Cell Reports,
Journal Year:
2024,
Volume and Issue:
43(8), P. 114631 - 114631
Published: Aug. 1, 2024
Enzymatic
modification
of
DNA
nucleobases
can
coordinate
gene
expression,
nuclease
protection,
or
mutagenesis.
We
recently
discovered
a
clade
phage-specific
cytosine
methyltransferase
(MT)
and
5-methylpyrimidine
dioxygenase
(5mYOX)
enzymes
that
produce
5-hydroxymethylcytosine
(5hmC)
as
precursor
for
enzymatic
hypermodifications
on
viral
genomes.
Here,
we
identify
phage
MT-
5mYOX-associated
glycosyltransferases
(GTs)
catalyze
linkage
diverse
sugars
to
5hmC
nucleobase
substrates.
Metavirome
mining
revealed
thousands
biosynthetic
clusters
containing
with
predicted
roles
in
sugar
hypermodification.
developed
platform
high-throughput
screening
GT-containing
pathways,
relying
the
Escherichia
coli
metabolome
substrate
pool.
successfully
reconstituted
several
pathways
isolated
modifications
appended
cytosine,
including
mono-,
di-,
tri-saccharides
comprised
hexoses,
N-acetylhexosamines,
heptose.
These
findings
expand
our
knowledge
nucleic
acids
origins
corresponding
sugar-installing
enzymes.
PLoS Biology,
Journal Year:
2023,
Volume and Issue:
21(2), P. e3001922 - e3001922
Published: Feb. 13, 2023
A
universal
taxonomy
of
viruses
is
essential
for
a
comprehensive
view
the
virus
world
and
communicating
complicated
evolutionary
relationships
among
viruses.
However,
there
are
major
differences
in
conceptualisation
approaches
to
classification
nomenclature
virologists,
clinicians,
agronomists,
other
interested
parties.
Here,
we
provide
recommendations
guide
construction
coherent
taxonomy,
based
on
expert
scientific
consensus.
Firstly,
assignments
should
be
congruent
with
best
attainable
reconstruction
their
histories,
i.e.,
taxa
monophyletic.
This
fundamental
principle
currently
included
International
Committee
Taxonomy
Viruses
(ICTV)
code
only
rank
species.
Secondly,
phenotypic
ecological
properties
may
inform,
but
not
override,
relatedness
placement
ranks.
Thirdly,
alternative
classifications
that
consider
attributes,
such
as
being
vector-borne
(e.g.,
"arboviruses"),
infecting
certain
type
host
"mycoviruses,"
"bacteriophages")
or
displaying
specific
pathogenicity
"human
immunodeficiency
viruses"),
serve
important
clinical
regulatory
purposes
often
create
polyphyletic
categories
do
reflect
relationships.
Nevertheless,
ought
maintained
if
they
needs
communities
play
practical
role.
considered
called
taxonomies.
Finally,
while
an
evolution-based
framework
enables
discovered
by
metagenomics
incorporated
into
ICTV
requirements
quality
control
sequence
data
used
these
assignments.
Combined,
four
principles
will
enable
future
development
expansion
true
diversity
becomes
apparent.
The ISME Journal,
Journal Year:
2024,
Volume and Issue:
18(1)
Published: Jan. 1, 2024
Nearly
all
organisms
are
hosts
to
multiple
viruses
that
collectively
appear
be
the
most
abundant
biological
entities
in
biosphere.
With
recent
advances
metagenomics
and
metatranscriptomics,
known
diversity
of
substantially
expanded.
Comparative
analysis
these
using
advanced
computational
methods
culminated
reconstruction
evolution
major
groups
enabled
construction
a
virus
megataxonomy,
which
has
been
formally
adopted
by
International
Committee
on
Taxonomy
Viruses.
This
comprehensive
taxonomy
consists
six
realms,
aspired
monophyletic
assembled
based
conservation
hallmark
proteins
involved
capsid
structure
formation
or
genome
replication.
The
different
taxa
differ
host
range
accordingly
ecological
niches.
In
this
review
article,
we
outline
latest
developments
megataxonomy
discoveries
will
likely
lead
reassessment
some
taxa,
particular,
split
three
current
realms
into
two
more
independent
realms.
We
then
discuss
correspondence
between
distribution
among
niches,
as
well
abundance
versus
cells
habitats.
across
environments
appears
primarily
determined
ranges,
i.e.
virome
is
shaped
composition
biome
given
habitat,
itself
affected
abiotic
factors.
Journal of General Virology,
Journal Year:
2023,
Volume and Issue:
104(5)
Published: May 4, 2023
The
taxonomy
of
viruses
is
developed
and
overseen
by
the
International
Committee
on
Taxonomy
Viruses
(ICTV),
which
scrutinizes,
approves
ratifies
taxonomic
proposals,
maintains
a
list
virus
taxa
with
approved
names
(https://ictv.global).
ICTV
has
approximately
180
members
who
vote
simple
majority.
Taxon-specific
Study
Groups
established
have
combined
membership
over
600
scientists
from
wider
virology
community;
they
provide
comprehensive
expertise
across
range
known
are
major
contributors
to
creation
evaluation
proposals.
Proposals
can
be
submitted
anyone
will
considered
irrespective
Group
support.
Thus,
within
community
realized
democratic
decision-making
process.
upholds
distinction
between
or
replicating
genetic
element
as
physical
entity
taxon
category
it
assigned.
This
reflected
nomenclature
species
taxon,
now
mandated
in
binomial
format
(genus
+
epithet)
typographically
distinct
viruses.
Classification
below
rank
(such
as,
genotypes
strains)
not
remit
ICTV.
article,
authored
Executive
Committee,
explains
principles
organization,
function,
processes
resources
ICTV,
aim
encouraging
greater
understanding
interaction
among
community.
Biomolecules,
Journal Year:
2023,
Volume and Issue:
13(4), P. 584 - 584
Published: March 24, 2023
The
order
Crassvirales
comprises
dsDNA
bacteriophages
infecting
bacteria
in
the
phylum
Bacteroidetes
that
are
found
a
variety
of
environments
but
especially
prevalent
mammalian
gut.
This
review
summarises
available
information
on
genomics,
diversity,
taxonomy,
and
ecology
this
largely
uncultured
viral
taxon.
With
experimental
data
from
handful
cultured
representatives,
highlights
key
properties
virion
morphology,
infection,
gene
expression
replication
processes,
phage-host
dynamics.
Viruses,
Journal Year:
2024,
Volume and Issue:
16(8), P. 1191 - 1191
Published: July 25, 2024
Computational
models
of
homologous
protein
groups
are
essential
in
sequence
bioinformatics.
Due
to
the
diversity
and
rapid
evolution
viruses,
grouping
sequences
from
virus
genomes
is
particularly
challenging.
The
low
similarities
genes
viruses
require
specific
approaches
for
sequence-
structure-based
clustering.
Furthermore,
annotation
public
databases
not
as
consistent
up
date
many
cellular
genomes.
To
tackle
these
problems,
we
have
developed
VOGDB,
which
a
database
orthologous
groups.
VOGDB
multi-layer
that
progressively
viral
into
connected
by
increasingly
remote
similarity.
first
layer
based
on
pair-wise
similarities,
second
profile
alignments,
third
uses
predicted
structures
find
most
allow
more
sensitive
homology
searches
novel
increase
chance
predicting
annotations
or
inferring
phylogeny.
VOGD
B
all
RefSeq
partially
reannotates
them.
updated
with
every
release.
unique
feature
inclusion
both
prokaryotic
eukaryotic
same
clustering
process,
makes
it
possible
explore
old
evolutionary
relationships
two
freely
available
at
vogdb.org
under
CC
BY
4.0
license.
Journal of Evolutionary Biology,
Journal Year:
2023,
Volume and Issue:
36(11), P. 1551 - 1567
Published: Nov. 1, 2023
Abstract
Social
interactions
among
viruses
occur
whenever
multiple
viral
genomes
infect
the
same
cells,
hosts,
or
populations
of
hosts.
Viral
social
range
from
cooperation
to
conflict,
throughout
world,
and
affect
every
stage
lifecycle.
The
ubiquity
these
means
that
they
can
determine
population
dynamics,
evolutionary
trajectory,
clinical
progression
infections.
At
time,
in
raise
new
questions
for
theory,
providing
opportunities
test
extend
existing
frameworks
within
evolution.
Many
exist
at
this
interface:
Insights
into
evolution
have
immediate
implications
our
understanding
fundamental
biology
manifestation
diseases.
However,
are
currently
limited
because
biologists
only
rarely
study
viruses.
Here,
we
bridge
gap
by
(1)
summarizing
ways
which
interact
socially,
including
consequences
evolvability;
(2)
outlining
some
open
raised
could
challenge
concepts
theory;
(3)
illustrative
examples,
data
sources,
conceptual
questions,
studying
natural
history
diverse
pervasive,
with
potential
explore
challenges
present
biology.
