Stress Granules
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cellular biology Cell biology (also cellular biology or cytology) is a branch of biology that studies the Anatomy, structure, Physiology, function, and behavior of cell (biology), cells. All living organisms are made of cells. A cell is the basic unit of life th ...
, stress granules are
biomolecular condensate In biochemistry, biomolecular condensates are a class of membrane-less organelles and organelle subdomains, which carry out specialized functions within the cell. Unlike many organelles, biomolecular condensate composition is not controlled ...
s in the
cytosol The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells ( intracellular fluid (ICF)). It is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondri ...
composed of
proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...
and
RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...
that assemble into 0.1–2 μm membraneless organelles when the
cell Cell most often refers to: * Cell (biology), the functional basic unit of life * Cellphone, a phone connected to a cellular network * Clandestine cell, a penetration-resistant form of a secret or outlawed organization * Electrochemical cell, a de ...
is under stress. The mRNA molecules found in stress granules are stalled
translation Translation is the communication of the semantics, meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The English la ...
pre-initiation complexes associated with 40S
ribosomal Ribosomes () are macromolecular machines, found within all cells, that perform biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to fo ...
subunits, translation initiation factors, poly(A)+ mRNA and RNA-binding proteins (RBPs). While they are membraneless organelles, stress granules have been proposed to be associated with the
endoplasmatic reticulum The endoplasmic reticulum (ER) is a part of a transportation system of the eukaryotic cell, and has many other important functions such as protein folding. The word endoplasmic means "within the cytoplasm", and reticulum is Latin for "little ne ...
. There are also
nuclear Nuclear may refer to: Physics Relating to the nucleus of the atom: *Nuclear engineering *Nuclear physics *Nuclear power *Nuclear reactor *Nuclear weapon *Nuclear medicine *Radiation therapy *Nuclear warfare Mathematics * Nuclear space *Nuclear ...
stress granules. This article is about the
cytosolic The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells ( intracellular fluid (ICF)). It is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondri ...
variety.


Proposed functions

The function of stress granules remains largely unknown. Stress granules have long been proposed to have a function to protect RNA from harmful conditions, thus their appearance under stress. The accumulation of RNA into dense globules could keep them from reacting with harmful chemicals and safeguard the information coded in their
RNA sequence A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nu ...
. Stress granules might also function as a decision point for untranslated mRNA. Molecules can go down one of three paths: further storage, degradation, or re-initiation of
translation Translation is the communication of the semantics, meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The English la ...
. Conversely, it has also been argued that stress granules are not important sites for mRNA storage nor do they serve as an intermediate location for mRNA in transit between a state of storage and a state of degradation. Efforts to identify all RNA within stress granules (the stress granule
transcriptome The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The ...
) in an unbiased way by sequencing RNA from biochemically purified stress granule "cores" have shown that RNA are not recruited to stress granules in a sequence-specific manner, but rather generically, with longer and/or less-optimally translated transcripts being enriched. These data imply that the stress granule transcriptome is influenced by the valency of RNA (for proteins or other RNA) and by the rates of RNA run-off from
polysome A polyribosome (or polysome or ergosome) is a group of ribosomes bound to an mRNA molecule like “beads” on a “thread”. It consists of a complex of an mRNA molecule and two or more ribosomes that act to translate mRNA instructions into p ...
s. The latter is further supported by recent single molecule imaging studies. Furthermore, it was estimated that only about 15% of the total mRNA in the cell is localized to stress granules, suggesting that stress granules only influence a minority of mRNA in the cell and may not be as important for mRNA processing as previously thought. That said, these studies represent only a snapshot in time, and it is likely that a larger fraction of mRNA are at one point stored in stress granules due to those RNA transiting in and out. The stress proteins that are the main component of stress granules in plant cells are molecular chaperones that sequester, protect, and possibly repair proteins that unfold during heat and other types of stress. Therefore, any association of mRNA with stress granules may simply be a side effect of the association of partially unfolded RNA-binding proteins with stress granules, similar to the association of mRNA with
proteasome Proteasomes are essential protein complexes responsible for the degradation of proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are called proteases. Proteasomes are found inside all e ...
s.


RNA damage

DHX9 is a distinct stress granule that has helicase activity capable of acting on
double-stranded RNA Double-stranded RNA (dsRNA) is RNA with two complementary strands found in cells. It is similar to DNA but with the replacement of thymine by uracil and the adding of one oxygen atom. Despite the structural similarities, much less is known about ...
, but not on
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
, to promote cell survival. DHX9 acts as a non-membrane bound cytoplasmic compartment to safeguard daughter cells from parental RNA damage. Assembly of DHX9 stress granules appears to be a dedicated mechanism in mammalian cells for protecting against RNA crosslinking damage.


Formation

Environmental stressors trigger cellular signaling, eventually leading to the formation of stress granules. ''
In vitro ''In vitro'' (meaning ''in glass'', or ''in the glass'') Research, studies are performed with Cell (biology), cells or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in ...
'', these stressors can include heat, cold,
oxidative stress Oxidative stress reflects an imbalance between the systemic manifestation of reactive oxygen species and a biological system's ability to readily detoxify the reactive intermediates or to repair the resulting damage. Disturbances in the normal ...
(sodium arsenite), endoplasmic reticulum stress (
thapsigargin Thapsigargin is a non-competitive inhibitor of the sarco/endoplasmic reticulum Ca2+ ATPase ( SERCA). Structurally, thapsigargin is classified as a guaianolide, and is extracted from a plant, '' Thapsia garganica''. It is a tumor promoter in ...
), proteasome inhibition (
MG132 MG132 is a potent, reversible, and cell-permeable proteasome inhibitor ( Ki = 4 nM). It belongs to the class of synthetic peptide aldehydes. It reduces the degradation of ubiquitin-conjugated proteins in mammalian cells and permeable strains o ...
), hyperosmotic stress,
ultraviolet radiation Ultraviolet radiation, also known as simply UV, is electromagnetic radiation of wavelengths of 10–400 nanometers, shorter than that of visible light, but longer than X-rays. UV radiation is present in sunlight and constitutes about 10% of t ...
, inhibition of
eIF4A The eukaryotic initiation factor-4A (eIF4A) family consists of 3 closely related proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of Messenger RNA, mRNA to 40S ribosome, ribosomal subunits. In addition these prot ...

pateamine A
hippuristanol Hippuristanol is a small molecule found in the coral '' Isis hippuris'' which was discovered by Jerry Pelletier and others of McGill University in Montreal, Quebec, Canada. It appears to have anti-viral activity and may hold promise as a cancer ...
, or RocA), nitric oxide accumulation after treatment with 3-morpholinosydnonimine (SIN-1), perturbation of pre- mRNA splicing, and other stressors, like
puromycin Puromycin is an antibiotic protein synthesis inhibitor which causes premature chain termination during translation. Inhibition of translation Puromycin is an aminonucleoside antibiotic, derived from the '' Streptomyces alboniger'' bacterium, ...
, which result in disassembled
polysome A polyribosome (or polysome or ergosome) is a group of ribosomes bound to an mRNA molecule like “beads” on a “thread”. It consists of a complex of an mRNA molecule and two or more ribosomes that act to translate mRNA instructions into p ...
s. Many of these stressors result in the activation of particular stress-associated
kinase In biochemistry, a kinase () is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule don ...
s (HRI, PERK, PKR, and GCN2), translational inhibition and stress granule formation. Stress granules will also form upon Gαq activation in a mechanism that involves the release of stress granule associated proteins from the cytosolic population of the Gαq effector
phospholipase C Phospholipase C (PLC) is a class of membrane-associated enzymes that cleave phospholipids just before the phosphate group (see figure). It is most commonly taken to be synonymous with the human forms of this enzyme, which play an important role i ...
β. Stress granule formation is often downstream of the stress-activated
phosphorylation In biochemistry, phosphorylation is described as the "transfer of a phosphate group" from a donor to an acceptor. A common phosphorylating agent (phosphate donor) is ATP and a common family of acceptor are alcohols: : This equation can be writ ...
of eukaryotic translation initiation factor
eIF2α Eukaryotic translation initiation factor 2 subunit 1 (eIF2α) is a protein that in humans is encoded by the ''EIF2S1'' gene. Function The protein encoded by this gene is the alpha (α) subunit of the translation initiation factor eIF2 prote ...
; this does not hold true for all types of stressors that induce stress granules, for instance, eIF4A inhibition. Further downstream,
prion A prion () is a Proteinopathy, misfolded protein that induces misfolding in normal variants of the same protein, leading to cellular death. Prions are responsible for prion diseases, known as transmissible spongiform encephalopathy (TSEs), w ...
-like aggregation of the protein
TIA-1 TIA1 or Tia1 cytotoxic granule-associated rna binding protein is a 3'UTR mRNA binding protein that can bind the 5'TOP sequence of 5'TOP mRNAs. It is associated with programmed cell death (apoptosis) and regulates alternative splicing of the gene ...
promotes the formation of stress granules. The term
prion A prion () is a Proteinopathy, misfolded protein that induces misfolding in normal variants of the same protein, leading to cellular death. Prions are responsible for prion diseases, known as transmissible spongiform encephalopathy (TSEs), w ...
-like is used because aggregation of
TIA-1 TIA1 or Tia1 cytotoxic granule-associated rna binding protein is a 3'UTR mRNA binding protein that can bind the 5'TOP sequence of 5'TOP mRNAs. It is associated with programmed cell death (apoptosis) and regulates alternative splicing of the gene ...
is
concentration In chemistry, concentration is the abundance of a constituent divided by the total volume of a mixture. Several types of mathematical description can be distinguished: '' mass concentration'', '' molar concentration'', '' number concentration'', ...
dependent, inhibited by chaperones, and because the aggregates are resistant to
proteases A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do ...
. It has also been proposed that
microtubules Microtubules are polymers of tubulin that form part of the cytoskeleton and provide structure and shape to eukaryotic cells. Microtubules can be as long as 50 micrometres, as wide as 23 to 27  nm and have an inner diameter between 11 an ...
play a role in the formation of stress granules, perhaps by transporting granule components. This hypothesis is based on the fact that disruption of microtubules with the chemical
nocodazole Nocodazole is an antineoplastic agent which exerts its effect in cells by interfering with the polymerization of microtubules. Microtubules are one type of fibre which constitutes the cytoskeleton, and the dynamic microtubule network has se ...
blocks the appearance of the granules. Furthermore, many signaling molecules have been shown to regulate the formation or dynamics of stress granules; these include the "master energy sensor" AMP-activated protein kinase (AMPK), the O-GlcNAc transferase enzyme (OGT), and the pro-apoptotic kinase
ROCK1 ROCK1 is a protein serine/threonine kinase also known as rho-associated, coiled-coil-containing protein kinase 1. Other common names are ROKβ and P160ROCK. ROCK1 is a major downstream effector of the small GTPase RhoA and is a regulator of the ...
.


Potential roles of RNA-RNA interactions

RNA
phase transitions In physics, chemistry, and other related fields like biology, a phase transition (or phase change) is the physical process of transition between one state of a medium and another. Commonly the term is used to refer to changes among the basic Sta ...
driven in part by intermolecular RNA-RNA interactions may play a role in stress granule formation. Similar to intrinsically disordered proteins, total RNA extracts are capable of undergoing phase separation in physiological conditions ''in vitro''.
RNA-seq RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also k ...
analyses demonstrate that these assemblies share a largely overlapping
transcriptome The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The ...
with stress granules, with RNA enrichment in both being predominately based on the length of the RNA. Further, stress granules contain many
RNA helicase Helicases are a class of enzymes that are vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic double helix, separating the two hybridized ...
s, including the DEAD/H-box helicase
Ded1p
DDX3,
eIF4A1 Eukaryotic initiation factor 4A-I (also known as eIF4A1 or DDX2A) is a 46 kDa cytosolic protein that, in humans, is encoded by the ''EIF4A1'' gene, which is located on chromosome 17. It is the most prevalent member of the eIF4A protein family, fa ...
, and RHAU. In yeast, catalytic ''ded1'' mutant alleles give rise to constitutive stress granules ATPase-deficient DDX3X (the mammalian homolog of Ded1) mutant alleles are found in pediatric
medulloblastoma Medulloblastoma is a common type of primary brain cancer in children. It originates in the part of the brain that is towards the back and the bottom, on the floor of the skull, in the cerebellum, or posterior fossa. The brain is divided into two ...
, and these coincide with constitutive granular assemblies in patient cells. These mutant DDX3 proteins promote stress granule assembly in
HeLa HeLa () is an immortalized cell line used in scientific research. It is the oldest human cell line and one of the most commonly used. HeLa cells are durable and prolific, allowing for extensive applications in scientific study. The line is ...
cells. In mammalian cells, RHAU mutants lead to reduced stress granule dynamics. Thus, some hypothesize that RNA aggregation facilitated by intermolecular RNA-RNA interactions plays a role in stress granule formation, and that this role may be regulated by RNA
helicases Helicases are a class of enzymes that are vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic double helix, separating the two hybridized n ...
. There is also evidence that RNA within stress granules is more compacted, compared to RNA in the
cytoplasm The cytoplasm describes all the material within a eukaryotic or prokaryotic cell, enclosed by the cell membrane, including the organelles and excluding the nucleus in eukaryotic cells. The material inside the nucleus of a eukaryotic cell a ...
, and that the RNA is found to be post-translationally modified by
N6-methyladenosine ''N''6-Methyladenosine (m6A) was originally identified and partially characterised in the 1970s, and is an abundant modification in mRNA and DNA. It is found within some viruses, and most eukaryotes including mammals, insects, plants and yeast. I ...
(m6A) on its 5' ends or RNA acetylation ac4C. Recent work has shown that the highly abundant translation initiation factor and DEAD-box protein eIF4A limits stress granule formation. It does so through its ability to bind ATP and RNA, acting analogously to protein chaperones like
Hsp70 The 70 kilodalton heat shock proteins (Hsp70s or DnaK) are a family of conserved ubiquitously expressed heat shock proteins. Proteins with similar structure exist in virtually all living organisms and play crucial roles in the development of can ...
.


Connection with processing bodies

Stress granules and
P-bodies In cellular biology, P-bodies, or processing bodies, are distinct foci formed by phase separation within the cytoplasm of a eukaryotic cell consisting of many enzymes involved in mRNA turnover. P-bodies are highly conserved structures and have ...
(processing bodies) share
RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...
and
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
components, both appear under stress, and can physically associate with one another. As of 2018, of the ~660 proteins identified as localizing to stress granules, ~11% also have been identified as processing body-localized proteins (see below). The protein
G3BP1 Ras GTPase-activating protein-binding protein 1 is an enzyme that in humans is encoded by the ''G3BP1'' gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nuc ...
is necessary for the proper docking of processing bodies and stress granules to each other, which may be important for the preservation of polyadenylated mRNA. Although some protein components are shared between stress granules and processing bodies, the majority of proteins in either structure are uniquely localized to either structure. While both stress granules and P-bodies are associated with
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...
, processing bodies have been long proposed to be sites of mRNA degradation because they contain
enzymes An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as pro ...
such as DCP1/2 and
XRN1 5′-3′ exoribonuclease 1 (Xrn1) is a protein that in humans is encoded by the XRN1 gene. Xrn1 hydrolyses RNA in the 5′ to 3′ direction. Function This gene encodes a member of the 5′-3′ exonuclease family. The encoded protein may be ...
that are known to degrade mRNA. However, others have demonstrated that mRNA associated with processing bodies are largely translationally repressed but not degraded. It has also been proposed that mRNA selected for degradation are passed from stress granules to processing bodies, though there is also data suggesting that processing bodies precede and promote stress granule formation.


Protein composition of stress granules

The complete
proteome A proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. P ...
of stress granules is still unknown, but efforts have been made to catalog all of the proteins that have been experimentally demonstrated to transit into stress granules. Importantly, different
stressors A stressor is a chemical or biological agent, environmental condition, external stimulus or an event seen as causing stress to an organism. Psychologically speaking, a stressor can be events or environments that individuals might consider dema ...
can result in stress granules with different protein components. Many stress granule-associated proteins have been identified by transiently stressing cultured cells and utilizing
microscopy Microscopy is the technical field of using microscopes to view subjects too small to be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of microscopy: optical mic ...
to detect the localization of a protein of interest either by expressing that protein fused to a
fluorescent protein Fluorescent proteins include: * Green fluorescent protein The green fluorescent protein (GFP) is a protein that exhibits green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the ...
(i.e.
green fluorescent protein The green fluorescent protein (GFP) is a protein that exhibits green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish ''Aequorea victo ...
(GFP)) and/or by fixing cells and using
antibodies An antibody (Ab) or immunoglobulin (Ig) is a large, Y-shaped protein belonging to the immunoglobulin superfamily which is used by the immune system to identify and neutralize antigens such as bacteria and viruses, including those that caus ...
to detect the protein of interest along with known protein markers of stress granules (
immunocytochemistry Immunocytochemistry (ICC) is a common laboratory technique that is used to anatomically visualize the localization of a specific protein or antigen in cells by use of a specific primary antibody that binds to it. The primary antibody allows vis ...
). In 2016, stress granule "cores" were experimentally identified and then biochemically purified for the first time. Proteins in the cores were identified in an unbiased manner using
mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...
. This technical advance lead to the identification of hundreds of new stress granule-localized proteins. The proteome of stress granules has also been experimentally determined by using two slightly different proximity labeling approaches. One of these proximity labeling approaches is the ascorbate peroxidase (APEX) method, in which cells are engineered to express a known stress granule protein, such as
G3BP1 Ras GTPase-activating protein-binding protein 1 is an enzyme that in humans is encoded by the ''G3BP1'' gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nuc ...
, fused to a modified ascorbate peroxidase enzyme called APEX. Upon incubating the cells in
biotin Biotin (also known as vitamin B7 or vitamin H) is one of the B vitamins. It is involved in a wide range of metabolic processes, both in humans and in other organisms, primarily related to the utilization of fats, carbohydrates, and amino acids. ...
and treating the cells with
hydrogen peroxide Hydrogen peroxide is a chemical compound with the formula . In its pure form, it is a very pale blue liquid that is slightly more viscosity, viscous than Properties of water, water. It is used as an oxidizer, bleaching agent, and antiseptic, usua ...
, the APEX enzyme will be briefly activated to biotinylate all proteins in close proximity to the protein of interest, in this case G3BP1 within stress granules. Proteins that are biotinylated can then be isolated via
streptavidin Streptavidin is a 52 Atomic mass unit, kDa protein (tetramer) purified from the bacterium ''Streptomyces avidinii''. Streptavidin Homotetramer, homo-tetramers have an extraordinarily high affinity for biotin (also known as vitamin B7 or vitamin ...
and identified using
mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...
. The APEX technique was used to identify ~260 stress granule-associated proteins in several cell types, including
neurons A neuron (American English), neurone (British English), or nerve cell, is an membrane potential#Cell excitability, excitable cell (biology), cell that fires electric signals called action potentials across a neural network (biology), neural net ...
, and with various stressors. Of the 260 proteins identified in this study, ~143 had not previously been demonstrated to be stress granule-associated. Another proximity labeling method used to determine the proteome of stress granules is BioID. BioID is similar to the APEX approach, in that a biotinylating protein (BirA* instead of APEX) was expressed in cells as a fusion protein with several known stress granule-associated proteins. Proteins in close proximity to BirA* will be biotinylated and are then identified by
mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...
. Youn et al. used this method to identify/predict 138 proteins as stress granule-associated and 42 as processing body-associated. A curated database of stress granule-associated proteins can be found her

The following is a list of proteins that have been demonstrated to localize to stress granules (compiled from ):


References


Further reading

* *
— molecular details of stress granule assembly & function * {{refend


External links

Laboratories:
Anderson lab, post-transcriptional control & inflammatory response

Zhou lab, neurodegenerative disease




Cell biology