médecine/sciences,
Journal Year:
2022,
Volume and Issue:
38(12), P. 990 - 998
Published: Dec. 1, 2022
Il
est
maintenant
bien
établi
que
les
virus
ont
joué
un
rôle
important
dans
l’évolution
des
eucaryotes
modernes.
Dans
cette
revue,
nous
commentons
le
qu’ils
pu
jouer
l’eucaryogenèse.
Nous
discutons
analyses
phylogénétiques
qui
mettent
en
évidence
l’origine
virale
de
plusieurs
protéines
clés
la
biologie
moléculaire
et
observations
récentes
qui,
par
analogie,
pourraient
suggérer
une
origine
du
noyau
cellulaire.
mettons
parallèle
complexité
avec
l’unicité
leur
virosphère
avançons
l’hypothèse
selon
laquelle
mécanismes
différenciation
cellulaire
auraient
source
ceux
mis
œuvre
pour
transformer
cellules
infectées
virales.
Frontiers in Microbiology,
Journal Year:
2025,
Volume and Issue:
16
Published: Feb. 19, 2025
DNA
replication
is
an
essential
process
enabling
the
duplication
of
before
cell
division.
This
typically
starts
at
origins
(ori),
which
are
specific
sequences
(except
in
higher
eukaryotes,
where
they
not
very
well
defined
and
correspond
to
a
broad
chromosomal
region
preferentially
happens)
recognized
by
initiator
protein
complex,
leading
unwinding
opening
DNA.
In
bacteria,
DnaA
(Rashid
Berger,
2024),
while
archaea
it
initiated
Orc/Cdc6
proteins
(Orc1/Cdc6
Archaea
Orc1-6
Cdc6
eukaryotes;
Bell
Dutta,
2002;Matsunaga
et
al.,
2007;Majerník
Chong,
2008;Ojha
Swati,
2010).
Bacteria
possess
single
ori
(Gao,
2015),
whereas
eukaryotes
can
have
hundreds
thousands
(Hu
Stillman,
2023;Tian
2024).
archaea,
number
varies
between
species,
ranging
from
one
four
(Myllykallio
2000;Lundgren
2004;Duggin
2008;Farkas
2011;Pelve
2012;Hawkins
2013).
Then,
(DnaA
or
Orc1/Cdc6)
recruit
replicative
helicase
(DnaB
for
Mcm
MCM
complex
eucaryotes)
that
unwinds
begins
with
loading
other
components
(primase,
polymerases
etc.).Positioned
evolutionarily
bacteria
(Dombrowski
2021;Imachi
2020),
offer
unique
vantage
point
understanding
mechanisms
drive
cellular
life.
While
were
initially
thought
share
strategies
due
their
prokaryotic
nature,
studies
shown
employ
hybrid
system
incorporating
features
both
bacterial
eukaryotic
processes.
These
microorganisms
genes
operons
circular
genomic
like
but
metabolism
more
closely
related
cells
(Edgell
Doolittle,
1997;Raymann
2014).
evolutionary
bridge
makes
fascinating
subjects
scientific
inquiry,
offering
insights
could
reshape
our
molecular
biology.The
study
has
garnered
increasing
attention
over
past
decade,
especially
since
was
live
without
(Hawkins
Recent
demonstrated
use
multiple
different
levels
activity,
homologous
recombination
plays
important
role
2013;Gehring
2017;Mc
Teer
2024;Liman
article
aims
explore
latest
findings
on
archaeal
replication,
focusing
key
Hawkins
al.
(2013),
Mc
(2024),
Liman
(2024).
works
only
challenge
traditional
views
also
highlight
complexity
flexibility
archaea.DNA
fundamental
life,
yet
processes
employed
defy
simple
classification.
Historically,
scientists
grouped
structure,
Carl
Woese
coworkers
revolutionized
this
perception
demonstrating
existence
three
distinct
domains
life
(Fox
1977).
Although
still
debated
whether
ancestors
(Imachi
2020;Dombrowski
2021;Da
Cunha
2022),
certain
aspects
biology
remain
intriguing.
Research
recently
Gehring
(2017)
andMc
reveals
reality.
combination
bacterial-like
eukaryotic-like
mechanisms,
might
retain
even
ancient
suggests
represent
linking
modern
systems.
One
most
striking
discoveries
Euryarchaeota
Haloferax
volcanii
(2024)
RadA
involved
reducing
expression
increases
utilization
two
Euryarchaeota,
Thermococcus
barophilus
kodakarensis,
respectively.
reveal
recombination-dependent
(RDR)
used
some
partly
entirely
ensures
proper
replication.
However,
all
ori,
nor
do
RDR
(Samson
2013;Yang
2015).
relies
formation
D-loop
through
strand
invasion
recombination,
then
serves
as
platform
initiate
firstly
described
T4
phage
(Mosig,
1998;Kreuzer,
2000;Malkova
Ira,
special
system,
using
R-loop
(a
RNA
invades
double
replication)
(Miller
2003).
Similar
Escherichia
coli
(iSDR
recombinase
cSDR
R-loop)
(BIR)
unable
weakly
able
form
colonies
replicate
error
(Michel
Bernander,
2014).Interestingly,
Cyanobacteria
dnaA
(Richter
1998;Ran
2010;Ohbayashi
2016;Ohbayashi
2020).
Ohbayashi
(2016)
suggested
fire
asynchronously
strain
explain
results.
could,
least
Cyanobacteria,
be
accordance
found
archaea.
Unfortunately,
no
investigated
importance
RecA,
recombinase,
Cyanobacteria.
Such
research
necessary
determine
if
another
unknown
initiation
pathway.
suggest
shared
origin
potentially
dating
back
LUCA
(Last
Universal
Common/Cellular
Ancestor).In
my
opinion,
these
"classical"
models
merely
exceptions
rule
critical
refining
forms.
Their
systems
blur
boundaries
serve
living
early
life.Forterre
(2002
2013)
proposed
machineries,
differ
Archaea/Eucarya,
result
viral
transfer
descendants
LUCA.
Similarly,
Koonin
(2014)
explained
variety
associated
respective
may
evolved
primordial
pool,
surviving
selfish
elements.
Two
ultimately
adopted
successful
Archaea,
later
Eukaryotes.
Since
RecA/RAD51/RadA
family
shares
common
ancestor
(Lin
2006;Chintapalli
2013),
why
similar
such
iSDR
BIR,
many
organisms.
Kowalczykowski
(2000)
RecA-like
provided
way
primitive
organisms.Since,
been
ATPase
AAA+
domain
DnaA/Orc/Cdc6
same
period
(Iyer
2003),
obtained
fusion
gene
(specific
binds
actual
DnaA/Orc/Cdc6)
independently
descendant
gave
archaea/eukarya
Thus
possible
present
Genome
remains
mysterious
composed
(Forterre,
1999
;Koonin
2020)
now
genome
hypothesis
based
non-homology
polymerase,
helicases
primase
universal
worked
Topo
IA
given
virus
(PCNA,
RFC
example)
To
go
further
theory,
RNA-binding
repair
(Bader
2020;Klaric
2021),
known
bind
RNA,
BRCA1,
KU,
RPA,
RAD52,
RAD51,
RecA
(Kirkpatrick
1992;Kim
1992;Yoo
Dynan,
1998;Keskin
2014;Sharma
2015;Thomas
2023).
For
review,
specifically
proteins,
tempting
think
proteins-the
ancestor-already
RNA-LUCA,
perform
word,
first
(and
repair)
(in
LUCA's
descendants).
actually
support
view
generated
Polymerase
LUCA)
(RecA
(Kasahara
2000)
acted
ancestral
initiation.
taken
archaea/eukaryotes.In
case,
viruses
already
carried
RecA/RadA/RAD51
and/or
initiators,
transmitted
descendants.
Supporting
hypothesis,
originate
extrachromosomal
genetic
elements,
Robinson
(2007)
(2013,
fourth
H.
chromosome).
seen
organisms
mobile
elements
absorbed
regulated
machinery
Therefore,
independent,
co-opted
create
efficient,
centralized
restart
particularly
preceded,
co-existed
with,
emergence
primary
method
Some
retained
mechanism
(archaea,
cyanobacteria?)
(bacteria
eukaryotes)
genomes
under
conditions.Whereas
seems
main
appears
principal
T.
kodakarensis
laboratory
conditions
(Gehring
mainly
during
stationary
phase
except
when
RadA,
expressed
(Mc
underscore
versatility
far
adaptable
than
bacteria.
adaptability,
I
believe,
positions
how
forms
extreme
environments.
Furthermore,
inherently
simpler
propose
appearance
relied
recombination-based
processes,
today
repair,
material
(Fig.
1).
reinforces
notion
innovation
often
arises
co-option
existing,
selfish,
abundantly
literature
(Hurst
Werren,
2001;Hazen
2010;Koonin,
2016;Haudiquet
2022;Kumon
Lampson,
2022;Widen
2023).In
conclusion,
represents
area
bridges
gap
prokaryotes
eukaryotes.
studies,
those
(2017),
versatile
nature
long-standing
assumptions
greater
previously
recognized.
More
effort
should
directed
towards
studying
RDR.
Badel
mention
Aeropyrum
pernix,
barophilus,
uses
actively
phase,
suggesting
Crenarchaeota,
exponential
phase.Additionally,
analyzing
potential
provide
insights.
Moreover,
because
Deinococcales
deeply
branched
tree
ESDSA
(extended
synthesis-dependent
annealing;
Zahradka
2006),
double-strand
break
would
interesting
test
capacity
dnaA.Archaea's
ability
survive
environments
provides
valuable
limits
Earth
planets.
By
manage
high-stress
conditions,
we
better
understand
pressures
shaped
forms.Moving
forward,
interdisciplinary
integrating
biology,
biochemistry,
biotechnology
will
unlocking
full
discoveries.
biological
curiosities;
central
life's
history
hold
promise
future
biotechnological
advancements.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: May 6, 2025
Abstract
Archaeal
membrane
lipids
are
markedly
distinct
from
those
in
bacteria
and
eukaryotes,
serving
as
unique
biomarkers
for
unraveling
their
ecological
biogeochemical
roles.
Recent
advancements
lipidomics
have
facilitated
detailed
cellular-level
characterizations
of
lipid
compounds.
However,
the
lack
a
comprehensive
dedicated
database
has
severely
limited
large-scale,
high-throughput
investigations
archaeal
lipids.
We
present
ArchLips,
containing
218,868
silico
molecular
structures
tandem
mass
spectra
199,248
corresponding
ArchLips
enables
rapid
accurate
identification
characterized
compounds
both
pure
cultures
environmental
samples,
transformative
tool
enhancing
our
understanding
diversity
evolutionary
significance
within
global
ecosystems.
Frontiers in Bioinformatics,
Journal Year:
2023,
Volume and Issue:
3
Published: Sept. 1, 2023
The
origin
of
eukaryotes
was
among
the
most
important
events
in
history
life,
spawning
a
new
evolutionary
lineage
that
led
to
all
complex
multicellular
organisms.
However,
timing
this
event,
crucial
for
understanding
its
environmental
context,
has
been
difficult
establish.
fossil
and
biomarker
records
are
sparse
molecular
clocks
have
thus
far
not
reached
consensus,
with
dates
spanning
2.1-0.91
billion
years
ago
(Ga)
critical
nodes.
Notably,
time
estimates
last
common
ancestor
typically
hundreds
millions
younger
than
Great
Oxidation
Event
(GOE,
2.43-2.22
Ga),
leading
researchers
question
presumptive
link
between
oxygen.
We
obtained
estimate
using
genetic
data
both
archaeal
bacterial
origin,
latter
rarely
used
past
studies.
also
avoided
potential
calibration
biases
may
affected
earlier
conservative
interval
2.2-1.5
Ga,
an
even
narrower
core
2.0-1.8
eukaryotes,
period
closely
aligned
rise
further
reconstructed
biological
complexity
across
tree
life
three
universal
measures:
cell
types,
genes,
genome
size.
found
temporally
consistent
followed
pattern
similar
This
suggests
causal
relationship
stemming
from
increased
energy
needs
fulfilled
by
mLife,
Journal Year:
2022,
Volume and Issue:
1(4), P. 359 - 367
Published: Dec. 1, 2022
The
work
of
Carl
Woese
and
his
colleagues
the
Urbana
University
has
been
one
most
important
breakthroughs
in
biology
last
century
(for
historical
sketches,
see
Refs.1,
2).
pioneered
use
macromolecule
sequences
to
decipher
relationships
between
all
organisms,
fulfilling
Darwin's
dream
get
a
"fairly
true
genealogical
trees
each
great
kingdom
nature"3.
He
went
even
beyond
this
objective
since
he
was
finally
able
identify
connect
nature
(which
called
domains)
into
single
tree.
apex
discovery
1977
an
entire
new
domain
life,
hidden
before
our
eyes,
Archaea4.
16S
ribosomal
RNA
(rRNA)
as
molecular
chronometer
later
probe
for
PCR
not
only
revealed
third
life
but
also
paved
way
detection
identification
microorganisms
that
were
yet
amenable
cultivation5.
I
deeply
affected
when
passed
away
10
years
ago
because
my
three
scientific
heroes:
together
with
James
Watson,
DNA
double-helix,
Wang,
topoisomerases
(the
Ws).
surprised
still
shocked
despite
monumental
achievements,
death
completely
ignored
French
media,
suspect
it
same
countries
worldwide.
Notably,
died
day
famous
horse,
Ourasi,
had
won
several
competitions
such
"le
grand
prix
de
l'arc
Triumphe."
horse
made
headlines
media
day,
including
prime-time
TV
news.
could
resist
sending
short
piece
entitled
"the
scientist
horse"
Journal
Liberation
which
emphasize
difference
treatment
(and
like
horses)
greatest
scientists
century.
It
published
online
version
journal
link
now
removed,
you
can
read
at
end
fourth
chapter
book,
Microbes
from
Hell1.
ardent
activist
promoting
vision
living
world
by
discoveries.
criticized
misleading
prokaryotic/eukaryotic
paradigm,
classification
organisms
is
based
on
phenotypic
features,
sequel
anthropic
lower
higher
ones,
humans
top
classifications6.
paradigm
establish
15
Archaea7.
Therefore,
George
Fox
their
seminar
paper
Proc
Natl
Acad
Sci
USA
1977,
already
firmly
established.
prokaryote/eukaryote
easy
explain
(with
or
without
nucleus)
quickly
became
pillar
cellular
organisms8.
dichotomy
welcomed
cytologists
biologists
alike
modern
classification,
be
opposed
five-kingdom
favored
zoologists
botanists9.
This
probably
explains
why
so
many
biologists,
strongly
time
Woese's
proposal
though
data2,
10,
11
(see
Ref.12
answer
Ernst
Mayer).
Why
should
we
change
winning
team?
Here,
will
briefly
describe
various
encounters
Woese,
focusing
agreements
disagreements
concerning
universal
tree
Last
Universal
Common
Ancestor
(LUCA),
which,
according
definitely
less
recognized
major
question
today"13.
discuss
how
legacy
challenged
occasions
reactions.
Unfortunately,
no
longer
among
us
defend
legacy.
All
aware
existence
Archaea
recognize
merit
revealing
deep
divide
"prokaryotic
world,"
too
(in
opinion)
believe
view
fundamentally
wrong
favor
pre-Woesian
evolutionary
model.
dominant
one,
paralleled
virus/phage
virosphere,
layman
politicians
journalists
ignore
(still
confused
Bacteria).
More
troublesome
fact
(except
those
working
Archaea)
are
unaware
vastly
underestimate
importance.
seems
remind
generations
importance
history
science
fight
ideas
think
they
forefront
science.
discovered
reading
1981
review
Scientific
American
described
"Archaebacteria"
possibility
studying
"primary
kingdom"
determine
common
ancestor
domains,
progenote14.
turning
point
career
immediately
stop
replication
Bacteria
(Escherichia
coli)
started
Archaea,
polymerases.
Thanks
inspiration
help
few
pioneers
field,
especially
Wolfram
Zillig15,
rapidly
accumulate
significant
results
study
Halobacterium
halobium
Sulfolobus
acidocaldarius16,
17.
first
publications
topic,
invited
Zillig
participate
second
meeting
organized
Martinsried
Institute,
near
Munich
1985.
gave
me
opportunity
time.
vividly
remember
memorable
sparring
Lake
took
place
meeting.
Based
electron
microscopic
pictures
ribosomes,
just
two
papers
Science18,
19
proposed
replacing
"urkingdoms"
(Figure
1A)
four
1B).
In
unrooted
tree,
ribosome
structure,
Archaebacteria
split
"Archaebacteria
proper,"
limited
halophiles
methanogens,
urkingdom,
Eocytes,
grouping
other
thermophilic
archaea,
Thermococcus
Thermoplasma18.
Lake,
who
spoke
first,
violently
attacked
explained
him
different
values
versus
genotypic
data.
came
back
shivering
much
argument
opinion
people
present
explanation.
structural
signatures
Jim
used
define
Eocyte
indeed
observed
mesophilic
methanogen,
Methanococcus
vanielli29.
paper,
although
Science,
cited
today,
whereas
Lake's
1984
proponents
two-domains
(2D)
hypothesis
below)
supporting
favorite
hypothesis30,
31.
discouraged
failure
held
Victoria
Canadian
east
coast
fresh
arguments.
meantime,
learned
phylogenetic
techniques
designed
method
own,
parsimony32,
produced
rRNA
Thermoplasma
removed
Eocytes33.
If
root
localized
bacteria
obtains
2D
trees,
1988
(Ref.33)
clearly
(instead
1984)
description
1D).
After
talk
meeting,
stage
conclude
speaker
brought
arguments
theory.
striking
contrast
mute
Canada,
leaving
coworker
Gary
Olsen
against
Lake34.
seemed
bit
ongoing
debate.
How
realize
scenario
good
one?
wondering
mathematician
here
settle
dispute.
realized
myself
problem
primarily
mathematical
(today,
speaking
about
choose
best
model)
more
data
sets22.
fed
up
meetings
eager
person
opponents.
Besides
conflict
rejection
theory
evolutionists,
Mayer
Lynn
Margulis,
continue
support
paradigm2.
My
encounter
thus
delayed
until
1994,
very
beginning
genomic
era.
Despite
reluctance
attend
meetings,
joined
friendship
Zillig,
influential
bringing
gospel
Europe15.
We
waiting
genome
sequenced
(most
likely
bacterial
one),
Roger
Garret
Aarhus
Denmark35
small
roundtable
five
colleagues,
one)
archaeal
selected
mammoth
task.
Each
participant
name
archaeon
floor
expected
(hoping
would
one).
"We
sequence
least
five,"
declared
stupefaction
incredulity.
fact,
right
genomes
available
century,
Craig
Venter's
team
done
collaboration
1996
(Methanocaldococcus
vannielii)36.
example
lifetime.
being
heroes,
did
hesitate
disagree
him.
strong
proponent
rooting
groups
1980s37,
38.
obtained
combining
analysis
paralogous
proteins
originated
gene
duplication
LUCA.
For
time,
Hervé
Philippe,
these
reliable
attraction
long
branch
separated
corresponding
respective
outgroup39,
40.
suspected
preferred
Bacteria.
Indeed,
rooted
justify
changing
Archaea20
hoped
topology
simply
extreme
environments
1C).
while,
disagreed
Eukaryotes
domains.
liked
idea
some
eukaryotic
spliceosome,
possibly
Of
course,
rejected
have
old
division.
When
Philippe
defended
reporting
presence
bacterial-like
genes
than
eukaryotic-like
genomes39,
ridiculed
quantitative
qualitative,
quality
hallmark
translation
apparatus
studies41.
soon
right,
allowing
parsimonious
distribution
domains
life27
1E).
However,
cannot
solved
analyses
reasonable
guess
comparative
(Box
1).
LUCA
smaller
33–34
ribosomes
contain
around
60–80
proteins27.
mechanism
biosynthesis
simpler,
protein
involved
process42.
initiation
transcription
specific,
factor
set
elongation
Finn
Werner)43.
RNA,
explaining
replication,
replicase,
primase,
helicase,
homologous
Arkarya
Bacteria44
(Arkarya
clade
Eukarya)27.
(processivity
factor)
might
introduced
independently
lineages
viruses.
ATPase
synthase
ATP
fermentation
subunit
essential
synthesis
Arkarya45.
These
reasoning
sophistication
fundamental
mechanisms
takes
lineages.
Alternative
hypotheses
(complex
LUCA)
involve
replacement
Arkaryal
features
ones
vice
versa
ones.
There
obvious
selection
pressure
suggested
replacement,
except
simplification
branch40.
Although
simpler
progenote,
sensu
Fox21,
46,
sophisticated
membrane
pumps
capable
faithful
synthesis27.
seminal
"The
concept
evolution"46,
unfaithful
apparatus.
Again,
gap
exists
hand
Eukarya
evolution
always
parsimonious,
remain
open
possible
alternatives47.
partly
agree
LUCA,
do
stricto
sensu,
translate
mRNA
message
rather
faithfully.
conclusion
contained
transfer
(tRNA)
modifications
crucial
translation.
A
provided
Kae1
Sua5
t6A
biosynthesis,
tRNA
modification
ANN
codons.
need
additional
factors
perform
task
sufficient
synthesize
mitochondria,
suggesting
mitochondria
recapitulates
LUCA27.
adopted
promoted
so-called
"bacterial
branch,"
never
considered
finding
Eukarya.
departure
cladistic
rules
due
fear
weakening
three-domain
promoted.
if
follows
rules,
usually
assumed,
two-domain
Bacteria,
naming
Arkarya27.
Probably
bypassing
case
2002,
Darwinian
threshold
transition
period
ancestors
Archaeal
Ancestor,
LACA;
Bacterial
LBCA;
Eukaryotic
LECA),
hereafter
referred
ancestors21.
moment
transmission
genetic
information
moves
predominantly
horizontal
mode
lateral
(LGT)
vertical
mode.
assumed
LGTs
allow
organisms.
Accordingly,
argue
applicable
threshold,
separation
leading
Killing
birds
once,
tempo
dramatically
decreased
emergence
ancestors.
dramatic
reduction
observations
early
looking
shape
tree13.
rate
within
extrapolated
ancestors,
born
formation
Earth!
LGT
prevalence
correct
rarely
LGT48,
49.
2006,
replicated
repaired
faithfully
RNA50.
viruses
triggers
independent
RNA-to-DNA
transitions,
domain.
To
delight,
reject
agreed
refer
USA.
respond
critics
challenge
life.
prevalent
once
thought,
sometimes
far
apart
led
buzz
forgetting
trumpeting
"Darwin
wrong"
discussion
Ref.51).
profoundly
views,
authors
jokingly
percent"52
networks53.
save
upper
part
(those
context.
chance
meet
another
2003
personal
discussions
evolution.
little
afraid
knowledge
previous
disagreement
negative
impact
encounter.
case;
friendly,
real
lover
something
give
happy
figure
1982,
someone
remembered
review14.
Lund
Sweden
honor
awarded
Crafoord
prize
Royal
Swedish
Academy
Sciences.
received
King
Sweden,
Gustav
XVI,
descendant
Marshal
Napoleon
Bernadotte,
unexpected
turn
history.
occasion
humor
mimicked
official
dinner
ritual
master
ceremony
Chap.
4
Ref.1).
prize,
3
Nobel
(both
terms
money
ceremony!),
exception
complete
absence
press
coverage.
pity
Prize.
speak
archaea.
deserved
medicine,
considering
markers
microorganism
medicine.
recent
Svante
Pääbo
sequencing
Neanderthal
confirms
advances
fields
prize.
wonder
opposition
adversaries
evolutionists
played
role
final
distinction.
met
2007
Illinois
Urbana-Champaign
celebrate
30th
anniversary
Archaea.
"hidden
your
eyes"
resembling
visible,
decades
cousins
under
microscope.
visit
laboratory
opening
box
containing
film
two-dimensional
gel
chromatography
collection
oligonucleotides
after
digestion
Methanobacterium
thermoautotrophicum
RNase
T1
1
Ref.15).
honored
own
university
surrounded
friends
introduce
countries,
Karl
Stetter
Germany,
Yoshizumi
Ishino
Japan,
David
Prangishvili
former
USSR.
2012,
reawakening
Asgard
archaea24,
25.
am
really
reacted
twist
biology.
imagine
disturbed,
view.
decade,
paraphyletic,
considers
belong
1F).
make
things
worse,
often
depicted
fusions
(one
mitochondria)
archaeon,
Margulis
highly
despised
(figure
Ref14).
Archaebacteria,
hence
illustrated
contrasting
eukaryotes
emerged
fusion
prokaryotes
(only
time)14.
much.
going
past
becoming
one.
classical
during
decade
fast-evolving
species
sets,
combined
difficulty
recovering
testifying
monophyly
reviews
results,
Ref.54).
does
mean
archaea
breakthrough
provide
exciting
understand
Phylogenetic
odd
Signature
Proteins
(ESPs)
extensive
proto-eukaryotes54.
Studying
reconstruct
proto-eukaryotic
lineage.
proto-eukaryotes
suggests
thriving
LECA
environments,
indicating
shed
light
type
environment
inhabited
cultivated
Candidatus
Prometheoarchaem
synthrophicum,
turned
out
dependent
growth
its
physical
association
methanogenic
archaeon55.
tour
force
concluded
publication
genomics
"most
them,
all,
symbiotic
interactions."
tempting
suggest
facilitated
interactions
Asgard54.
One
live
ectosymbionts
today.
search
associations
biotopes
adventure
young
(or
young)
microbial
ecologists54.
assault
three-domains
concept,
deny
prokaryotic
At
2020,
heralded
putting
nail
coffin.
From
10,575
genomes,
381
markers,
"1.16
trillions
non
amino-acids,"
separates
shorter
previously
thought56.
branches
separating
altogether.
correct,
there
reason
separate
reunified
domain,
pre-Woese
area.
Looking
cursorily
claim,
flaws
conclusion.
included
6
34
shared
proteins.
They
is,
instance,
gyrase,
recruited
(Ref.
50
references
therein).
subsequently
refuted
Moody
identified
both
paralogy
Zhu
colleagues49.
noticed
14
include
priori
unbelievable
aim
measure
distance
68
others
25%
sampled
Strikingly,
(a
prerequisite
kind
analysis)
recovered
22
trees49.
indicated
that,
transferred
other.
review,
Refs.23,
57)
confirmed
recently
using
data,
non-ribosomal
proteins22,
48,
Long
lengths
criterion
determining
besides
widespread
domains48,
58.
Failure
consider
Weiss
colleagues59.
reported
355
supposed
starting
"6.1
million
protein-coding
genes"
"286,514
clusters."
showed
metabolism
similar
Clostridia
genome,
"prokaryote"
progenote.
thrived
high
temperatures
reverse
enzymes
found
mesophiles
hyperthermophiles,
gyrases
formed
monophyletic
analysis,
them
short,
gyrase
intermixed,
domains58.
reanalysis
colleagues'
Berkemer
McGlynn
82%
all),
LUCA48.
again
underrepresented
low
diversity.
looked
arrived
Using
criteria
represented
distantly
related
phylums,
15–20
"LUCA"
(unpublished
observations).
proteome
table.
scenarios
origin
International Journal of Molecular Sciences,
Journal Year:
2023,
Volume and Issue:
24(22), P. 16169 - 16169
Published: Nov. 10, 2023
The
recently
observed
circadian
oscillations
of
the
intestinal
microbiota
underscore
profound
nature
human-microbiome
relationship
and
its
importance
for
health.
Together
with
discovery
clocks
in
non-photosynthetic
gut
bacteria
rhythms
anucleated
cells,
these
findings
have
indicated
possibility
that
virtually
all
microorganisms
may
possess
functional
biological
clocks.
However,
they
also
raised
many
essential
questions
concerning
fundamentals
timekeeping,
evolution,
origin.
This
narrative
review
provides
a
comprehensive
overview
recent
literature
molecular
chronobiology,
aiming
to
bring
together
latest
evidence
on
structure
mechanisms
driving
microbial
while
pointing
potential
applications
this
knowledge
medicine.
Moreover,
it
discusses
hypotheses
regarding
evolution
timing
describes
functions
peroxiredoxins
cells
their
contribution
cellular
clockwork.
diversity
among
various
human-associated
role
transcriptional
post-translational
timekeeping
are
addressed.
Finally,
metabolic
oscillators
host-microbiome
communication
is
presented.
mLife,
Journal Year:
2024,
Volume and Issue:
3(1), P. 119 - 128
Published: March 1, 2024
Abstract
Saccharolobus
islandicus
REY15A
represents
one
of
the
very
few
archaeal
models
with
versatile
genetic
tools,
which
include
efficient
genome
editing,
gene
silencing,
and
robust
protein
expression
systems.
However,
plasmid
vectors
constructed
for
this
crenarchaeon
thus
far
are
based
solely
on
pRN2
cryptic
plasmid.
Although
coexists
pRN1
in
its
original
host,
early
attempts
to
test
pRN1‐based
consistently
failed
yield
any
stable
host–vector
system
Sa.
.
We
hypothesized
that
failure
could
be
due
occurrence
CRISPR
immunity
against
archaeon.
identified
a
putative
target
sequence
orf904
encoding
replicase
(target
N1).
Mutated
targets
(N1a,
N1b,
N1c)
were
then
designed
tested
their
capability
escape
host
by
using
interference
assay.
The
results
revealed
triggered
archaeon,
whereas
all
three
mutated
did
not,
indicating
mutations
evaded
immunity.
These
incorporated
into
individually,
yielding
corresponding
backbones
shuttle
plasmids
(pN1aSD,
pN1bSD,
pN1cSD).
transformation
pN1aSD
pN1bSD
functional
vectors,
but
pN1cSD
lost
replication.
indicate
missense
conserved
helicase
domain
pN1c
inactivated
replicase.
further
showed
pRN2‐based
stably
maintained
cells
either
alone
or
combination,
yielded
dual
study
important
model.
The
main
objective
is
to
offer
a
functionally
coherent
counter-narrative
the
polarized
views
prevailing
now
about
complex
‘Eukaryogenesis
problem’
versus
“primitive”
nature
ascribed
so-called
“Prokaryotes”
(termed
Akaryotes
herein).
paradigm
shift
presented
aims
at
bridging
conceptual
gap
between
rudimentary
beginnings
of
biomolecular
cooperativity
on
pristine
Earth
(the
Origins
Life
or
OoL)
and
lineage-wise
diversification
toward
Darwinean
speciation
in
Tree
(or
ToL).
Although
research
field
as
whole
not
aware
corresponding
‘Prokaryogenesis
problem’,
evolutionary
process
resulting
partly
independent
archaeal
bacterial
cell
types
fully
understood.
present
paper
provides
an
explanation
for
these
problems
based
coevolutionary
complementarity
multiple
levels.
unconventional
model
connects
various
stages
from
“neighborhood
selection”
film-like
layers
unbounded
“surface
protoplasm”
short
“statistical
proteins”,
via
closely
knit
“peptide/RNA
partnership”
“making
genes”,
genomes”
several
RNA-to-DNA
transitions.
Three
virus-related
plasmids
carrying
different
DNA
replicases
may
have
initiated
vertical
stability
hereditable
lineages
that
led
three
“domains”
organismal
life,
with
fourth
lineage
ending
eukaryotic
organelles.
These
transitions
established
late-comer
fundamental
biomolecules.