Characterizing functional differences in sea anemone Hsp70 isoforms using budding yeast

Acute heat priming promotes short-term climate resilience of early life stages in a model sea anemone

Across diverse taxa, sublethal exposure to abiotic stressors early in life can lead to benefits such as increased stress tolerance upon repeat exposure. This phenomenon, known as hormetic priming, is largely unexplored in early life stages of marine invertebrates, which are increasingly threatened by anthropogenic climate change. To investigate this phenomenon, larvae of the sea anemone and model marine invertebrate Nematostella vectensis were exposed to control (18 °C) or elevated (24 °C, 30 °C, 35 °C, or 39 °C) temperatures for 1 h at 3 days post-fertilization (DPF), followed by return to control temperatures (18 °C). The animals were then assessed for growth, development, metabolic rates, and heat tolerance at 4, 7, and 11 DPF. Priming at intermediately elevated temperatures (24 °C, 30 °C, or 35 °C) augmented growth and development compared to controls or priming at 39 °C. Indeed, priming at 39 °C hampered developmental progression, with around 40% of larvae still in the planula stage at 11 DPF, in contrast to 0% for all other groups. Total protein content, a proxy for biomass, and respiration rates were not significantly affected by priming, suggesting metabolic resilience. Heat tolerance was quantified with acute heat stress exposures, and was significantly higher for animals primed at intermediate temperatures (24 °C, 30 °C, or 35 °C) compared to controls or those primed at 39 °C at all time points. To investigate a possible molecular mechanism for the observed changes in heat tolerance, the expression of heat shock protein 70 (HSP70) was quantified at 11 DPF. Expression of HSP70 significantly increased with increasing priming temperature, with the presence of a doublet band for larvae primed at 39 °C, suggesting persistent negative effects of priming on protein homeostasis. Interestingly, primed larvae in a second cohort cultured to 6 weeks post-fertilization continued to display hormetic growth responses, whereas benefits for heat tolerance were lost; in contrast, negative effects of short-term exposure to extreme heat stress (39 °C) persisted. These results demonstrate that some dose-dependent effects of priming waned over time while others persisted, resulting in heterogeneity in organismal performance across ontogeny following priming. Overall, these findings suggest that heat priming may augment the climate resilience of marine invertebrate early life stages via the modulation of key developmental and physiological phenotypes, while also affirming the need to limit further anthropogenic ocean warming.

Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel

Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.

The C-terminal domain of Hsp70 is responsible for paralog-specific regulation of ribonucleotide reductase

The Hsp70 family of molecular chaperones is well-conserved and expressed in all organisms. In budding yeast, cells express four highly similar cytosolic Hsp70s Ssa1, 2, 3 and 4 which arose from gene duplication. Ssa1 and 2 are constitutively expressed while Ssa3 and 4 are induced upon heat shock. Recent evidence suggests that despite their amino acid similarity, these Ssas have unique roles in the cell. Here we examine the relative importance of Ssa1-4 in the regulation of the enzyme ribonucleotide reductase (RNR). We demonstrate that cells expressing either Ssa3 or Ssa4 as their sole Ssa are compromised for their resistance to DNA damaging agents and activation of DNA damage response (DDR)-regulated transcription. In addition, we show that the steady state levels and stability of RNR small subunits Rnr2 and Rnr4 are reduced in Ssa3 or Ssa4-expressing cells, a result of decreased Ssa-RNR interaction. Interaction between the Hsp70 co-chaperone Ydj1 and RNR is correspondingly decreased in cells only expressing Ssa3 and 4. Through studies of Ssa2/4 domain swap chimeras, we determined that the C-terminal domain of Ssas are the source of this functional specificity. Taking together, our work suggests a distinct role for Ssa paralogs in regulating DNA replication mediated by C-terminus sequence variation.

Cells require molecular chaperones to fold proteins into their active conformation. A major mystery however is why cells express so many highly-related and apparently redundant Hsp70 paralogs. We examined the role of four Hsp70 paralogs in budding yeast (Ssa1, 2, 3 and 4) on the activity of the ribonucleotide reductase (RNR complex). Importantly, we demonstrate there is selectivity of RNR subunits for Ssa1 and Ssa2 subunits, which is dictated by the co-chaperone Ydj1. Taken together, our work provides new insight into the functional specificity of Hsp70 paralogs using a native client protein.

Pseudogene HSPA7 is a poor prognostic biomarker in Kidney Renal Clear Cell Carcinoma (KIRC) and correlated with immune infiltrates

Background

Pseudogenes played important roles in tumorigenesis, while there are nearly no reports about the expression and roles of HSPA7 in the cancer.

Methods

Firstly, we used Logistic regression, the KS test, the GEPIA database, UALCAN database and qRT-PCR to analyze the expression level of HSPA7 in KIRC, then we used the Cox regression and the Kaplan–Meier curve to analyze the overall survival (OS) of KIRC patients with different Clinico-pathological parameters. Thirdly, we used the multivariate Cox analysis of influencing factors to compare the correlation between the HSPA7 expression level and the clinical parameters. Finally, we used multi-GSEA analysis and the Tumor Immunoassay Resource (TIMER) database to explore the functional role of HSPA7 in KIRC

Results

The HSPA7 is highly expressed in KIRC tumor tissues, and its expression is related to clinico-pathological features and survival in KIRC patients. GSEA analysis displayed the high expression of HSPA7 in KIRC were related to several tumor-related and immune-related pathways. With the TIMER database analysis we showed that HSPA7 levels were correlated with the CD4⁺ T cells, neutrophils and Dendritic Cell.

Conclusions

Our study showed that HSPA7 is very important in the tumor progression and may act as a poor prognostic biomarker for KIRC tumor by modulating immune infiltrating cells.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-021-02141-1.

Rapid deacetylation of yeast Hsp70 mediates the cellular response to heat stress

Hsp70 is a highly conserved molecular chaperone critical for the folding of new and denatured proteins. While traditional models state that cells respond to stress by upregulating inducible HSPs, this response is relatively slow and is limited by transcriptional and translational machinery. Recent studies have identified a number of post-translational modifications (PTMs) on Hsp70 that act to fine-tune its function. We utilized mass spectrometry to determine whether yeast Hsp70 (Ssa1) is differentially modified upon heat shock. We uncovered four lysine residues on Ssa1, K86, K185, K354 and K562 that are deacetylated in response to heat shock. Mutation of these sites cause a substantial remodeling of the Hsp70 interaction network of co-chaperone partners and client proteins while preserving essential chaperone function. Acetylation/deacetylation at these residues alter expression of other heat-shock induced chaperones as well as directly influencing Hsf1 activity. Taken together our data suggest that cells may have the ability to respond to heat stress quickly though Hsp70 deacetylation, followed by a slower, more traditional transcriptional response.

Dataset of Nematostella vectensis Hsp70 isoform interactomes upon heat shock

Nematostella vectensis is an estuarine sea anemone that has emerged as a model species to characterize molecular responses to physiological stressors due to its exposure to diverse, extreme abiotic conditions. In marine cnidarians, Hsp70 proteins can be effective biomarkers to determine mechanisms of physiological acclimation and evolutionary adaptations to environmental stress: a pressing issue as concerns about climate change grow. Here we show the results of affinity purification mass spectrometry of three Nematostella vectensis Hsp70 isoforms, NvHsp70A, B and D when expressed in untreated and heat shocked yeast cells lacking their native Hsp70s. We identified a total of 1031 interactors for the three NvHsp70 isoforms, 549 or which were shared. NvHsp70 isoform interactions altered substantially under heat stress with 17% of NvHsp70A, 51% of NvHsp70B and 20% of NvHsp70D interactions increasing after exposure to 39 °C for 2 hours. For further interpretation of the data presented in this article, please see the research article “Dynamic remodeling of the interactomes of Nematostella vectensis Hsp70 isoforms under heat shock”.

Dynamic remodeling of the interactomes of Nematostella vectensis Hsp70 isoforms under heat shock

Heat shock protein 70s (Hsp70s) are a highly conserved class of molecular chaperones that fold a large proportion of the proteome. Nematostella vectensis (Nv) is an estuarine sea anemone that has emerged as a model species to characterize molecular responses to physiological stressors due to its exposure to diverse, extreme abiotic conditions. Previous transcriptional data has shown dramatic differences among expression profiles of three NvHsp70 isoforms (NvHsp70A, B and D) under stress but it is unknown if, and to what extent, the client proteins for these chaperones differ. In order to determine client specificity, NvHsp70A, B and D were expressed in Saccharomyces cerevisiae budding yeast lacking native Hsp70 and interacting proteins for each Hsp70 were determined with mass spectrometry in yeast ambient and heat shock conditions. Our analyses showed <50% of identified interacting proteins were common to all three anemone Hsp70s and 3-18% were unique to an individual Hsp70. Mapping of temperature induced interactions suggest that under stress a proportion of clients are transferred from NvHsp70A and NvHsp70D to NvHsp70B. Together, these data suggest a diverse set of interacting proteins for Hsp70 isoforms that likely determines the precise functions for Hsp70s in organismal acclimation and potentially adaptation. BIOLOGICAL SIGNIFICANCE: Although the Hsp70 family of molecular chaperones has been studied for >50 years, it is still not fully understood why organisms encode and express many highly-similar Hsp70 isoforms. The prevailing theory is that these isoforms have identical function, but are expressed under unique cellular conditions that include heat shock to cope with increased number of unfolded/misfolded proteins. The sea anemone Nematostella vectensis encodes three Hsp70 isoforms A, B and D that when expressed in yeast demonstrate unique functionalities. This study provides the interactome of NvHsp70s A, B and D and demonstrates that Hsp70 isoforms, while highly similar in sequence, have unique co-chaperone and client interactors.

Not quite the SSAme: unique roles for the yeast cytosolic Hsp70s

The Heat Shock Protein 70s (Hsp70s) are an essential family of proteins involved in folding of new proteins and triaging of damaged proteins for proteasomal-mediated degradation. They are highly conserved in all organisms, with each organism possessing multiple highly similar Hsp70 variants (isoforms). These isoforms have been previously thought to be identical in function differing only in their spatio-temporal expression pattern. The model organism Saccharomyces cerevisiae (baker's yeast) expresses four Hsp70 isoforms Ssa1, 2, 3 and 4. Here, we review recent findings that suggest that despite their similarity, Ssa isoforms may have unique cellular functions.

Analyzing the Functionality of Non-native Hsp70 Proteins in Saccharomyces cerevisiae

Yeast are an ideal system to study Heat Shock Protein 70 (Hsp70) function in a cellular context. This protocol was generated to analyze the function of non-native Hsp70 proteins by expressing them as the sole cytosolic Hsp70 in yeast. As an initial step, Hsp70 variants (such as Ssa1 point mutants and non-yeast versions such as Nematostella vectensis NvHsp70A, B and D) are cloned into an appropriate expression plasmid. Next, these plasmids are transformed into ssa1-4Δ yeast [expressing native Ssa1 from an uracil-based (URA3) plasmid] which are subsequently cured of the original yeast on 5-Fluroorotic Acid (5-FOA). The resulting cells can be screened for a variety of phenotypes which match to the activity of well-studied cellular pathways.