A protein blueprint of the diatom CO2-fixing organelle
Cell,
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 1, 2024
Язык: Английский
DiatOmicBase: a versatile gene‐centered platform for mining functional omics data in diatom research
The Plant Journal,
Год журнала:
2025,
Номер
121(6)
Опубликована: Март 1, 2025
SUMMARY
Diatoms
are
prominent
microalgae
found
in
all
aquatic
environments.
Over
the
last
20
years,
thanks
to
availability
of
genomic
and
genetic
resources,
diatom
species
such
as
Phaeodactylum
tricornutum
Thalassiosira
pseudonana
have
emerged
valuable
experimental
model
systems
for
exploring
topics
ranging
from
evolution
cell
biology,
(eco)physiology,
biotechnology.
Since
first
genome
sequencing
projects
initiated
more
than
years
ago,
numerous
genome‐enabled
datasets
been
generated,
based
on
RNA‐Seq
proteomics
experiments,
epigenomes,
ecotype
variant
analysis.
Unfortunately,
these
generated
by
various
laboratories,
often
disparate
formats
challenging
access
analyze.
Here
we
present
DiatOmicBase,
a
portal
gathering
comprehensive
omics
resources
P.
T.
facilitate
exploration
dispersed
public
design
new
experiments
prior‐art.
DiatOmicBase
provides
gene
annotations,
transcriptomic
profiles
browser
with
variants,
histone
methylation
marks,
transposable
elements,
non‐coding
RNAs,
read
densities
experiments.
We
developed
semi‐automatically
updated
module
explore
both
publicly
available
users'
private
datasets.
Using
gene‐level
expression
data,
users
can
perform
exploratory
data
analysis,
differential
expression,
pathway
biclustering,
co‐expression
network
Users
create
heatmaps
visualize
pre‐computed
comparisons
selected
subsets.
Automatic
other
bioinformatic
tools
comparative
functional
genomics
is
also
provided.
Focusing
currently
centralized
,
showcase
several
examples
how
strengthens
molecular
research
diatoms,
making
organisms
accessible
broad
community.
Язык: Английский
Overexpression of Plastid Acetyl-CoA Carboxylase Confers Stress Tolerances with Increased Levels of Unsaturated Fatty Acids in the Marine Diatom Phaeodactylum tricornutum
Marine Biotechnology,
Год журнала:
2025,
Номер
27(2)
Опубликована: Март 26, 2025
Язык: Английский
Multiphase CO2-dependent photosynthesis in marine diatoms
Frontiers in Photobiology,
Год журнала:
2025,
Номер
3
Опубликована: Апрель 2, 2025
Diatoms,
one
of
the
most
ubiquitous
phytoplankton
in
oceans,
have
evolved
a
pyrenoid-based
CO
2
-concentrating
mechanism
(CCM)
to
utilize
limited
seawater
for
photosynthesis.
Recent
proteomics
analyses
and
molecular
biological
tools
deepened
our
understanding
mechanisms
involved
diatom
chloroplast
architecture
CCM.
Here,
we
provide
an
update
knowledge
processes
high
affinity
photosynthesis
dissolved
inorganic
carbon
(DIC)
diatoms.
Based
on
phenotype
genome-edited
mutants,
propose
model
CCM
composed
four
phases
-dependent
at
(I)
less
than
0.1
mM,
(II)
0.1–2
(III)
2–10
(IV)
more
10
mM
DIC
concentrations,
which
rate-determining
steps
are
capture
unfixed
stroma
Phases
I
II,
evolution
pyrenoid-penetrating
thylakoid
lumen
Phase
III,
transport
IV.
Under
natural
containing
mainly
form
HCO
3
−
,
marine
diatoms
is
likely
primarily
shifting
II
when
available
limited.
Язык: Английский
New avenues in photosynthesis: from light harvesting to global modeling
Physiologia Plantarum,
Год журнала:
2025,
Номер
177(2)
Опубликована: Март 1, 2025
Abstract
Photosynthesis
underpins
life
on
Earth,
serving
as
the
primary
energy
source
while
regulating
global
carbon
and
water
cycles,
thereby
shaping
climate
vegetation.
Advancing
photosynthesis
research
is
essential
for
improving
crop
productivity
refining
models
across
scales,
ultimately
addressing
critical
challenges
such
food
security
environmental
sustainability.
This
minireview
synthesizes
a
selection
of
recent
advancements
presented
at
2nd
European
Congress
Research,
focusing
efficiency
modelling
scales.
We
explore
strategies
to
optimize
light
harvesting
fixation,
leading
canopy
level
improvements.
Alongside
synthetic
biology,
we
examine
advances
in
harnessing
natural
variability
key
photosynthetic
traits,
considering
both
methodological
innovations
vast
reservoir
opportunities
they
present.
Additionally,
highlight
unique
insights
gained
from
plants
adapted
extreme
environments,
offering
pathways
improve
resilience
simultaneously.
emphasize
importance
holistic
approach,
integrating
dynamic
modeling
metabolic
processes
bridge
these
advancements.
Beyond
improvements,
discuss
progress
simulations,
particularly
through
improved
parametrization
mesophyll
conductance,
crucial
enhancing
leaf‐to‐global
scale
simulations.
Recognizing
need
greater
interdisciplinary
collaboration
tackle
grand
put
research,
two
initiatives
launched
congress—an
open
science
platform
dedicated
journal
plant
ecophysiology.
conclude
this
with
forward‐looking
outline,
highlighting
next
steps
toward
achieving
meaningful
improvements
photosynthesis,
yield,
modeling.
Язык: Английский
The thylakoid membrane remodeling protein VIPP1 forms bundled oligomers in tobacco chloroplasts
PLANT PHYSIOLOGY,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 8, 2025
The
thylakoid
membrane
(TM)
serves
as
the
scaffold
for
oxygen-evolving
photosynthesis,
hosting
protein
complexes
responsible
light
reactions
and
ATP
synthesis.
Vesicle
inducing
in
plastid
1
(VIPP1),
a
key
TM
remodeling,
has
been
recognized
essential
homeostasis.
In
vitro
studies
of
cyanobacterial
VIPP1
demonstrated
its
ability
to
form
large
homo-oligomers
(2
MDa)
manifesting
ring-like
or
filament-like
assemblies
associated
with
membranes.
Similarly,
Chlamydomonas
reinhardtii
assembles
into
rods
that
encapsulate
liposomes
stacked
spiral
structures.
However,
nature
chloroplasts,
particularly
Arabidopsis,
remains
uncharacterized.
Here,
we
expressed
Arabidopsis
thaliana
fused
GFP
(AtVIPP1-GFP)
tobacco
(Nicotiana
tabacum)
chloroplasts
performed
transmission
electron
microscopy
(TEM).
A
purified
AtVIPP1-GFP
fraction
was
enriched
long
filamentous
tubule-like
Detailed
TEM
observations
fixed
resin-embedded
tissues
identified
situ
appeared
colocalize
fluorescence.
Electron
tomography
AtVIPP1
oligomers
consisted
bundled
filaments
near
membranes,
some
which
connected
inner
chloroplast
envelope
at
their
contact
sites.
observed
bundles
were
never
detected
wild-type
but
vipp1
mutants
expressing
AtVIPP1-GFP.
Taken
together,
propose
are
dominant
represent
static
state
vivo.
Язык: Английский
From algae to plants: understanding pyrenoid-based CO2-concentrating mechanisms
Trends in Biochemical Sciences,
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 1, 2024
Язык: Английский
Spotlight on “A protein blueprint of the diatom CO 2 -fixing organelle” by Nam et al. (2024) and “Diatom pyrenoids are encased in a protein shell that enables efficient CO 2 fixation” by Shimakawa et al. (2024)
Journal of Mitochondria Plastids and Endosymbiosis,
Год журнала:
2024,
Номер
3(1)
Опубликована: Дек. 24, 2024
Recent
studies
by
Nam
et
al.
and
Shimakawa
published
in
Cell
(2024)
have
elucidated
the
protein
composition
of
diatom
pyrenoids
constructing
protein–protein
interaction
networks
for
centric
Thalassiosira
pseudonana
using
vivo
photo-crosslinking
with
Rubisco
pennate
Phaeodactylum
tricornutum.
These
investigations
identified
a
family
proteins
that
form
pyrenoid
sheath,
termed
"Shell"
proteins.
Knockout
experiments
revealed
absence
or
malformation
these
sheaths
leads
to
altered
structures
impaired
growth
under
atmospheric
CO2
conditions.
The
research
highlights
are
enclosed
lattice-like
proteinaceous
sheaths,
as
demonstrated
through
multiscale
imaging
techniques.
findings
provide
insights
into
convergent
evolution
across
various
algal
lineages
suggest
potential
strategies
engineering
crop
plants
enhance
agricultural
yields.
Язык: Английский