Anticipating
alien
cells
with
alternative
genetic
codes:
away
from
the
alanine
world!
Vladimir
Kubyshkin
1,2
and
Nediljko
Budisa
1,2
Can
we
make
life
with
a
different
genetic
amino
acid
repertoire?
Can
we
expect
organisms
which
would
keep
newly
given
genetic
code
associations
permanently?
To
address
these
questions,
we
would
like
to
analyze
the
existent
genetic
code
amino
acid
repertoire
as
formed
from
derivatives
of
alanine.
Derivation
from
alanine
leads
to
the
a-helix
based
biological
world,
the
Alanine
World,
whereas
variations
in
the
side-chains
enable
tertiary
folding
and
subsequent
chemical
versatility
of
the
proteome.
Proline,
glycine
and
pyrrolysine
are
the
rudiments
in
the
current
genetic
code,
indicating
that
the
original
set
could
be
different.
Furthermore,
from
the
perspective
of
peptide
chemistry,
it
shall
be
possible
to
recruit
these
alternative
scaffolds
for
the
construction
of
synthetic
or
alternative
life.
This
would
allow
for
a
completely
new
biological
world,
potentially
as
functional
and
versatile
as
the
existing
one.
Pursuing
these
options
offers
a
strategy
for
a
complete
re-
design
or
even
de-novo
creation
of
living
organisms
based
on
entirely
different
chemical
make-up,
with
completely
new
set
of
solutions
for
both
near
and
distant
future
biotechnologies.
Addresses
1
Institute
of
Chemistry,
Technical
University
of
Berlin,
Mu
¨ller-Breslau-
Str.
10,
Berlin
10623,
Germany
2
Department
of
Chemistry,
University
of
Manitoba,
Dysart
Rd
.144,
Winnipeg
R3T
2N2,
Manitoba,
Canada
Corresponding
authors:
Kubyshkin,
Vladimir
(vladimir.
Budisa,
Nediljko
(nediljko.budisa@tu-berlin.
de,
Current
Opinion
in
Biotechnology
2019,
60:242–249
This
review
comes
from
a
themed
issue
on
Chemical
biotechnology
Edited
by
Sven
Panke
and
Thomas
Ward
For
a
complete
overview
see
the
Issue
and
the
Editorial
Available
online
3rd
July
2019
https://doi.org/10.1016/j.copbio.2019.05.006
0958-1669/ã
2019
The
Authors.
Published
by
Elsevier
Ltd.
This
is
an
open
access
article
under
the
CC
BY-NC-ND
license
(http://creative-
commons.org/licenses/by-nc-nd/4.0/).
“We
are
about
to
win
chemical
influence
on
the
design
of
the
organism,
and
this
should
lead
to
the
strangest
phenomena,
to
changes
in
shape,
which
leave
everything
behind,
what
has
been
achieved
by
breeding
and
crossing.”
Emil
Fischer,
1890
[1].
Introduction
Life
on
Earth
is
a
reservoir
of
evolutionary
and
adaptive
innovations,
which
accumulated
over
time.
In
order
to
understand,
manipulate
and
engineer
it,
we
need
to
formulate
the
basic
principles
governing
it,
and
rational-
ize
relationships
between
the
principal
components
of
life
biochemistry.
We
are
particularly
interested
in
the
chem-
ical
identity
of
living
systems,
represented
by
the
basic
chemical
composition
of
the
biochemical
components.
Among
these,
the
main
focus
of
attention
is
given
to
the
biopolymeric
scaffolds,
nucleic
acids
and
polypeptides.
The
transition
between
these
two
biopolymeric
levels
or
‘worlds’
occurs
according
to
the
central
dogma
of
molec-
ular
biology
(Figure
1),
which
has
been
formulated
as
follows:
“The
Central
Dogma
states
that
once
‘information’
has
passed
into
protein
it
cannot
get
out
again.
In
more
detail,
the
transfer
of
information
from
nucleic
acid
to
nucleic
acid
or
from
nucleic
acid
to
protein
may
be
possible,
but
transfer
from
protein
to
protein,
or
from
protein
to
nucleic
acid
is
impossible”
[2].
On
the
basis
of
the
Central
Dogma,
the
nucleic
acids
are
mainly
viewed
as
informational
polymers,
whereas
the
interpretation
of
this
information
occurs
at
the
level
of
the
proteins,
where
amino
acid
sequences
fold
into
func-
tional
protein
bodies.
The
hierarchy
of
the
biopolymer
scaffolds
immediately
suggests
that
the
manipulation
with
the
life
systems
can
be
performed
on
two
levels:
nucleic
acids
(genes)
and
proteins.
Manipulation
of
the
informa-
tional
elements,
genes,
is
a
particular
goal
of
synthetic
biology,
as
a
method
towards
new
biological
species
[3].
The
exchange
and
spread
of
the
genetic
information
also
occur
naturally
in
the
course
of
horizontal
and
vertical
gene
transfers,
which
effectively
connects
the
living
species
on
Earth
into
a
large
communication
network
[4].
Transfer
of
the
genetic
information
between
species
is
an
important
mechanism,
which
allows
biological
species
to
gain
new
functions
and
innovations
from
across
the
biosphere.
None-
theless,
this
mechanism
is
based
on
the
common
set
of
chemical
building
block
elements,
a
universal
set
of
chem-
ical
bases:
polymeric
scaffolds,
nucleobases
[5,6],
amino
acid
side
chains,
and
so
on.
It
has
been
hypothesized
that
redesign
or
expansion
of
this
set
can
provide
an
alternative
way
towards
chemical
innovations,
thereby
forming
new
species
with
an
alternative
chemical
identity
[7
].
Over
the
past
few
decades,
a
large
progress
has
been
made
towards
manipulations
with
the
set
of
20(+3)
canonical
Available
online
at
www.sciencedirect.com
ScienceDirect
Current
Opinion
in
Biotechnology
2019,
60:242–249
www.sciencedirect.com
(coded)
amino
acids.
Nowadays,
it
is
almost
routinely
possible
to
perform
a
single
protein
expression
in
vivo
with
the
amino
acid
building
blocks
well
beyond
the
canonical
ones
[8
].
This
multitude
of
possibilities
is
even
greater
for
in
vitro
protein
translation
assays,
as
these
allow
a
relatively
free
redefinition
of
the
genetic
code
set
[9,10].
However,
the
currently
available
methods
and
approaches
to
emancipate
or
re-assign
the
meaning
of
codons
in
an
entire
living
(microbial)
organisms
are
still
in
the
infancy
stage
of
development.
Redesign
of
the
amino
acid
compo-
sition
on
the
proteome
level
requires
application
of
a
pressure
to
organisms.
The
desired
pressure
is
usually
created
experimentally
either
by
constructing
a
stringent
genetic
set-up
[11
,12
,13
]
or
through
long-term
cultiva-
tion
in
gradually
changing
supply
medium
(so-called
adap-
tive
laboratory
evolution)
[14
],
or
both.
In
this
way,
aromatic
amino
acids
such
as
para-acetylphenyl-alanine
or
biphenyl-alanine
or
thienopyrrolyl-alanine
have
been
appended
to
the
canonical
amino
acid
repertoire
in
geneti-
cally
modified
Escherichia
coli
organisms.
Although
these
achievements
are
impressive,
we
never-
theless
believe
that
they
need
to
be
critically
scrutinized,
not
by
questioning
the
rigor
of
the
experimental
genetic
setup,
but
the
concept
itself.
The
main
efforts
in
this
research
field
are
aimed
at
generating
genetically
encoded
side-chain
modifications
with
minimal
distur-
bance
in
local
microenvironments
for
interesting
aca-
demic
questions
or
simple
technological
solutions
[15,16].
However,
in
order
to
provide
a
solid
basis
for
the
design
of
synthetic
life
based
on
radically
different
chemical
makeup,
the
experiments
should
be
designed
so
that
a
newly
introduced
amino
acid
should
provide
an
advantage
to
the
synthetic
cells.
Ideally,
they
should
provide/endow
them
with
new
chemical
functions
and
processes
accompanied
with
a
complete
redesign
of
the
proteome
architecture.
To
this
end,
we
would
like
to
offer
a
simple
retrospective
view
on
the
genetic
code,
and
formulate
a
strategic
alternative
to
the
existing
canonical
amino
acid
repertoire.
At
the
core
of
our
argument,
we
want
to
emphasize
that
most
of
the
canonical
amino
acids
are
derivatives
of
alanine,
and
in
this
sense,
we
are
living
in
the
Alanine
World.
We
believe
that
alternative
potential
scenarios,
Worlds,
can
provide
strategic
solutions
for
the
biotechnology
of
the
distant
future,
enabling
entirely
alienated
life
in
a
test
tube.
Molecular
evolution
and
development
of
the
genetic
code
Let
us
make
a
little
journey
back
in
the
history.
The
emergence
of
protein
biosynthesis
and
the
parallel
devel-
opment
of
the
genetic
code
was
the
key
event
in
evolution
of
life
as
we
know
it.
This
is
due
to
the
fact
that
the
genetic
code
assigns
nucleic
acids
with
their
amino
acid
‘meanings’,
thus
enabling
genetic
development,
and
this
is
also
track-
able
by
phylogenetic
analysis
[17
].
The
hypothesis
of
the
RNA
World
directly
follows
from
the
central
dogma
[18,19
]
(Figure
1).
According
to
this
hypothesis,
RNA
molecules
were
the
functional
molecular
entities
in
the
early
phase
of
the
development
of
life
comprising
the
RNA
World,
whereas
the
emergence
of
protein
biosynthesis
lead
to
the
outbreak
of
the
Protein
World.
The
ancestor
molecules
to
those
known
as
tRNA
had
associations
with
particular
amino
acids
which
were
established
beforehand,
while
the
original
amino
acyl-RNA
were
either
cofactors
or
metabolic
components
for
biosynthetic
purposes
[20,21].
Already
followingfrom
this
simple
picture,onecanimagine
that
few
amino
acids
were
inevitably
present
in
the
RNA
attached
form,
and
these
were
available
for
use
in
transla-
tion.
Glycine
and
aspartic
acid
bear
carbon-skeletons,
which
are
metabolic
precursors
for
nucleobases,
serine
is
a
metabolic
precursor
of
glycine
and
pteridine-bound
C1-
units
(which
were
also
available
through
ancient
C1-metab-
olism),
alanine
is
a
simplest
carrier
of
nitrogen
required
for
nucleobase
synthesis
and
so
on.
Thus,
one
can
find
simple
and
easy
metabolic
justification
for
the
biochemical
occur-
rence
of
amino
acids
before
the
protein
biosynthesis
has
started.
Perhaps,oneoftheweirdest
initial
components
was
proline,
which
is
a
cyclic
amino
acid,
devoid
of
side-chain
functional
groups.
However,
one
should
not
be
distracted
by
the
simplicity
of
this
structure.
Proline,
in
fact,
may
be
attributed
a
very
special
role,
since
its
amine-functional
group
is
an
efficient
catalyst
in
reactions
known
as
conden-
sation
reactions.
Catalyzed
condensations
along
with
trans-
aldolase/ketolase
reactions
are
essential
sources
for
sugars,
the
backbone
entities
of
RNA
biopolymers.
Thus,
a
primi-
tive
Pro-tRNA
ester
could
have
served
the
role
of
a
catalytic
center;
otherwise
this
was
a
part
of
a
catalytic
cascade
for
sugar
metabolism
[22].
Subsequently,
the
synthesis
of
proline
would
require
its
metabolic
precursors,
either
glu-
tamic
acid
or
ornithine,
the
latter
is
also
direct
precursor
for
arginine,
a
component
of
the
existing
genetic
code.
Thereby,
proline
and
its
precursors
may
have
been
avail-
able
before
the
advent
of
protein
biogenesis.
Synthetic
life
with
alternative
genetic
codes
Kubyshkin
and
Budisa
243
Figure
1
transcription
RNA World Protein World
reverse
transcription
translation
replication
Life evolution:
(ribozymes doing catalysis) (enzymes doing catalysis)
DNA RNA Proteins
Current Opinion in Biotechnology
The
central
dogma
of
molecular
biology
states
there
is
solely
a
unidirectional
flow
of
information
in
living
systems.
The
RNA
World
hypothesis
logically
follows
from
the
central
dogma.
www.sciencedirect.com
Current
Opinion
in
Biotechnology
2019,
60:242–249
Following
the
Frozen
Accident
theory
of
Crick
[23],
protein
biosynthesis
started
with
an
original
set
of
amino
acids
and
was
expanding
its
repertoire
until
the
point
when
further
recruitment
would
generate
too
many
detrimental
problems.
Although,
there
are
different
theories,
hypoth-
eses
and
opinions
on
how
the
amino
acid
repertoire
was
expanding,
we
are
particularly
attracted
by
the
concept
proposed
recently
by
Hartman
and
Smith
[24
,25,26
].
According
to
the
proposed
scenario,
the
original
set
was
restricted
only
to
codons
containing
GC
letters.
Further
expansion
of
the
repertoire
required
recruitment
of
addi-
tional
nucleobases,
and
subsequently
the
letter
A
was
recruited,
followed
by
the
U
letter.
The
elegance
of
the
GC-GCA-GCAU
scheme
is
that
it
can
be
easily
correlated
to
the
hierarchy
of
protein
folding
[27]
(Figure
2)
as
well
as
with
the
metabolic
significances
of
the
initial
amino
acids
listed
above.
The
original
amino
acid
set
coded
by
GC
contained
glycine,
alanine,
proline,
and
one
cationic
amino
acid
(now:
arginine),
the
amino
acids
needed
for
the
nucleotide
biosynthesis.
From
the
folding
perspective
though,
polypeptides
based
on
this
set
would
be
dominated
by
extended
and
relatively
low
stable
structures,
and
subsequently
would
be
maily
dis-
ordered.
However,
these
would
already
be
able
to
adhere
to
polyanionic
RNA
molecules
due
to
the
positive
net
charge
provided
by
the
cationic
amino
acids.
In
the
next
phase,
the
addition
of
the
A-letter
allowed
the
acquisition
of
a
number
of
polar
amino
acids.
The
GCA-phase
enabled
the
formation
of
the
a-helix,
the
most
important
secondary
structure
motif
in
common
biochemistry.
For-
mation
of
tertiary
structure
and
the
membrane
interaction
was
made
possible
in
the
next
GCAU-phase,
after
the
addition
of
the
U
letter
allowed
recruitment
of
hydropho-
bic
amino
acids.
The
late
addition
of
hydrophobic
amino
acids
can
be
proposed
to
arise
from
the
high
metabolic
complexity
and
costs
of
their
biosynthesis.
Thus,
the
recruitment
of
the
RNA
letters
built
the
coding
space
of
mRNA,
while
the
amino
acid
counterparts
were
acquired
from
metabolic
sources.
Coevolution
of
these
two
components
built
up
the
genetic
code
[28].
The
sequence
of
amino
acid
recruitment
correlates
well
with
the
complexity
of
their
metabolic
synthesis:
while
the
first
wave
of
evolutionary
genetic
code
expansion
(GCA
phase)
has
acquired
the
amino
acids
that
are
only
a
few
steps
away
from
the
core
metabolism,
the
acquisition
of
the
amino
acids
in
the
GCAU
expansion
wave
required
development
of
more
complex
biosynthetic
pathways.
From
this,
it
can
be
speculated
that
the
metabolic
availability
of
the
amino
acids
played
a
key
role
in
the
development
of
protein
biogenesis.
This
statement
can
be
explained
by
the
fact
that
the
genetic
code
contains
tyrosine
(
para-hydroxyphenylalanine),
but
does
not
contain
g-hydroxyproline,
which
is
just
as
abundant
in
modern
biochemistry.
Simple
metabolic
considerations
suggest
that
hydroxylation
in
the
g-posi-
tion
in
the
proline
residue
occurs
in
nature
by
oxidation
with
molecular
oxygen
[29],
a
molecular
species
absent
in
the
genetic
code
formation
phase
[30].
At
the
same
time,
tyrosine
biosynthesis
does
not
require
oxidation
with
oxygen,
as
this
amino
acid
can
be
derived
directly
from
prephenate,
a
common
precursor
for
tyrosine
and
phenylalanine.
244
Chemical
biotechnology
Figure
2
available AA-RNA
structure
primary:
secondary:
tertiary: no no
shortcut possible!
GC-phase GCA-phase GCAU-phase
globular fold
transmembrane elements
in formation
extended structures, unstructured
polyproline-II, β-stranded
α-helix, β-sheet
defined defined
defined
transmembrane polyproline helix
Gly, Ala, Orn (Arg), Pro
(backbone-forming)
Asp, Glu, Gln, Asn,
Thr, Ser, His
(polar)
Met, Leu, Val,
Ile, Phe, Tyr, Trp
(hydrophobic)
Lys, Cys
core metabolism complex metabolism
growth of the amino acid repertoire
Protein World
(Alanine
World)
RNA World
Current Opinion in Biotechnology
The
GC-GCA-GCAU-scheme
of
the
genetic
code
development
as
summarized
by
Hartman
and
Smith
with
chemical
interpretation.
The
polypeptide
structure
complexity
and
the
amino
acid
metabolic
complexity
increase
from
earlier
to
later
phases.
Current
Opinion
in
Biotechnology
2019,
60:242–249
www.sciencedirect.com
The
Alanine
World
and
its
alternatives
From
the
perspective
of
peptide
science,
the
set
of
the
first
amino
acids,
glycine,
proline,
alanine
and
one
cat-
ionic
species
should
generate
a
rather
undefined
poly-
peptide
backbone
folding,
dominated
by
extended
con-
formations.
However,
from
this
point
further
expansion
of
the
genetic
code
repertoire
went
solely
into
the
direction
of
structural
derivatives
of
alanine.
Not
a
single
non-
alanine
based
amino
acid
was
recruited
into
the
protein
biosynthesis
after
the
adoption
of
alanine
as
the
preferred
motif.
For
example,
a
phenyl-group
containing
amino
acid
in
the
genetic
code
repertoire
is
phenylalanine,
and
not
phenylglycine,
phenylproline
or
phenyllysine.
From
this
point
of
view,
the
existent
Protein
World
should
rather
be
called
the
Alanine
World.
Very
important
feature
of
alanine
is
the
fact
that
this
amino
acid
residue
exhibits
the
greatest
a-helical
propensity
[31,32].
We
thus
would
like
to
outline
the
following
key
attributes
of
the
Alanine
World:
1)
the
polypeptide
structure
is
chiral
as
follows
from
chirality
of
the
L-building
blocks;
2)
the
amino
acid
building
blocks
have
a
backbone
(alanine)
part
and
the
side-chain
function;
therefore,
point
mutations
usually
do
not
impact
the
backbone
fold,
but
change/alter
the
chemical
function;
3)
the
chemical
function
is
close
to
the
backbone;
therefore,
accumulation
of
the
mutations
can
impact
the
secondary
structure;
4)
the
backbone
is
capable
of
donating
and
accepting
the
hydrogen
bond;
therefore,
the
proteome
is
dominated
by
the
hydrogen-
bond
based
structures;
among
them
a-helix
is
the
most
common.
These
attributes
provide
an
empirical
basis
for
any
experiment
in
protein
engineering.
However,
one
should
clearly
realize
they
are
essentially
derived
from
the
fact
that
the
most
canonical
amino
acids
are
structur-
ally
derived
from
alanine.
For
example,
‘alanine
scan’
is
the
common
approach
in
biochemical
science
that
fully
relies
on
attribute
2),
and
it
often
fails
when
approaching
glycine
or
proline,
since
these
amino
acids
do
not
share
same
alanine-based
backbone
architecture.
The
Alanine
World
features
are
so
common,
that
they
usually
remain
unnoticed
unless
these
are
addressed
in
the
frame
of
peptide
studies
with
radically
different
chemical
alternatives.
Nonetheless,
from
the
chemical
standpoint,
the
Alanine
World
is
not
the
only
way
in
which
a
peptide
scaffold
can
be
decorated
with
a
rich
number
of
functional
elements.
Each
of
the
starting
amino
acids
can
propose
its
own
alternative
development
of
the
protein
chemistry
as
schematically
illustrated
on
Figure
3.
Especially
rich
is
proline-based
peptide
chemistry.
Substitutions
based
on
the
core
structure
of
proline
lead
to
scaffolds
able
to
adopt
extended
polyproline-II
helix,
which
is
also
a
generic
secondary
structure
allowed
for
other
a-amino
acids
[33].
In
the
Alanine
World
the
polyproline-II
extended
helix
is
obscured
due
to
the
competition
with
more
stable
hydrogen-bonded
structures.
However,
this
is
one
of
the
dominant
structures
in
the
so-called
‘disordered’
or
‘denatured’
state
[34],
as
well
as
in
the
initial
proteome
in
the
GC-phase
(Figure
2).
Construction
of
polyproline-II
structures
based
on
proline
analogues
creates
a
rather
stable
secondary
fold.
Polyproline-II
folded
peptideshave
already
demonstrated
their
ability
to
interact
with
nucleic
acids
[35
],
secondary
messengers
[36],
and
membranes
[37,38].
Conversely,
assembly
of
polyproline-II
helices
into
colla-
gen
triple
helix
has
been
explored
by
nature,
and
this
is
triggered
by
post-translational
hydroxylation
of
proline
residues
in
procollagen
[39].
Alternatively,
the
assembly
of
polyproline
helices
into
bundles
has
been
recently
described
for
antifreeze
proteins
[40,41].
Until
very
recently
it
was
not
clear
whether
the
polypro-
line-II
helix
could
feature
in
hydrophobic
sequences,
since
the
extended
nature
of
this
structure
usually
favors
water
solvation.
Kubyshkin
and
Budisa
[42,43]
and
others
[44,45]
demonstrated
with
the
help
of
some
proline
analogues
that
absence
of
hydrophobic
polyproline-II
helices
in
living
nature
is
not
caused
by
fundamental
limitation
of
the
structure
itself.
Moreover,
we
recently
showed
that
polyproline-II
helix
is
capable
of
forming
transmembrane
elements
[46
].
Thus,
we
created
a
shortcut
in
the
Hartman-Smith
scheme,
by
making
an
artificial
transmembrane
element
bypassing
development
of
the
a-helix
(Figure
2).
Recently,
it
has
also
been
shown
that
incorporation
of
the
polyproline
helices
into
the
collagen
superstructures
is
fully
compatible
with
the
hydrophobic
environment
[47
].
These
solid
experimen-
tal
facts
allow
us
to
conclude
that
there
are
no
fundamen-
tal
limitations
that
would
preclude
proline
and
the
poly-
proline-II
helix
from
becoming
a
competent
life-building
constituent.
Thus,
the
Proline
World
is
a
fully
conceivable
option,
which
was
neglected
by
nature
most
likely
due
to
a
number
of
limitations
arising
from
metabolic
schemes
in
existing
living
cells.
Further
analysis
demonstrates
that
other
amino
acids
from
the
initial
GC-phase
set
could
also
give
rise
each
to
its
own
set
of
other
chemical
solutions.
This
can
be
illustrated
by
the
placement
of
the
functional
group
in
the
glycine
backbone
bypassing
the
1-carbon
atom
linker,
for
example
in
phenylglycine
(Glycine
World).
Alternatively,
a
placement
of
a
functional
substituent
on
the
nitrogen
rather
than
Ca-atom
generates
structures
called
peptoids
(Sarcosine
World),
the
structures
that
are
per
se
non-chiral
(Figure
3).
Although,
peptoids
do
not
usually
demon-
strate
a
defined
secondary
fold
[48],
they
are
prone
to
forming
multiple
cis-trans
isomers,
with
tertiary
fold
that
could
potentially
stabilize
their
conformations.
Interac-
tion
of
hydrophobic
peptoids
with
membranes
is
also
evident
[49],
although,
no
defined
transmembrane
pep-
toid
has
been
reported,
despite
efforts
[50].
Other
alternatives
could
be
a
placement
of
a
substituent
on
the
distant
d-amino
or
e-amino
group
of
ornithine
or
Synthetic
life
with
alternative
genetic
codes
Kubyshkin
and
Budisa
245
www.sciencedirect.com
Current
Opinion
in
Biotechnology
2019,
60:242–249
lysine
that
give
rise
to
the
Ornithine
or
Lysine
World.
The
idea
behind
the
Ornithine/Lysine
World
could
be
uncou-
pling
of
the
backbone
secondary
structure
from
the
functional
groups,
by
using
a
sufficiently
distant
linker,
longer
than
a
single
methylene
unit.
As
the
result,
the
development
of
the
secondary
structure
can
be
uncoupled
from
the
chemical
features
of
the
side
chain
functions,
and
proceed
in
parallel.
Occurrence
of
pyrro-
lysine
(Figure
3),
a
special
canonical
amino
acid
encoded
in
some
methanogens
highlights
significance
of
this
scenario.
There
are
certainly
more
available
options,
which
do
not
have
rudimentary
traces
in
the
genetic
code
amino
acid
repertoire.
For
example,
a,a-dialkyl
structures
(deriva-
tives
of
aminoisobutyric
acid)
form
peptide
structures
called
peptaibols,
which
feature
a
set
of
secondary
folds
including
a-helix,
3
10
-helix
and
very
unusual
fully
extended
2.0
5
-helix,
which
is
not
represented
in
natural
proteomes
[51,52].
In
fact,
modern
peptide
and
foldamer
research
allows
to
propose
a
notable
number
of
potential
backbone
carriers
for
geometric
arrangement
of
the
bio-
chemical
functional
groups;
among
these
proline,
glycine
and
ornithine
are
taken
here
as
examples
because
these
are
preserved
in
the
modern
genetic
code.
Away
from
the
Alanine
World!
Our
analysis
of
the
evolutionary
development
of
the
amino
acid
repertoire
allows
us
to
speculate
that
the
selection
of
the
amino
acid
structures
was
dictated
by
their
metabolic
availability
in
the
GCA-phase,
whereas
in
the
GCAU-phase
the
hydrophobic
motif
was
appended
to
the
already
established
a-helix-based
architecture.
This
is
what
has
led
to
the
Alanine
World
with
biochemistry
dominated
by
the
a-helix
and
other
features
of
the
common
protein
architecture,
as
outlined
above.
What
if
the
set
of
chemical
options
offered
by
the
Alanine
World
had
already
been
explored
in
the
course
of
life’s
246
Chemical
biotechnology
Figure
3
Ornithine/Lysine World
Alanine World
attachment linker
functional group
H-bond donor H-bond acceptor
Rʹ = CH3 for Thr, Val, Ile
R = H for other
α-helix > β-strand/sheet >
polyproline-II helix
Sarcosine World
pyrrolysine
Glycine World
Proline World
functional group R
distant from backbone
charge repulsion between side chains
no H-bond donor
H-bonding suppressed
Backbone restricted to polyproline-II helix
Peptoids
when R = CH3 - sarcosine
R-function directly on backbone,
e.g. phenylglycine with R = Ph
extended
secondary
structures
compact
secondary
structures (α-helix)
H-bonds donor
distant linker
functional group R
distant from backbone
side-chain functions
backbone folding
Current Opinion in Biotechnology
Some
suggestions
for
possibilities
in
alternative
developments
of
the
proteome
based
on
the
initial
GC-phase
available
amino
acid
set
(glycine,
proline,
alanine
and
cationic
amino
acid).
Current
Opinion
in
Biotechnology
2019,
60:242–249
www.sciencedirect.com
evolution?
A
positive
answer
would
mean
that
our
attempts
to
add
new
side-chain
functionalities
without
redesigning
the
core
structure
of
the
building
blocks
are
not
radical
changes,
rather
mere
variations
within
the
Alanine
World
[53].
We
should
therefore
be
able
to
consider
a
number
of
strategic
chemical
alternatives,
which
should
enable
rede-
sign
of
the
genetic
code
repertoire
without
compromising
chemical
versatility
and
cellular
functionality.
One
possi-
ble
approach
to
accomplish
this
task
could
be
to
establish
a
stable
self-sustainable
system
with
all
integrated
func-
tions
based
on
a
different
type
of
the
underlying
chemical
skeleton
(secondary
structure).
Exchange
of
the
core
amino
acid
structure
(e.g.
Proline
World
or
Sarcosine
World),
uncoupling
of
the
secondary
fold
from
the
side-
chain
propensities
(Ornithine
World)
or
other
options
inspired
from
peptide
and
foldamer
studies
could
open
avenues
for
a
complete
redesign
of
protein
folding,
and
create
or
evolve
a
completely
different
form
of
life
based
on
these
building
blocks.
Fortunately,
modern
chemical
synthesis
provides
many
sources
for
the
amino
acid
ana-
logues
and
related
structures
required
for
such
develop-
ments.
It
is
thus
relatively
easy
to
supply
model
biochem-
ical
systems
with
a
number
of
man-made
amino
acids,
thereby
mimicking
their
metabolic
availability
in
the
cells.
We
thus
suggest
that
alternative
synthetic
life
forms
can
be
constructed
along
with
this
path.
Thereby,
we
are
about
to
change
the
basic
chemical
implementation
of
life
but
not
the
fundamental
principles
on
which
life
is
built
such
as
defined
by,
for
example,
Ga
´nti
‘Chemoton
Model’
[54].
We
anticipate
experiments
within
both
approaches
that
currently
dominate
synthetic
biology
and
xenobiol-
ogy,
so-called
top-down
and
bottom-up
[55].
The
top-
down
approach
is
usually
based
on
adaptive
laboratory
evolution
protocols
to
alienate
the
current
genetic
code,
starting
with
building
blocks
that
are
similar
to
canonical
ones.
Over
the
course
of
generations
of
evolutionary
adaptation
and
metabolic
rearrangements
[56],
these
building-block
structures
could
be
further
diversified
until
they
are
completely
different
from
those
present
in
the
original
ancestral
cells.
Another
potential
direction,
the
bottom-up
approach,
should
enable
de
novo
design
by
using
simple
boundary
systems
such
as
artificial
vesicles
or
compartments
[57],
which
should
evolve
into
a
truly
alternative
life
from
scratch.
This
should
be
a
life
with
radically
different
chemistries
and
genetic
codes
from
the
beginning
—
a
life
we
do
not
know
yet.
Finally,
we
believe
that
escaping
the
Alanine
World
is
a
very
complex
and
rather
long-term
goal.
However,
once
achieved,
this
will
enable
us
to
answer
many
fundamental
questions
about
the
origins
and
limits
of
life,
at
the
same
time
providing
entirely
unique
and
innovative
biotech-
nological
solutions
for
medicinal
chemistry
and
material
science.
In
addition,
dependence
on
noncanonical
amino
acid
components
and
in
general
of
synthetic
building
blocks
or
precursors
could
be
considered
as
the
built-in
biological
safety
tool
in
resulting
alien
organisms,
thus
enabling
complete
biocontainment
that
is
parallel
life
exists
in
complete
genetic
isolation
from
the
‘old’
biolog-
ical
world
[58].
Conflict
of
interest
statement
Nothing
declared.
Acknowledgements
VK
acknowledges
the
DFG
research
group
1805
for
a
post-doctoral
position.
NB
acknowledges
the
Award
for
Tier
1
Canada
Research
Chair
in
Chemical
Synthetic
Biology
by
the
Canadian
Federal
Government.
References
and
recommended
reading
Papers
of
particular
interest,
published
within
the
period
of
review,
have
been
highlighted
as:
of
special
interest
of
outstanding
interest
1.
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E:
In
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Fischer
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Gesammelte
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Edited
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M.
Springer;
1915:796-809.
2.
Crick
FHC:
On
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Symposia
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the
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for
Experimental
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Number
XII:
The
Biological
Replication
of
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Cambridge
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1958:138-163.
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Acevedo-Rocha
C,
Budisa
N:
Xenomicrobiology:
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2016,
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http://dx.doi.org/10.1111/1751-7915.12398.
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N:
On
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2018,
164:16-25
http://
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RJ,
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2018,
46:196-202
http://dx.doi.org/10.1016/j.
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Biocontainment
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operate
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the
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in
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60:242–249
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http://dx.doi.org/
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[11],
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amino
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was
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