Molecular chaperones in protein folding and proteostasis. Nature. 2011;475:324-332. [PMID: 21776078 DOI: 10.1038/nature10317]

Glycogen synthase is required for heat shock-mediated autophagy induction in neuronal cells

Autophagy is an essential cellular process that facilitates the degradation of aggregated proteins and damaged organelles to maintain cellular homeostasis and promote cell survival. Recent studies have indicated a direct role for glycogen synthase (GS) in activating neuronal autophagy and in conferring protection against cytotoxic misfolded proteins. Since heat shock induces protein misfolding and autophagy is an essential component of the heat shock response that clears the misfolded proteins, we looked at the possible role of GS in heat shock response pathways in neuronal cells. We demonstrate an increase in the activity and level of GS and a concomitant increase in the glycogen level during the heat shock and post-heat shock recovery period. These changes had a direct correlation with autophagy induction. We further demonstrate that heat shock transcription factor 1 regulates the level and activation of GS during heat shock and that GS is essential for the induction of autophagy during heat stress in neuronal cells. Intriguingly, the partial knock-down of GS led to increased death due to heat shock in neuronal cells and Drosophila. Our study offers a novel insight into the role of GS and glycogen metabolic pathways in heat shock response in neuronal cells.

A study of alpha-synuclein and poly(N-isopropylacrylamide) complex formation through detailed atomistic simulations

This work presents an investigation of the influence of poly(N-isopropylacrylamide) (PNIPAM) polymer on the structural dynamics of intrinsically disordered alpha-synuclein (α-syn) protein, exploring the formation and intricate features of the resulting α-syn/PNIPAM complexes. Using atomistic molecular dynamics (MD) simulations, our study analyzes the impact of initial configuration, polymer molecular weight, and protein mutations on the α-syn and the α-syn/PNIPAM complex. Atomistic simulations, of a few μs, of the protein/polymer complex reveal crucial insights into molecular interactions within the complex, emphasizing a delicate balance of forces governing its stability and structural evolution. Our findings indicate that PNIPAM polymer engages in significant non-polar interactions with the non-amyloid component (NAC) region of α-syn, which plays a crucial role in fibril formation, under various conditions such as the mutations in the protein structure and polymer chain length. Especially the PNIPAM polymer with a 40mer monomer exhibits a stabilizing effect on the structural properties of the protein, reducing intramolecular interactions that contribute to misfolding. These findings, which delve into protein/polymer interactions, hold promise as potential guidance for therapeutic strategies in various neurodegenerative disorders.

Metabolaging: a new geroscience perspective linking aging pathologies and metabolic dysfunction

With age, our metabolic systems undergo significant alterations, which can lead to a cascade of adverse effects that are implicated in both metabolic disorders, such as diabetes, and in the body's ability to respond to acute stress and trauma. To elucidate the metabolic imbalances arising from aging, we introduce the concept of "metabolaging." This framework encompasses the broad spectrum of metabolic disruptions associated with the hallmarks of aging, including the functional decline of key metabolically active organs, like the adipose tissue. By examining how these organs interact with essential nutrient-sensing pathways, "metabolaging" provides a more comprehensive view of the systemic metabolic imbalances that occur with age. This concept extends to understanding how age-related metabolic disturbances can influence the response to acute stressors, like burn injuries, highlighting the interplay between metabolic dysfunction and the ability to handle severe physiological challenges. Finally, we propose potential interventions that hold promise in mitigating the effects of metabolaging and its downstream consequences.

ENO1/Hsp70 Interaction Domains: In Silico and In Vitro Insight for a Putative Therapeutic Target in Cancer

Alpha-enolase (ENO1) is a multifunctional protein with oncogenic roles. First described as a glycolytic enzyme, the protein performs different functions according to its cellular localization, post-translational modifications, and binding partners. Cell surface-localized ENO1 serves as a plasminogen-binding receptor, and it has been detected in several cell types, including various tumor cells. The plasminogen system plays a crucial role in pathological events, such as tumor cell invasion and metastasis. We have previously demonstrated that the interaction of ENO1 with the multifunctional chaperone Hsp70 increases its surface localization and the migratory and invasive capacity of breast cancer cells, thus representing a novel potential target to counteract the metastatic potential of tumors. Here, we have used computational approaches to map the putative binding region of ENO1 to Hsp70 and predict the key anchoring amino acids, also called hot spots. In vitro coimmunoprecipitation experiments were then used to validate the in silico prediction of the protein-protein interaction. This work outcome will be further used as a guide for the design of potential ENO1/HSP70 inhibitors.

TTC7A missense variants in intestinal disease can be classified by molecular and cellular phenotypes

Biallelic mutations in tetratricopeptide repeat domain 7A (TTC7A) give rise to intestinal and immune disorders. However, our understanding of the genotype-phenotype relationship is limited, because TTC7A variants are mostly compound heterozygous and the disease phenotypes are highly diverse. This study aims to clarify how different TTC7A variants impact the severity of intestinal epithelial disorders. We individually characterized the molecular and cellular consequences of 11 different TTC7A missense mutations in TTC7A knockout Caco-2 cells. We examined variant-specific RNA expression profiles, TTC7A protein abundance, and endoplasmic reticulum (ER) stress by using RNA sequencing and imaging flow cytometry. For six variants we detected no significant alterations on these assays, suggesting that protein function may not be severely compromised. However, for five variants we observed molecular phenotypes, with overlapping gene expression signatures between specific variants. Remarkably, the TTC7AE71K variant displayed a unique expression profile, along with reduced TTC7A RNA and protein expression, which set it apart from all other variants. The findings from this study offer a better understanding of the role of specific TTC7A variants in disease and provide a framework for the classification of the variants based on the severity of impact. We propose a classification system for TTC7A variants that could help diagnosis, guide future treatment decisions and may aid in developing effective molecular therapies for patients that carry specific TTC7A variants.

Chaperone dysfunction in motor neuron disease: new insights from studies of the SMN complex

Spinal muscular atrophy and amyotrophic lateral sclerosis are devastating neurodegenerative diseases characterized by motor neuron loss. Although these 2 disorders have distinct genetic origins, recent studies suggest that they share common etiological mechanisms rooted in proteostatic dysfunction. At the heart of this emerging understanding is the survival motor neuron (SMN) complex.

Protein Quality Control is a Master Modulator of Molecular Evolution in Bacteria

The bacterial protein quality control (PQC) network comprises a set of genes that promote proteostasis (proteome homeostasis) through proper protein folding and function via chaperones, proteases, and protein translational machinery. It participates in vital cellular processes and influences organismal development and evolution. In this review, we examine the mechanistic bases for how the bacterial PQC network influences molecular evolution. We discuss the relevance of PQC components to contemporary issues in evolutionary biology including epistasis, evolvability, and the navigability of protein space. We examine other areas where proteostasis affects aspects of evolution and physiology, including host-parasite interactions. More generally, we demonstrate that the study of bacterial systems can aid in broader efforts to understand the relationship between genotype and phenotype across the biosphere.

Hallmarks of aging: A user's guide for comparative biologists

Since the first description of a set of characteristics of aging as so-called hallmarks or pillars in 2013/2014, these characteristics have served as guideposts for the research in aging biology. They have been examined in a range of contexts, across tissues, in response to disease conditions or environmental factors, and served as a benchmark for various anti-aging interventions. While the hallmarks of aging were intended to capture generalizable characteristics of aging, they are derived mostly from studies of rodents and humans. Comparative studies of aging including species from across the animal tree of life have great promise to reveal new insights into the mechanistic foundations of aging, as there is a great diversity in lifespan and age-associated physiological changes. However, it is unclear how well the defined hallmarks of aging apply across diverse species. Here, we review each of the twelve hallmarks of aging defined by Lopez-Otin in 2023 with respect to the availability of data from diverse species. We evaluate the current methods used to assess these hallmarks for their potential to be adapted for comparative studies. Not unexpectedly, we find that the data supporting the described hallmarks of aging are restricted mostly to humans and a few model systems and that no data are available for many animal clades. Similarly, not all hallmarks can be easily assessed in diverse species. However, for at least half of the hallmarks, there are methods available today that can be employed to fill this gap in knowledge, suggesting that these studies can be prioritized while methods are developed for comparative study of the remaining hallmarks.

Understanding the molecular diversity of synapses

Synapses are composed of thousands of proteins, providing the potential for extensive molecular diversity to shape synapse type-specific functional specializations. In this Review, we explore the landscape of synaptic diversity and describe the mechanisms that expand the molecular complexity of synapses, from the genotype to the regulation of gene expression to the production of specific proteoforms and the formation of localized protein complexes. We emphasize the importance of examining every molecular layer and adopting a systems perspective to understand how these interconnected mechanisms shape the diverse functional and structural properties of synapses. We explore current frameworks for classifying synapses and methodologies for investigating different synapse types at varying scales, from synapse-type-specific proteomics to advanced imaging techniques with single-synapse resolution. We highlight the potential of synapse-type-specific approaches for integrating molecular data with cellular functions, circuit organization and organismal phenotypes to enable a more holistic exploration of neuronal phenomena across different scales.

Multiple Chaperone DnaK-FliC Flagellin Interactions are Required for Pseudomonas aeruginosa Flagellum Assembly and Indicate a New Function for DnaK

The DnaK (Hsp70) protein is an essential ATP-dependent chaperone foldase and holdase found in most organisms. In this study, combining multiple experimental approaches we determined FliC as major interaction partner of DnaK in the opportunistic bacterial pathogen Pseudomonas aeruginosa. Implementing immunofluorescence microscopy and electron microscopy techniques DnaK was found extracellularly associated to the assembled filament in a regular pattern. dnaK repression led to intracellular FliC accumulation and motility impairment, highlighting DnaK essentiality for FliC export and flagellum assembly. SPOT-membrane peptide arrays coupled with artificial intelligence analyses suggested a highly dynamic DnaK-FliC interaction landscape involving multiple domains and transient complexes formation. Remarkably, in vitro fast relaxation imaging (FReI) experiments mimicking ATP-deprived extracellular environment conditions exhibited DnaK ATP-independent holdase activity, regardless of its co-chaperone DnaJ and its nucleotide exchange factor GrpE. We present a model for the DnaK-FliC interactions involving dynamic states throughout the flagellum assembly stages. These results expand the classical view of DnaK chaperone functioning and introduce a new participant in the Pseudomonas flagellar system, an important trait for bacterial colonisation and virulence.

Intraspecific divergence within Microcystis aeruginosa mediates the dynamics of freshwater harmful algal blooms under climate warming scenarios

Intraspecific biodiversity can have ecosystem-level consequences and may affect the accuracy of ecological forecasting. For example, rare genetic variants may have traits that prove beneficial under future environmental conditions. The cyanobacterium responsible for most freshwater harmful algal blooms worldwide, Microcystis aeruginosa, occurs in at least three types. While the dominant type occurs in eutrophic environments and is adapted to thrive in nutrient-rich conditions, two additional types have recently been discovered that inhabit oligotrophic and eutrophic environments and have genomic adaptations for survival under nutrient limitation. Here, we show that these oligotrophic types are widespread throughout the Eastern USA. By pairing an experimental warming study with gene expression analyses, we found that the eutrophic type may be most susceptible to climate warming. In comparison, oligotrophic types maintained their growth better and persisted longer under warming. As a mechanistic explanation for these patterns, we found that oligotrophic types responded to warming by widespread elevated expression of heat shock protein genes. Reduction of nutrient loading has been a historically effective mitigation strategy for controlling harmful algal blooms. Our results suggest that climate warming may benefit oligotrophic types of M. aeruginosa, potentially reducing the effectiveness of such mitigation efforts. In-depth study of intraspecific variation may therefore improve forecasting for understanding future whole ecosystem dynamics.

A special focus on polyadenylation and alternative polyadenylation in neurodegenerative diseases: A systematic review

Neurodegenerative diseases (NDDs) are one of the prevailing conditions characterized by progressive neuronal loss. Polyadenylation (PA) and alternative polyadenylation (APA) are the two main post-transcriptional events that regulate neuronal gene expression and protein production. This systematic review analyzed the available literature on the role of PA and APA in NDDs, with an emphasis on their contributions to disease development. A comprehensive literature search was performed using the PubMed, Scopus, Cochrane, Google Scholar, Embase, Web of Science, and ProQuest databases. The search strategy was developed based on the framework introduced by Arksey and O'Malley and supplemented by the inclusion and exclusion criteria. The study selection was performed by two independent reviewers. Extraction and data organization were performed in accordance with the predefined variables. Subsequently, quantitative and qualitative analyses were performed. Forty-seven studies were included, related to a variety of NDDs, namely Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Disease induction was performed using different models, including human tissues, animal models, and cultured cells. Most investigations were related to PA, although some were related to APA or both. Amyloid precursor protein (APP), Tau, SNCA, and STMN2 were the major genes identified; most of the altered PA patterns were related to mRNA stability and translation efficiency. This review particularly underscores the key roles of PA and APA in the pathogenesis of NDDs through their mechanisms that contribute to gene expression dysregulation, protein aggregation, and neuronal dysfunction. Insights into these mechanisms may lead to new therapeutic strategies focused on the modulation of PA and APA activities. Further research is required to investigate the translational potential of targeting these pathways for NDD treatment.

Unfolded protein response: An essential element of intestinal homeostasis and a potential therapeutic target for inflammatory bowel disease

Different physiological and pathological situations can produce alterations in the cell's endoplasmic reticulum (ER), leading to a condition known as ER stress, which can trigger an intricate intracellular signal transduction system known as the unfolded protein response (UPR). UPR is primarily tailored to restore proteostasis and ER equilibrium; otherwise, if ER stress persists, it can cause programmed cell death as a cytoprotective mechanism and drive inflammatory processes. Therefore, since intestinal cells strongly rely on UPR for their biological functions and unbalanced UPR has been linked to inflammatory, metabolic, and immune disorders, here we discussed the role of the UPR within the intestinal tract, focusing on the UPR contribution to inflammatory bowel disease development. Importantly, we also highlighted the promising potential of UPR components as therapeutic targets for intestinal inflammatory diseases.

Impact of bioaugmentation on psychrophilic anaerobic digestion of corn straw

In order to investigate the mechanisms by which bioaugmentation affects psychrophilic anaerobic digestion (AD), this study introduced a psychrophilic methanogenic culture into the sequencing batch of psychrophilic AD systems. The findings demonstrated that bioaugmentation boosted the abundance of Smithella (23.2 times), Syntrophobacter (9.9 times), and Methanothrix (1.4 times) in the psychrophilic AD systems, accelerating acetate and propionate degradation and improving methane production (26 %). Metagenomic analysis showed that bioaugmentation increased the relative abundance of genes related to propionate degradation and methane production, such as propionyl-CoA synthetase (45 %) and acetyl-CoA synthetase (11 %). At the cellular level, genes related to prevention of cell damage and promotion of membrane fluidity were upregulated. This study revealed the effect of bioaugmentation on microbial metabolic activities related to conversion of propionate to methane and cold tolerance in psychrophilic AD.

Beyond protein folding: The pleiotropic functions of PPIases in cellular processes and microbial virulence

Peptidyl prolyl cis/trans isomerases (PPIases), a ubiquitously distributed superfamily of enzymes, associated with signal transduction, trafficking, assembly, biofilm formation, stress tolerance, cell cycle regulation, gene expression and tissue regeneration, is a key regulator of metabolic disorders and microbial virulence. This review assumes an integrative approach, to provide a holistic overview of the structural and functional diversity of PPIases, examining their conformational dynamics, cellular distribution, and physiological significance. We explore their intricate involvement in cellular processes and virulence modulation in both eukaryotic and prokaryotic systems. Additionally, we evaluate the potential of these molecular chaperones as drug targets and vaccine candidates, emphasizing their relevance in therapeutic development. By synthesizing recent findings and providing a broader perspective on these proteins, this review aims to enhance our understanding of their multifaceted roles in biology and their potential applications in medicine.

Blocking constitutive autophagy rescues the loss of acquired heat resistance in Arabidopsis fes1a

High temperature is one of several major abiotic stresses that can cause substantial loss of crop yields. Heat shock proteins (HSPs) are key components of heat stress resistance. Mutation of FES1A, an auxiliary molecular chaperone of HSP70, leads to defective acquired thermotolerance. Autophagy is a positive regulator of basal thermotolerance and a negative regulator of heat stress memory, but its function in acquired thermotolerance is unclear. We found that blocking constitutive autophagy rescued the heat sensitivity of fes1a in Arabidopsis thaliana. Immunoblot and proteomic analyses showed that the rescue was not due to increased HSP levels. Instead, proteomic analysis and confocal microscopy studies revealed that knocking out the core autophagy-related (ATG) genes leads to accumulation of peroxisomes, thus upregulating the metabolic pathways within the peroxisomes. Accumulation of peroxisomes promotes both reactive oxygen species scavenging and indole-3-acetic acid (IAA) production in atg7 fes1a. Overexpression of ABCD1/PXA1/CTS, a peroxisomal ATP-binding cassette transporter, in atg7 fes1a leads to abnormal peroxisomal function and subsequently thermosensitivity. Moreover, we found that exogenous application of indole-3-butyric acid, IAA or naphthalene-1-acetic acid rescued fes1a heat sensitivity. We propose that autophagy is detrimental to the survival of the fes1a mutant, which has acquired thermosensitivity.

Response mechanism of ethanol-tolerant Saccharomyces cerevisiae strain ES-42 to increased ethanol during continuous ethanol fermentation

BACKGROUND

Continuous fermentation offers advantages in improving production efficiency and reducing costs, making it highly competitive for industrial ethanol production. A key requirement for Saccharomyces cerevisiae strains used in this process is their tolerance to high ethanol concentrations, which enables them to adapt to continuous fermentation conditions. To explore how yeast cells respond to varying levels of ethanol stress during fermentation, a two-month continuous fermentation was conducted. Cells were collected at different ethanol concentrations (from 60 g/L to 100 g/L) for comparative transcriptomic analysis.

RESULTS

During continuous fermentation, as ethanol concentration increased, the expression of genes associated with cytoplasmic ribosomes, translation, and fatty acid biosynthesis progressively declined, while the expression of genes related to heat shock proteins (HSPs) and ubiquitin-mediated protein degradation gradually increased. Besides, cells exhibited distinct responses to varying ethanol concentrations. At lower ethanol concentrations (nearly 70 g/L), genes involved in mitochondrial ribosomes, oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, antioxidant enzymes, ergosterol synthesis, and glycerol biosynthesis were specifically upregulated compared to those at 60 g/L. This suggests that cells enhanced respiratory energy production, ROS scavenging capacity, and the synthesis of ergosterol and glycerol to counteract stress. At relatively higher ethanol concentrations (nearly 80 g/L), genes involved in respiration and ergosterol synthesis were inhibited, while those associated with glycolysis and glycerol biosynthesis were notably upregulated. This suggests a metabolic shift from respiration towards enhanced glycerol synthesis. Interestingly, the longevity-regulating pathway seemed to play a pivotal role in mediating the cellular adaptations to different ethanol concentrations. Upon reaching an ethanol concentration of 100 g/L, the aforementioned metabolic activities were largely inhibited. Cells primarily focused on enhancing the clearance of denatured proteins to preserve cellular viability.

CONCLUSIONS

This study elucidated the mechanisms by which an ethanol-tolerant S. cerevisiae strain adapts to increasing ethanol concentrations during continuous fermentation. The findings suggest that the longevity-regulating pathway may play a critical role in adapting to varying ethanol stress by regulating mitochondrial respiration, glycerol synthesis, ergosterol synthesis, antioxidant enzyme, and HSPs. This work provides a novel and valuable understanding of the mechanisms that govern ethanol tolerance during continuous fermentation.

Assessment of Hsp90β-selective inhibitor safety and on-target effects

The heat shock protein 90 (Hsp90) family of molecular chaperones mediates the folding and activation of ~ 400 client proteins, many of which contribute to oncogenesis. As a result, Hsp90 pan-inhibitors, which inhibit all four Hsp90 isoforms, have been investigated in the clinic for the treatment of cancer. Unfortunately, detrimental side effects were observed and hindered the clinical development of pan-Hsp90 inhibitors. The two most common on-target toxicities, cardio-toxicity and ocular-toxicity, have been attributed to inhibition of the Hsp90α isoform. As an alternative strategy, Hsp90β-selective inhibitors have been developed, which have shown promising anti-cancer activity in vitro and in vivo in combination with immune-checkpoint blockade therapy. This study aims to assess the potential risks of cardio-toxicity and ocular-toxicity exhibited by Hsp90β-selective inhibitors in vitro. In summary, the Hsp90β-selective NDNB1182 was found to avoid the cardio- and ocular-toxicity typical of Hsp90 pan-inhibitors (e.g. 17-AAG), providing a promising path toward the generation of isoform-selective Hsp90 inhibitors.

Modeling the navigating forces behind BSA aggregation in a microfluidic chip

Microfluidic chips are powerful tools for investigating numerous variables including chemical and physical parameters on protein aggregation. This study investigated the aggregation of bovine serum albumin (BSA) in two different systems: a vial-based static system and a microfluidic chip-based dynamic system in which BSA aggregation was induced successfully. BSA aggregation induced in a microfluidic chip on a timescale of seconds enabled a dynamic investigation of the forces driving the aggregation process. This study employed a combination of experimental approaches, including biophysical and microscopic methods, and computational simulations using MATLAB and COMSOL Multiphysics. Obtained results revealed that Brownian movement, advective mixing, and laminar flow applied in favor of the formation of amyloid-like aggregates through the entire pathway. Furthermore, heating provided the necessary energy for the initial BSA's partial unfolding. In the following, space restriction and the cumulative effects of repulsive electrostatic and attractive van der Waals forces contributed to forming BSA clusters as a partially unfolded intermediate in the first few seconds of the aggregation process. Consequently, the synergistic effects of hydrodynamic forces (including shear force), hydrophobic interaction, and space restriction resulted in the deposition of larger aggregates on the channel sidewalls. Due to the elevated local concentration of BSA clusters alongside the strong shear force toward the channel sidewalls, the deposited structures underwent a structural conversion to form amyloid-like aggregates within a few seconds. In this study, we not only elucidated the molecular mechanisms underlying BSA aggregation but also highlighted the forces driving the aggregation process in microfluidic systems, explaining how it occurs within a timescale of seconds.

When HSFs bring the heat-mapping the transcriptional circuitries of HSF-type regulators in Candida albicans

Heat shock factor (HSF)-type regulators are stress-responsive transcription factors widely distributed among eukaryotes, including fungi. They carry a four-stranded winged helix-turn-helix DNA-binding domain considered as the signature domain for HSFs. The genome of the opportunistic yeast Candida albicans encodes four HSF members, namely, Sfl1, Sfl2, Skn7, and the essential regulator, Hsf1. C. albicans HSFs do not only respond to heat shock and/or temperature variation but also to CO2 levels, oxidative stress, and quorum sensing, acting this way as central decision makers. In this minireview, I follow on the heels of my mSphere of Influence commentary (2020) to provide an overview of the repertoire of HSF regulators in Saccharomyces cerevisiae and C. albicans and describe how their genetic perturbation in C. albicans, coupled with genome-wide expression and location analyses, allow to map their transcriptional circuitry. I highlight how they can regulate, in common, a crucial developmental program: filamentous growth.

A novel peptide encoded by circSRCAP confers resistance to enzalutamide by inhibiting the ubiquitin-dependent degradation of AR-V7 in castration-resistant prostate cancer

BACKGROUND

The sustained activation of androgen receptor splice variant-7 (AR-V7) is a key factor in the resistance of castration-resistant prostate cancer (CRPC) to second-generation anti-androgens such as enzalutamide (ENZ). The AR/AR-V7 protein is regulated by the E3 ubiquitin ligase STUB1 and a complex involving HSP70, but the precise mechanism remains unclear.

METHODS

High-throughput RNA sequencing was used to identify differentially expressed circular RNAs (circRNAs) in ENZ-resistant and control CRPC cells. The coding potential of circSRCAP was confirmed by polysome profiling and LC-MS. The function of circSRCAP was validated in vitro and in vivo using gain- and loss-of-function assays. Mechanistic insights were obtained through immunoprecipitation analyses.

RESULTS

A novel ENZ-resistant circRNA, circSRCAP, was identified and shown to be upregulated in ENZ-resistant C4-2B (ENZR-C4-2B) cells, correlating with increased AR-V7 protein levels. circSRCAP is generated via splicing by eIF4A3, forming a loop structure and is exported from the nucleus by the RNA helicase DDX39A. Mechanistically, circSRCAP encodes a 75-amino acid peptide (circSRCAP-75aa) that inhibits the ubiquitination of AR/AR-V7's co-chaperone protein HSP70 by disrupting the interaction with the E3 ligase STUB1. This process results in the upregulation of AR-V7 expression and promotes ENZ resistance in CRPC cells. Xenograft tumor models further confirmed the role of circSRCAP in CRPC progression and its potential as a therapeutic target for ENZ-resistant CRPC.

CONCLUSIONS

circSRCAP provides an epigenetic mechanism influencing AR-V7 stability and offers a promising therapeutic target for treating ENZ-resistant CRPC.

Exploring the effects of dietary methionine supplementation on European seabass mucosal immune responses against Tenacibaculum maritimum

Introduction

Dietary methionine supplementation has been shown to enhance immunity and disease resistance in fish. However, excessive intake may lead to adverse effects. The present study aimed to evaluate the immune status of European seabass (Dicentrarchus labrax) fed increasing levels of dietary methionine supplementation and to investigate the early immune response to Tenacibaculum maritimum.

Methods

For this purpose, juvenile European seabass were fed one of three experimental diets containing methionine at 8.6 mg/g (CTRL), 18.5 mg/g (MET2), and 29.2 mg/g (MET3) for four weeks, followed by a bath challenge with T. maritimum.

Results

While higher methionine intake reduced hemoglobin levels, no other significant changes in the immune status were observed. However, after infection, fish fed higher methionine levels exhibited a dose-dependent decrease in the mRNA expression of some proinflammatory genes. Similarly, RNA sequencing analysis of skin tissue revealed an attenuated immune response in the MET2 group at 24 hours post-infection, with few proinflammatory genes upregulated, which intensified at 48 h, potentially due to advanced tissue colonization by T. maritimum. The MET3 group displayed the least pronounced immune response, along with the enrichment of some immune-related pathways among the downregulated transcripts. These findings, together with the lower mRNA expression of proinflammatory genes in the head kidney and the higher mortality rates observed in this group, suggest a potential impairment of the immune response.`.

Discussion

Overall, these findings indicate that dietary methionine supplementation may significantly influence both systemic and local immune responses in European seabass, highlighting the need for careful consideration when supplementing diets with methionine.

Engineering a membrane protein chaperone to ameliorate the proteotoxicity of mutant huntingtin

Toxic protein aggregates are associated with various neurodegenerative diseases, including Huntington's disease (HD). Since no current treatment delays the progression of HD, we develop a mechanistic approach to prevent mutant huntingtin (mHttex1) aggregation. Here, we engineer the ATP-independent cytosolic chaperone PEX19, which targets peroxisomal membrane proteins to peroxisomes, to remove mHttex1 aggregates. Using yeast toxicity-based screening with a random mutant library, we identify two yeast PEX19 variants and engineer equivalent mutations into human PEX19 (hsPEX19). These variants effectively delay mHttex1 aggregation in vitro and in cellular HD models. The mutated hydrophobic residue in the α4 helix of hsPEX19 variants binds to the N17 domain of mHttex1, thereby inhibiting the initial aggregation process. Overexpression of the hsPEX19-FV variant rescues HD-associated phenotypes in primary striatal neurons and in Drosophila. Overall, our data reveal that engineering ATP-independent membrane protein chaperones is a promising therapeutic approach for rational targeting of mHttex1 aggregation in HD.

Modification of peroxidase activity and proteome in maize exposed to cadmium in the presence of galactoglucomannan oligosaccharides

We tested the effects of galactoglucomannan oligosaccharides (GGMOs) and/or cadmium (Cd) on peroxidase activity and the proteome in maize (Zea mays L.) roots and leaves. Our previous work confirmed that GGMOs ameliorate the symptoms of Cd stress in seedlings. Here, the plants were hydroponically cultivated for 7 days, and the protein content and peroxidase activity were estimated in intracellular, neutral cell wall, and acidic cell wall protein fractions. The peroxidase activity varied between the plant organs as well as among the fractions and treatments. The GGMOs in the presence of Cd did not significantly influence content of peroxidases but modulated their activity, which implies posttranslational regulation. The changes in the content of various proteins (e.g., related to the defence reactions, cell wall structure/metabolism, and activation of plant hormones) caused by GGMOs and Cd indicate possible protective mechanisms that improve the vitality of maize seedlings exposed to metal stress. GGMOs partially reverted Cd-induced protein disbalance, which was a reoccurring phenomenon of mitigation in leaves.

Exploring the impact of lipid nanoparticles on protein stability and cellular proteostasis

Lipid nanoparticles (LNPs) have become pivotal in advancing modern medicine, from mRNA-based vaccines to gene editing with CRISPR-Cas9 systems. Though LNPs based therapeutics offer promising drug delivery with satisfactory clinical safety profiles, concerns are raised regarding their potential nanotoxicity. Here, we explore the impacts of LNPs on protein stability in buffer and cellular protein homeostasis (proteostasis) in HepG2 cells. First, we show that LNPs of different polyethylene glycol (PEG) molar ratios to total lipid ratio boost protein aggregation propensity by reducing protein stability in cell lysate and blood plasma. Second, in HepG2 liver cells, these LNPs induce global proteome aggregation, as imaged by a cellular protein aggregation fluorescent dye (AggStain). Such LNPs induced proteome aggregation is accompanied by decrease in cellular micro-environmental polarity as quantified by a solvatochromic protein aggregation sensor (AggRetina). The observed local polarity fluctuations may be caused by the hydrophobic contents of LNPs that promote cellular proteome aggregation. Finally, we exploit RNA sequencing analysis (RNA-Seq) to reveal activation of unfolded protein response (UPR) pathway and other proteostasis genes upon LNPs treatment. Together, these findings highlight that LNPs may induce subtle proteome stress by compromising protein stability and proteostasis even without obvious damage to cell viability.

Shallow-water mussels (Mytilus galloprovincialis) adapt to deep-sea environment through transcriptomic and metagenomic insights

Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.

Exploring Novel Antibiotics by Targeting the GroEL/GroES Chaperonin System

Infectious diseases have affected 13.7 million patients, placing a heavy burden on society. Furthermore, inappropriate and unrequited utilization of antibiotics has led to antimicrobial resistance worldwide. However, well-established targeted screening of environmental isolates or compound libraries has produced limited new drugs. The current situation, in which drug development is delayed, bacterial evolution is occurring, and drug resistance is emerging, requires the development of new targets and/or new strategies to combat infections. Some novel antibacterial strategies have been proposed, among which disruption of protein balance by inhibiting transcription and translation machinery is one of the proven effective antimicrobial strategies. Molecular chaperonins could mediate the correct folding of proteins, especially under conditions such as high temperature and pressure. The GroEL/ES system has been confirmed as one of the key molecular chaperones for bacterial viability. Recent data have revealed the antibacterial activities of GroEL/ES-targeted compounds, highlighting the potential role of GroEL/ES in the development of novel antibiotics. In this brief review, we discuss the function of the GroEL/ES system and summarize the inhibitors of the GroEL/ES system. The GroEL/ES system may represent a promising drug target for the exploration of novel antibiotics.

Allosteric CDC37 Inhibitor Disrupts Chaperone Complex to Block CDK4/6 Maturation

Cell division cycle 37 (CDC37) is a member of the molecular chaperone family and acts as a cochaperone of heat shock protein 90 (HSP90), which is overexpressed in many cancer types as a regulator of protein kinase maturation. In this process, CDC37 selectively recognizes and stabilizes protein kinases by forming a HSP90-CDC37-kinase chaperone complex. The protein-protein interactions (PPIs) of HSP90-CDC37 and CDC37-kinase complexes contribute to malignant tumors, as oncogenic kinases in malignant cells depend upon CDC37 expression. Thus, inhibiting CDC37 to disrupt HSP90-CDC37-kinase chaperone complex reveals as a promising way to achieve selective inhibition of oncogenic kinase maturation. Herein, we report a small-molecule CDC37 inhibitor called DDO-6079 that simultaneously inhibits HSP90-CDC37 and CDC37-CDK4/6 chaperone complex by binding to an allosteric site on CDC37. DDO-6079 selectively inhibited the maturation of multiple oncogenic kinases to escape heat shock response (HSR). Furthermore, DDO-6079 decreased the thermostability of CDK6, reversed the resistance of CDK6 to palbociclib (a successful CDK4/6 inhibitor) in colorectal cancer cells and exhibited efficacy in vivo. Together, the results revealed that DDO-6079 is a first-in-class small molecule CDC37 inhibitor that disrupts the HSP90-CDC37-kinase chaperone complex and provides a new way to block kinase maturation.

Improving functional protein generation via foundation model-derived latent space likelihood optimization

A variety of deep generative models have been adopted to perform de novo functional protein generation. Compared to 3D protein design, sequence-based generation methods, which aim to generate amino acid sequences with desired functions, remain a major approach for functional protein generation due to the abundance and quality of protein sequence data, as well as the relatively low modeling complexity for training. Although these models are typically trained to match protein sequences from the training data, exact matching of every amino acid is not always essential. Certain amino acid changes (e.g., mismatches, insertions, and deletions) may not necessarily lead to functional changes. This suggests that maximizing the training data likelihood beyond the amino acid sequence space could yield better generative models. Pre-trained protein large language models (PLMs) like ESM2 can encode protein sequences into a latent space, potentially serving as functional validators. We propose training functional protein sequence generative models by simultaneously optimizing the likelihood of training data in both the amino acid sequence space and the latent space derived from a PLM. This training scheme can also be viewed as a knowledge distillation approach that dynamically re-weights samples during training. We applied our method to train GPT-like models (i.e., autoregressive transformers) for antimicrobial peptide (AMP) and malate dehydrogenase (MDH) generation tasks. Computational experiments confirmed that our method outperformed various deep generative models (e.g., generative adversarial net, variational autoencoder, and GPT model without the proposed training strategy) on these tasks, demonstrating the effectiveness of our multi-likelihood optimization strategy.

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

Revival of the Escherichia coli heat shock response after two decades with a small Hsp in a critical but distinct act

The heat stress response is an essential defense mechanism in all organisms. Heat shock proteins (Hsps) are produced in response to thermal stress, with their expression levels regulated by heat shock transcription factors. In Escherichia coli, the key transcription factor σ32 positively regulates Hsp expression. Studies from over two decades ago revealed that σ32 abundance is negatively controlled under normal conditions, mainly through degradation mechanisms involving DnaK, GroEL, and FtsH. Beyond this established mechanism, recent findings indicate that a small heat shock protein IbpA also plays a role in the translational regulation of σ32, adding a new layer to the established model. This review highlights the role of a new actor, IbpA, which strongly suppresses σ32 expression under non-stress conditions and markedly increases it during heat shock.

Structural Analysis of Plasma-Induced Oxidation and Electric Field Effect on the Heat Shock Protein (Hsp60) Structure: A Computational Viewpoint

In recent years, there has been an increase in the study of the mechanisms behind plasma oncology. For this, many wet lab experiments and computational studies were conducted. Computational studies give an advantage in examining protein structures that are costly to extract in enough amounts to analyze the biophysical properties following plasma treatment. Therefore, in this work, we studied the effect of plasma oxidation and electric field on the human mitochondrial heat shock protein (mHsp60). Hsp60, alias chaperonin, is one of the most conserved proteins expressed across all species. Hence, we performed molecular dynamic simulations to calculate the root-mean-square deviation, root-mean-square fluctuation, and solvent-accessible surface area of mHsp60 with and without oxidation. In addition to the oxidation state, we also applied an electric field (0.003 and 2.0 V/nm) to check the changes in the mHsp60 protein. Through simulations, we observed that the electric field strongly affects the structure of mHsp60 protein compared with the oxidation. The combination of oxidation and electric field effect increases the destabilization of the mHsp60 structure compared with their respective control states.

Regulation of physiological and pathological condensates by molecular chaperones

Biomolecular condensates are dynamic membraneless compartments that regulate a myriad of cellular functions. A particular type of physiological condensate called stress granules (SGs) has gained increasing interest due to its role in the cellular stress response and various diseases. SGs, composed of several hundred RNA-binding proteins, form transiently in response to stress to protect mRNAs from translation and disassemble when the stress subsides. Interestingly, SGs contain several aggregation-prone proteins, such as TDP-43, FUS, hnRNPA1, and others, which are typically found in pathological inclusions seen in autopsy tissues from amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients. Moreover, mutations in these genes lead to the familial form of ALS and FTD. This has led researchers to propose that pathological aggregation is seeded by aberrant SGs: SGs that fail to properly disassemble, lose their dynamic properties, and become pathological condensates which finally 'mature' into aggregates. Here, we discuss the evidence supporting this model for various ALS/FTD-associated proteins. We further continue to focus on molecular chaperone-mediated regulation of ALS/FTD-associated physiological condensates on one hand, and pathological condensates on the other. In addition to SGs, we review ALS/FTD-relevant nuclear condensates, namely paraspeckles, anisosomes, and nucleolar amyloid bodies, and discuss their emerging regulation by chaperones. As the majority of chaperoning mechanisms regulate physiological condensate disassembly, we highlight parallel themes of physiological and pathological condensation regulation across different chaperone families, underscoring the potential for early disease intervention.

Inducers and modulators of protein aggregation in Alzheimer's disease - Critical tools for understanding the foundations of aggregate structures

Amyloidogenic protein aggregation is a pathological hallmark of Alzheimer's Disease (AD). As such, this critical feature of the disease has been instrumental in guiding research on the mechanistic basis of disease, diagnostic biomarkers and preventative and therapeutic treatments. Here we review identified molecular triggers and modulators of aggregation for two of the proteins associated with AD: amyloid beta and tau. We aim to provide an overview of how specific molecular factors can impact aggregation kinetics and aggregate structure to promote disease. Looking toward the future, we highlight some research areas of focus that would accelerate efforts to effectively target protein aggregation in AD.

All-Trans Retinoic Acid-Induced Cell Surface Heat Shock Protein 90 Mediates Tau Protein Internalization and Degradation in Human Microglia

This study investigates the role of all-trans retinoic acid (ATRA) in modulating the expression of heat shock protein 90 (Hsp90) and its influence on the uptake and degradation of tau proteins in immortalized human microglia cells. We demonstrate that ATRA significantly upregulates Hsp90 expression in a concentration-dependent manner, enhancing both extracellular and intracellular Hsp90 levels. Our results show that ATRA-treated cells exhibit increased tau protein uptake via caveolae/raft-dependent endocytosis pathways. This uptake is mediated by surface Hsp90, as evidenced by the inhibition of tau internalization using an extracellular Hsp90-selective inhibitor. Further, we establish that the exogenously added full-sized monomeric tau proteins bind to Hsp90. The study also reveals that ATRA-enhanced tau uptake is followed by effective degradation through both lysosomal and proteasomal pathways. We observed a significant reduction in intracellular tau levels in ATRA-treated cells, which was reversed by lysosome or proteasome inhibitors, suggesting the involvement of both degradation pathways. Our findings highlight the potential therapeutic role of ATRA in Alzheimer's disease and related tauopathies. By enhancing Hsp90 expression and facilitating tau degradation, ATRA could contribute to the clearance of pathological tau proteins, offering a promising strategy for mitigating neurodegeneration. This research underscores the need for further exploration into the molecular mechanisms of tau protein internalization and degradation, which could provide valuable insights into the treatment of neurodegenerative diseases.

Exploration of small-molecule inhibitors targeting Hsp110 as novel therapeutics

The heat shock protein (HSP) 110 family has a key role as a unique class of molecular chaperones maintaining cellular proteostasis in eukaryotes. Abnormal activation of Hsp110 has been implicated in several diseases. Given its important role in pathogenesis, Hsp110 has become a novel drug target for disease diagnosis and targeted therapy. Thus, targeting Hsp110 or its interactions with client proteins offers new therapeutic approaches. Recent studies of small-molecule inhibitors that target Hsp110 in vitro and in vivo have yielded encouraging results. In this review, we provide an overview of novel therapeutics targeting Hsp110, mainly inhibitors of protein-protein interactions (PPIs), together with a brief discussion of the relevant challenges, opportunities, and future directions.

Astrocytic proteostasis in the tale of aging and neurodegeneration

Homeostasis of proteins (proteostasis), which governs protein processing, folding, quality control, and degradation, is a fundamental cellular process that plays a pivotal role in various neurodegenerative diseases and in the natural aging process of the mammalian brain. While the role of neuronal proteostasis in neuronal physiology is well characterized, the contribution of proteostasis of glial cells, particularly of astrocytes, has received fairly less attention in this context. Here, we summarize recent data highlighting proteostasis dysfunction in astrocytes and its putative implication to neurodegenerative diseases and aging. We discuss how distinct proteostasis nodes and pathways in astrocytes may specifically contribute to brain function and different age-associated pathologies. Finally, we argue that the understanding of astrocytic proteostasis role in neuronal physiology and functional decay may arise as a potential new avenue of intervention in neurodegenerative diseases and grant relevant data in the biology of aging.

A nucleolar mechanism suppresses organismal proteostasis by modulating TGFβ/ERK signalling

The protein homeostasis (proteostasis) network encompasses a myriad of mechanisms that maintain the integrity of the proteome by controlling various biological functions, including protein folding and degradation. Alas, ageing-associated decline in the efficiency of this network enables protein aggregation and consequently the development of late-onset neurodegenerative disorders, such as Alzheimer's disease. Accordingly, the maintenance of proteostasis through late stages of life bears the promise to delay the emergence of these devastating diseases. Yet the identification of proteostasis regulators is needed to assess the feasibility of this approach. Here we report that knocking down the activity of the nucleolar FIB-1-NOL-56 complex protects model nematodes from proteotoxicity of the Alzheimer's disease-causing amyloid-β peptide and of abnormally long poly-glutamine stretches. This mechanism promotes proteostasis across tissues by modulating the activity of TGFβ signalling and by enhancing proteasome activity. Our findings point at research avenues towards the development of proteostasis-promoting therapies for neurodegenerative maladies.

Quiescent cells maintain active degradation-mediated protein quality control requiring proteasome, autophagy, and nucleus-vacuole junctions

Many cells spend a major part of their life in quiescence, a reversible state characterized by a distinct cellular organization and metabolism. In glucose-depleted quiescent yeast cells, there is a metabolic shift from glycolysis to mitochondrial respiration, and a large fraction of proteasomes are reorganized into cytoplasmic granules containing disassembled particles. Given these changes, the operation of protein quality control (PQC) in quiescent cells, in particular the reliance on degradation-mediated PQC and the specific pathways involved, remains unclear. By examining model misfolded proteins expressed in glucose-depleted quiescent yeast cells, we found that misfolded proteins are targeted for selective degradation requiring functional 26S proteasomes. This indicates that a significant pool of proteasomes remains active in degrading quality control substrates. Misfolded proteins were degraded in a manner dependent on the E3 ubiquitin ligases Ubr1 and San1, with Ubr1 playing a dominant role. In contrast to exponentially growing cells, the efficient clearance of certain misfolded proteins additionally required intact nucleus-vacuole junctions (NVJ) and Cue5-independent selective autophagy. Our findings suggest that proteasome activity, autophagy, and NVJ-dependent degradation operate in parallel. Together, the data demonstrate that quiescent cells maintain active PQC that relies primarily on selective protein degradation. The necessity of multiple degradation pathways for the removal of misfolded proteins during quiescence underscores the importance of misfolded protein clearance in this cellular state.

From Molecular to Radionuclide and Pharmacological Aspects in Transthyretin Cardiac Amyloidosis

Amyloidosis is a rare pathology characterized by protein deposits in various organs and tissues. Cardiac amyloidosis (CA) can be caused by various protein deposits, but transthyretin amyloidosis (ATTR) and immunoglobulin light chain (AL) are the most frequent pathologies. Protein misfolding can be induced by several factors such as oxidative stress, genetic mutations, aging, chronic inflammation, and neoplastic disorders. In ATTR cardiomyopathy (ATTR-CM), the amyloid fibrils can be found in the myocardium interstitial space and are associated with arrhythmias and heart failure. In pathological situations, the transthyretin (TTR) configuration is destroyed by proteolytic action, leading to monomers that further misfold and aggregate to form the amyloid fibrils. 99mTc-Pyrophosphate (99m-Tc-PYP), 99mTc 3,3-diphosphono-1,2-propanodicarboxylic acid (99m-Tc-DPD) and 99m-Tc hydroxy-methylene-Dyphosphonate (99m-Tc-HMDP) are used to detect myocardium amyloid deposits due to their ability to detect calcium ions that are present in the amyloid fibrils through dystrophic calcification. ATTR-CM therapy acts on different stages of the amyloidogenic process, including liver TTR synthesis, TTR tetramer destabilization, and misfolding of the monomers. The main aim of this narrative review is to present ATTR-CM, starting with molecular changes regarding the protein misfolding process and radionuclide aspects and finishing with pharmacological approaches.

Secreted extracellular heat shock protein gp96 and inflammatory cytokines are markers of severe malaria outcome

Malaria caused by Plasmodium spp., is a major public health issue in sub-Saharan Africa. The fight against malaria has stalled due to increasing resistance to treatments and insecticides. There is an urgent need to focus on new therapeutic targets to combat malaria effectively. This study aimed to measure the secreted heat shock protein gp96 levels in both malaria patients and controls. Indeed, gp96 plays a crucial role in parasite survival within the host and in establishing a successful infection. Therefore, gp96 could be a promising target for antimalarial drugs. In our study, we included 60 malaria patients, 30 with severe malaria (SM) and 30 with uncomplicated malaria (UM). Additionally, 28 controls were included. Using the ELISA method, we measured gp96 levels in the participants' blood samples. We then used the Mann-Whitney or analyse of variance tests to calculate descriptive statistics and determined the correlation between gp96 level and parasitemia using Spearman's rank correlation test. The study found that gp96 levels in the plasma significantly increased in malaria patients (23.86 ng/mL) compared to control (5.88 ng/mL), with a P < 0.0001. Interestingly, there was a significant difference between SM (27.56 ng/mL) and UM (13.9 ng/mL), with a P-value of 0.001. These findings are accompanied by significantly higher parasitemia and elevated proinflammatory cytokines such as IL-17A and IL-1β levels in SM patients compared to UM and controls. Furthermore, there was no significant positive correlation between gp96 levels and parasitemia/proinflammatory cytokines. Our research has revealed, for the first time, that individuals with SM have significantly higher levels of gp96 in the context of high parasitemia and proinflammatory cytokines. Our preliminary results will be taken further to evaluate gp96 as a valuable biomarker for the diagnosis of SM and a potential target for antimalarial drug discovery.

Bioinformatics analysis and alternative polyadenylation in Heat Shock Proteins 70 (HSP70) family members

OBJECTIVE

The Heat Shock Protein 70 (HSP70) family is a highly conserved group of molecular chaperones essential for maintaining cellular homeostasis. These proteins are necessary for protein folding, assembly, and degradation and involve cell recovery from stress conditions. HSP70 proteins are upregulated in response to heat shock, oxidative stress, and pathogenic infections. Their primary role is preventing protein aggregation, refolding misfolded proteins, and targeted degradation of irreparably damaged proteins. Given their involvement in fundamental cellular processes and stress responses, HSP70 proteins are critical for cell survival and modulating disease outcomes in cancer, neurodegeneration, and other pathologies. The present study aims to understand domain architecture, physicochemical properties, phosphorylation, ubiquitination, and alternative polyadenylation site prediction in various HSP70 members.

METHOD

SMART and InterProScan software were used for domain analysis. EXPASY Protparam, NetPhos 3.1 server DTU, and MUbisiDa were used for physicochemical analysis, phosphorylation, and ubiquitination site analysis, respectively. Alternative polyadenylation was studied using the EST database.

RESULT

Domain analysis shows that coiled-coil and nucleotide-binding domains are present in some of the HSP70 members. Five HSP70 family members have alternate polyadenylation sites in their 3'UTR.

CONCLUSION

The present work has provided valuable insights into their structure, functions, interactome, and polyadenylation patterns. Studying their therapeutic potential in diseases like cancer can be helpful.

Comparative analysis of BAG1 and BAG2: Insights into their structures, functions and implications in disease pathogenesis

As BAG family members, Bcl-2 associated athanogene family protein 1 (BAG1) and 2 (BAG2) are implicated in multiple cellular processes, including apoptosis, autophagy, protein folding and homeostasis. Although structurally similar, they considerably differ in many ways. Unlike BAG2, BAG1 has four isoforms (BAG1L, BAG1M, BAG1S and BAG1 p29) displaying different expression features and functional patterns. BAG1 and BAG2 play different cellular functions by interacting with different molecules to participate in the regulation of various diseases, including cancer/tumor and neurodegenerative diseases. Commonly, BAG1 acts as a protective factor to predict a good prognosis of patients with some types of cancer or a risk factor in some other cancers, while BAG2 is regarded as a risk factor to promote cancer/tumor progression. In neurodegenerative diseases, BAG2 commonly acts as a neuroprotective factor. In this review, we summarized the differences in molacular structure and biological function between BAG1 and BAG2, as well as the influences of them on pathogenesis of diseases, and explore the prospects for their clinical therapy application by specifying the activators and inhibitors of BAG1 and BAG2, which might provide a better understanding of the underlying pathogenesis and developing the targeted therapy strategies for diseases.

Correlation between lncRNAs with human molecular chaperons in cancer immunopathogenesis and drug resistance

The development of cancer immunology heavily relies on the interaction between long non-coding RNAs (lncRNAs) and molecular chaperones. By participating in gene regulation, lncRNAs interact with molecular chaperones, which play a critical role in protein folding and stress responses, to influence oncogenic pathways. This interaction has an impact on both the immune cells within the tumor microenvironment and the tumor cells themselves. Understanding these mechanisms provides valuable insights into innovative approaches for diagnosis and treatment. Targeting the lncRNA-chaperone axis has the potential to strengthen anti-tumor immunity and enhance cancer treatment outcomes. Further research is necessary to uncover specific associations, identify biomarkers, and develop personalized therapies aimed at disrupting this axis, which could potentially revolutionize cancer diagnosis and treatment.

Deciphering the Vulnerability of Pollen to Heat Stress for Securing Crop Yields in a Warming Climate

Climate change is leading to more frequent and severe extreme temperature events, negatively impacting agricultural productivity and threatening global food security. Plant reproduction, the process fundamental to crop yield, is highly susceptible to heatwaves, which disrupt pollen development and ultimately affect seed-set and crop yields. Recent research has increasingly focused on understanding how pollen grains from various crops react to heat stress at the molecular and cellular levels. This surge in interest over the last decade has been driven by advances in genomic technologies, such as single-cell RNA sequencing, which holds significant potential for revealing the underlying regulatory reprogramming triggered by heat stress throughout the various stages of pollen development. This review focuses on how heat stress affects gene regulatory networks, including the heat stress response, the unfolded protein response, and autophagy, and discusses the impact of these changes on various stages of pollen development. It highlights the potential of pollen selection as a key strategy for improving heat tolerance in crops by leveraging the genetic variability among pollen grains. Additionally, genome-wide association studies and population screenings have shed light on the genetic underpinnings of traits in major crops that respond to high temperatures during male reproductive stages. Gene-editing tools like CRISPR/Cas systems could facilitate precise genetic modifications to boost pollen heat resilience. The information covered in this review is valuable for selecting traits and employing molecular genetic approaches to develop heat-tolerant genotypes.

Beyond Misfolding: A New Paradigm for the Relationship Between Protein Folding and Aggregation

Aggregation is intricately linked to protein folding, necessitating a precise understanding of their relationship. Traditionally, aggregation has been viewed primarily as a sequential consequence of protein folding and misfolding. However, this conventional paradigm is inherently incomplete and can be deeply misleading. Remarkably, it fails to adequately explain how intrinsic and extrinsic factors, such as charges and cellular macromolecules, prevent intermolecular aggregation independently of intramolecular protein folding and structure. The pervasive inconsistencies between protein folding and aggregation call for a new framework. In all combined reactions of molecules, both intramolecular and intermolecular rate (or equilibrium) constants are mutually independent; accordingly, intrinsic and extrinsic factors independently affect both rate constants. This universal principle, when applied to protein folding and aggregation, indicates that they should be treated as two independent yet interconnected processes. Based on this principle, a new framework provides groundbreaking insights into misfolding, Anfinsen's thermodynamic hypothesis, molecular chaperones, intrinsic chaperone-like activities of cellular macromolecules, intermolecular repulsive force-driven aggregation inhibition, proteome solubility maintenance, and proteinopathies. Consequently, this paradigm shift not only refines our current understanding but also offers a more comprehensive view of how aggregation is coupled to protein folding in the complex cellular milieu.

PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3-4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84

BACKGROUND

Rice blast caused by Pyricularia oryzae is a major threat to rice production worldwide. Tainung 84 (TNG84) is an elite japonica rice cultivar developed through the traditional pedigree method. It has maintained superior blast resistance since its release in 2010. This study aimed to investigate the genetic factors underlying the durable resistance of TNG84 in Taiwan.

RESULTS

Quantitative trait locus (QTL) mapping was conducted using 122 F2 individuals and F2:3 families derived from the cross of TNG84 and a susceptible japonica cultivar Tainan 11 (TN11). Using 733 single nucleotide polymorphisms (SNPs) obtained through genotyping-by-sequencing and three P. oryzae isolates (D41-2, 12CY-MS1-2, and 12YL-TT4-1) belonging to different physiological races and Pot2 lineages, a major QTL was identified in the region of 52-54 cM (9.54-15.16 Mb) on chromosome 12. Fine-mapping using 21 F5:6 recombinants delimited the QTL to a 140.4-kb region (10.78 to 10.93 Mb) containing the known resistance gene Ptr. Sequencing analysis indicated that TNG84 carries the resistant PtrA allele and TN11 carries the susceptible PtrD allele. Investigation of the Ptr haplotypes in 41 local japonica rice cultivars revealed that eight PtrA-containing cultivars (19.5%) consistently exhibited good field resistance in Taiwan from 2008 to 2024. Subsequently, a few F5:6 lines (P026, P044, P092, and P167) lacking the resistant Ptr allele were observed to exhibit a resistant phenotype against P. oryzae 12YL-TT4-1-lab. Trait-marker association analyses using eight F6:7 homozygous recombinants, 378 BC1F2 from P044 backcrossed to TN11, and 180 BC1F2 from P092 backcrossed to TN11, identified Piz-t on chromosome 6 and a new QTL located between 3.3 Mb and 4.4 Mb on chromosome 12 (designated as qBR12_3.3-4.4). Analysis of 12 selected BC1F2:3 lines derived from P044 demonstrated that in the absence of Ptr and Piz-t, qBR12_3.3-4.4 alone reduced the disease severity index from approximately 6.3 to 3.9.

CONCLUSIONS

PtrA is likely the primary gene responsible for the broad-spectrum and durable resistance of TNG84. Piz-t confers narrow-spectrum resistance, while qBR12_3.3-4.4 contributes partial resistance. The discovery of qBR12_3.3-4.4 has provided a new source of blast resistance, and the markers developed in this study can be utilized in future breeding programs.

Biomimetic Folding Strategies for Chemical Synthesis of Disulfide-Bonded Peptides and Proteins

Disulfide-bonded peptides and proteins, including hormones, toxins, growth factors, and others, are abundant in living organisms. These molecules play crucial physiological roles such as regulating cell and organism growth, development, and metabolism. They have also found widespread applications as drugs or tool molecules in biomedical and pharmaceutical research. However, the chemical synthesis of disulfide-bonded proteins is complicated by the challenges associated with their folding. This review focuses on the latest advancements in disulfide-bonded peptide and protein folding technologies. Particularly, it highlights biomimetic folding strategies that emulate the naturally occurring oxidative folding processes in nature. These strategies include chaperone-assisted folding, glycosylation-assisted folding, and organic-based oxidative folding methods. The review also anticipates future directions in folding technology. Such research offers innovative approaches for the chemical synthesis of complex proteins that are otherwise difficult to fold.

Life History Differences Between Lepidoptera Larvae and Blattodea Nymphs Lead to Different Energy Allocation Strategies and Cellular Qualities

Different life histories result in different strategies to allocate energy in biosynthesis, including growth and reproduction, and somatic maintenance. One of the most notable life history differences between Lepidoptera and Blattodea species is that the former grow much faster than the latter, and during metamorphosis, a large amount of tissue in Lepidoptera species disintegrates. In this review, using Lepidoptera caterpillars and cockroach nymphs as examples, we show that, due to these differences in growth processes, cockroach nymphs spend 20 times more energy on synthesizing one unit of biomass (indirect cost of growth) than butterfly caterpillars. Because of the low indirect cost of growth in caterpillars, the fraction of metabolic energy allocated to growth is six times lower, and that for maintenance is seven times higher in caterpillars, compared to cockroach nymphs, despite caterpillar's higher growth rates. Moreover, due to the higher biosynthetic energy cost in cockroach nymphs, they have better cellular qualities, including higher proteasomal activity for protein quality control and higher resistance to oxidative stress. We also show that under food restriction conditions, the fraction of assimilated energy allocated to growth was reduced by 120% in cockroach nymphs, as they lost body weight under food restriction, while this reduction was only 14% in hornworms, and the body mass increased at a lower rate. Finaly, we discuss future research, especially the difference in adult lifespans associated with the energetic differences.