Cells,
Journal Year:
2021,
Volume and Issue:
10(5), P. 1039 - 1039
Published: April 28, 2021
Monomeric
GTPases,
which
belong
to
the
Ras
superfamily,
are
small
proteins
involved
in
many
biological
processes.
They
fine-tuned
regulated
by
guanine
nucleotide
exchange
factors
(GEFs)
and
GTPase-activating
(GAPs).
Several
families
have
been
identified
organisms
from
different
kingdoms.
Overall,
most
studied
Ras,
Rho,
Rab,
Ran,
Arf,
Miro.
Recently,
a
new
family
named
Big
GTPases
was
reported.
As
general
rule,
of
all
five
characteristic
motifs
(G1–G5),
some
specific
features
for
each
described.
Here,
we
present
an
exhaustive
analysis
these
GTPase
fungi,
using
56
genomes
belonging
phyla.
For
this
purpose,
used
distinct
approaches
such
as
phylogenetics
sequences
analysis.
The
main
functions
described
monomeric
fungi
include
morphogenesis,
secondary
metabolism,
vesicle
trafficking,
virulence,
discussed
here.
Their
participation
during
fungus–plant
interactions
is
reviewed
well.
Annual Review of Microbiology,
Journal Year:
2020,
Volume and Issue:
74(1), P. 291 - 313
Published: July 14, 2020
In
this
review,
we
discuss
the
current
status
and
future
challenges
for
fully
elucidating
fungal
tree
of
life.
last
15
years,
advances
in
genomic
technologies
have
revolutionized
systematics,
ushering
field
into
phylogenomic
era.
This
has
made
unthinkable
possible,
namely
access
to
entire
genetic
record
all
known
extant
taxa.
We
first
review
highlight
areas
where
additional
effort
will
be
required.
then
analytical
imposed
by
volume
data
methods
recover
most
accurate
species
given
sea
gene
trees.
Highly
resolved
deeply
sampled
trees
are
being
leveraged
novel
ways
study
radiations,
delimitation,
metabolic
evolution.
Finally,
critical
issue
incorporating
unnamed
uncultured
dark
matter
taxa
that
represent
vast
majority
diversity.
Natural Product Reports,
Journal Year:
2022,
Volume and Issue:
39(8), P. 1557 - 1573
Published: Jan. 1, 2022
Covering:
2002
to
2020In
their
natural
environment,
fungi
must
compete
for
resources.
It
has
been
hypothesized
that
this
competition
likely
induces
the
biosynthesis
of
secondary
metabolites
defence.
In
a
quest
discover
new
chemical
diversity
from
fungal
cultures,
growing
trend
recapitulate
competitive
environment
in
laboratory,
essentially
co-culture.
This
review
covers
fungal-fungal
co-culture
studies
beginning
with
first
literature
report
2002.
Since
then,
there
number
reported
as
result
studies.
Specifically,
discusses
and
provides
insights
into
(1)
rationale
pairing
strains,
(2)
ways
grow
co-culture,
(3)
different
approaches
screening
co-cultures
diversity,
(4)
determining
metabolite-producing
strain,
(5)
final
thoughts
regarding
approach.
Our
goal
is
provide
set
practical
strategies
generate
unique
products
research
community
can
utilize.
Biotechnology Advances,
Journal Year:
2021,
Volume and Issue:
54, P. 107866 - 107866
Published: Nov. 12, 2021
Natural
products
from
fungi
represent
an
important
source
of
biologically
active
metabolites
notably
for
therapeutic
agent
development.
Genome
sequencing
revealed
that
the
number
biosynthetic
gene
clusters
(BGCs)
in
is
much
larger
than
expected.
Unfortunately,
most
them
are
silent
or
barely
expressed
under
laboratory
culture
conditions.
Moreover,
many
nature
uncultivable
cannot
be
genetically
manipulated,
restricting
extraction
and
identification
bioactive
these
species.
Rapid
exploration
tremendous
cryptic
fungal
BGCs
necessitates
development
heterologous
expression
platforms,
which
will
facilitate
efficient
production
natural
cell
factories.
Host
selection,
BGC
assembly
methods,
promoters
used
expression,
metabolic
engineering
strategies
compartmentalization
pathways
key
aspects
consideration
to
develop
such
a
microbial
platform.
In
present
review,
we
summarize
current
progress
on
above
challenges
promote
research
effort
relevant
fields.
Journal of Fungi,
Journal Year:
2023,
Volume and Issue:
9(3), P. 362 - 362
Published: March 15, 2023
Fungi
represent
an
important
source
of
bioactive
secondary
metabolites
(SMs),
which
have
wide
applications
in
many
fields,
including
medicine,
agriculture,
human
health,
and
other
industries.
The
genes
involved
SM
biosynthesis
are
usually
clustered
adjacent
to
each
into
a
region
known
as
biosynthetic
gene
cluster
(BGC).
recent
advent
diversity
genetic
genomic
technologies
has
facilitated
the
identification
cryptic
or
uncharacterized
BGCs
their
associated
SMs.
However,
there
still
challenges
that
hamper
broader
exploration
industrially
metabolites.
advanced
CRISPR/Cas
system
revolutionized
fungal
engineering
enabled
discovery
novel
compounds.
In
this
review,
we
firstly
introduce
relationships
with
SMs,
followed
by
brief
summary
conventional
strategies
for
engineering.
Next,
range
state-of-the-art
CRISPR/Cas-based
tools
been
developed
review
these
methods
fungi
research
on
Finally,
limitations
systems
discussed
directions
future
proposed
order
expand
improve
efficiency
Microbial Genomics,
Journal Year:
2023,
Volume and Issue:
9(4)
Published: April 28, 2023
Bacterial
secondary
metabolites,
synthesized
by
enzymes
encoded
in
biosynthetic
gene
clusters
(BGCs),
can
underlie
microbiome
homeostasis
and
serve
as
commercialized
products,
which
have
historically
been
mined
from
a
select
group
of
taxa.
While
evolutionary
approaches
proven
beneficial
for
prioritizing
BGCs
experimental
characterization
efforts
to
uncover
new
natural
dedicated
bioinformatics
tools
designed
comparative
analysis
within
focal
taxa
are
limited.
We
thus
developed
l
ineage
s
pecific
nalysis
(
lsa
BGC;
https://github.com/Kalan-Lab/lsaBGC
)
aid
exploration
microdiversity
trends
across
homologous
groupings
BGCs,
cluster
families
(GCFs),
any
bacterial
interest.
BGC
enables
rapid
direct
identification
GCFs
genomes,
calculates
statistics
conservation
genes,
builds
framework
allow
base
resolution
mining
novel
variants
through
metagenomic
exploration.
Through
application
the
suite
four
genera
commonly
found
skin
microbiomes,
we
insights
into
evolution
diversity
their
BGCs.
show
that
virulence-associated
carotenoid
staphyloxanthin
Staphylococcus
aureus
is
ubiquitous
genus
.
one
GCF
encoding
biosynthesis
showcases
evidence
plasmid-mediated
horizontal
transfer
(HGT)
between
species,
another
appears
be
transmitted
vertically
amongst
sub-clade
skin-associated
Further,
latter
GCF,
well
conserved
S.
,
has
lost
most
epidermidis
common
species
on
human
also
regarded
commensal.
identify
thousands
single-nucleotide
(SNVs)
Corynebacterium
tuberculostearicum
sp.
complex,
narrow,
multi-species
clade
features
prevalent
healthy
microbiomes.
Although
SNVs
were
approximately
10
times
likely
correspond
synonymous
changes
when
located
top
five
percentile
sites,
identified
defied
this
trend
predicted
amino
acid
functionally
key
enzymatic
domains.
Ultimately,
beyond
supporting
investigations
provides
important
functionalities
discovery
or
directed
modification
products.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: July 8, 2024
Abstract
Copy
number
variation
(CNV)
can
drive
rapid
evolution
in
changing
environments.
In
microbial
pathogens,
such
adaptation
is
a
key
factor
underpinning
epidemics
and
colonization
of
new
niches.
However,
the
genomic
determinants
remain
poorly
understood.
Here,
we
systematically
investigate
CNVs
large
genome
sequencing
dataset
spanning
worldwide
collection
1104
genomes
from
major
wheat
pathogen
Zymoseptoria
tritici
.
We
found
overall
strong
purifying
selection
acting
on
most
CNVs.
Genomic
defense
mechanisms
likely
accelerated
gene
loss
over
episodes
continental
colonization.
Local
along
climatic
gradients
was
facilitated
by
affecting
secondary
metabolite
production
general.
One
strongest
loci
for
highly
conserved
NAD-dependent
Sirtuin
family.
The
CNV
locus
localizes
to
an
~68-kb
Starship
mobile
element
unique
species
carrying
genes
expressed
during
plant
infection.
has
lost
ability
transpose,
demonstrating
how
ongoing
domestication
cargo-carrying
selfish
elements
contribute
selectable
within
populations.
Our
work
highlights
standing
copy
numbers
at
global
scale
be
driving
metabolic
species.
Microbiology Spectrum,
Journal Year:
2024,
Volume and Issue:
12(2)
Published: Jan. 9, 2024
Fungal
secondary
metabolites
(SMs)
contribute
to
the
diversity
of
fungal
ecological
communities,
niches,
and
lifestyles.
Many
SMs
have
one
or
more
medically
industrially
important
activities
(e.g.,
antifungal,
antibacterial,
antitumor).
The
genes
necessary
for
SM
biosynthesis
are
typically
located
right
next
each
other
in
genome
known
as
biosynthetic
gene
clusters
(BGCs).
However,
whether
bioactivity
can
be
predicted
from
specific
attributes
BGCs
remains
an
open
question.
We
adapted
machine
learning
models
that
bacterial
BGC
data
with
accuracies
high
80%
data.
trained
our
predict
cytotoxic/antitumor
on
two
sets:
(i)
(data
set
comprised
314
BGCs)
(ii)
(314
(1,003
BGCs).
found
had
balanced
between
51%
68%,
whereas
training
56%
68%.
low
prediction
accuracy
bioactivities
likely
stems
small
size
set;
this
lack
data,
coupled
finding
including
did
not
substantially
change
currently
limits
application
approaches
studies.
With
>15,000
characterized
SMs,
millions
putative
genomes,
increased
demand
novel
drugs,
efforts
systematically
link
urgently
needed.IMPORTANCEFungi
key
sources
natural
products
iconic
penicillin
statins.
DNA
sequencing
has
revealed
there
pathways
but
chemical
structures
>99%
produced
by
these
remain
unknown.
used
artificial
intelligence
diverse
pathways.
predictions
were
generally
low,
because
only
very
few
known.
products,
present
study
suggests
is
urgent
need
identify
pathways,
their
bioactivities.
Natural Product Reports,
Journal Year:
2024,
Volume and Issue:
41(10), P. 1543 - 1578
Published: Jan. 1, 2024
This
review
highlights
methods
for
studying
structure
activity
relationships
of
natural
products
and
proposes
that
these
are
complementary
could
be
used
to
build
an
iterative
computational-experimental
workflow.
Organic Letters,
Journal Year:
2025,
Volume and Issue:
27(4), P. 1036 - 1041
Published: Jan. 22, 2025
Bioactivity-guided
isolation
identified
the
main
antifungal
compounds
produced
by
Acrophialophora
levis
as
new
polyhydroxy-polyketides
acrophialocinol
(1)
and
acrophialocin
(2).
Their
biosynthesis
was
elucidated
heterologous
reconstitution
in
Aspergillus
oryzae
involves
an
α-ketoglutarate-dependent
dioxygenase-catalyzed
α-hydroxylation,
resulting
formation
of
a
tertiary
alcohol
that
is
indispensable
for
activity.
Furthermore,
self-resistance
toward
mediated
conserved
RTA1-like
protein
encoded
acr
biosynthetic
gene
cluster.