New Phytologist,
Год журнала:
2023,
Номер
238(5), С. 1908 - 1923
Опубликована: Март 8, 2023
Summary
In
plants,
the
switch
to
autotrophic
growth
involves
germination
followed
by
postgermination
seedling
establishment.
When
environmental
conditions
are
not
favorable,
stress
hormone
abscisic
acid
(ABA)
signals
plants
postpone
establishment
inducing
expression
of
transcription
factor
ABI5.
The
levels
ABI5
determine
efficiency
ABA‐mediated
developmental
arrest.
molecular
mechanisms
regulating
stability
and
activity
during
transition
light
less
known.
Using
genetic,
molecular,
biochemical
approach,
we
found
that
two
B‐box
domain
containing
proteins
BBX31
BBX30
alongwith
inhibit
in
a
partially
interdependent
manner.
also
characterized
as
microProteins
miP1a
miP1b,
respectively,
based
on
their
small
size,
single
domain,
ability
interact
with
multidomain
proteins.
miP1a/BBX31
miP1b/BBX30
physically
stabilize
it
promote
its
binding
promoters
downstream
genes.
reciprocally
induces
directly
promoter.
thereby
form
positive
feedback
loop
arrest
seedlings.
Cell Systems,
Год журнала:
2024,
Номер
15(7), С. 662 - 672.e4
Опубликована: Июнь 13, 2024
Transcription
factors
can
promote
gene
expression
through
activation
domains.
Whole-genome
screens
have
systematically
mapped
domains
in
transcription
but
not
non-transcription
factor
proteins
(e.g.,
chromatin
regulators
and
coactivators).
To
fill
this
knowledge
gap,
we
employed
the
domain
predictor
PADDLE
to
analyze
proteomes
of
Arabidopsis
thaliana
Saccharomyces
cerevisiae.
We
screened
18,000
predicted
from
>800
genes
both
species,
confirming
that
89%
candidate
contain
active
fragments.
Our
work
enables
annotation
hundreds
nuclear
as
putative
coactivators,
many
which
never
been
ascribed
any
function
plants.
Analysis
peptide
sequence
compositions
reveals
how
distribution
key
amino
acids
dictates
activity.
Finally,
validated
short,
"universal"
with
comparable
performance
state-of-the-art
used
for
genome
engineering.
approach
genome-wide
discovery
across
diverse
eukaryotes.
Frontiers in Cell and Developmental Biology,
Год журнала:
2022,
Номер
10
Опубликована: Ноя. 1, 2022
The
human
body
is
programmed
with
definite
quantities,
magnitudes,
and
proportions.
At
the
microscopic
level,
such
sizes
manifest
in
individual
cells
-
different
cell
types
are
characterized
by
distinct
whereas
of
same
type
highly
uniform
size.
How
do
a
population
maintain
uniformity
size,
how
changes
target
size
programmed?
A
convergence
recent
historical
studies
suggest
just
as
thermostat
maintains
room
temperature
proliferating
animal
similarly
maintained
homeostatic
mechanisms.
In
this
review,
we
first
summarize
old
new
literature
on
existence
checkpoints,
then
discuss
additional
advances
study
homeostasis
that
involve
feedback
regulation
cellular
growth
rate.
We
further
progress
molecules
underlie
checkpoints
mechanisms
specify
setpoints.
Lastly,
less-well
explored
teleological
question:
why
does
matter
what
functional
importance
control?
iScience,
Год журнала:
2022,
Номер
25(12), С. 105547 - 105547
Опубликована: Ноя. 10, 2022
Protein
coding
genes
were
originally
identified
with
sequence-based
definitions
that
included
a
100-codon
cutoff
to
avoid
annotating
irrelevant
open
reading
frames.
However,
many
active
proteins
contain
less
than
100
amino
acids.
Indeed,
functional
genetics,
ribosome
profiling,
and
proteomic
profiling
have
short,
translated
frames,
including
those
biologically
peptide
products
(microproteins).
Yet,
functions
for
most
of
these
remain
unknown.
Because
microproteins
often
act
as
key
signals
or
fine-tune
processes,
animal
development
has
already
revealed
handful
provides
an
ideal
context
uncover
additional
microprotein
functions.
mRNAs
during
early
are
maternally
provided
hinder
targeted
mutagenesis
approaches
characterize
developmental
The
recently
established,
RNA-targeting
CRISPR-Cas13d
system
in
zebrafish
overcomes
this
barrier
produces
potent
knockdown
mRNA,
enables
flexible,
efficient
interrogation
development.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Сен. 12, 2023
Abstract
Transcription
factors
promote
gene
expression
via
trans-regulatory
activation
domains.
Although
whole
genome
scale
screens
in
model
organisms
(e.g.
human,
yeast,
fly)
have
helped
identify
domains
from
transcription
factors,
such
been
less
extensively
used
to
explore
the
occurrence
of
non-transcription
factor
proteins,
as
transcriptional
coactivators,
chromatin
regulators
and
some
cytosolic
leaving
a
blind
spot
on
what
role
these
proteins
could
play
regulating
transcription.
We
utilized
domain
predictor
PADDLE
mine
entire
proteomes
two
eukaryotes,
Arabidopsis
thaliana
Saccharomyces
cerevisiae
(
1
).
characterized
18,000
fragments
covering
predicted
>800
genes
both
species,
experimentally
validated
that
89%
contained
capable
activating
yeast.
Peptides
with
similar
sequence
composition
show
broad
range
activities,
which
is
explained
by
arrangement
key
amino
acids.
also
annotated
hundreds
nuclear
putative
coactivators;
many
never
ascribed
any
function
plants.
Furthermore,
our
library
contains
>250
non-nuclear
containing
peptides
across
eukaryotic
lineages,
suggesting
there
are
unknown
biological
roles
beyond
Finally,
we
validate
short,
‘universal’
activate
yeast
plants
comparable
or
stronger
performance
state-of-the-art
Overall,
dual
host
screen
provides
blueprint
how
systematically
discover
novel
genetic
parts
for
synthetic
biology
wide
diversity
eukaryotes.
Significance
Statement
Activation
critical
expression.
mapping
has
carried
out
previous
genome-wide
screens,
their
explored.
utilize
an
new
proteins.
derived
>750
transcription,
discovering
potentially
coactivators
Importantly,
can
representing
unique
tools.
Biochemistry,
Год журнала:
2023,
Номер
62(21), С. 3050 - 3060
Опубликована: Окт. 9, 2023
Over
the
past
decade,
advances
in
genomics
have
identified
thousands
of
additional
protein-coding
small
open
reading
frames
(smORFs)
missed
by
traditional
gene
finding
approaches.
These
smORFs
encode
peptides
and
proteins,
commonly
termed
micropeptides
or
microproteins.
Several
these
newly
discovered
microproteins
biological
functions
operate
through
interactions
with
proteins
protein
complexes
within
cell.
CYREN1
is
a
characterized
microprotein
that
regulates
double-strand
break
repair
mammalian
cells
interaction
Ku70/80
heterodimer.
binds
to
stabilizes
breaks
recruits
machinery
needed
for
nonhomologous
end
join
repair.
In
this
study,
we
examined
biochemical
properties
better
understand
explain
its
cellular
interactions.
Our
findings
support
an
intrinsically
disordered
structure
allows
it
enriches
several
including
SF3B1
via
distinct
short
linear
motif
(SLiMs)
on
CYREN1.
Since
many
are
predicted
be
disordered,
exemplar
how
interact
other
reveals
unknown
scaffolding
function
may
link
NHEJ
splicing.
