Tardigrade small heat shock proteins can limit desiccation-induced protein aggregation

Small heat shock proteins as relevant biomarkers for anthropogenic stressors in earthworms

Anthropogenic stressors in terrestrial ecosystems require focused research on adaptive responses in soil organisms such as Eisenia fetida, a model earthworm species. We analyzed the gene expression of five small heat shock proteins (sHSPs) in response to various stressors: heat stress (31 and 35 °C), desiccation (10 % and 20 % humidity), and chemical exposure (bisphenol A and endosulfan) under standard and elevated temperatures. Under moderate heat (31 °C), early upregulation of sHSP transcripts suggests their involvement in initial stress responses, possibly mitigating protein aggregation. At the higher temperature (35 °C), three sHSPs served as a defense against severe protein aggregation, a significant finding as previous studies identified only one activated heat shock protein (HSP70) in E. fetida under similar conditions. Desiccation stress at 10 % humidity activated more sHSPs than at 20 % humidity, and the expression profile at 10 % humidity closely resembled that observed under heat stress, suggesting overlapping adaptation pathways. Heat combined with chemical stress, particularly endosulfan, elevated sHSP transcription and underscored the potential of these proteins as biomarkers in multi-stressor environments. Monomeric sHSPs from E. fetida, which share homology with human sHSPs, showed the highest activity across all stressors, suggesting their key role in earthworm adaptation.

A TT1-SCE1 module integrates ubiquitination and SUMOylation to regulate heat tolerance in rice

Heat stress poses a significant threat to grain yield. As an α2 subunit of the 26S proteasome, TT1 has been shown to act as a critical regulator of rice heat tolerance. However, the heat tolerance mechanisms mediated by TT1 remain elusive. In this study, we unveiled that small ubiquitin-like modifier (SUMO)-conjugating enzyme 1 (SCE1), which interacts with TT1 and acts as a downstream component of TT1, is engaged in TT1-mediated 26S proteasome degradation. We showed that SCE1 functions as a negative regulator of heat tolerance in rice, which is associated with its ubiquitination modification. Furthermore, we observed that small heat-shock proteins (sHSPs) such as Hsp24.1 and Hsp40 can undergo SUMOylation mediated by SCE1, leading to increased accumulation of sHSPs in the absence of SCE1. Reducing protein levels of SCE1 significantly enhanced grain yield under high-temperature stress by improving seed-setting rate and rice grain filling capacity. Taken together, these results uncover the critical role of SCE1 in the TT1-mediated heat tolerance pathway by regulating the abundance of sHSPs and SUMOylation, and ultimately modulating rice heat tolerance. These findings underscore the great potential of the TT1-SCE1 module in improving the heat tolerance of crops.

A bacterial expression cloning screen reveals single-stranded DNA-binding proteins as potent desicco-protectants

Desiccation kills most cells. Some proteins have been identified to help certain cells survive desiccation, but many protein protectants are likely to be unknown. Moreover, the mechanisms ensuring protection of key cellular components are incompletely understood. We devised an expression-cloning approach to discover further protectants. We expressed cDNA libraries from two species of tardigrades in E. coli, and we subjected the bacteria to desiccation to select for survivors. Sequencing the populations of surviving bacteria revealed enrichment of mitochondrial single-stranded DNA-binding proteins (mtSSBs) from both tardigrade species. Expression of mtSSBs in bacteria improved desiccation survival as strongly as the best tardigrade protectants known to date. We found that DNA-binding activity of mtSSBs was necessary and sufficient to improve the desiccation tolerance of bacteria. Although tardigrade mtSSBs were among the strongest protectants we found, single-stranded DNA binding proteins in general offered some protection. These results identify single-stranded DNA-binding proteins as potent desicco-protectants.

Multi-omics landscape and molecular basis of radiation tolerance in a tardigrade

Tardigrades are captivating organisms known for their resilience in extreme environments, including ultra-high-dose radiation, but the underlying mechanisms of this resilience remain largely unknown. Using genome, transcriptome, and proteome analysis of Hypsibius henanensis sp. nov., we explored the molecular basis contributing to radiotolerance in this organism. A putatively horizontally transferred gene, DOPA dioxygenase 1 (DODA1), responds to radiation and confers radiotolerance by synthesizing betalains-a type of plant pigment with free radical-scavenging properties. A tardigrade-specific radiation-induced disordered protein, TRID1, facilitates DNA damage repair through a mechanism involving phase separation. Two mitochondrial respiratory chain complex assembly proteins, BCS1 and NDUFB8, accumulate to accelerate nicotinamide adenine dinucleotide (NAD+) regeneration for poly(adenosine diphosphate-ribosyl)ation (PARylation) and subsequent poly(adenosine diphosphate-ribose) polymerase 1 (PARP1)-mediated DNA damage repair. These three observations expand our understanding of mechanisms of tardigrade radiotolerance.

An evaluation of thermal tolerance in six tardigrade species in an active and dry state

Tardigrades are known for their ability to survive extreme conditions. Reports indicate that tardigrade thermal tolerance is enhanced in the desiccated state; however, these reports have almost always used a single tardigrade species and drying/heating methods vary between studies. Using six different species of tardigrades we confirm that desiccation enhances thermal tolerance in tardigrades. Furthermore, we show that differences in thermal tolerance exist between tardigrade species both when hydrated and desiccated. While Viridiscus viridianus survives the highest temperatures in the hydrated state of any species tested here, under hydrated conditions, the thermal tolerance of V. viridianus is restricted to an acute transient stress. Furthermore, unlike other stresses, such as desiccation, where mild initial exposure preconditions some species to survive subsequent harsher treatment, for V. viridianus exposure to mild thermal stress in the hydrated state does not confer protection to harsher heating. Our results suggest that while tardigrades have the capacity to tolerate mild thermal stress while hydrated, survival of high temperatures in a desiccated state is a by-product of tardigrades' ability to survive desiccation.

A small heat shock protein (SlHSP17.3) in tomato plays a positive role in salt stress

Small heat shock proteins (sHSPs) are molecular chaperones that are widely present in plants and play a vital role in the response of plants to various environmental stimuli. This study employed transgenic Arabidopsis to investigate the impact of the new tomato (Solanum lycopersicum) sHSP protein (SlHSP17.3) on salt stress tolerance. Transient conversion analysis of Arabidopsis protoplasts revealed that SlHSP17.3 localized to the cytoplasm. Furthermore, as suggested by expression analysis, salt stress stimulated SlHSP17.3 expression, suggesting that SlHSP17.3 is involved in the salt stress response of plants. SlHSP17.3-overexpressing plants presented greater germination rates, fresh weights, chlorophyll contents, and Fv/Fm ratios, as well as longer root lengths, lower reactive oxygen species (ROS) levels, and lighter cell membrane injury under salt stress. Furthermore, certain stress-related genes (AtCOR15, AtDREB1B, and AtHSFA2) were up-regulated in salt-stressed transgenic plants. Overall, SlHSP17.3 overexpression improved the salt stress resistance of transgenic plants, mainly through increasing AtCOR15, AtDREB1B, and AtHSFA2 expression.

Protein surface chemistry encodes an adaptive tolerance to desiccation

Cellular desiccation - the loss of nearly all water from the cell - is a recurring stress in an increasing number of ecosystems that can drive protein unfolding and aggregation. For cells to survive, at least some of the proteome must resume function upon rehydration. Which proteins tolerate desiccation, and the molecular determinants that underlie this tolerance, are largely unknown. Here, we apply quantitative and structural proteomic mass spectrometry to show that certain proteins possess an innate capacity to tolerate rehydration following extreme water loss. Structural analysis points to protein surface chemistry as a key determinant for desiccation tolerance, which we test by showing that rational surface mutants can convert a desiccation sensitive protein into a tolerant one. Desiccation tolerance also has strong overlap with cellular function, with highly tolerant proteins responsible for production of small molecule building blocks, and intolerant proteins involved in energy-consuming processes such as ribosome biogenesis. As a result, the rehydrated proteome is preferentially enriched with metabolite and small molecule producers and depleted of some of the cell's heaviest consumers. We propose this functional bias enables cells to kickstart their metabolism and promote cell survival following desiccation and rehydration.

HSPB6: A lipid-dependent molecular chaperone inhibits α-synuclein aggregation

The process of protein misfolding and aggregation is associated with various cytotoxic effects. Understanding how this phenomenon is regulated by the protein homeostasis system, however, is difficult, since it takes place through a complex non-linear network of coupled microscopic steps, including primary nucleation, fibril elongation, and secondary nucleation, which depend on environmental factors. To address this problem, we studied how the aggregation of α-synuclein, a protein associated with Parkinson's disease, is modulated by molecular chaperones and lipid membranes. We focused on small heat shock proteins (sHSPs/HSPBs), which interact with proteins and lipids and are upregulated during aging, a major risk factor for protein misfolding diseases. HSPBs act on different microscopic steps to prevent α-synuclein aggregation, with HSPB6 showing a lipid-dependent chaperone activity. Our findings provide an example of how HSPBs diversified their mechanisms of action to reach an efficient regulation of protein misfolding and aggregation within the complex cellular environment.

Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades

Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.

Tardigrade secretory proteins protect biological structures from desiccation

Tardigrades, microscopic animals that survive a broad range of environmental stresses, express a unique set of proteins termed tardigrade-specific intrinsically disordered proteins (TDPs). TDPs are often expressed at high levels in tardigrades upon desiccation, and appear to mediate stress adaptation. Here, we focus on the proteins belonging to the secreted family of tardigrade proteins termed secretory-abundant heat soluble ("SAHS") proteins, and investigate their ability to protect diverse biological structures. Recombinantly expressed SAHS proteins prevent desiccated liposomes from fusion, and enhance desiccation tolerance of E. coli and Rhizobium tropici upon extracellular application. Molecular dynamics simulation and comparative structural analysis suggest a model by which SAHS proteins may undergo a structural transition upon desiccation, in which removal of water and solutes from a large internal cavity in SAHS proteins destabilizes the beta-sheet structure. These results highlight the potential application of SAHS proteins as stabilizing molecules for preservation of cells.

The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation

Tardigrades can survive remarkable doses of ionizing radiation, up to about 1,000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but the damage is repaired. We show that this species has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme-making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important in vivo for tardigrade radiation tolerance. We hypothesize that the tardigrades' ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.

Reexamining the diverse functions of arginine in biochemistry

Arginine in a free-state and as part of peptides and proteins shows distinct tendency to form clusters. In free-form, it has been found useful in cryoprotection, as a drug excipient for both solid and liquid formulations, as an aggregation suppressor, and an eluent in protein chromatography. In many cases, the mechanisms by which arginine acts in all these applications is either debatable or at least continues to attract interest. It is quite possible that arginine clusters may be involved in many such applications. Furthermore, it is possible that such clusters are likely to behave as intrinsically disordered polypeptides. These considerations may help in understanding the roles of arginine in diverse applications and may even lead to better strategies for using arginine in different situations.

Elevated external temperature affects cell ultrastructure and heat shock proteins (HSPs) in Paramacrobiotus experimentalis Kaczmarek, Mioduchowska, Poprawa, & Roszkowska, 2020

Increasing temperature influences the habitats of various organisms, including microscopic invertebrates. To gain insight into temperature-dependent changes in tardigrades, we isolated storage cells exposed to various temperatures and conducted biochemical and ultrastructural analysis in active and tun-state Paramacrobiotus experimentalis Kaczmarek, Mioduchowska, Poprawa, & Roszkowska, 2020. The abundance of heat shock proteins (HSPs) and ultrastructure of the storage cells were examined at different temperatures (20 °C, 30 °C, 35 °C, 37 °C, 40 °C, and 42 °C) in storage cells isolated from active specimens of Pam. experimentalis. In the active animals, upon increase in external temperature, we observed an increase in the levels of HSPs (HSP27, HSP60, and HSP70). Furthermore, the number of ultrastructural changes in storage cells increased with increasing temperature. Cellular organelles, such as mitochondria and the rough endoplasmic reticulum, gradually degenerated. At 42 °C, cell death occurred by necrosis. Apart from the higher electron density of the karyoplasm and the accumulation of electron-dense material in some mitochondria (at 42 °C), almost no changes were observed in the ultrastructure of tun storage cells exposed to different temperatures. We concluded that desiccated (tun-state) are resistant to high temperatures, but not active tardigrades (survival rates of tuns after 24 h of rehydration: 93.3% at 20 °C, 60.0% at 35 °C, 33.3% at 37 °C, 33.3% at 40 °C, and 20.0% at 42 °C).

The major inducible small heat shock protein HSP20-3 in the tardigrade Ramazzottius varieornatus forms filament-like structures and is an active chaperone

The tardigrade Ramazzottius varieornatus has remarkable resilience to a range of environmental stresses. In this study, we have characterised two members of the small heat shock protein (sHSP) family in R. varieornatus, HSP20-3 and HSP20-6. These are the most highly upregulated sHSPs in response to a 24 h heat shock at 35 0C of adult tardigrades with HSP20-3 being one of the most highly upregulated gene in the whole transcriptome. Both R. varieornatus sHSPs and the human sHSP, CRYAB (HSPB5), were produced recombinantly for comparative structure-function studies. HSP20-3 exhibited a superior chaperone activity than human CRYAB in a heat-induced protein aggregation assay. Both tardigrade sHSPs also formed larger oligomers than CRYAB as assessed by size exclusion chromatography and transmission electron microscopy of negatively stained samples. Whilst both HSP20-3 and HSP20-6 formed particles that were variable in size and larger than the particles formed by CRYAB, only HSP20-3 formed filament-like structures. The particles and filament-like structures formed by HSP20-3 appear inter-related as the filament-like structures often had particles located at their ends. Sequence analyses identified two unique features; an insertion in the middle region of the N-terminal domain (NTD) and preceding the critical-sequence identified in CRYAB, as well as a repeated QNTN-motif located in the C-terminal domain of HSP20-3. The NTD insertion is expected to affect protein-protein interactions and subunit oligomerisation. Removal of the repeated QNTN-motif abolished HSP20-3 chaperone activity and also affected the assembly of the filament-like structures. We discuss the potential contribution of HSP20-3 to protein condensate formation.

A review on oligomeric polydispersity and oligomers-dependent holding chaperone activity of the small heat-shock protein IbpB of Escherichia coli

Inclusion body-associated proteins IbpA and IbpB of MW 16 KDa are the two small heat-shock proteins (sHSPs) of Escherichia coli, and they have only holding, but not folding, chaperone activity. In vitro holdase activity of IbpB is more than that of IbpA, and in combination, they synergise. Both IbpA and IbpB monomers first form homodimers, which as building blocks subsequently oligomerize to make heavy oligomers with MW of MDa range; for IbpB, the MW range of heavy oligomers is 2.0-3.0 MDa, whereas for IbpA oligomers, the values in MDa are not so specified/reported. By temperature upshift, such large oligomers of IbpB, but not of IbpA, dissociate to make relatively small oligomeric assemblies of MW around 600-700KDa. The larger oligomers of IbpB are assumed to be inactive storage form, which on facing heat or oxidative stress dissociate into smaller oligomers of ATP-independent holding chaperone activity. These smaller oligomers bind with stress-induced partially denatured/unfolded and thereby going to be aggregated proteins, to give them protection against permanent damage and aggregation. On withdrawal of stress, IbpB transfers the bound substrate protein to the ATP-dependent bi-chaperone system DnaKJE-ClpB, having both holdase and foldase properties, to finally refold the protein. Of the two sHSPs IbpA and IbpB of E. coli, this review covers the recent advances in research on IbpB only.

The beauty and complexity of the small heat shock proteins: a report on the proceedings of the fourth workshop on small heat shock proteins

The Fourth Cell Stress Society International workshop on small heat shock proteins (sHSPs), a follow-up to successful workshops held in 2014, 2016 and 2018, took place as a virtual meeting on the 17-18 November 2022. The meeting was designed to provide an opportunity for those working on sHSPs to reconnect and discuss their latest work. The diversity of research in the sHSP field is reflected in the breadth of topics covered in the talks presented at this meeting. Here we summarise the presentations at this meeting and provide some perspectives on exciting future topics to be addressed in the field.

A Year at the Forefront of Proteostasis and Aging

During aging, animals experience a decline in proteostasis activity, including loss of stress-response activation, culminating in the accumulation of misfolded proteins and toxic aggregates, which are causal in the onset of some chronic diseases. Finding genetic and pharmaceutical treatments that can increase organismal proteostasis and lengthen life is an ongoing goal of current research. The regulation of stress responses by cell non-autonomous mechanisms appears to be a potent way to impact organismal healthspan. In this Review, we cover recent findings in the intersection of proteostasis and aging, with a special focus on articles and preprints published between November 2021 and October 2022. A significant number of papers published during this time increased our understanding of how cells communicate with each other during proteotoxic stress. Finally, we also draw attention to emerging datasets that can be explored to generate new hypotheses that explain age-related proteostasis collapse.