Huge
phages
(genome
size
≥
200
kb)
have
been
detected
in
diverse
habitats
worldwide,
infecting
a
variety
of
prokaryotes.
However,
their
evolution
and
adaptation
strategy
soils
remain
poorly
understood
due
to
the
scarcity
soil-derived
genomes.
Here,
we
conduct
size-fractioned
(<
0.22
μm)
metagenomic
analysis
across
130-year
chronosequence
glacier
foreland
Tibetan
Plateau
discovered
412
novel
viral
operational
taxonomic
units
(vOTUs)
huge
phages.
The
phylogenomic
gene-shared
network
gained
insights
into
unique
evolutionary
history
compared
with
smaller
Their
communities
revealed
distinct
pattern
between
early
(≤
41
years)
late
stages
(>
based
on
macrodiveristy
(interspecies
diversity)
analysis.
A
significant
increase
diversity
following
retreat
were
observed
according
current
database.
distributed
sites
within
stage
demonstrated
remarkable
higher
microdiversity
(intraspecies
other
geographic
range
such
as
intra
stage,
suggesting
that
glacial
is
key
drivers
phage
speciation.
Alongside
shift
communities,
also
noted
an
functional
transition
stages.
identification
abundant
CRISPR-Cas12
type
IV
restriction-modification
(RM)
systems
indicates
complex
mechanisms
for
adaptive
immunity.
Overall,
this
study
unravels
importance
climate
change
shaping
composition,
evolution,
function
soil
further
understanding
vital
broader
inclusion
ecosystem
models.
Nature,
Год журнала:
2024,
Номер
630(8018), С. 984 - 993
Опубликована: Июнь 26, 2024
Abstract
Genomic
rearrangements,
encompassing
mutational
changes
in
the
genome
such
as
insertions,
deletions
or
inversions,
are
essential
for
genetic
diversity.
These
rearrangements
typically
orchestrated
by
enzymes
that
involved
fundamental
DNA
repair
processes,
homologous
recombination,
transposition
of
foreign
material
viruses
and
mobile
elements
1,2
.
Here
we
report
IS110
insertion
sequences,
a
family
minimal
autonomous
elements,
express
structured
non-coding
RNA
binds
specifically
to
their
encoded
recombinase.
This
bridge
contains
two
internal
loops
encoding
nucleotide
stretches
base-pair
with
target
donor
DNA,
which
is
element
itself.
We
demonstrate
target-binding
donor-binding
can
be
independently
reprogrammed
direct
sequence-specific
recombination
between
molecules.
modularity
enables
into
genomic
sites,
well
programmable
excision
inversion.
The
system
expands
diversity
nucleic-acid-guided
systems
beyond
CRISPR
interference,
offering
unified
mechanism
three
rearrangements—insertion,
inversion—that
required
design.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Апрель 22, 2024
Gene
editing
has
the
potential
to
solve
fundamental
challenges
in
agriculture,
biotechnology,
and
human
health.
CRISPR-based
gene
editors
derived
from
microbes,
while
powerful,
often
show
significant
functional
tradeoffs
when
ported
into
non-native
environments,
such
as
cells.
Artificial
intelligence
(AI)
enabled
design
provides
a
powerful
alternative
with
bypass
evolutionary
constraints
generate
optimal
properties.
Here,
using
large
language
models
(LLMs)
trained
on
biological
diversity
at
scale,
we
demonstrate
first
successful
precision
of
genome
programmable
editor
designed
AI.
To
achieve
this
goal,
curated
dataset
over
one
million
CRISPR
operons
through
systematic
mining
26
terabases
assembled
genomes
meta-genomes.
We
capacity
our
by
generating
4.8x
number
protein
clusters
across
CRISPR-Cas
families
found
nature
tailoring
single-guide
RNA
sequences
for
Cas9-like
effector
proteins.
Several
generated
comparable
or
improved
activity
specificity
relative
SpCas9,
prototypical
effector,
being
400
mutations
away
sequence.
Finally,
an
AI-generated
editor,
denoted
OpenCRISPR-1,
exhibits
compatibility
base
editing.
release
OpenCRISPR-1
publicly
facilitate
broad,
ethical
usage
research
commercial
applications.
Nature Microbiology,
Год журнала:
2024,
Номер
9(7), С. 1873 - 1883
Опубликована: Июнь 20, 2024
Historically
neglected
by
microbial
ecologists,
soil
viruses
are
now
thought
to
be
critical
global
biogeochemical
cycles.
However,
our
understanding
of
their
distribution,
activities
and
interactions
with
the
microbiome
remains
limited.
Here
we
present
Global
Soil
Virus
Atlas,
a
comprehensive
dataset
compiled
from
2,953
previously
sequenced
metagenomes
composed
616,935
uncultivated
viral
genomes
38,508
unique
operational
taxonomic
units.
Rarefaction
curves
Atlas
indicate
that
most
diversity
unexplored,
further
underscored
high
spatial
turnover
low
rates
shared
units
across
samples.
By
examining
genes
associated
functions,
also
demonstrate
potential
impact
carbon
nutrient
cycling.
This
study
represents
an
extensive
characterization
provides
foundation
for
developing
testable
hypotheses
regarding
role
virosphere
in
biogeochemistry.
Nature Microbiology,
Год журнала:
2024,
Номер
9(3), С. 737 - 750
Опубликована: Фев. 6, 2024
Viruses
are
often
studied
using
metagenome-assembled
sequences,
but
genome
incompleteness
hampers
comprehensive
and
accurate
analyses.
Contig
Overlap
Based
Re-Assembly
(COBRA)
resolves
assembly
breakpoints
based
on
the
de
Bruijn
graph
joins
contigs.
Here
we
benchmarked
COBRA
ocean
soil
viral
datasets.
accurately
joined
assembled
sequences
achieved
notably
higher
accuracy
than
binning
tools.
From
231
published
freshwater
metagenomes,
obtained
7,334
bacteriophage
clusters,
~83%
of
which
represent
new
phage
species.
Notably,
~70%
these
were
circular,
compared
with
34%
before
We
expanded
sampling
huge
phages
(≥200
kbp),
largest
was
curated
to
completion
(717
kbp).
Improved
genomes
from
Rotsee
Lake
provided
context
for
metatranscriptomic
data
indicated
in
situ
activity
phages,
whiB-encoding
cysC-
cysH-encoding
phages.
improves
contiguity
completeness,
thus
reliability
analyses
gene
content,
diversity
evolution.
The
prokaryotic
antiviral
defense
systems
are
crucial
for
mediating
prokaryote-virus
interactions
that
influence
microbiome
functioning
and
evolutionary
dynamics.
Despite
the
prevalence
significance
of
systems,
their
responses
to
abiotic
stress
ecological
consequences
remain
poorly
understood
in
soil
ecosystems.
We
established
microcosm
with
varying
concentrations
hexavalent
chromium
(Cr(VI))
investigate
adaptive
modifications
under
stress.
Utilizing
hybrid
metagenomic
assembly
long-read
short-read
sequencing,
we
discovered
were
more
diverse
prevalent
heavily
polluted
soils,
which
was
corroborated
by
meta-analyses
public
datasets
from
various
heavy
metal-contaminated
sites.
As
Cr(VI)
concentration
increased,
prokaryotes
favoring
mutualism
gradually
supplanted
those
incurring
high
costs.
Additionally,
as
enriched
exhibited
synchronization
microbial
metal
resistance
genes.
Furthermore,
proportion
carried
mobile
genetic
elements
(MGEs),
including
plasmids
viruses,
increased
approximately
43%
39%,
respectively,
rising
Cr
concentrations.
This
trend
is
conducive
strengthening
dissemination
sharing
resources
within
communities.
Overall,
our
study
reveals
modification
ecosystems
stress,
well
positive
contributions
establishing
evolution
resistance.
These
findings
advance
understanding
adaptation
stressful
environments
may
inspire
novel
approaches
manipulation
bioremediation.
Video
Abstract.
