How Do Viruses Interact with Stress-Associated RNA
Richard E. Lloyd*
Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
The Stress of Virus Infections Activates Cellular
Host mRNAs are always dynamically exchanged between
translating and non-translating pools. Non-translating pools are
organized into specialized RNA granules called stress granules
(SGs) and processing bodies (P-bodies, PBs), which have funda-
mental roles in inhibition and degradation of host mRNAs
(Figure 1) . Virus infection usually results in interference in
many cell processes in ways that directly induce stress responses.
Cells respond to many types of stress by transient global inhibition
of protein synthesis in order to promote cell survival through
restricted consumption of nutrients and energy. This can also
redirect gene expression and resources to damage repair pathways.
The most common form of global translation arrest comes by
restricting production of ternary complex consisting of eukaryotic
initiation factor 2(eIF2)NGTPNmet-tRNAimet, which must bind
40 S ribosome subunits to facilitate mRNA scanning and start
codon selection at the initiation step. Restriction of ternary
complex formation is accomplished by phosphorylation of the
alpha subunit of eIF2 by one of four conserved eIF2a kinases that
sense various types of cell stress . Restriction of translation from
activation of eIF2 kinases results in accumulation of stalled
preinitiation complexes containing 40 S ribosomal subunits. After
translation repression by this means, or alternate mechanisms such
as cleavage of eIF4G scaffold protein or inhibition of eIF4E
helicase, cells respond by organizing mRNPs with stalled
translation initiation complexes into SG foci. The mechanism of
SG formation is poorly understood but involves mRNP remod-
eling that incorporates new proteins that may nucleate SGs and
involves mRNP transport on microtubules (Figure 1). SGs may
facilitate rapid reactivation of translation upon stress recovery
since ribosome preinitiation complexes are retained in an
assembled state. SGs may also promote cell survival during stress
since they sequester components of apoptotic signal transduction
pathways such as RACK1 .
SGs and PBs have fundamental roles in inhibition and
degradation of host mRNAs, and thus will affect the metabolic
fate of viral mRNAs. Viruses interfere with the cellular gene
expression machinery, thus it is no surprise that many viruses
interact in different ways with both SG and PB responses and
components to control virus replication and antiviral responses.
Although SG formation is frequently induced by virus infection,
many differences exist in the dynamics and outcome of the stress
responses induced by various viruses.
Viruses Control SG Formation
No virus infection can succeed if viral mRNA is sequestered into
translationally silenced mRNPs that aggregate in SG structures.
Thus, viruses have evolved counter measures to prevent this fate.
Species from many virus families can be organized into groups
based on how they repress SGs. For instance, one group of viruses
transiently triggers SG formation early in replicative cycles but
restricts SGs later. Many of these viruses, such as poliovirus,
alphavirus, and orthoreovirus, have replication cycles that activate
eIF2a kinases ; however, mammalian orthoreoviruses can
induce SG by viral entry alone . This basic host–virus
relationship is conserved in nature since insect dicistrovirus also
antagonizes SG formation . Another group of viruses effectively
represses SG formation throughout infection, which is only
revealed when their defective mutant viruses induce SGs or SG-
like structures. These include herpes simplex virus mutant lacking
the vhs host shutoff gene  and influenza virus with NS1 mutants
Many viruses within the above groups overtly block the host
cell’s ability to form SGs at some point during infection. This is
often measured by loss of cellular SG formation in response to
oxidative stress from arsenite treatment, which is the most
accepted standard for canonical SG formation. Viruses that block
this response include poliovirus, orthoreovirus, human immuno-
deficiency virus 1 (HIV-1), cardiovirus, junin virus, and rotavirus
(reviewed in ). Viral gene expression leads to suppression of the
cellular SG response through an expanding variety of mechanisms.
Only a few have been elucidated in any detail, but one common
pattern emerging is destruction or sequestration of key host factors
required for SG formation. For instance, poliovirus 3C protease
cleaves the key SG-nucleating protein G3BP , which prevents
colocalization of initiation factors, ribosome subunits, and mRNA
in silenced SG foci. Another SG-nucleating protein, TIA1,
continues to aggregate after G3BP cleavage , but only in
smaller vestigial foci that are stripped of initiation factors and most
mRNA . The flaviviruses West Nile virus and dengue virus
sequester other SG-nucleating proteins, TIA1 and TIAR, in
replication complexes , and dengue virus may also sequester
SG proteins G3BP1, caprin1, and USP10 as well as PB marker
protein DDX6 (also known as RCK/p54) . HTLV-1 Tax
protein interacts with HDAC-6, which is crucial for SG formation
and maintenance . Dicistrovirus also blocks formation of
complete SGs by preventing inclusion of paralogs of TIA1 and
G3BP . Viruses that sequester key SG-nucleating components
in novel aggregates may also be diverting SG assembly pathways
to aid replication as discussed below.
Citation: Lloyd RE (2012) How Do Viruses Interact with Stress-Associated RNA
Granules? PLoS Pathog 8(6): e1002741. doi:10.1371/journal.ppat.1002741
Editor: Vincent Racaniello, Columbia University, United States of America
Published June 28, 2012
Copyright: ? 2012 Richard E. Lloyd. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
Funding: This work was supported by NIH grant AI50237. The funders had no
role in study design, data collection and analysis, decision to publish, or
preparation of the manuscript.
Competing Interests: The author has declared that no competing interests
* E-mail: email@example.com
PLoS Pathogens | www.plospathogens.org1June 2012 | Volume 8 | Issue 6 | e1002741
Viruses Can Disrupt PBs and RNA Decay
SGs are dynamically linked to PBs, which are another type of
RNA granule packed with translationally silenced mRNPs and
many enzymes of the RNA decay machinery . SGs and PBs
are thought to transiently bind and exchange mRNP cargo in
association with remodeling of the mRNP protein constituents,
and PBs may promote SG assembly [16,17]. Since PBs are
proposed to be sites where RNA decay of translationally repressed
mRNA occurs, it is likely that viruses will antagonize PB functions
that could otherwise lead to decay of viral mRNA. Indeed, West
Nile virus and hepatitis C virus (HCV) infection leads to a
progressive decline in PB foci after 24–36 h infection [12,18].
HCV replication is stimulated by PB RNA helicase DDX3, which
binds HCV core protein , and PB components Rck/p54,
Lsm1, and PatL1 are required for HCV replication [20,21].
Knockdown of certain PB components (Lsm1, DDX6) also
reduced HCV replication, suggesting that PB components (as well
as SG components) are required for HCV replication or assembly
. Some of these basic relationships are conserved in insect
viruses since cricket paralysis virus partly disperses PB foci
containing overexpressed marker proteins . Poliovirus and
coxsackievirus B3 also disrupt PBs, but much more aggressively,
leading to total loss of PBs by 3–4 h after infection. In this case,
virus infection results in cleavage or degradation of key compo-
nents of the RNA decay pathway, Xrn1, Dcp1a, and Pan3,
involved in both 59 and 39 mediated RNA decay . Sindbis
virus also antagonizes viral RNA decay by selective movement of
HuR protein out of the nucleus where it binds and stabilizes viral
transcripts . HuR is known to antagonize inclusion of mRNA
in PBs .
Viruses Can Co-Opt Components of SGs and PBs
for New Functions in Replication or Assembly
As canonical SGs do not commonly co-exist with active virus
replication, it seems the overall effect of SGs on virus replication
usually appears to be negative and is selected against. However,
some viruses may co-opt and misdirect the SG response of cells to
facilitate steps in virus replication. In this way the initial host
response to stress could have a positive impact on certain virus
infections, though significant aggregation of stalled translation
initiation complexes is disallowed. For example, vaccinia virus
(VV) may subvert SG-nucleating proteins and other constituents
into novel aggregates that share some SG properties such as
colocalized G3BP and initiation factors eIF4G and eIF4E but
differ in that they contain no silenced mRNAs; rather, they
Figure 1. Stress granule and P-body assembly and interference by viruses. Virus infection causes stress at multiple levels that reduces host
translation through activation of eIF2 kinases or other means and converts active polysome mRNPs into stalled translation initiation complex mRNPs.
A complex series of events involving nucleation of several stress granule marker proteins such as G3BP, Tia-1/TIAR, and HDAC6 plus transport on
microtubules (MT) leads to aggregates of translation initiation complex mRNPs in stress granules. Alternatively, mRNPs can be stripped of initiation
factors and ribosome subunits, associate with GW182, undergo Pan2/3-mediated deadenylation, MT transport, and association of other RNA decay
factors (e.g., Xrn1, Dcp1a, DDX6, GW182 and Lsm components of the exosome), and become concentrated in P-bodies. Decapping and decay occur
outside P-bodies and also within them. Specific points/proteins where viruses interact with and inhibit RNA granule assembly pathways are shown.
PLoS Pathogens | www.plospathogens.org2 June 2012 | Volume 8 | Issue 6 | e1002741
contain VV mRNA instead. These structures form within and
adjacent to viral replication factories and may help vaccinia
segregate replication and packaging activities away from transla-
tion . In an analogous way, HCV recruits several components
of SGs to viral replication factories where they colocalize with
HCV core protein. Recruited SG proteins include G3BP1,
ataxin2, and PABP, which form alternative ring-like structures
surrounding lipid droplets . Finally, both HCV and dengue
virus RNA are reported to bind G3BP [13,26], and West Nile
virus promotes plus strand RNA replication by using TIAR to
bind a stem-loop structure on minus strand RNA templates
[12,27]. The interactions of SG-nucleating proteins with viral
RNA and formation of novel viral foci containing SG proteins
indicates viral foci may share common assembly mechanisms with
SGs or PBs. The specific functions of redirected host proteins in
virus replication or assembly have not yet been characterized.
SGs and PBs May Function as Antiviral
Components of Innate Immune Responses
Since many virus families repress SGs or PBs, these RNA
granules may represent components of an integrated cellular stress
response that has distinct antiviral properties. The formation of
SGs is potentially antiviral on several functional levels. First, they
sequester host translation initiation factors that may be limiting
(e.g., eIF4E, eIF4G, eIF4A, eIF4B, and eIF3) and 40 S ribosome
subunits, which are critical for viruses to translate their transcripts
efficiently. Second, SGs sequester IRES transactivating factors
(PTB, PCBP2, and UNR) required by classes of viruses (e.g.,
picornaviruses) for efficient IRES-mediated translation [11,28].
Third, any other mRNA binding proteins that function in aspects
of virus replication are likely to be concentrated in SGs as
passengers on silenced mRNPs. As mentioned above, both HCV
and West Nile virus apparently co-opt SG-nucleating proteins
G3BP and TIA1/TIAR in or near replication complexes; thus,
stable formation of functional SGs containing these factors may
antagonize replication [12,18]. Thus, the overall act of SG-
mediated sequestration of needed factors away from general
cytoplasmic pools can be viewed as generally antiviral.
In agreement with this, some experiments suggest that SG or at
least SG components may function to repress productive virus
infections. Expression of a cleavage-resistant mutant of G3BP that
stabilized SGs against virus attack reduced replicative output of
poliovirus . Mouse embryo fibroblasts with TIA1 knocked out
displayed increased virus production from several families of
viruses, including vesicular stomatitis virus, Sindbis virus, and
herpes simplex virus .
Formation of SG during infection could also sequester viral
mRNA transcripts directly into these silenced non-translating
pools, but interestingly, where this has been examined, there is no
significant incorporation of viral mRNAs into SGs . Possible
exceptions are sequestration of HIV-1 transcripts via Nef mRNA
interaction with SAM68 causing SG inclusion  and APO-
BEC3G protein binding to HIV RNA that may shunt RNA into
SGs and PBs .
Apoptosis is another cell stress response that is largely antiviral
in consequence; however, SG formation may signal survival and
antagonize cell death. SG can block apoptosis by inhibiting the
JNK/SAPK pathway via sequestration of RACK1 and other
apoptosis-promoting factors into SG . Thus, virus modulation
of SG formation may require fine tuning to sequester sufficient
pro-apoptotic factors while liberating sufficient pro-viral factors
and translation apparatus to support efficient replication.
The complexity of virus–host relationships reveals common
pathways and mechanisms, but also many exceptions that are
virus-specific. This is evident in viral responses to SGs and PBs as
viruses adapted their variable replication strategies to this common
host impediment to replication.
It is also important to recognize that not all SGs are equivalent,
as those induced by different stressors (e.g., heat shock) can contain
some unique components that may influence their assembly or
function . Future work with viruses will reveal more
mechanisms that can block SG formation, thus revealing novel
insights into SG assembly. It will be interesting to learn how SG
functions in integrated stress responses and if SG assembly itself
further signals stress responses in forward feedback loops or
antagonizes them in negative feedback loops, and to what extent
crosstalk with Toll-like receptor or interferon signaling pathways
occurs. Hopefully the lessons learned will translate into novel
therapies to control viral gene expression and aid infection control
and provide new insights into cancer and stress-associated
I apologize to colleagues whose work was not cited here owing to space
limitations. I thank Lucas Reineke for proofreading.
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