingis catalyzed
bythat
aaRSs
in the modern
The free
energy
change
in aminoacyl
adenylate
greater than
in aminoacyl
tRNA
(ester) hydrolysis
[28], which
that the
activated
aminoacyl
grouptocan
be spontaneously
biological
systems).
As the formation
of means
aminoacyl
adenylate
has
been proven
occur
prebiotically [29], a
from adenylate
to the 3′-end
of the
tRNA (the amino
second acids
step being
catalyzed
by aaRSs
in In this
model transferred
system of tRNA
aminoacylation
based
on activated
has been
proposed
[30].
the modern biological systems). As the formation of aminoacyl adenylate has been proven to 1occur
system, the aminoacyl phosphate oligonucleotide and the universal CCA sequence at the 3 -end of the
prebiotically [29], a model system of tRNA aminoacylation based on activated amino acids has been
minihelix are in close proximity to each other and are bridged by another oligonucleotide. Surprisingly,
proposed [30]. In this system, the aminoacyl phosphate oligonucleotide and the universal CCA
the formation
-aminoacyl-minihelix
wasin detected
with atosignificant
over by
that of a
sequenceof
at an
theL3′-end
of the minihelix are
close proximity
each other preference
and are bridged
D-aminoacyl-minihelix,
in
the
ratio
of
approximately
4:1
[30]
(Figure
4).
Chiral
selectivity
is likely
another oligonucleotide. Surprisingly, the formation of an L-aminoacyl-minihelix was detected with
significant
preference over
of a D-aminoacyl-minihelix,
in the
ratio of approximately
4:1 [30] by the
due to athe
steric hindrance.
The that
approach
of oxygen (Nu) to the
carbonyl
carbon is described
˝ [31] and
(Figureangle
4). Chiral
selectivity
likely due angle
to the steric
hindrance. The
approach
of the
oxygen
(Nu) to
Bürgi-Dunitz
defined
as theisNu´C=O
of approximately
105
position
of the
an amino
carbonyl
carbon
is in
described
by thechiral
Bürgi-Dunitz
defined
as itthe
Nu−C=O
of RNA
acid side
chain is
crucial
determining
selectivityangle
[32–35].
Here,
is clear
that angle
D-ribose
approximately 105° [31] and the position of an amino acid side chain is crucial in determining chiral
determines homochirality of L-amino acids, so the next question is about the origin of D-ribose in RNA.
selectivity [32–35]. Here, it is clear that D-ribose RNA determines homochirality of L-amino acids, so
Template-directed
auto-oligomerization using all possible combinations of homochiral and heterochiral
the next question is about the origin of D-ribose in RNA. Template-directed auto-oligomerization
1 ,31 -cyclophosphates occurred chiral-selectively,
diastereomers
of short
pyranosyl-RNA
using all
possible
combinations oligonucleotide
of homochiral 2and
heterochiral diastereomers of short
resulting
in all D- or alloligonucleotide
L-products [36].
Therefore, similarly-produced
RNAs couldresulting
have been
composed
pyranosyl-RNA
2′,3′-cyclophosphates
occurred chiral-selectively,
in all
Dallall
L-products
[36].The
Therefore,
similarly-produced
RNAs
have been
composed
of all
- orLall
of all Dor
- or
L-libraries.
important
point here is that
thecould
sequences
contained
in the
D-Dor
-libraries
-libraries.
important
here is that
the sequences
contained
in exceed
the D- or
would Lnot
be the The
same,
becausepoint
the number
of possible
sequences
would
theL-libraries
number would
of sequences
not be the same, because the number of possible sequences would exceed the number of sequences
actually formed during the process of extending RNA length. A specific sequence in only D-libraries may
actually formed during the process of extending RNA length. A specific sequence in only D-libraries
have exhibited an important unknown chemical propensity for establishing the RNA world; alternatively,
may have exhibited an important unknown chemical propensity for establishing the RNA world;
it mightalternatively,
have been itchance
that led
the use
L-amino
acids
in the translational
system. system.
might have
beentochance
thatofled
to the use
of L-amino
acids in the translational
4. Chiral-selective
aminoacylationofofan
anRNA
RNA minihelix.
aminoacylation
with with
FigureFigure
4. Chiral-selective
aminoacylation
minihelix.Non-enzymatic
Non-enzymatic
aminoacylation
an aminoacyl phosphate oligonucleotide and a bridging nucleotide occurs with the clear preference
an aminoacyl phosphate oligonucleotide and a bridging nucleotide occurs with the clear preference for
for L- over D-amino acids. The arrow indicates nucleophilic attack of 3′-O of the terminal adenosine
L- over D-amino acids. The arrow indicates nucleophilic attack of 31 -O of the terminal adenosine on the
carbonyl carbon of the aminoacyl phosphate linkage.
Chiral selectivity is likely due to steric hindrance
4
of the side chain of D-amino acids.
1690
Life 2015, 5, page–page
on the carbonyl carbon of the aminoacyl phosphate linkage. Chiral selectivity is likely due to steric
hindrance of the side chain of D-amino acids.
Life 2015, 5, 1687–1699
5. The CCA Sequence of tRNAs and the Origin of the Genetic Code
5. The
Sequence
ofpossess
tRNAs aand
the Origin of CCA
the Genetic
Code
AllCCA
tRNA
molecules
single-stranded
sequence
(C74C75A76) at their 3′-ends [5].
1 -ends [5].
Weiner
and
Maizels
proposed
the
genomic
tag
model,
which
postulates
that tRNA-like
All tRNA molecules possess a single-stranded CCA sequence (C74C75A76)
at their 3structural
motifs with
CCA first
evolvedthe
asgenomic
3′-terminal
in RNA
for
replication
instructural
the RNA motifs
world
Weiner
and Maizels
proposed
tag tags
model,
whichgenomes
postulates
that
tRNA-like
1
[37].
This
model,
therefore,
hypothesizes
that
ancient
linear
RNA
genomes
also
possessed
tRNA-like
with CCA first evolved as 3 -terminal tags in RNA genomes for replication in the RNA world [37]. This
structures
with the
3′-terminalthat
CCA
as a replication
The tRNA-like
model, therefore,
hypothesizes
ancient
linear RNAinitiation
genomes site
also [37].
possessed
tRNA-like structures
structures
1
may the
have
arisen early
and
an essential
theThe
earliest
replicating
systems.
Conserved
with
3 -terminal
CCA
as aplayed
replication
initiationrole
sitein
[37].
tRNA-like
structures
may have
arisen
throughout
evolution,
these
structures
are
important
in
the
contemporary
world
as
well,
as
early and played an essential role in the earliest replicating systems. Conserved throughout evolution,
evidenced
by
their
function
in
a
wide
variety
of
replicative
processes
in
the
modern
biological
these structures are important in the contemporary world as well, as evidenced by their function in a
systems
[38–40].
wide
variety
of replicative processes in the modern biological systems [38–40].
Replication
startingwith
withGG
GG
could
have
favored
because
of hydrogen
strong hydrogen
bonds
Replication starting
could
have
beenbeen
favored
because
of strong
bonds between
between
pairs (compared
to A:Uand
pairs)
and strong
stacking
thedinucleotide.
GG dinucleotide.
Moreover,
G:C pairsG:C
(compared
to A:U pairs)
strong
stacking
of the of
GG
Moreover,
the
1
the
addition
of
a
non-templated
3′-terminal
nucleotide
(typically
A),
which
commonly
occurs
in
addition of a non-templated 3 -terminal nucleotide (typically A), which commonly occurs in modern
modern
polymerases,
would
be
favorable
as
the
stacking
of
A
stabilizes
the
terminal
base
pair
[41–43].
polymerases, would be favorable as the stacking of A stabilizes the terminal base pair [41–43].
Similar
to aaRSs,
aaRSs,ribosomal
ribosomalsubunits
subunits(large
(large
and
small)
functionally
separated
[44,45].
Similar to
and
small)
areare
alsoalso
functionally
separated
[44,45].
The
The
CCA
end
of
the
minihelix
domain
of
tRNA
interacts
with
the
large
subunit,
and
peptide
bond
CCA end of the minihelix domain of tRNA interacts with the large subunit, and peptide bond formation
formation
occurs
at the
peptidyl center
transferase
center
(PTC). the
In contrast,
the
end tRNA
of thehalf
other
tRNA
occurs at the
peptidyl
transferase
(PTC).
In contrast,
end of the
other
interacts
half interacts
theand
small
subunit
and serves
decode
triplets bybinding
codon-anticodon
with
the small with
subunit
serves
to decode
mRNAtotriplets
bymRNA
codon-anticodon
(Figure 5).
binding
(Figure
5).
The
CCA
sequence
of
tRNA
is
known
to
be
important
in
the
reaction
The CCA sequence of tRNA is known to be important in the reaction with the ribosomewith
[46];the
in
ribosome
[46];
in
particular,
the
specific
base-pairing
of
C74
and
C75
with
G2252
and
G2251
in 23S
particular, the specific base-pairing of C74 and C75 with G2252 and G2251 in 23S rRNA (Escherichia
coli
rRNA
(Escherichia
coli numbering),
respectively,
are transferase
essential foractivity
peptidyl
transferase
activity
[47].
numbering),
respectively,
are essential
for peptidyl
[47].
Furthermore,
A76
of
Val has been shown necessary for the editing activity of ValRS [48].
Val
Furthermore,
A76
of
tRNA
tRNA has been shown necessary for the editing activity of ValRS [48].
Recently,
it has
has been
been proposed
proposed that
that an
an RNA
RNA with
with the
the CCA-3
CCA-3′1 terminus
origin of
Recently, it
terminus was
was the
the origin
of
Gly
Gly anticodon
Gly
Gly
tRNA
[49,50].
Considering
the
fact
that
the
second
and
third
nucleotides
of
tRNA
are
tRNA
[49,50]. Considering the fact that the second and third nucleotides of tRNA
anticodon
C35
andand
C36,
respectively,
and
the
half-sized
are C35
C36,
respectively,
and
thefollowing
followingnucleotide
nucleotideisismostly
mostly adenosine
adenosine (A37),
(A37), half-sized
hairpin-like
to form
form full-length
full-length
hairpin-like RNA
RNA molecules
molecules with
with the
the CCA
CCA terminus
terminus might
might have
have been
been ligated
ligated to
Gly
Gly
1
tRNA
[49,50]
(Figure
6a).
A
minihelix
with
the
UCCA-3′
terminus
is
known
to
form
a
structure
in
tRNA
[49,50] (Figure 6a). A minihelix with the UCCA-3 terminus is known to form a structure
1
which
the
3′-sequence
folds
back
[51]
(Figure
6b).
This
is
in
contrast
to
a
minihelix
with
the
ACCA-3′
in which the 3 -sequence folds back [51] (Figure 6b). This is in contrast to a minihelix with the
terminus,
which does
not does
adopt
conformation
[43,51].[43,51].
Glycyl Glycyl
adenylate
could could
have have
been
ACCA-31 terminus,
which
notthis
adopt
this conformation
adenylate
1
produced
prebiotically,
and
the
A
would
be
expected
to
pair
with
the
U
in
the
UCCA-3′
of
been produced prebiotically, and the A would be expected to pair with the U in the UCCA-3 of the
the
minihelix
of the
minihelix [52].
[52]. The
The Gly
Gly residue
residue would
would be
be transferred
transferred to
to the
the OH
OH group
group of
the 3′-terminal
31 -terminal adenosine
adenosine of
of
the
minihelix
because
of
their
close
proximity
in
the
folded-back
structure
(Figure
6b).
The
transfer
the minihelix because of their close proximity in the folded-back structure (Figure 6b). The transfer is
is
thermodynamically
favorable.
thermodynamically favorable.
Figure 5. Evolution of ribosomes and its relation to tRNAs. The CCA end of the minihelix interacts with
the large ribosomal subunit for peptide bond formation, and the end of the other tRNA half interacts
with the small ribosomal subunit for decoding mRNA
5 triplets through codon-anticodon interactions.
1691
Life 2015, 5, page–page
Figure 5. Evolution of ribosomes and its relation to tRNAs. The CCA end of the minihelix interacts with
the5,large
ribosomal subunit for peptide bond formation, and the end of the other tRNA half interacts
Life 2015,
1687–1699
with the small ribosomal subunit for decoding mRNA triplets through codon-anticodon interactions.
Figure
Figure 6.
6. Plausible
Plausible Gly
Gly assignment
assignment in
in the
the primordial
primordial genetic
genetic code.
code. (a)
(a) The
The sequence
sequence of
of the
the full-length
full-length
Gly
1
tRNA
may be
be the
the product
product of
of tandem
tandem ligation
ligation of
of tRNA
tRNA half
half with
with the
the NCCA-3
NCCA-3′ terminus.
terminus. The
The joint
joint
tRNAGly may
1 terminus of
position
corresponds
exactly
to
the
canonical
intron
insertion
point;
and
(b)
the
UCCA-3
position corresponds exactly to the canonical intron insertion point; and (b) the UCCA-3′ terminus of
the
a folded-back
structure.
TheThe
A ofAglycyl
adenylate
would
base pair
the minihelix
minihelix(or
(ortRNA)
tRNA)forms
forms
a folded-back
structure.
of glycyl
adenylate
would
basewith
pair
1 , and nucleophilic attack of 31 -O of the terminal adenosine on the carbonyl carbon of
the
U
in
UCCA-3
with the U in UCCA-3′, and nucleophilic attack of 3′-O of the terminal adenosine on the carbonyl
the
acylof
phosphate
group in glycyl
accomplish
glycylationglycylation
[52].
carbon
the acyl phosphate
groupadenylate
in glycyl would
adenylate
would accomplish
[52].
There is a bias in base distribution at the discriminator base position (position 73), and more than
There is a bias in base distribution at the discriminator base position (position 73), and more
half tRNAs have A at this position; U preceding CCA-31 is not more common. However, eubacterial
than half
tRNAs have A 1 at this position; U preceding CCA-3′ is not more common. However,
tRNAGly has the UCCA-3
terminus (with U73 at the discriminator position), which may indicate
eubacterial tRNAGly has the UCCA-3′ terminus (with U73 at the discriminator position), which may
a vestige of the primordial tRNA. Although the reaction can occur in all amino acids theoretically,
indicate a vestige of the primordial tRNA. Although the reaction can occur in all amino acids
plausible processes of the genetic code formation could be just briefly speculated below, based on the
theoretically, plausible processes of the genetic code formation could be just briefly speculated
features of tRNAGly and the current genetic
code.
below, based on the features of tRNAGly and the current genetic code.
First, in terms of prebiotic formation of aminoacyl adenylate, Gly is the most probable because
First, in terms of prebiotic formation of aminoacyl adenylate, Gly is the most probable because
it is not only the simplest and most abundant amino acid, but also has been shown to be formed
it is not only the simplest and most abundant amino acid, but also has been shown to be formed in
in the conditions of the primitive Earth or even in space [53,54]. Second, in terms of the tRNA
the conditions of the primitive Earth or even in space
[53,54]. Second, in terms of the tRNA
sequences, tRNACys
from all three kingdoms and tRNAGln from the eukaryotic cytoplasm also possess
sequences, tRNACys from all three kingdoms and tRNAGln from the eukaryotic cytoplasm also
U73 [5]. However, Gln and Cys are produced from Glu and Ser, respectively, in biosynthetic pathways
possess U73 [5]. However, Gln and Cys are produced from Glu and Ser, respectively, in biosynthetic
and both Gln and Cys could have been incorporated later in the coevolution theory of the genetic
pathways and both Gln and Cys could have been incorporated later in the coevolution theory of the
code [55,56]. Consistent with this idea, enzymes of aerobic thermophiles contain fewer or even no
genetic code [55,56]. Consistent with this idea, enzymes of aerobic thermophiles contain fewer or
Cys residues [57–60]. In fact, the Cβ -Sγ bond of Cys is easily broken in aerobic and high temperature
even no Cys residues [57–60]. In fact, the Cβ-Sγ bond of Cys is easily broken in aerobic and high
conditions [61]. Furthermore, the possibility that Lys or Arg were introduced first is not ruled out
temperature conditions [61]. Furthermore, the possibility that Lys or Arg were introduced first is not
because they may have added chemical functionality to ribozymes, which required cations. However,
ruled out because they may have added chemical functionality to ribozymes, which required
Lys and Arg are biosynthesized from Asp and Glu, respectively, so they could have been incorporated
cations. However, Lys and Arg are biosynthesized from Asp and Glu, respectively, so they could
later in evolution, similar to Gln and Cys [55,56].
have been incorporated later in evolution,
similar to Gln and Cys [55,56].
The tRNA mutant with the GGA-31 terminus (together with the C2252/C2251 double mutant in
The tRNA mutant with the GGA-3′ terminus (together with the C2252/C2251 double mutant in
23S rRNA) can function in peptidyl transfer [62]. Here, strong hydrogen bonding between G:C pairs
23S rRNA) can function in peptidyl transfer [62]. Here, strong hydrogen bonding between G:C pairs
would be retained in the interaction with the ribosome, but the tRNA with GGA-31 would not form the
would be retained in the interaction with the ribosome, but the tRNA with GGA-3′would not form
folded-back structure anymore. Hence, this mutant could not have been utilized in glycylation using
the folded-back structure anymore. Hence, this mutant could not have been utilized in glycylation
glycyl adenylate.
using glycyl adenylate.
So far, the detection of stereochemical interactions between amino acids and their coding
So far, the detection of stereochemical interactions between amino acids and their coding
nucleotides has not been fully successful and the results are inconclusive [63–68]. Therefore, the
nucleotides has not been fully successful and the results are inconclusive [63–68]. Therefore, the
genetic code may have evolved from the assignment of Gly in the process beyond a strict frozen
genetic code may have evolved from the assignment of Gly in the process beyond a strict frozen
accident [52].
accident [52].
6. Origins of the Ribosome PTC and tRNA
The PTC is composed of only RNA molecules with the closest proteins detected approximately
18 Å away [47,69], which clearly suggests that the6ribosome is a ribozyme [70]. The CCA termini of
1692
Life 2015, 5, page–page
6. Origins of the Ribosome PTC and tRNA
The PTC is composed of only RNA molecules with the closest proteins detected approximately
18 Å away [47,69], which clearly suggests that the ribosome is a ribozyme [70]. The CCA termini of
two tRNA molecules specifically interact with domain V of 23S rRNA, assembling the central part of
two
tRNAwhere
molecules
specifically attack
interactofwith
domain Vgroup
of 23SofrRNA,
assembling on
thethe
central
part
the PTC,
the nucleophilic
the α-amino
aminoacyl-tRNA
carbonyl
of
the
PTC,
where
the
nucleophilic
attack
of
the
α-amino
group
of
aminoacyl-tRNA
on
the
carbonyl
carbon of peptidyl-tRNA leads to the formation of a peptide bond [47]. A simple model system has
carbon
of peptidyl-tRNA
to the
formation
of a peptide
bond [47].[71].
A simple model system has
also proved
the occurrenceleads
of this
reaction
and validated
its chemistry
also proved
occurrence
of this
reaction
and
validated
itsribosomal
chemistrysubunits
[71].
Crystal the
structures
of both
bacterial
and
archaeal
large
clearly show that two
Crystal
structures
of
both
bacterial
and
archaeal
large
ribosomal
subunits
clearly
show that
L-shaped RNA units similar in size to tRNA form a symmetrical pocket [72,73] (Figure
7). two
The
L-shaped
similar in
sizeistolikely
tRNAassociated
form a symmetrical
[72,73]
7). The
structure
structure RNA
of theunits
primordial
PTC
with the pocket
formation
of (Figure
the peptide
bond.
Two
of
the primordial
PTC is likely
associatedcould
with have
the formation
of the
Two L-shaped
RNAs
L-shaped
RNAs placed
symmetrically
functioned
as apeptide
scaffoldbond.
for proper
positioning
of
placed
have functioned
as a scaffold
for proper of
positioning
the two reactant
the twosymmetrically
reactant RNAcould
molecules
[44,72,73] (Figure
7). Duplication
half-sizedofhairpin-like
RNA
RNA
molecules
(Figure some
7). Duplication
half-sized and,
hairpin-like
RNAcould
molecules
molecules
might[44,72,73]
have produced
tRNA-likeofstructures
ultimately,
have might
formedhave
the
produced
some
tRNA-like
structures
and,
ultimately,
could
have
formed
the
PTC.
In
addition,
other
PTC. In addition, other tRNA-like molecules could have evolved to function as “adaptors.” The
tRNA-like
have
evolved to association
function as of
“adaptors.”
The proto-PTC
may peptide
have assisted
proto-PTCmolecules
may havecould
assisted
symmetrical
the two CCA
units, favoring
bond
symmetrical
association of the two CCA units, favoring peptide bond formation [44,72,73].
formation [44,72,73].
In the
translational
system,
the distance
between
the CCA
and tRNAand
anticodon
themodern
modern
translational
system,
the distance
between
theterminus
CCA terminus
tRNA
(~75
Å) (Figure
1) is
quite important
ensure the
perfect the
alignment
both structures
the
anticodon
(~75 Å)
(Figure
1) is quite to
important
to ensure
perfect of
alignment
of both within
structures
ribosome.
L-shape
ofL-shape
tRNA isof
also
required
the interaction
with protein
factors
at each
step
within the The
ribosome.
The
tRNA
is alsofor
required
for the interaction
with
protein
factors
at
of
thestep
ribosomal
[74]. Therefore,
L-shapethe
of modern
must be
retained.
in the
each
of the cycle
ribosomal
cycle [74]. the
Therefore,
L-shape tRNA
of modern
tRNA
must Then,
be retained.
transition
of the
proto-ribosomes
to modern ribosomes,
proteins
must have
takenmust
the functional
place
Then, in the
transition
of the proto-ribosomes
to modern
ribosomes,
proteins
have taken
the
of
RNA,
as
evidenced
by
release
factors
that
mimic
tRNA
structure
[75,76].
functional place of RNA, as evidenced by release factors that mimic tRNA structure [75,76].
Life 2015, 5, 1687–1699
Figure 7.
7. A putative
putative mechanism
mechanism of symmetrical
symmetrical primordial PTC formation. (a)
(a) The central loop of
domain V in 23S rRNA forms
forms aa symmetrical
symmetrical pocket.
pocket. The
core
unit
structures
from the Haloarcula
Haloarcula
The
angles, complexed with
marismortui 50S subunit (PDB code: 1VQN)
1VQN) are shown at two different angles,
1 -end. The
substrates mimicking the tip of tRNA 33′-end.
The AA- and
and P-core units are shown as blue and green
spheres, respectively
respectively[73];
[73];(b)
(b)the
theP-core
P-core
unit
overlaps
well
with
tRNA
(yellow;
1EHZ);
spheres,
unit
overlaps
well
with
tRNA
(yellow;
PDBPDB
code:code:
1EHZ);
and
and
(c)
comparison
of
the
shapes
of
the
P-core
unit,
A-core
unit,
and
tRNA
after
appropriate
rotation.
(c) comparison of the shapes of the P-core unit, A-core unit, and tRNA after appropriate rotation.
7. Evolution
7.
Evolutionof
ofthe
theGenetic
GeneticCode
Codeand
andtRNA
tRNA
Rodin and
and Ohno
Ohno have
have suggested
suggested the
the process
process of
of short
short RNA
RNA extension
extension to
to the
the modern
modern tRNA-like
tRNA-like
Rodin
cloverleaf
[77].
The
11
base
pair-long
double-stranded
palindrome
with
complementary
triplets in
in
cloverleaf [77]. The 11 base pair-long double-stranded palindrome with complementary triplets
1
1
the
center,
each
flanked
by
NCCA-3′
and
5′-UGGN,
can
replicate
into
a
similar
25
base
pair-long
the center, each flanked by NCCA-3 and 5 -UGGN, can replicate into a similar 25 base pair-long
palindrome with
with aa complementary
complementary triplet
triplet in
in the
the middle,
middle, after
after the
the addition
addition of
of the
the folded-back
folded-back triplet
triplet
palindrome
hook.
Then,
self-templating
elongation
of
both
palindromes
should
result
in
the
formation
of
two
hook. Then, self-templating elongation of both palindromes should result in the formation of two
1
1
helices
with
internal
complementary
triplets.
Finally,
the
removal
of
5′-UGGN
from
the
5′-terminus
helices with internal complementary triplets. Finally, the removal of 5 -UGGN from the 5 -terminus
produces the
themodern
moderntRNA-like
tRNA-like
cloverleaf.
In this
process,
an intermediate
hairpin
in the
produces
cloverleaf.
In this
process,
an intermediate
hairpin
placesplaces
in the center
a single-stranded triplet (plausible anticodon), which might represent the original anticodon-codon
7
pair at the 1-2-3 positions of current tRNAs [77].
1693
Life 2015, 5, page–page
center a single-stranded triplet (plausible anticodon), which might represent the original
anticodon-codon pair at the 1-2-3 positions of current tRNAs [77].
Ala has a unique G3U70 base pair in the acceptor stem, and the wobble base pair has been
tRNA
Life 2015,
5, 1687–1699
shown to be a critical recognition site by AlaRS [78,79]. If the modern tRNA-aaRS system has
evolved from the primordial tRNA-aaRS system, the primordial genetic code should have resided
Ala has a unique G3U70 base pair in the acceptor stem, and the wobble base pair has been
in thetRNA
minihelix
region and the recognition domain should have been also located in the primitive
shown
to be a the
critical
recognitionof
site
AlaRS [78,79].
If code.
the modern
tRNA-aaRS
system
has evolved
aaRSs, before
establishment
thebyuniversal
genetic
From this
standpoint,
G3U70
may be
from
the of
primordial
tRNA-aaRS
the primordial
genetic
code should
have
resided
in and
the
a vestige
the primordial
geneticsystem,
code, which
may be called
“operational
RNA
code”
[13,14]
minihelix
region
and
the
recognition
domain
should
have
been
also
located
in
the
primitive
aaRSs,
is thought to precede the universal genetic code referred to by de Duve as “the second genetic
before
the establishment of the universal genetic code. From this standpoint, G3U70 may be a vestige
code” [80].
of theThe
primordial
code,
which
may be called
“operational
RNA code”bases
[13,14]
is thought
to
n (where
number genetic
of possible
RNA
sequences
composed
of four nucleotide
is 4and
n is the
precede
the
universal
genetic
code
referred
to
by
de
Duve
as
“the
second
genetic
code”
[80].
number of nucleotides). In terms of genuinely mathematical estimation without any consideration of
The number
of possible
RNA
sequences
of four nucleotide
bases chain
is 4n (where
is the
functional
frequency,
the total
mass
neededcomposed
for the formation
of nucleotide
of the nlength
number
of
nucleotides).
In
terms
of
genuinely
mathematical
estimation
without
any
consideration
of
similar to that of modern tRNA (~76 nucleotides) would be around ¹⁄₂₅th of the total mass of the
functional
frequency,
the
total
mass
needed
for
the
formation
of
nucleotide
chain
of
the
length
similar
Earth. However, for half-tRNA (~35 nucleotides), the required mass would be at most 100 to
g,
1{25 th of the total mass of the Earth. However,
that
of modern
tRNA (~76
nucleotides)
would
be around
suggesting
plausibility
of the
formation
of modern
tRNAs
via ligation of two half-sized hairpin-like
for
half-tRNA
(~35
nucleotides),
thestudies
required
wouldofbethe
at most
g, suggesting
plausibility
of
RNA
molecules
(Figure
8). Several
onmass
the origin
tRNA100
molecule,
including
statistical
the
formation
of
modern
tRNAs
via
ligation
of
two
half-sized
hairpin-like
RNA
molecules
(Figure
8).
analysis, also indicate that most tRNA sequences have vestiges of double-hairpin duplication [81–
Several
studies
on the origin
of the tRNA
statistical
analysis,
indicate
84]. Pairing
between
the acceptor
stem molecule,
bases andincluding
anticodon
stem/loop
bases also
in the
5′-halfthat
andmost
the
tRNA
sequences
have
vestiges
of
double-hairpin
duplication
[81–84].
Pairing
between
the
acceptor
3′-half molecules of tRNAs fit the double hairpin folding. Helices can be formed by the acceptor
stem
anticodon
stem/loop
in thestem/loop
51 -half and
the 31(N26–N34),
-half molecules
fit the
stem bases
regionand
(mainly
N1–N8)
and the bases
anticodon
region
and of
bytRNAs
the acceptor
double
hairpin
folding.
Helices
can
be
formed
by
the
acceptor
stem
region
(mainly
N1–N8)
and
the
stem region (N66–N73) and the anticodon stem/loop with extra loop region (N39–N47); they should
anticodon
stem/loop
region
(N26–N34),
and
by
the
acceptor
stem
region
(N66–N73)
and
the
anticodon
be located near or on the retained D- or T-stem/loop [82]. This fact strongly suggests that the double
stem/loop
with extra
region (N39–N47);
they should
be located
near ortoonthe
themodern
retainedtRNA
D- or
hairpin formation
in loop
the ancient
prebiotic world
underlies
the evolution
T-stem/loop
[82].
This
fact
strongly
suggests
that
the
double
hairpin
formation
in
the
ancient
prebiotic
structure (Figures 1 and 8).
worldThus,
underlies
the evolutionfull-length
to the modern
tRNA
structure
(Figures
andformed
8).
the contemporary
tRNA
molecules
could
have 1been
by the ligation of
Thus,
the
contemporary
full-length
tRNA
molecules
could
have
been
formed
by the ligation
half-sized hairpin-like RNA structures (Figure 8). In the evolution of codon assignments,
it of
is
half-sized
hairpin-like
RNA
structures
(Figure
8).
In
the
evolution
of
codon
assignments,
it
is
important
important to minimize the effects of mutations, i.e., similar amino acids are assigned in close
to
minimize
the
of mutations,
amino
acids are
assigned
in close
positions
[85]. Gly
If
positions
[85].
If effects
half-sized
tRNA withi.e.,
thesimilar
UCCA-3′
terminus
is the
ancestral
molecules
of tRNA
1 terminus is the ancestral molecules of tRNAGly (Figure 6a), Gly
half-sized
tRNA
with
the
UCCA-3
Gly
(Figure 6a), Gly might be a strong candidate for the first piece of the genetic code [52,86] and tRNA
might
a strongacandidate
first piecetRNA.
of the In
genetic
code [52,86]
and tRNAGly
might represent
might be
represent
vestige offor
thethe
primordial
this picture,
Gly-containing
primitive
peptides
a
vestige
the primordial
tRNA. In this
picture,
Gly-containing
primitive
peptides
have
could
haveofpreceded
the protein-based
evolution
of life.
β-turns stabilized
by β-sheets
arecould
thought
to
preceded
the
protein-based
evolution
of
life.
β-turns
stabilized
by
β-sheets
are
thought
to
be
plausible
be plausible active sites of early enzymes [87], and Gly together with Pro are often present in β-turns
active
sitesPro
of early
enzymes
[87], and
Gly together
with Pro are
often present
in β-turns
[68,88,89].
[68,88,89].
has also
been shown
to destruct
the G-quartet
structure,
and NGG
(the anticodon
of
Pro )
Pro
Pro
has
also
been
shown
to
destruct
the
G-quartet
structure,
and
NGG
(the
anticodon
of
tRNA
tRNA ) may have been involved in the establishment of the genetic code through Pro-dependent
may
have been
involved in the establishment
of the genetic
code through
G-quartet
formation/destruction
[68]. Interestingly,
G-quadruplex
motifsPro-dependent
are found at G-quartet
both the
formation/destruction
[68]. Interestingly,
motifs
are3′-termini
found at both
the 51 -termini
of
5′-termini of 5′-untranslated
regions and G-quadruplex
immediately after
the
of coding
sequences,
1 -untranslated regions and immediately after the 31 -termini of coding sequences, suggesting their
5
suggesting their important role in translation as well as transcription [90]. In addition,
important
role in
translation
as well astotranscription
[90]. In
addition,
hasformation
been suggested
G-quadruplex
has
been suggested
be a primordial
scaffold
forG-quadruplex
peptide bond
using
to
be a primordial scaffold
for peptide bond formation using aminoacyl-tRNAs [91].
aminoacyl-tRNAs
[91].
Figure 8. The double-hairpin model of tRNA formation. The acceptor stem bases and anticodon
Figure 8. The double-hairpin model of tRNA formation. The acceptor stem bases and anticodon
stem/loop bases in tRNA 5′-half and 3′-half fit the double-hairpin folding, suggesting that the
stem/loop bases in tRNA 51 -half and 31 -half fit the double-hairpin folding, suggesting that the
8 evolved to the structure of modern tRNA [81,82].
primordial double-hairpin RNA molecules could have
The anticodon is adjacent to the “D-hairpin” [82].
1694
Life 2015, 5, 1687–1699
Hydrophobic binding energy of a methylene group is about 1 kcal/mol, and the probability of an
amino acid to be replaced by another one with additional methylene group would be about 1{5 [92].
Although modern aaRSs achieve strict discrimination between these two different amino acids using
editing mechanisms (error rate as low as 1{40, 000 [93]), a simple thermodynamic process alone makes
it impossible to discriminate with such a high fidelity. Therefore, the primordial genetic code could
have been non-selective for several sets of amino acids with similar side chains. Gly (and also Ala,
a similar amino acid with an additional methylene group) and Pro might have been the first candidates
assigned by the primordial genetic code [52,68]. Strict discrimination could have evolved with the
development of a biosynthetic system for amino acids and an editing mechanism involving aaRSs.
8. Concluding Remarks
After the discovery of tRNA by Zamecnik, Crick refused to believe that it was indeed the adaptor
since the size was much bigger than he had expected. In fact, tRNA could have originated from a
smaller-sized RNA. However, the question remains as to whether the minihelix is the real progenitor
of modern tRNA. Probably, the most primitive tRNA was composed of oligonucleotides similar in size
to that proposed by Rodin and Ohno [77]. What is the real origin of the genetic code? What happened
during the evolution of the full-length tRNA from a primitive tRNA? These are still critical issues that
should be further investigated.
Acknowledgments: I would like to thank Koichi Ito for the valuable comments on the manuscript and support
in the assembly of the figures, and Satoshi Akanuma for helpful discussions. This work was supported by the
Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology
(MEXT), Japan (Grant No. 25291082).
Conflicts of Interest: The author declares no conflict of interest.
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