bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Апрель 12, 2024
Abstract
Chemical
waste
with
toxic
effects
is
released
into
the
environment
by
industrial
and
urban
activities.
Pseudomonas
putida
,
a
rhizosphere
bacterium,
harbors
wide
variety
of
genes
capable
degrading
hydrocarbons
xenobiotic
compounds
in
its
natural
environment.
This
bacterium
also
large
set
metal
resistance
genes.
Most
studies
that
identify
involved
P.
focus
on
over/underexpressed
may
miss
other
important
for
whose
expression
does
not
change.
In
this
study,
we
used
Tn-seq
approach
to
determine
essential
genome
required
growth
presence
an
excess
metals
culture
medium.
enables
detection
mutants
reduced
or
increased
fitness
excess.
We
validated
our
screen
identifying
known
gene
such
as
czcA-1
(
PP_0043
),
cadA-3
PP_5139
cadR
PP_5140
)
pcoA2
PP_5380
).
Their
were
underrepresented
zinc,
cadmium
(for
copper
respectively.
demonstrate
targeted
mutagenesis
complementation
assay
PP_5337
PP_0887
are
putative
transcriptional
regulators
resistance,
respectively,
.
The
study
revealed
role
two
genes,
PP_1663
PP_5002
cobalt
first
evidence
linking
these
highlights
incomplete
understanding
mechanisms
Bacteria
are
highly
adaptable
and
grow
in
diverse
niches,
where
they
often
interact
with
eukaryotic
organisms.
These
interactions
different
hosts
span
the
entire
spectrum
from
symbiosis
to
pathogenicity
thus
determine
lifestyle
of
bacterium.
Knowledge
genetic
determinants
involved
animal
plant
host
colonization
by
pathogenic
mutualistic
bacteria
is
not
only
crucial
discover
new
drug
targets
for
disease
management
but
also
developing
novel
biostimulant
strategies.
In
last
decades,
significant
progress
genome-wide
high-throughput
technologies
such
as
transposon
insertion
sequencing
has
led
identification
pathways
that
enable
efficient
colonization.
However,
extent
which
similar
genes
play
a
role
this
process
yet
unclear.
This
review
highlights
commonalities
specificities
bacterial
important
bacteria-host
interaction.
New Phytologist,
Год журнала:
2022,
Номер
236(1), С. 235 - 248
Опубликована: Июнь 16, 2022
Plant
diseases
are
an
important
threat
to
food
production.
While
major
pathogenicity
determinants
required
for
disease
have
been
extensively
studied,
less
is
known
on
how
pathogens
thrive
during
host
colonization,
especially
at
early
infection
stages.
Here,
we
used
randomly
barcoded-transposon
insertion
site
sequencing
(RB-TnSeq)
perform
a
genome-wide
screen
and
identify
key
bacterial
fitness
of
the
vascular
pathogen
Xanthomonas
campestris
pv
(Xcc)
cauliflower
plant
(Brassica
oleracea).
This
high-throughput
analysis
was
conducted
in
hydathodes,
natural
entry
Xcc,
xylem
sap
synthetic
media.
Xcc
did
not
face
strong
bottleneck
hydathode
infection.
In
total,
181
genes
were
identified
plant-associated
environments
with
functional
enrichment
involved
metabolism
but
only
few
previously
be
virulence.
The
biological
relevance
12
independently
confirmed
by
phenotyping
single
mutants.
Notably,
show
that
XC_3388,
protein
no
function
(DUF1631),
plays
role
adaptation
virulence
possibly
through
c-di-GMP-mediated
regulation.
study
revealed
yet
unsuspected
social
behaviors
adopted
individuals
when
confined
inside
hydathodes
Postharvest Biology and Technology,
Год журнала:
2024,
Номер
211, С. 112816 - 112816
Опубликована: Фев. 12, 2024
Foodborne
illness
linked
to
fruit
and
vegetables
poses
a
major
challenge
public
health
horticulture
production.
Processed
lettuce
has
been
implicated
in
recurrent
outbreaks
of
pathogenic
Shiga
toxin-producing
Escherichia
coli
(STEC)
infection.
We
hypothesized
that
plant
defenses
elicited
by
mechanical
injury
may
effect
STEC
inhibition
cut
leaves.
Intact
leaves
31
cultivars
(Lactuca
spp.)
selected
from
>500
accessions
based
on
their
resistance
common
insect
pests
the
necrotrophic
drop
pathogen
were
assessed
for
serovar
O157:H7
(EcO157)
survival
under
cold
storage
conditions.
The
previously
ranked
also
phenotypes
such
as
other
phytopathogens
physiological
traits.
Total
leaf
phenolic
compounds,
anthocyanins,
reactive
oxygen
species
(ROS);
phenylalanine
lyase
(PAL),
peroxidase
(POD),
polyphenol
oxidase
(PPO)
activity
quantified
each
cultivar.
Principal
Component
Analysis
(PCA)
K-means
cluster
analysis
applied
group
EcO157
population
decline
lettuce.
In
five
cultivars,
high
herbivorous
insects
(aphids,
miners
thrips),
diseases
(lettuce
drop,
downy
mildew,
Impatiens
Necrotic
Spot
Virus),
disorder
tipburn
was
associated
with
up
42-fold
cold-stored
(shredded)
leaves,
11-fold
difference
intact
vs
(ΔD).
these
24-fold
greater
than
cultivar
lowest
decline,
8-fold
mean
all
(P
<
0.01).
Resistance
hemibiotrophic
causing
bacterial
spot,
Xanthomonas
hortorum
pv.
vitians,
not
indicative
this
system.
High
PAL
activity,
anthocyanin
content
(PPA);
POD
0.05).
One
susceptibility
phytopathogens,
low
levels
defense
metabolism
nevertheless
showed
inhibition,
suggesting
inhibitory
characteristics
at
play.
Basal
immunity
pathways
strong
wound
response
inform
about
enteric
minimally
processed
postharvest
related
traits
identified
study
serve
breed
new
genotypes
intrinsically
enhanced
microbial
safety.
ABSTRACT
Encoded
within
many
microbial
genomes,
biosynthetic
gene
clusters
(BGCs)
underlie
the
synthesis
of
various
secondary
metabolites
that
often
mediate
ecologically
important
functions.
Several
studies
and
bioinformatics
methods
developed
over
past
decade
have
advanced
our
understanding
both
pangenomes
BGC
evolution.
In
this
minireview,
we
first
highlight
challenges
in
broad
evolutionary
analysis
BGCs,
including
delineation
boundaries
clustering
BGCs
across
genomes.
We
further
summarize
key
findings
from
comparative
genomics
on
conservation
taxa
habitats
discuss
potential
fitness
effects
different
settings.
Afterward,
recent
research
showing
importance
genomic
context
production
evolution
is
highlighted.
These
draw
parallels
to
recent,
broader,
investigations
gene-to-gene
associations
pangenomes.
Finally,
describe
mechanisms
by
which
evolve,
ranging
acquisition
or
origination
entire
micro-evolutionary
trends
individual
genes.
An
outlook
how
expansions
capabilities
some
might
support
theories
open
are
result
adaptive
also
discussed.
conclude
with
remarks
about
future
work
leveraging
longitudinal
metagenomics
diverse
ecosystems
likely
significantly
improve
genomes
BGCs.
Environmental Microbiology,
Год журнала:
2025,
Номер
27(5)
Опубликована: Апрель 29, 2025
ABSTRACT
Industrial
and
urban
activities
release
toxic
chemical
waste
into
the
environment.
Pseudomonas
putida
,
a
soil
bacterium,
is
known
to
degrade
hydrocarbons
xenobiotics,
possesses
numerous
genes
associated
with
heavy
metal
tolerance.
Most
studies
on
tolerance
in
P.
focus
solely
over‐
or
underexpressed
genes,
potentially
overlooking
important
unchanged
expression.
This
study
employed
Tn‐seq
approach
identify
essential
required
for
growth
under
stress.
method
enables
identification
of
mutants
altered
fitness
presence
excess
metals.
The
screen
successfully
identified
number
implicated
resistance,
including
czcA‐1
cadA‐3
cadR
pcoA2
thereby
validating
approach.
Further
analyses
using
targeted
mutagenesis
complementation
assays
revealed
PP_5337
as
putative
transcriptional
regulator
involved
copper
two‐component
system
RoxSR
(
PP_0887/PP_0888
)
key
determinant
cadmium
Additionally,
PP_1663
PP_5002
were
contributing
cobalt
tolerance,
respectively.
provides
first
evidence
linking
these
highlighting
gaps
our
understanding
mechanisms
demonstrating
utility
identifying
novel
determinants.
Frontiers in Plant Science,
Год журнала:
2023,
Номер
14
Опубликована: Май 8, 2023
Dickeya
and
Pectobacterium
species
are
necrotrophic
pathogens
that
macerate
stems
(blackleg
disease)
tubers
(soft
rot
of
Solanum
tuberosum.
They
proliferate
by
exploiting
plant
cell
remains.
also
colonize
roots,
even
if
no
symptoms
observed.
The
genes
involved
in
pre-symptomatic
root
colonization
poorly
understood.
Here,
transposon-sequencing
(Tn-seq)
analysis
solani
living
macerated
tissues
revealed
126
important
for
competitive
tuber
lesions
207
stem
lesions,
including
96
common
to
both
conditions.
Common
included
acr
the
detoxification
defense
phytoalexins
kduD,
kduI,
eda
(=kdgA),
gudD,
garK,
garL,
garR
assimilation
pectin
galactarate.
In
colonization,
Tn-seq
highlighted
83
genes,
all
different
from
those
lesion
encode
exploitation
organic
mineral
nutrients
(dpp,
ddp,
dctA,
pst)
glucuronate
(kdgK
yeiQ)
synthesis
metabolites:
cellulose
(celY
bcs),
aryl
polyene
(ape),
oocydin
(ooc).
We
constructed
in-frame
deletion
mutants
bcsA,
ddpA,
apeH,
pstA
genes.
All
were
virulent
infection
assays,
but
they
impaired
roots.
addition,
ΔpstA
mutant
was
its
capacity
progeny
tubers.
Overall,
this
work
distinguished
two
metabolic
networks
supporting
either
an
oligotrophic
lifestyle
on
roots
or
a
copiotrophic
lesions.
This
novel
traits
pathways
understanding
how
D.
pathogen
efficiently
survives
persists
environment,
colonizes
Infection and Immunity,
Год журнала:
2024,
Номер
92(8)
Опубликована: Авг. 13, 2024
ABSTRACT
Interbacterial
antagonism
involves
all
major
phyla,
occurs
across
the
full
range
of
ecological
niches,
and
has
great
significance
for
environment,
clinical
arena,
agricultural
industrial
sectors.
Though
earliest
insight
into
interbacterial
traces
back
to
discovery
antibiotics,
a
paradigm
shift
happened
when
it
was
learned
that
protein
secretion
systems
(e.g.,
types
VI
IV
systems)
deliver
toxic
“effectors”
against
competitors.
However,
link
between
Gram-negative
type
II
system
(T2SS),
which
exists
in
many
pathogens
environmental
species,
is
not
evident
prior
reviews
on
bacterial
competition
or
T2SS
function.
A
current
examination
literature
revealed
four
examples
one
its
known
substrates
having
bactericidal
activity
Gram-positive
target
another
Gram-negative.
When
further
studied,
effectors
proved
be
peptidases
peptidoglycan
competitor.
There
are
also
reports
various
bacteriolytic
enzymes
occurring
culture
supernatants
some
other
these
activities
suggested.
Thus,
can
mediator
antagonism,
possible
T2SSs
have
antibacterial
outputs.
Yet,
at
present,
remains
relatively
understudied
role
competition.
Arguably,
there
need
analyze
broader
species
their
antagonism.
Such
investigation
offers,
among
things,
pathway
toward
developing
new
antimicrobials
treating
disease.
Essays in Biochemistry,
Год журнала:
2023,
Номер
67(3), С. 455 - 470
Опубликована: Март 24, 2023
Xanthomonas
plant
pathogens
can
infect
hundreds
of
agricultural
plants.
These
bacteria
exploit
sophisticated
molecular
strategies
based
on
multiple
secretion
systems
and
their
associated
virulence
factors
to
overcome
the
defenses,
including
physical
barrier
imposed
by
cell
walls
innate
immune
system.
Xanthomonads
are
equipped
with
a
broad
diverse
repertoire
Carbohydrate-Active
enZymes
(CAZymes),
which
besides
enabling
utilization
complex
carbohydrates
as
carbon
energy
source,
also
play
pivotal
roles
in
bacterial
lifestyle
host.
CAZymes
xanthomonads
often
organized
multienzymatic
similar
Polysaccharide
Utilization
Loci
(PUL)
from
Bacteroidetes
known
CUT
(from
Carbohydrate
TonB-dependent
transporters).
recognized
synthesize
distinct
exopolysaccharides
xanthan
gum
untapped
biofilm
formation.
Here,
we
summarize
current
knowledge
multifaceted
xanthomonads,
connecting
function
pathogenicity
tissue
specificity.