Molecular Biology and Evolution,
Journal Year:
2022,
Volume and Issue:
40(1)
Published: Dec. 31, 2022
Escherichia
coli
have
served
as
important
model
organisms
for
over
a
century-used
to
elucidate
key
aspects
of
genetics,
evolution,
molecular
biology,
and
pathogenesis.
However,
defining
which
strains
actually
belong
this
species
is
erratic
unstable
due
shifts
in
the
characters
criteria
used
distinguish
bacterial
species.
Additionally,
many
isolates
designated
E.
are
genetically
more
closely
related
Shigella
than
other
coli,
creating
situation
entire
genus
its
four
encompassed
within
single
coli.
We
evaluated
all
complete
genomes
assigned
closest
relatives
according
biological
concept
(BSC),
using
evidence
reproductive
isolation
gene
flow
(i.e.,
homologous
recombination
case
asexual
bacteria)
ascertain
boundaries.
The
BSC
establishes
uniform,
consistent,
objective
principle
that
allows
species-level
classification
across
domains
life
does
not
rely
on
either
phenotypic
or
genotypic
similarity
defined
type-specimen
membership.
Analyzing
total
1,887
sequenced
comparing
our
results
genome-based
methods,
we
found
few
barriers
among
strains,
clades,
phylogroups,
Shigella.
Due
utility
recognizing
constitute
true
species,
designate
form
genetic
cohesive
group
members
coliBIO.
Nature,
Journal Year:
2022,
Volume and Issue:
613(7943), P. 332 - 339
Published: Dec. 21, 2022
Abstract
Asgard
archaea
are
considered
to
be
the
closest
known
relatives
of
eukaryotes.
Their
genomes
contain
hundreds
eukaryotic
signature
proteins
(ESPs),
which
inspired
hypotheses
on
evolution
cell
1–3
.
A
role
ESPs
in
formation
an
elaborate
cytoskeleton
and
complex
cellular
structures
has
been
postulated
4–6
,
but
never
visualized.
Here
we
describe
a
highly
enriched
culture
‘
Candidatus
Lokiarchaeum
ossiferum’,
member
phylum,
thrives
anaerobically
at
20
°C
organic
carbon
sources.
It
divides
every
7–14
days,
reaches
densities
up
5
×
10
7
cells
per
ml
significantly
larger
genome
compared
with
single
previously
cultivated
strain
represent
5%
its
protein-coding
genes,
including
four
actin
homologues.
We
imaged
enrichment
using
cryo-electron
tomography,
identifying
Ca
L.
ossiferum’
basis
characteristic
expansion
segments
their
ribosomes.
Cells
exhibited
coccoid
bodies
network
branched
protrusions
frequent
constrictions.
The
envelope
consists
membrane
surface
structures.
long-range
extends
throughout
bodies,
twisted
double-stranded
architecture
filaments
is
consistent
F-actin.
Immunostaining
indicates
that
comprise
Lokiactin—one
most
conserved
archaea.
propose
actin-based
predated
emergence
first
eukaryotes
was
crucial
feature
phylum
by
scaffolding
The
dichotomy
that
separates
prokaryotic
from
eukaryotic
cells
runs
deep.
transition
pro-
to
eukaryote
evolution
is
poorly
understood
due
a
lack
of
reliable
intermediate
forms
and
definitions
regarding
the
nature
first
host
could
no
longer
be
considered
prokaryote,
common
ancestor,
FECA.
last
LECA,
was
complex
cell
united
all
traits
characterising
biology
including
mitochondrion.
role
endosymbiotic
organelle
in
this
radical
towards
life
is,
however,
sometimes
questioned.
In
particular
discovery
asgard
archaea
has
stimulated
discussions
pre-endosymbiotic
complexity
Here
we
review
differences
similarities
among
models
view
as
isolated
coincidental
events
archaeal
or,
on
contrary,
result
response
endosymbiosis.
Inspecting
perspective
endosymbiont
uncovers
can
explained
having
evolved
solution
housing
semi-autonomous
why
addition
another
endosymbiont,
plastid,
added
extra
compartments.
Mitochondria
provided
selective
pressures
for
origin
(and
continued
maintenance)
complexity.
Moreover,
they
also
energetic
benefit
throughout
eukaryogenesis
evolving
thousands
gene
families
unique
eukaryotes.
Hence,
synthesis
current
data
lets
us
conclude
such
Golgi
apparatus,
nucleus,
autophagosomes,
meiosis
sex
an
imposes.
Nature Microbiology,
Journal Year:
2023,
Volume and Issue:
8(2), P. 231 - 245
Published: Jan. 19, 2023
Abstract
‘
Candidatus
Methanophagales’
(ANME-1)
is
an
order-level
clade
of
archaea
responsible
for
anaerobic
methane
oxidation
in
deep-sea
sediments.
The
diversity,
ecology
and
evolution
ANME-1
remain
poorly
understood.
In
this
study,
we
use
metagenomics
on
hydrothermal
samples
to
expand
diversity
uncover
the
effect
virus–host
dynamics.
Phylogenetic
analyses
reveal
a
deep-branching,
thermophilic
family,
Methanospirareceae’,
closely
related
short-chain
alkane
oxidizers.
Global
phylogeny
near-complete
genomes
show
that
hydrogen
metabolism
within
ancient
trait
was
vertically
inherited
but
differentially
lost
during
lineage
diversification.
Metagenomics
also
uncovered
16
undescribed
virus
families
so
far
exclusively
targeting
archaea,
showing
unique
structural
replicative
signatures.
expansive
virome
contains
metabolic
gene
repertoire
can
influence
host
through
virus-mediated
displacement.
Our
results
suggest
evolutionary
continuum
between
oxidizers
underscore
effects
viruses
dynamics
methane-driven
ecosystems.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: June 29, 2024
Abstract
Argonaute
proteins
are
the
central
effectors
of
RNA-guided
RNA
silencing
pathways
in
eukaryotes,
playing
crucial
roles
gene
repression
and
defense
against
viruses
transposons.
Eukaryotic
Argonautes
subdivided
into
two
clades:
AGOs
generally
facilitate
miRNA-
or
siRNA-mediated
silencing,
while
PIWIs
piRNA-mediated
silencing.
It
is
currently
unclear
when
how
Argonaute-based
mechanisms
arose
diverged
during
emergence
early
evolution
eukaryotes.
Here,
we
show
that
Asgard
archaea,
closest
prokaryotic
relatives
an
evolutionary
expansion
took
place.
In
particular,
a
deep-branching
PIWI
protein
(HrAgo1)
encoded
by
genome
Lokiarchaeon
‘
Candidatus
Harpocratesius
repetitus’
shares
common
origin
with
eukaryotic
proteins.
Contrasting
known
use
single-stranded
DNA
as
guides
and/or
targets,
HrAgo1
mediates
cleavage,
facilitates
expressed
human
cells
supplied
miRNA
precursors.
A
cryo-EM
structure
HrAgo1,
combined
quantitative
single-molecule
experiments,
reveals
displays
structural
features
target-binding
modes
mix
those
AGO
Thus,
this
archaeal
may
have
retained
ancestral
molecular
architecture
preceded
functional
mechanistic
divergence
PIWIs.
The
origin
of
eukaryotes
was
a
key
event
in
the
history
life.
Current
leading
hypotheses
propose
that
symbiosis
between
an
asgardarchaeal
host
cell
and
alphaproteobacterial
endosymbiont
represented
crucial
step
eukaryotic
metabolic
cross-feeding
partners
provided
basis
for
their
subsequent
evolutionary
integration.
A
major
unanswered
question
is
whether
metabolism
modern
bears
any
vestige
this
ancestral
syntrophy.
Here
we
systematically
analyse
origins
gene
repertoires
mediating
central
carbon
metabolism.
Our
phylogenetic
sequence
analyses
reveal
repertoire
chimeric,
with
contributions
from
Asgardarchaeota
Alphaproteobacteria
operating
predominantly
glycolysis
tricarboxylic
acid
cycle,
respectively.
also
extent
to
which
interplay
has
been
remodelled
via
loss,
transfer
subcellular
retargeting
>2
billion
years
since
cells,
identify
genetic
other
prokaryotic
sources
addition
endosymbiont.
work
demonstrates
that,
contrast
previous
assumptions,
preserves
information
about
nature
original
asgardarchaeal–alphaproteobacterial
interactions
supports
syntrophy
scenarios
cell.
Analysis
identifies
Alphaproteobacteria,
microbial
taxa,
followed
by
retargeting,
have
over
time.
Nature Microbiology,
Journal Year:
2022,
Volume and Issue:
7(7), P. 948 - 952
Published: June 27, 2022
Asgard
archaea
have
recently
been
identified
as
the
closest
archaeal
relatives
of
eukaryotes.
Their
ecology,
and
particularly
their
virome,
remain
enigmatic.
We
reassembled
closed
chromosome
Candidatus
Odinarchaeum
yellowstonii
LCB_4,
through
long-range
PCR,
revealing
CRISPR
spacers
targeting
viral
contigs.
found
related
viruses
in
genomes
diverse
prokaryotes
from
geothermal
environments,
including
other
archaea.
These
open
research
avenues
into
ecology
evolution
