Journal of Dental Research,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 20, 2025
The
difficulty
of
establishing
a
relationship
between
archaea
and
oral
diseases
such
as
dental
caries
stems
from
the
challenges
detecting,
identifying,
isolating
these
microorganisms.
This
study
aimed
to
detect
in
publicly
available
datasets
comprising
caries-free
saliva
plaque
by
using
tailored
bioinformatic
pipeline
for
shotgun
sequencing
analysis.
A
systematic
search
was
performed
identify
studies
metagenomics
or
metatranscriptomics
on
samples
obtained
individuals
with
caries.
Two
reviewers
selected
based
eligibility
criteria.
Sequencing
metadata
each
were
retrieved
SRA
Bioproject.
count
table
generated
database
mapping
reads
against
an
genome
database,
specifically
this
study,
stringent
filtering
parameters
greater
than
97%
similarity
90%
query
coverage.
Archaeal
prevalence
determined
arbitrary
cutoff
point
(>500
reads).
An
effect
size
meta-analysis
determine
overall
prevalence.
Phyloseq
DESeq2
packages
used
alpha
beta
diversities,
differential
abundance
different
taxonomic
levels,
expression
comparing
samples.
Spearman
correlation
bacteriome.
yielded
154
titles,
which
collection
7
8
obtained.
Of
397
samples,
N
=
63
positive
postfiltering,
putative
20%
(confidence
interval
0%–40%)
identifying
Euryarchaeota
,
Thermoplasmatota
Nitrosphaeria
.
Methanogens
present
both
groups
(
Methanobrevibacter
spp.,
Methanosarcina
Methanosphaera
)
positively
correlated
Stenotrophomonas
Streptococcus
Actinomyces
Abiotrophia
Gemella
Corynebacterium
Several
methanogenesis
genes,
including
methyl-coenzyme
M
reductase,
catalyzes
final
step
methane
production
methanogens,
underexpressed
caries-active
compared
Saliva
emerged
sites
low-abundance
archaea,
genes
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Feb. 15, 2024
Abstract
Archaea
play
indispensable
roles
in
global
biogeochemical
cycles,
yet
many
crucial
cellular
processes,
including
cell-shape
determination,
are
poorly
understood.
Haloferax
volcanii
,
a
model
haloarchaeon,
forms
rods
and
disks,
depending
on
growth
conditions.
Here,
we
used
combination
of
iterative
proteomics,
genetics,
live-cell
imaging
to
identify
mutants
that
only
form
or
disks.
We
compared
the
proteomes
with
wild-type
cells
across
phases,
thereby
distinguishing
between
protein
abundance
changes
specific
cell
shape
those
related
phases.
The
results
identified
diverse
set
proteins,
predicted
transporters,
transducers,
signaling
components,
transcriptional
regulators,
as
important
for
determination.
Through
phenotypic
characterization
deletion
strains,
established
rod-determining
factor
A
(RdfA)
disk-determining
(DdfA)
required
formation
respectively.
also
structural
an
actin
homolog
plays
role
disk-shape
morphogenesis,
which
named
volactin.
Using
imaging,
determined
volactin’s
localization
showed
its
dynamic
polymerization
depolymerization.
Our
provide
insights
into
archaeal
possible
implications
understanding
evolution
morphology
regulation
domains.
Endosomal
sorting
complexes
required
for
transport
(ESCRT)
play
key
roles
in
protein
between
membrane-bounded
compartments
of
eukaryotic
cells.
Homologs
many
ESCRT
components
are
identifiable
various
groups
archaea,
especially
Asgardarchaeota,
the
archaeal
phylum
that
is
currently
considered
to
include
closest
relatives
eukaryotes,
but
not
bacteria.
We
performed
a
comprehensive
search
homologs
archaea
and
reconstructed
evolution
using
phylogenetic
tree
Vps4
ATPase
(ESCRT
IV)
as
scaffold
sensitive
sequence
analysis
comparison
structural
models
identify
previously
unknown
proteins.
Several
distinct
systems
outside
Asgard
were
identified,
including
proteins
structurally
similar
ESCRT-I
ESCRT-II,
several
other
domains
involved
suggesting
an
early
origin
these
components.
Additionally,
distant
CdvA
identified
Thermoproteales
which
likely
uncharacterized
cell
division
system
archaea.
propose
evolutionary
scenario
from
ancestral
building
blocks,
namely,
ATPase,
ESCRT-III
components,
wH
(winged
helix-turn-helix
fold)
possibly
also
coiled-coil,
Vps28-like
domains.
The
last
common
ancestor
encompassed
complex
was
sorting.
Subsequent
either
simplification,
TACK
superphylum,
where
co-opted
division,
or
complexification
Asgardarchaeota.
In
connection
ubiquitin
signature
already
established.IMPORTANCEAll
cells
possess
intracellular
membrane
organization.
central
role
remodeling
essential
cellular
functionality
eukaryotes.
Recently,
it
has
been
shown
includes
known
encode
systems.
employed
structure
comparisons
reconstruct
subunits,
some
can
be
predicted
participate
division.
results
this
reconstruction
indicate
encoded
evolved
toward
greater
complexity,
particular,
established.
Frontiers in Microbiology,
Journal Year:
2023,
Volume and Issue:
13
Published: Jan. 10, 2023
The
origin
of
the
FtsZ/tubulin
protein
family
was
extremely
relevant
for
life
since
these
proteins
are
present
in
nearly
all
organisms,
carrying
out
essential
functions
such
as
cell
division
or
forming
a
major
part
cytoskeleton
eukaryotes.
Therefore,
investigating
early
evolution
could
reveal
crucial
aspects
diversification
three
domains
life.
In
this
study,
we
revisited
phylogenies
an
extensive
prokaryotic
diversity,
focusing
on
main
evolutionary
events
that
occurred
during
its
evolution.
We
found
evidence
last
universal
common
ancestor
FtsZ
Bacteria
and
Archaea.
bacteria,
ftsZ
genes
genomically
associated
with
bacterial
gene
cluster,
while
archaea,
duplicated
prior
to
archaeal
diversification,
one
copies
is
biosynthesis
genes.
Archaea
have
expanded
sequences
closely
related
eukaryotic
tubulins.
addition,
report
novel
CetZ-like
groups
Halobacterota
Asgardarchaeota.
Investigating
C-termini
paralogs
basal
tubulins,
show
CetZ,
well
plasmidic
TubZ
from
Firmicutes,
most
likely
originated
FtsZ.
Finally,
tubulins
restricted
Odinarchaeaota
Prosthecobacter
species,
they
seem
belong
different
molecular
systems.
However,
their
suggest
α/β-tubulins
pointing
potential
ancestrality
Current Opinion in Cell Biology,
Journal Year:
2023,
Volume and Issue:
85, P. 102274 - 102274
Published: Nov. 7, 2023
Every
cell
becomes
two
through
a
carefully
orchestrated
process
of
division.
Prior
to
division,
contractile
machinery
must
first
be
assembled
at
the
midzone
ensure
that
cut,
when
it
is
made,
bisects
separated
copies
genetic
material.
Second,
this
dynamically
tethered
limiting
plasma
membrane
so
as
bring
with
constricts.
Finally,
connecting
severed
generate
physically
separate
daughter
cells.
In
several
organisms
across
tree
life,
Endosomal
Sorting
Complex
Required
for
Transport
(ESCRT)-III
family
proteins
aid
division
by
forming
composite
polymers
function
together
Vps4
AAA-ATPase
constrict
and
cut
tube
nascent
cells
from
inside.
review,
we
discuss
unique
features
ESCRT-III
enable
play
role
in
many
archaea
eukaryotes.
Molecular Microbiology,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Feb. 25, 2024
While
there
is
a
considerable
body
of
knowledge
regarding
the
molecular
and
structural
biology
biochemistry
archaeal
information
processing
machineries,
far
less
known
about
nature
substrate
for
these
machineries-the
nucleoid.
In
this
article,
we
will
describe
recent
advances
in
our
understanding
three-dimensional
organization
chromosomes
model
organisms
crenarchaeal
phylum.
