Systemic control of protein synthesis through sequestration of translation and ribosome biogenesis factors during severe heat stress

Stress granules in atherosclerosis: Insights and therapeutic opportunities

Atherosclerosis, a complex inflammatory and metabolic disorder, is the underlying cause of several life-threatening cardiovascular diseases. Stress granules (SG) are biomolecular condensates composed of proteins and mRNA that form in response to stress. Recent studies suggest a potential link between SG and atherosclerosis development. However, there remain gaps in understanding SG role in atherosclerosis development. Here we provide a thorough analysis of the role of SG in atherosclerosis, covering cellular stresses stimulation, core components, and regulatory genes in SG formation. Furthermore, we explore atherosclerosis induced factors such as inflammation, low or oscillatory shear stress (OSS), and oxidative stress (OS) may impact SG formation and then the development of atherosclerotic lesions. We have assessed how changes in SG dynamics impact pro-atherogenic processes like endothelial dysfunction, lipid metabolism, and immune cell recruitment in atherosclerosis. In summary, this review emphasizes the complex interplay between SG and atherosclerosis that could open innovative directions for targeted therapeutic strategies in preventing or treating atherosclerotic cardiovascular diseases.

Osmotic stress induces formation of both liquid condensates and amyloids by a yeast prion domain

Liquid protein condensates produced by phase separation are involved in the spatiotemporal control of cellular functions, while solid fibrous aggregates (amyloids) are associated with diseases and/or manifest as infectious or heritable elements (prions). Relationships between these assemblies are poorly understood. The Saccharomyces cerevisiae release factor Sup35 can produce both fluid liquid-like condensates (e. g. at acidic pH) and amyloids (typically cross-seeded by other prions). We observed acidification-independent formation of Sup35-based liquid condensates in response to hyperosmotic shock in the absence of other prions, both at increased and physiological expression levels . The Sup35 prion domain, Sup35N, is both necessary and sufficient for condensate formation, while the middle domain, Sup35M antagonizes this process. Formation of liquid condensates in response to osmotic stress is conserved within yeast evolution. Notably, condensates of Sup35N/NM protein originated from the distantly related yeast Ogataea methanolica can directly convert to amyloids in osmotically stressed S. cerevisiae cells, providing a unique opportunity for real-time monitoring of condensate-to-fibril transition in vivo by fluorescence microscopy. Thus, cellular fate of stress-induced condensates depends on protein properties and/or intracellular environment.

Stress-dependent condensate formation regulated by the ubiquitin-related modifier Urm1

The ability of proteins and RNA to coalesce into phase-separated assemblies, such as the nucleolus and stress granules, is a basic principle in organizing membraneless cellular compartments. While the constituents of biomolecular condensates are generally well documented, the mechanisms underlying their formation under stress are only partially understood. Here, we show in yeast that covalent modification with the ubiquitin-like modifier Urm1 promotes the phase separation of a wide range of proteins. We find that the drop in cellular pH induced by stress triggers Urm1 self-association and its interaction with both target proteins and the Urm1-conjugating enzyme Uba4. Urmylation of stress-sensitive proteins promotes their deposition into stress granules and nuclear condensates. Yeast cells lacking Urm1 exhibit condensate defects that manifest in reduced stress resilience. We propose that Urm1 acts as a reversible molecular "adhesive" to drive protective phase separation of functionally critical proteins under cellular stress.

Role of J-domain Proteins in Yeast Physiology and Protein Quality Control

The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the folding of newly synthesized proteins to the disassembly and refolding of protein aggregates. This multifunctionality of Hsp70 is governed by J-domain proteins (JDPs), which act as indispensable co-chaperones that target specific substrates to Hsp70. The number of distinct JDPs present in a species always outnumbers Hsp70, documenting JDP function in functional diversification of Hsp70. In this review, we describe the physiological roles of JDPs in the Saccharomyces cerevisiae PQC system, with a focus on the abundant JDP generalists, Zuo1, Ydj1 and Sis1, which function in fundamental cellular processes. Ribosome-bound Zuo1 cooperates with the Hsp70 chaperones Ssb1/2 in folding and assembly of nascent polypeptides. Ydj1 and Sis1 cooperate with the Hsp70 members Ssa1 to Ssa4 to exert overlapping functions in protein folding and targeting of newly synthesized proteins to organelles including mitochondria and facilitating the degradation of aberrant proteins by E3 ligases. Furthermore, they act in protein disaggregation reactions, though Ydj1 and Sis1 differ in their modes of Hsp70 cooperation and substrate specificities. This results in functional specialization as seen in prion propagation and the underlying dominant role of Sis1 in targeting Hsp70 for shearing of prion amyloid fibrils.

Isoform-specific sequestration of protein kinase A fine-tunes intracellular signaling during heat stress

Protein kinase A (PKA) is a conserved kinase crucial for fundamental biological processes linked to growth, development, and metabolism. The PKA catalytic subunit is expressed as multiple isoforms in diverse eukaryotes; however, their contribution to ensuring signaling specificity in response to environmental cues remains poorly defined. Catalytic subunit activity is classically moderated via interaction with an inhibitory regulatory subunit. Here, a quantitative mass spectrometry approach is used to examine heat-stress-induced changes in the binding of yeast Tpk1-3 catalytic subunits to the Bcy1 regulatory subunit. We show that Tpk3 is not regulated by Bcy1 binding but, instead, is deactivated upon heat stress via reversible sequestration into cytoplasmic granules. These "Tpk3 granules" are enriched for multiple PKA substrates involved in various metabolic processes, with the Hsp42 sequestrase required for their formation. Hence, regulated sequestration of Tpk3 provides a mechanism to control isoform-specific kinase signaling activity during stress conditions.

K29-linked free polyubiquitin chains affect ribosome biogenesis and direct ribosomal proteins to the intranuclear quality control compartment

Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs) Ubp2 and Ubp14, and E3 ligases Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the intranuclear quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with ribosomopathies.

Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts

Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. Here we show that, in striking contrast, virtually all mRNA species condense in response to multiple unrelated stresses in budding yeast, length plays a minor role, and instead, stress-induced transcripts are preferentially excluded from condensates, enabling their selective translation. Using both endogenous genes and reporter constructs, we show that translation initiation blockade, rather than resulting ribosome-free RNA, causes condensation. These translation initiation-inhibited condensates (TIICs) are biochemically detectable even when stress granules, defined as microscopically visible foci, are absent or blocked. TIICs occur in unstressed yeast cells, and, during stress, grow before the appearance of visible stress granules. Stress-induced transcripts are excluded from TIICs primarily due to the timing of their expression, rather than their sequence features. Together, our results reveal a simple system by which cells redirect translational activity to newly synthesized transcripts during stress, with broad implications for cellular regulation in changing conditions.

eIF4F is a thermo-sensing regulatory node in the translational heat shock response

Heat-shocked cells prioritize the translation of heat shock (HS) mRNAs, but the underlying mechanism is unclear. We report that HS in budding yeast induces the disassembly of the eIF4F complex, where eIF4G and eIF4E assemble into translationally arrested mRNA ribonucleoprotein particles (mRNPs) and HS granules (HSGs), whereas eIF4A promotes HS translation. Using in vitro reconstitution biochemistry, we show that a conformational rearrangement of the thermo-sensing eIF4A-binding domain of eIF4G dissociates eIF4A and promotes the assembly with mRNA into HS-mRNPs, which recruit additional translation factors, including Pab1p and eIF4E, to form multi-component condensates. Using extracts and cellular experiments, we demonstrate that HS-mRNPs and condensates repress the translation of associated mRNA and deplete translation factors that are required for housekeeping translation, whereas HS mRNAs can be efficiently translated by eIF4A. We conclude that the eIF4F complex is a thermo-sensing node that regulates translation during HS.

An adaptive biomolecular condensation response is conserved across environmentally divergent species

Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.

Using a metabolomics approach to investigate the sensitivity of a potential Arctic-invader and its Arctic sister-species to marine heatwaves and traditional harvesting disturbances

Coastal species are threatened by fishing practices and changing environmental conditions, such as marine heatwaves (MHW). The mechanisms that confer tolerance to such stressors in marine invertebrates are poorly understood. However, differences in tolerance among different species may be attributed to their geographical distribution. To test the tolerance of species occupying different thermal ranges, we used two closely related bivalves the softshell clam Mya arenaria (Linnaeus, 1758), a cold-temperate invader with demonstrated potential for establishment in the Arctic, and the blunt gaper Mya truncata (Linnaeus, 1758), a native polar species. Clams were subjected to a thermal stress, mimicking a MHW, and harvesting stress in a controlled environment. Seven acute temperature changes (2, 7, 12, 17, 22, 27, and 32 °C) were tested at two harvesting disturbance intensities (with, without). Survival was measured after 12 days and three tissues (gills, mantle, and posterior adductor muscle) collected from surviving individuals for targeted metabolomic profiling. MHW tolerance differed significantly between species: 26.9 °C for M. arenaria and 17.8 °C for M. truncata, with a negligeable effect of harvesting. At the upper thermal limit, M. arenaria displayed a more profound metabolomic remodelling when compared to M. truncata, and this varied greatly between tissue types. Network analysis revealed differences in pathway utilization at the upper MHW limit, with M. arenaria displaying a greater reliance on multiple DNA repair and expression and cell signalling pathways, while M. truncata was limited to fewer pathways. This suggests that M. truncata is ill equipped to cope with warming environments. MHW patterning in the Northwest Atlantic may be a strong predictor of population survival and future range shifts in these two clam species. As polar environments undergo faster rates of warming compared to the global average, M. truncata may be outcompeted by M. arenaria expanding into its native range.

Contribution of the yeast bi-chaperone system in the restoration of the RNA helicase Ded1 and translational activity under severe ethanol stress

Preexposure to mild stress often improves cellular tolerance to subsequent severe stress. Severe ethanol stress (10% v/v) causes persistent and pronounced translation repression in Saccharomyces cerevisiae. However, it remains unclear whether preexposure to mild stress can mitigate translation repression in yeast cells under severe ethanol stress. We found that the translational activity of yeast cells pretreated with 6% (v/v) ethanol was initially significantly repressed under subsequent 10% ethanol but was then gradually restored even under severe ethanol stress. We also found that 10% ethanol caused the aggregation of Ded1, which plays a key role in translation initiation as a DEAD-box RNA helicase. Pretreatment with 6% ethanol led to the gradual disaggregation of Ded1 under subsequent 10% ethanol treatment in wild-type cells but not in fes1Δhsp104Δ cells, which are deficient in Hsp104 with significantly reduced capacity for Hsp70. Hsp104 and Hsp70 are key components of the bi-chaperone system that play a role in yeast protein quality control. fes1Δhsp104Δ cells did not restore translational activity under 10% ethanol, even after pretreatment with 6% ethanol. These results indicate that the regeneration of Ded1 through the bi-chaperone system leads to the gradual restoration of translational activity under continuous severe stress. This study provides new insights into the acquired tolerance of yeast cells to severe ethanol stress and the resilience of their translational activity.

An adaptive biomolecular condensation response is conserved across environmentally divergent species

Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.

K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ)

Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs), Ubp2 and Ubp14, and E3 ligases, Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the Ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the Intranuclear Quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with Ribosomopathies.

Genome-wide identification and analysis of HECT E3 ubiquitin ligase gene family in Ruditapes philippinarum and their involvement in the response to heat stress and Vibrio anguillarum infection

E3 ubiquitin ligase (E3s) plays an important role in ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains. However, the role of HECT E3 ubiquitin ligase in mollusk was rarely explored. In this study, we performed a genome-wide analysis of the HECT domain-containing gene in Ruditapes philippinarum to identify and predict the structural and functional characterization of HECT genes in response to abiotic and biotic stress. A total of sixteen members of HECT gene family were identified and analyzed for the gene structure, phylogenetic relation, three-dimensional structure, protein interaction network, and expression patterns. Experimental results demonstrated that Rph.HUWE1, Rph.HECTD1, Rph.Ubr5 were significantly up-regulated in response to heat stress and bacterial challenge. Taken together, our data provide insights into the potential function of HECT E3 ligase in heat stress and Vibrio anguillarum infection.

Stressful steps: Progress and challenges in understanding stress-induced mRNA condensation and accumulation in stress granules

Stress-induced condensation of mRNA and protein into massive cytosolic clusters is conserved across eukaryotes. Known as stress granules when visible by imaging, these structures remarkably have no broadly accepted biological function, mechanism of formation or dispersal, or even molecular composition. As part of a larger surge of interest in biomolecular condensation, studies of stress granules and related RNA/protein condensates have increasingly probed the biochemical underpinnings of condensation. Here, we review open questions and recent advances, including the stages from initial condensate formation to accumulation in mature stress granules, mechanisms by which stress-induced condensates form and dissolve, and surprising twists in understanding the RNA components of stress granules and their role in condensation. We outline grand challenges in understanding stress-induced RNA condensation, centering on the unique and substantial barriers in the molecular study of cellular structures, such as stress granules, for which no biological function has been firmly established.

Post-Transcriptional Dynamics is Involved in Rapid Adaptation to Hypergravity in Jurkat T Cells

The transcriptome of human immune cells rapidly reacts to altered gravity in a highly dynamic way. We could show in previous experiments that transcriptional patterns show profound adaption after seconds to minutes of altered gravity. To gain further insight into these transcriptional alteration and adaption dynamics, we conducted a highly standardized RNA-Seq experiment with human Jurkat T cells exposed to 9xg hypergravity for 3 and 15 min, respectively. We investigated the frequency with which individual exons were used during transcription and discovered that differential exon usage broadly appeared after 3 min and became less pronounced after 15 min. Additionally, we observed a shift in the transcript pool from coding towards non-coding transcripts. Thus, adaption of gravity-sensitive differentially expressed genes followed a dynamic transcriptional rebound effect. The general dynamics were compatible with previous studies on the transcriptional effects of short hypergravity on human immune cells and suggest that initial up-regulatory changes mostly result from increased elongation rates. The shift correlated with a general downregulation of the affected genes. All chromosome bands carried homogenous numbers of gravity-sensitive genes but showed a specific tendency towards up- or downregulation. Altered gravity affected transcriptional regulation throughout the entire genome, whereby the direction of differential expression was strongly dependent on the structural location in the genome. A correlation analysis with potential mediators of the early transcriptional response identified a link between initially upregulated genes with certain transcription factors. Based on these findings, we have been able to further develop our model of the transcriptional response to altered gravity.

GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents

Phase separation-based condensate formation is a novel working paradigm in biology, helping to rationalize many important cellular phenomena including the assembly of membraneless organelles. Uncovering the functional impact of cellular condensates requires a better knowledge of these condensates’ constituents. Herein, we introduce the webserver GraPES (Granule Protein Enrichment Server), a user-friendly online interface containing the MaGS and MaGSeq predictors, which provide propensity scores for proteins’ localization into cellular condensates. Our webpage contains models trained on human (Homo sapiens) and yeast (Saccharomyces cerevisiae) stress granule proteins. MaGS utilizes experimentally-based protein features for prediction, whereas MaGSeq is an entirely protein sequence-based implementation. GraPES is implemented in HTML/CSS and Javascript and is freely available for public use at https://grapes.msl.ubc.ca/. Documentation for using the provided webtools, descriptions of their methodology, and implementation notes can be found on the webpage.

Proteomic changes in broiler liver by body weight differences under chronic heat stress

The increasing global temperature is causing economic losses and animal welfare problems in the poultry industry. Because poultry do not have sweat glands, it is difficult for them to return to their usual body temperature. Heat stress has negative impact on production and health in broilers. Given the effects of chronic stress on broilers, the objective of this study was to identify physiological changes in differentially expressed proteins in broilers with different growth performances using liver tissue from 35-day-old chickens (Ross-308). Changes in protein levels were analyzed with two-dimensional gel electrophoresis (2DE) and mass spectrometry. This study contained 2 groups (control and heat treatment groups) with 8 replicates per group. After d 20, ten birds were assigned to each replicate. On d 35, the heat treatment group was subdivided into 2 groups, a heat stressed high body weight group (HH) and a heat stressed low body weight group (HL). Body weight was lower in the heat treatment group than that in the control group. In the heat treatment group, the HH group had a significantly higher body weight than the HL group. The expression of heat shock protein 70 significantly increased in the HL group. Protein spots with significant differences in 2DE analysis were screened and selected. Thirteen significant spots were excised and analyzed using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Among the 13 spots, 8 spots were identified. The identified spots were MRP-126, fatty acid binding protein, ferritin heavy chain, glutathione S-transferase, agmatinase; mitochondrial, alpha-enolase, 60 kDa heat shock protein; mitochondrial, and tubulin beta-7 chain. Our study has showed that high temperature stress aggravated oxidative stress in broilers, which resulted in comparatively slow growth to preserve body homeostasis.

Chaperones directly and efficiently disperse stress-triggered biomolecular condensates

Stresses such as heat shock trigger the formation of protein aggregates and the induction of a disaggregation system composed of molecular chaperones. Recent work reveals that several cases of apparent heat-induced aggregation, long thought to be the result of toxic misfolding, instead reflect evolved, adaptive biomolecular condensation, with chaperone activity contributing to condensate regulation. Here we show that the yeast disaggregation system directly disperses heat-induced biomolecular condensates of endogenous poly(A)-binding protein (Pab1) orders of magnitude more rapidly than aggregates of the most commonly used misfolded model substrate, firefly luciferase. Beyond its efficiency, heat-induced condensate dispersal differs from heat-induced aggregate dispersal in its molecular requirements and mechanistic behavior. Our work establishes a bona fide endogenous heat-induced substrate for long-studied heat shock proteins, isolates a specific example of chaperone regulation of condensates, and underscores needed expansion of the proteotoxic interpretation of the heat shock response to encompass adaptive, chaperone-mediated regulation.

Yeast stress granules at a glance

The formation of stress granules (SGs), membrane-less organelles that are composed of mainly messenger ribonucleoprotein assemblies, is the result of a conserved evolutionary strategy to cellular stress. During their formation, which is triggered by robust environmental stress, SGs sequester translationally inactive mRNA molecules, which are either forwarded for further processing elsewhere or stored during a period of stress within SGs. Removal of mRNA molecules from active translation and their sequestration in SGs allows preferential translation of stress response transcripts. By affecting the specificity of mRNA translation, mRNA localization and stability, SGs are involved in the overall cellular reprogramming during periods of environmental stress and viral infection. Over the past two decades, we have learned which processes drive SGs assembly, how their composition varies under stress, and how they co-exist with other subcellular organelles. Yeast as a model has been instrumental in our understanding of SG biology. Despite the specific differences between the SGs of yeast and mammals, yeast have been shown to be a valuable tool to the study of SGs in translation-related stress response. This review summarizes the data surrounding SGs that are formed under different stress conditions in Saccharomyces cerevisiae and other yeast species. It offers a comprehensive and up-to-date view on these still somewhat mysterious entities.

Dynamics and thermal sensitivity of ribosomal RNA maturation paths in plants

Ribosome biogenesis is a constitutive fundamental process for cellular function. Its rate of production depends on the rate of maturation of precursor ribosomal RNA (pre-rRNA). The rRNA maturation paths are marked by four dominant rate-limiting intermediates with cell-type variation of the processivity rate. We have identified that high temperature stress in plants, while halting the existing pre-rRNA maturation schemes, also transiently triggers an atypical pathway for 35S pre-rRNA processing. This pathway leads to production of an aberrant precursor rRNA, reminiscent of yeast 24S, encompassing 18S and 5.8S rRNA that do not normally co-occur together at sub-unit levels; this response is elicited specifically by high and not low temperatures. We show this response to be conserved in two other model crop plant species (Rice and Tomato). This pathway persists even after returning to normal growth conditions for 1 hour and is reset between 1-6 hours after stress treatment, likely, due to resumption of normal 35S pre-rRNA synthesis and processing. The heat-induced ITS2 cleavage-derived precursors and stalled P-A2-like precursors were heterogeneous in nature with a fraction containing polymeric (A) tails. Furthermore, high temperature treatment and subsequent fractionation resulted in polysome and precursor rRNA depletion.

eIF3a Destabilization and TDP-43 Alter Dynamics of Heat-Induced Stress Granules

Stress granules (SGs) are membrane-less assemblies arising upon various stresses in eukaryotic cells. They sequester mRNAs and proteins from stressful conditions and modulate gene expression to enable cells to resume translation and growth after stress relief. SGs containing the translation initiation factor eIF3a/Rpg1 arise in yeast cells upon robust heat shock (HS) at 46 °C only. We demonstrate that the destabilization of Rpg1 within the PCI domain in the Rpg1-3 variant leads to SGs assembly already at moderate HS at 42 °C. These are bona fide SGs arising upon translation arrest containing mRNAs, which are components of the translation machinery, and associating with P-bodies. HS SGs associate with endoplasmatic reticulum and mitochondria and their contact sites ERMES. Although Rpg1-3-labeled SGs arise at a lower temperature, their disassembly is delayed after HS at 46 °C. Remarkably, the delayed disassembly of HS SGs after the robust HS is reversed by TDP-43, which is a human protein connected with amyotrophic lateral sclerosis. TDP-43 colocalizes with HS SGs in yeast cells and facilitates cell regrowth after the stress relief. Based on our results, we propose yeast HS SGs labeled by Rpg1 and its variants as a novel model system to study functions of TDP-43 in stress granules disassembly.

Early Heat Exposure Effects on Proteomic Changes of the Broiler Liver under Acute Heat Stress

Simple Summary

Early heat exposure have been studied in the poultry industry as a method of reducing heat stress (HS) on poultry. However, the results of each study are inconsistent, and it has not been confirmed which mechanisms reduce HS by early heat exposure. Therefore, we tried to confirm the relaxation mechanism through proteomic analysis after applying early and acute heat exposure to broilers. The broilers were divided into three treatments, followed by CC (control group), CH (acute HS at the 35th day), and HH (early heat exposure at the fifth day and acute HS at the 35th day. Liver samples were collected and analyzed for proteomics and functional analysis. Proteins related to various functions, such as carbohydrate metabolism, fatty acid metabolism, energy metabolism, and the oxidation–reduction process, which were dramatically changed by acute HS, and were alleviated similar to the control group by early heat exposure. Through these results, the mechanism by which early heat exposure induces homeostasis during acute HS, and the possibility of the early heat exposure as a method of reducing HS were confirmed.

Abstract

As environmental temperatures continue to rise, heat stress (HS) is having a negative effect on the livestock industry. In order to solve this problem, many studies have been conducted to reduce HS. Among them, early heat exposure has been suggested as a method for reducing HS in poultry. In this study, we analyzed proteomics and tried to identify the metabolic mechanisms of early heat exposure on acute HS. A total of 48 chicks were separated into three groups: CC (control groups raised at optimum temperature), CH (raised with CC but exposed acute HS at the 35th day), and HH (raised with CC but exposed early heat at the fifth day and acute HS at the 35th day). After the whole period, liver samples were collected for proteomic analysis. A total of 97 differentially expressed proteins were identified by acute HS. Of these, 62 proteins recovered their expression levels by early heat exposure. We used these 62 proteins to determine the protective effects of early heat exposure. Of the various protein-related terms, we focused on the oxidative phosphorylation, fatty acid metabolism, carbohydrate metabolism, and energy production metabolism. Our findings suggest the possibility of early heat exposure effects in acute HS that may be useful in breeding or management techniques for producing broilers with high heat resistance.

Understanding and exploiting interactions between cellular proteostasis pathways and infectious prion proteins for therapeutic benefit

Several neurodegenerative diseases of humans and animals are caused by the misfolded prion protein (PrP^Sc), a self-propagating protein infectious agent that aggregates into oligomeric, fibrillar structures and leads to cell death by incompletely understood mechanisms. Work in multiple biological model systems, from simple baker's yeast to transgenic mouse lines, as well as in vitro studies, has illuminated molecular and cellular modifiers of prion disease. In this review, we focus on intersections between PrP and the proteostasis network, including unfolded protein stress response pathways and roles played by the powerful regulators of protein folding known as protein chaperones. We close with analysis of promising therapeutic avenues for treatment enabled by these studies.

The structure and function of deubiquitinases: lessons from budding yeast

Protein ubiquitination is a key post-translational modification that regulates diverse cellular processes in eukaryotic cells. The specificity of ubiquitin (Ub) signalling for different bioprocesses and pathways is dictated by the large variety of mono-ubiquitination and polyubiquitination events, including many possible chain architectures. Deubiquitinases (DUBs) reverse or edit Ub signals with high sophistication and specificity, forming an integral arm of the Ub signalling machinery, thus impinging on fundamental cellular processes including DNA damage repair, gene expression, protein quality control and organellar integrity. In this review, we discuss the many layers of DUB function and regulation, with a focus on insights gained from budding yeast. Our review provides a framework to understand key aspects of DUB biology.

The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins

Life is resilient because living systems are able to respond to elevated temperatures with an ancient gene expression program called the heat shock response (HSR). In yeast, the transcription of hundreds of genes is upregulated at stress temperatures. Besides stress protection conferred by chaperones, the function of the majority of the upregulated genes under stress has remained enigmatic. We show that those genes are required to directly counterbalance increased protein turnover at stress temperatures and to maintain the metabolism. This anaplerotic reaction together with molecular chaperones allows yeast to efficiently buffer proteotoxic stress. When the capacity of this system is exhausted at extreme temperatures, aggregation processes stop translation and growth pauses. The emerging concept is that the HSR is modular with distinct programs dependent on the severity of the stress.

Proteomic analysis reveals the direct recruitment of intrinsically disordered regions to stress granules in S. cerevisiae

Stress granules (SGs) are stress-induced membraneless condensates that store non-translating mRNA and stalled translation initiation complexes. Although metazoan SGs are dynamic compartments where proteins can rapidly exchange with their surroundings, yeast SGs seem largely static. To gain a better understanding of yeast SGs, we identified proteins that sediment after heat shock using mass spectrometry. Proteins that sediment upon heat shock are biased toward a subset of abundant proteins that are significantly enriched in intrinsically disordered regions (IDRs). Heat-induced SG localization of over 80 proteins were confirmed using microscopy, including 32 proteins not previously known to localize to SGs. We found that several IDRs were sufficient to mediate SG recruitment. Moreover, the dynamic exchange of IDRs can be observed using fluorescence recovery after photobleaching, whereas other components remain immobile. Lastly, we showed that the IDR of the Ubp3 deubiquitinase was critical for yeast SG formation. This work shows that IDRs can be sufficient for SG incorporation, can remain dynamic in vitrified SGs, and can play an important role in cellular compartmentalization upon stress.This article has an associated First Person interview with the first author of the paper.

Plant small heat shock proteins - evolutionary and functional diversity

Small heat shock proteins (sHSPs) are an ubiquitous protein family found in archaea, bacteria and eukaryotes. In plants, as in other organisms, sHSPs are upregulated by stress and are proposed to act as molecular chaperones to protect other proteins from stress-induced damage. sHSPs share an 'α-crystallin domain' with a β-sandwich structure and a diverse N-terminal domain. Although sHSPs are 12-25 kDa polypeptides, most assemble into oligomers with ≥ 12 subunits. Plant sHSPs are particularly diverse and numerous; some species have as many as 40 sHSPs. In angiosperms this diversity comprises ≥ 11 sHSP classes encoding proteins targeted to the cytosol, nucleus, endoplasmic reticulum, chloroplasts, mitochondria and peroxisomes. The sHSPs underwent a lineage-specific gene expansion, diversifying early in land plant evolution, potentially in response to stress in the terrestrial environment, and expanded again in seed plants and again in angiosperms. Understanding the structure and evolution of plant sHSPs has progressed, and a model for their chaperone activity has been proposed. However, how the chaperone model applies to diverse sHSPs and what processes sHSPs protect are far from understood. As more plant genomes and transcriptomes become available, it will be possible to explore theories of the evolutionary pressures driving sHSP diversification.

Changing faces of stress: Impact of heat and arsenite treatment on the composition of stress granules

Stress granules (SGs), hallmarks of the cellular adaptation to stress, promote survival, conserve cellular energy, and are fully dissolved upon the cessation of stress treatment. Different stresses can initiate the assembly of SGs, but arsenite and heat are the best studied of these stresses. The composition of SGs and posttranslational modifications of SG proteins differ depending on the type and severity of the stress insult, methodology used, cell line, and presence of overexpressed and tagged proteins. A group of 18 proteins showing differential localization to SGs in heat- and arsenite-stressed mammalian cell lines is described. Upon severe and prolonged stress, physiological SGs transform into more solid protein aggregates that are no longer reversible and do not contain mRNA. Similar pathological inclusions are hallmarks of neurodegenerative diseases. SGs induced by heat stress are less dynamic than SGs induced by arsenite and contain a set of unique proteins and linkage-specific polyubiquitinated proteins. The same types of ubiquitin linkages have been found to contribute to the development of neurodegenerative disorders such as Parkinson disease, Alzheimer disease, and amyotrophic lateral sclerosis (ALS). We propose heat stress-induced SGs as a possible model of an intermediate stage along the transition from dynamic, fully reversible arsenite stress-induced SGs toward aberrant SGs, the hallmark of neurodegenerative diseases. Stress- and methodology-specific differences in the compositions of SGs and the transition of SGs to aberrant protein aggregates are discussed. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization.

Condensation of Ded1p Promotes a Translational Switch from Housekeeping to Stress Protein Production

Cells sense elevated temperatures and mount an adaptive heat shock response that involves changes in gene expression, but the underlying mechanisms, particularly on the level of translation, remain unknown. Here we report that, in budding yeast, the essential translation initiation factor Ded1p undergoes heat-induced phase separation into gel-like condensates. Using ribosome profiling and an in vitro translation assay, we reveal that condensate formation inactivates Ded1p and represses translation of housekeeping mRNAs while promoting translation of stress mRNAs. Testing a variant of Ded1p with altered phase behavior as well as Ded1p homologs from diverse species, we demonstrate that Ded1p condensation is adaptive and fine-tuned to the maximum growth temperature of the respective organism. We conclude that Ded1p condensation is an integral part of an extended heat shock response that selectively represses translation of housekeeping mRNAs to promote survival under conditions of severe heat stress.

Non-translational Connections of eEF1B in the Cytoplasm and Nucleus of Cancer Cells

The human translation machinery includes three types of supramolecular complexes involved in elongation of the polypeptide chain: the ribosome, complex of elongation factors eEF1B and multienzyme aminoacyl-tRNA synthetase complex. Of the above, eEF1B is the least investigated assembly. Recently, a number of studies provided some insights into the structure of different eEF1B subunits and changes in their expression in cancer and other diseases. There is increasing agreement that possible disease-related functions of eEF1B are not necessarily related to its role in translation. This mini-review focuses on structural and functional features of the eEF1B complex while paying special attention to possible non-canonical functions of its subunits in cancer cells.

Composition-based prediction and rational manipulation of prion-like domain recruitment to stress granules

Mutations in a number of stress granule-associated proteins have been linked to various neurodegenerative diseases. Several of these mutations are found in aggregation-prone prion-like domains (PrLDs) within these proteins. In this work, we examine the sequence features governing PrLD localization to stress granules upon stress. We demonstrate that many yeast PrLDs are sufficient for stress-induced assembly into microscopically visible foci that colocalize with stress granule markers. Additionally, compositional biases exist among PrLDs that assemble upon stress, and these biases are consistent across different stressors. Using these biases, we have developed a composition-based prediction method that accurately predicts PrLD assembly into foci upon heat shock. We show that compositional changes alter PrLD assembly behavior in a predictable manner, while scrambling primary sequence has little effect on PrLD assembly and recruitment to stress granules. Furthermore, we were able to design synthetic PrLDs that were efficiently recruited to stress granules, and found that aromatic amino acids, which have previously been linked to PrLD phase separation, were dispensable for this recruitment. These results highlight the flexible sequence requirements for stress granule recruitment and suggest that PrLD localization to stress granules is driven primarily by amino acid composition, rather than primary sequence.

Distinct Features of Stress Granule Proteins Predict Localization in Membraneless Organelles

Recently generated proteomic data provides unprecedented insight into stress granule composition and stands as fruitful ground for further analysis. Stress granules are stress-induced biological assemblies that are of keen interest due to being linked to both long-term cell viability and a variety of protein aggregation-based diseases. Herein, we compile recently published stress granule composition data, formed specifically through heat and oxidative stress, for both mammalian (Homo sapiens) and yeast (Saccharomyces cerevisiae) cells. Interrogation of the data reveals that stress granule proteins are enriched in features that favor protein liquid-liquid phase separation, being highly disordered, soluble, and abundant while maintaining a high level of protein-protein interactions under basal conditions. Furthermore, these "stress granuleomes" are shown to be enriched for multidomained, RNA-binding proteins with increased potential for post-translational modifications. Findings are consistent with the notion that stress granule formation is driven by protein liquid-liquid phase separation. Furthermore, stress granule proteins appear poised near solubility limits while possessing the ability to dynamically alter their phase behavior in response to external threat. Interestingly, several features, such as protein disorder, are more prominent among stress granule proteins that share homologs between yeast and mammalian systems also found within stress-induced foci. We culminate results from our stress granule analysis into novel predictors for granule incorporation and validate the mammalian predictor's performance against multiple types of membraneless condensates and by colocalization microscopy.

The Cdc48-20S proteasome degrades a class of endogenous proteins in a ubiquitin-independent manner

The 26S proteasome is the major degradation machinery for soluble proteins in eukaryotes. Recent evidence reveals the existence of an alternative ATP-powered protein degradation complex, the Cdc48-20S proteasome complex, and we have identified yeast Sod1, a copper-zinc superoxide dismutase, as an endogenous substrate protein. Here, we identified yeast Ths1, an essential threonyl tRNA synthetase, as another endogenous substrate protein of the Cdc48-20S proteasome. In order to analyze the degradation mechanism in more details, we established an in vitro degradation system reconstituted using purified yeast components. Recombinant Sod1 and Ths1 directly interacted with Cdc48, and were degraded in a Cdc48-20S proteasome-dependent manner. Because the substrate proteins were purified from E. coli cells, no eukaryotic modifications including ubiquitination and phosphorylation exist. Therefore, although the 26S proteasome requires ubiquitination for specific recognition of the substrate proteins, the Cdc48-20S proteasome can degrade a class of substrate proteins without any modifications.

Cellular sequestrases maintain basal Hsp70 capacity ensuring balanced proteostasis

Maintenance of cellular proteostasis is achieved by a multi-layered quality control network, which counteracts the accumulation of misfolded proteins by refolding and degradation pathways. The organized sequestration of misfolded proteins, actively promoted by cellular sequestrases, represents a third strategy of quality control. Here we determine the role of sequestration within the proteostasis network in Saccharomyces cerevisiae and the mechanism by which it occurs. The Hsp42 and Btn2 sequestrases are functionally intertwined with the refolding activity of the Hsp70 system. Sequestration of misfolded proteins by Hsp42 and Btn2 prevents proteostasis collapse and viability loss in cells with limited Hsp70 capacity, likely by shielding Hsp70 from misfolded protein overload. Btn2 has chaperone and sequestrase activity and shares features with small heat shock proteins. During stress recovery Btn2 recruits the Hsp70-Hsp104 disaggregase by directly interacting with the Hsp70 co-chaperone Sis1, thereby shunting sequestered proteins to the refolding pathway.

The prion-like protein kinase Sky1 is required for efficient stress granule disassembly

Stress granules are membraneless protein- and mRNA-rich organelles that form in response to perturbations in environmental conditions. Stress granule formation is reversible, and persistent stress granules have been implicated in a variety of neurodegenerative disorders, including amyotrophic lateral sclerosis. However, characterization of the factors involved in dissolving stress granules is incomplete. Many stress granule proteins contain prion-like domains (PrLDs), some of which have been linked to stress granule formation. Here, we demonstrate that the PrLD-containing yeast protein kinase Sky1 is a stress granule component. Sky1 is recruited to stress granules in part via its PrLD, and Sky1's kinase activity regulates timely stress granule disassembly during stress recovery. This effect is mediated by phosphorylation of the stress granule component Npl3. Sky1 can compensate for defects in chaperone-mediated stress granule disassembly and vice-versa, demonstrating that cells have multiple overlapping mechanisms for re-solubilizing stress granule components.

Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function

In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.

The Co-chaperone Cns1 and the Recruiter Protein Hgh1 Link Hsp90 to Translation Elongation via Chaperoning Elongation Factor 2

The Hsp90 chaperone machinery in eukaryotes comprises a number of distinct accessory factors. Cns1 is one of the few essential co-chaperones in yeast, but its structure and function remained unknown. Here, we report the X-ray structure of the Cns1 fold and NMR studies on the partly disordered, essential segment of the protein. We demonstrate that Cns1 is important for maintaining translation elongation, specifically chaperoning the elongation factor eEF2. In this context, Cns1 interacts with the novel co-factor Hgh1 and forms a quaternary complex together with eEF2 and Hsp90. The in vivo folding and solubility of eEF2 depend on the presence of these proteins. Chaperoning of eEF2 by Cns1 is essential for yeast viability and requires a defined subset of the Hsp90 machinery as well as the identified eEF2 recruiting factor Hgh1.

Cellular sensing by phase separation: Using the process, not just the products

Phase separation creates two distinct liquid phases from a single mixed liquid phase, like oil droplets separating from water. Considerable attention has focused on how the products of phase separation-the resulting condensates-might act as biological compartments, bioreactors, filters, and membraneless organelles in cells. Here, we expand this perspective, reviewing recent results showing how cells instead use the process of phase separation to sense intracellular and extracellular changes. We review case studies in phase separation-based sensing and discuss key features, such as extraordinary sensitivity, which make the process of phase separation ideally suited to meet a range of sensory challenges cells encounter.

Principles of Stress Granules Revealed by Imaging Approaches

Eukaryotic cells contain a large number of RNA-protein assemblies, generically referred to as ribonucleoprotein (RNP) granules. Such RNP granules include stress granules and P-bodies in the cytosol and the nucleolus, Cajal bodies, and paraspeckles in the nucleus. A variety of imaging approaches have been used to reveal different components, structural features, and dynamics of RNP granules. In this review, we discuss imaging approaches that have been used to study stress granules and the insights gained from these experiments. A general theme is that these approaches can be transferred to other RNP granules to examine similar aspects of their composition, ultrastructure, dynamics and control.

Who's In and Who's Out-Compositional Control of Biomolecular Condensates

Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid-liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.

Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms

Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.

Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling

The folding of newly synthesized proteins to the native state is a major challenge within the crowded cellular environment, as non-productive interactions can lead to misfolding, aggregation and degradation1. Cells cope with this challenge by coupling synthesis with polypeptide folding and by using molecular chaperones to safeguard folding cotranslationally2. However, although most of the cellular proteome forms oligomeric assemblies3, little is known about the final step of folding: the assembly of polypeptides into complexes. In prokaryotes, a proof-of-concept study showed that the assembly of heterodimeric luciferase is an organized cotranslational process that is facilitated by spatially confined translation of the subunits encoded on a polycistronic mRNA4. In eukaryotes, however, fundamental differences—such as the rarity of polycistronic mRNAs and different chaperone constellations—raise the question of whether assembly is also coordinated with translation. Here we provide a systematic and mechanistic analysis of the assembly of protein complexes in eukaryotes using ribosome profiling. We determined the in vivo interactions of the nascent subunits from twelve hetero-oligomeric protein complexes of Saccharomyces cerevisiae at near-residue resolution. We find nine complexes assemble cotranslationally; the three complexes that do not show cotranslational interactions are regulated by dedicated assembly chaperones5–7. Cotranslational assembly often occurs uni-directionally, with one fully synthesized subunit engaging its nascent partner subunit, thereby counteracting its propensity for aggregation. The onset of cotranslational subunit association coincides directly with the full exposure of the nascent interaction domain at the ribosomal tunnel exit. The ribosome-associated Hsp70 chaperone Ssb8 is coordinated with assembly. Ssb transiently engages partially synthesized interaction domains and then dissociates before the onset of partner subunit association, presumably to prevent premature assembly interactions. Our study shows that cotranslational subunit association is a prevalent mechanism for the assembly of hetero-oligomers in yeast and indicates that translation, folding and assembly of protein complexes are integrated processes in eukaryotes.

Life and Work of Stress Granules and Processing Bodies: New Insights into Their Formation and Function

The dynamic formation of stress granules (SGs), processing bodies (PBs), and related RNA organelles regulates diverse cellular processes, including the coordination of functionally connected messengers, the translational regulation at the synapse, and the control of viruses and retrotransposons. Recent studies have shown that pyruvate kinase and other enzymes localize in SGs and PBs, where they become protected from stress insults. These observations may have implications for enzyme regulation and metabolic control exerted by RNA-based organelles. The formation of these cellular bodies is governed by liquid-liquid phase separation (LLPS) processes, and it needs to be strictly controlled to prevent pathogenic aggregation. The intracellular concentration of key metabolites, such as ATP and sterol derivatives, may influence protein solubility, thus affecting the dynamics of liquid organelles. LLPS in vitro depends on the thermal diffusion of macromolecules, which is limited inside cells, where the condensation and dissolution of membrane-less organelles are helped by energy-driven processes. The active transport by the retrograde motor dynein helps SG assembly, whereas the anterograde motor kinesin mediates SG dissolution; a tug of war between these two molecular motors allows transient SG formation. There is evidence that the efficiency of dynein-mediated transport increases with the number of motor molecules associated with the cargo. The dynein-dependent transport may be influenced by cargo size as larger cargos can load a larger number of motors. We propose a model based on this emergent property of dynein motors, which would be collectively stronger during SG condensation and weaker during SG breakdown, thus allowing kinesin-mediated dispersion.

A prion-like domain in Hsp42 drives chaperone-facilitated aggregation of misfolded proteins

The facilitated aggregation of misfolded proteins is a proteostasis strategy important for cell function and viability, but the molecular mechanisms are poorly understood. Grousl et al. reveal how the intrinsically disordered domains of the small heat shock protein Hsp42 promote and control the aggregation of misfolded proteins during stress conditions in yeast.

Chaperones with aggregase activity promote and organize the aggregation of misfolded proteins and their deposition at specific intracellular sites. This activity represents a novel cytoprotective strategy of protein quality control systems; however, little is known about its mechanism. In yeast, the small heat shock protein Hsp42 orchestrates the stress-induced sequestration of misfolded proteins into cytosolic aggregates (CytoQ). In this study, we show that Hsp42 harbors a prion-like domain (PrLD) and a canonical intrinsically disordered domain (IDD) that act coordinately to promote and control protein aggregation. Hsp42 PrLD is essential for CytoQ formation and is bifunctional, mediating self-association as well as binding to misfolded proteins. Hsp42 IDD confines chaperone and aggregase activity and affects CytoQ numbers and stability in vivo. Hsp42 PrLD and IDD are both crucial for cellular fitness during heat stress, demonstrating the need for sequestering misfolded proteins in a regulated manner.

Heat Shock Factor 1: From Fire Chief to Crowd-Control Specialist

HSF1 is the supposed master regulator of the heat shock response. In this issue of Molecular Cell, Solís et al. reveal that it has a much narrower job description: organizing a small team of molecular chaperones that keep the proteome moving.

The role of PKA in the translational response to heat stress in Saccharomyces cerevisiae

Cellular responses to stress stem from a variety of different mechanisms, including translation arrest and relocation of the translationally repressed mRNAs to ribonucleoprotein particles like stress granules (SGs) and processing bodies (PBs). Here, we examine the role of PKA in the S. cerevisiae heat shock response. Under mild heat stress Tpk3 aggregates and promotes aggregation of eIF4G, Pab1 and eIF4E, whereas severe heat stress leads to the formation of PBs and SGs that contain both Tpk2 and Tpk3 and a larger 48S translation initiation complex. Deletion of TPK2 or TPK3 impacts upon the translational response to heat stress of several mRNAs including CYC1, HSP42, HSP30 and ENO2. TPK2 deletion leads to a robust translational arrest, an increase in SGs/PBs aggregation and translational hypersensitivity to heat stress, whereas TPK3 deletion represses SGs/PBs formation, translational arrest and response for the analyzed mRNAs. Therefore, this work provides evidence indicating that Tpk2 and Tpk3 have opposing roles in translational adaptation during heat stress, and highlight how the same signaling pathway can be regulated to generate strikingly distinct physiological outputs.

Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows

In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Holstein cows were fed a high-straw, control-energy diet (CON; NE_L = 1.34 Mcal/kg) or overfed a moderate-energy diet (OVE; NE_L = 1.62 Mcal/kg) during the dry period. Blood for PMNL isolation and metabolite analysis was collected at −14 and +7 days relative to parturition. At an analysis of variance false discovery rate <0.05, energy intake (OVE vs CON) influenced 1806 genes. Dynamic Impact Approach bioinformatics analysis classified treatment effects on Kyoto Encyclopedia of Genes and Genomes pathways, including activated oxidative phosphorylation and biosynthesis of unsaturated fatty acids and inhibited RNA polymerase, proteasome, and toll-like receptor signaling pathway. This analysis indicates that processes critical for energy metabolism and cellular and immune function were affected with mixed results. However, overall interpretation of the transcriptome data agreed in part with literature documenting a potentially detrimental, chronic activation of PMNL in response to overfeeding. The widespread, transcriptome-level changes captured here confirm the importance of dietary energy adjustments around calving on the immune system.