Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Март 20, 2024
Abstract
Extracellular
electron
transfer
(EET)
via
microbial
nanowires
drives
globally-important
environmental
processes
and
biotechnological
applications
for
bioenergy,
bioremediation,
bioelectronics.
Due
to
highly-redundant
complex
EET
pathways,
it
is
unclear
how
microbes
wire
electrons
rapidly
(>10
6
s
−1
)
from
the
inner-membrane
through
outer-surface
directly
an
external
environment
despite
a
crowded
periplasm
slow
(<10
5
diffusion
among
periplasmic
cytochromes.
Here,
we
show
that
Geobacter
sulfurreducens
cytochromes
PpcABCDE
inject
into
OmcS
by
binding
transiently
with
differing
efficiencies,
least-abundant
cytochrome
(PpcC)
showing
highest
efficiency.
Remarkably,
this
defined
nanowire-charging
pathway
evolutionarily
conserved
in
phylogenetically-diverse
bacteria
capable
of
EET.
heme
reduction
potentials
are
within
200
mV
each
other,
midpoint
82
mV-higher
than
reported
previously.
This
could
explain
efficient
over
micrometres
at
ultrafast
(<200
fs)
rates
negligible
energy
loss.
Engineering
minimal
may
yield
chassis
improved
performance.
Язык: Английский
COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes
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.
Язык: Английский
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
Genome Research,
Год журнала:
2024,
Номер
34(10), С. 1595 - 1609
Опубликована: Окт. 1, 2024
Asgard
archaea
are
of
great
interest
as
the
progenitors
Eukaryotes,
but
little
is
known
about
mobile
genetic
elements
(MGEs)
that
may
shape
their
ongoing
evolution.
Here,
we
describe
MGEs
replicate
in
Atabeyarchaeia,
a
wetland
lineage
represented
by
two
complete
genomes.
We
used
soil
depth-resolved
population
metagenomic
data
sets
to
track
18
for
which
genome
structures
were
defined
and
precise
chromosome
integration
sites
could
be
identified
confident
host
linkage.
Additionally,
20.67
kbp
circular
plasmid
family-level
groups
viruses
linked
via
CRISPR
spacer
targeting.
Closely
related
40
possess
hypervariable
genomic
region
encoding
combinations
specific
genes
small
cysteine-rich
proteins
structurally
similar
restriction-homing
endonucleases.
One
10.9
integrative
conjugative
element
(ICE)
integrates
genomically
into
Язык: Английский
Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 6, 2024
ABSTRACT
Borgs
are
huge
extrachromosomal
elements
of
anaerobic
methane-oxidizing
archaea.
They
exist
in
exceedingly
complex
microbiomes,
lack
cultivated
hosts
and
have
few
protein
functional
annotations,
precluding
their
classification
as
plasmids,
viruses
or
other.
Here,
we
used
silico
structure
prediction
methods
to
investigate
potential
roles
for
∼10,000
Borg
proteins.
Prioritizing
analysis
multicopy
genes
that
could
signal
importance
lifestyles,
uncovered
highly
represented
de-ubiquitination-like
Zn-metalloproteases
may
counter
host
targeting
proteins
proteolysis.
Also
prevalent
clusters
production
diverse
glycoconjugates
contribute
decoration
the
cell
surface,
putative
capsid
predict
multimerize
into
hexagonal
arrays.
Features
including
megabase-scale
linear
genomes
with
inverted
terminal
repeats,
genomic
repertoires
energy
metabolism,
central
carbon
compound
transformations
translation,
pervasive
direct
repeat
regions
shared
giant
eukaryotes,
although
analyses
suggest
these
parallels
arose
via
convergent
evolution.
If
archaeal
they
would
fill
gap
tri(um)virate
all
three
domains
life.
One
Sentence
Summary
Protein
analyses,
informed
by
prediction,
revealed
share
numerous
features
eukaryotic
viruses,
suggesting
a
viral-like
lifestyle
evolutionary
convergence
large
across
Domains
Life.
Язык: Английский
Methanotrophic flexibility of Ca. Methanoperedens and its interactions with sulfate-1 reducing bacteria in the sediment of meromictic Lake Cadagno
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 8, 2024
Abstract
The
greenhouse
gas
methane
is
an
important
contributor
to
global
warming,
with
freshwater
sediments
representing
potential
sources.
Anaerobic
methane-oxidizing
archaea
mitigate
release
into
the
atmosphere
by
coupling
oxidation
of
reduction
extracellular
electron
acceptors
or
through
interspecies
transfer
microbial
partners.
Understanding
their
metabolic
flexibility
and
interactions
crucial
assess
role
in
cycling.
Here,
we
investigated
anoxic
meromictic
Lake
Cadagno
(Switzerland),
where
‘
Ca
.
Methanoperedens’
sulfate-reducing
bacteria
co-occur,
metagenomics
long-term
incubations.
Incubations
were
performed
different
acceptors,
revealing
that
manganese
oxides
supported
highest
CH
4
but
enriched
for
phylotypes
hardly
present
inoculum.
Combining
data
from
inoculum
incubations,
obtained
five
Ca.
genomes,
each
harboring
pathways.
In
a
reconstructed
Desulfobacterota
QYQD01
genome
observed
large
multi-heme
cytochromes,
type
IV
pili,
putative
loss
hydrogenases,
suggesting
facultative
syntrophic
Methanoperedens’.
We
also
screened
extrachromosomal
elements
including
BORGs.
This
research
deepens
our
understanding
interspecific
lakes.
Язык: Английский