Structural and functional properties of proteins interacting with small heat shock proteins

Insights into the antibacterial effectiveness of linalool against Shigella flexneri on pork surface: Changes in bacterial growth and pork quality

Shigella flexneri has the ability to contaminate pork and cause foodborne diseases. This study aimed to examine the effectiveness of linalool (a natural preservative) against S. flexneri and explore its potential application in contaminated pork. The results showed that linalool was capable of damaging the cell membrane and binding to the DNA of S. flexneri, and inhibiting biofilm formation and disrupting mature biofilms. The antibacterial effectiveness of linalool on the surface of pork was further demonstrated by analyzing the physicochemical properties of the pork (i.e., weight loss rate, pH value, color index, and TVB-N value) and its protein profiles. Linalool did not completely kill S. flexneri in pork at minimum bactericidal concentration (MBC) concentration and its antibacterial effect of linalool was stronger during the initial stage of storage. During storage, linalool influenced the abundance of specific proteins in the pork, particularly those involved in pathways related to fat metabolism. These findings offer novel insights into the antibacterial efficacy of linalool and its underlying mechanism in pork.

An increase in mitochondrial TOM activates apoptosis to drive retinal neurodegeneration

Intronic polymorphic TOMM40 variants increasing TOMM40 mRNA expression are strongly correlated to late onset Alzheimer's Disease. The gene product, hTomm40, encoded in the APOE gene cluster, is a core component of TOM, the translocase that imports nascent proteins across the mitochondrial outer membrane. We used Drosophila melanogaster eyes as an in vivo model to investigate the relationship between elevated Tom40 (the Drosophila homologue of hTomm40) expression and neurodegeneration. Here we provide evidence that an overabundance of Tom40 in mitochondria invokes caspase-dependent cell death in a dose-dependent manner, leading to degeneration of the primarily neuronal eye tissue. Degeneration is contingent on the availability of co-assembling TOM components, indicating that an increase in assembled TOM is the factor that triggers apoptosis and degeneration in a neural setting. Eye death is not contingent on inner membrane translocase components, suggesting it is unlikely to be a direct consequence of impaired import. Another effect of heightened Tom40 expression is upregulation and co-association of a mitochondrial oxidative stress biomarker, DmHsp22, implicated in extension of lifespan, providing new insight into the balance between cell survival and death. Activation of regulated death pathways, culminating in eye degeneration, suggests a possible causal route from TOMM40 polymorphisms to neurodegenerative disease.

Analysis of Heat Shock Proteins Based on Amino Acids for the Tomato Genome

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as HsfA that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and -0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs.

Heat shock proteins and viral infection

Heat shock proteins (HSPs) are a kind of proteins which mostly found in bacterial, plant and animal cells, in which they are involved in the monitoring and regulation of cellular life activities. HSPs protect other proteins under environmental and cellular stress by regulating protein folding and supporting the correctly folded structure of proteins as chaperones. During viral infection, some HSPs can have an antiviral effect by inhibiting viral proliferation through interaction and activating immune pathways to protect the host cell. However, although the biological function of HSPs is to maintain the homeostasis of cells, some HSPs will also be hijacked by viruses to help their invasion, replication, and maturation, thereby increasing the chances of viral survival in unfavorable conditions inside the host cell. In this review, we summarize the roles of the heat shock protein family in various stages of viral infection and the potential uses of these proteins in antiviral therapy.

Identification of the DcHsp20 gene family in carnation (Dianthus caryophyllus) and functional characterization of DcHsp17.8 in heat tolerance

33 heat shock protein 20 (Hsp20) genes were identified from the carnation genome whose expression were altered by abiotic stresses. DcHsp17.8 may function to improve the heat resistance of Arabidopsis. Heat shock proteins 20 (Hsp20s) mainly function as molecular chaperones that play crucial roles in relieving abiotic stresses such as heat stress. In this study, we identified and characterized 33 DcHsp20 genes from the carnation genome that were classified into 9 subfamilies. Gene structure analysis showed that 25 DcHsp20 genes contained 1 intron whilst the remaining 8 DcHsp20 genes did not contain introns. Motif analysis found that DcHsp20 proteins were relatively conserved. Cis-regulatory elements analysis of the Hsp20 promoters revealed a number of cis-regulatory elements that regulate growth and development, hormone and stress responses. Gene expression analysis revealed that DcHsp20 genes had multiple response patterns to heat stress. The largest range of induction occurred in DcHsp17.8 after 1 h of heat stress. Under cold stress, or treatment with saline or abscisic acid, the expression of most DcHsp20 genes was inhibited. To further understand the function of DcHsp20 genes in response to heat stress, we overexpressed DcHsp17.8 in Arabidopis and the plants showed improved heat tolerance, O₂^- and H₂O₂ activities and photosynthetic capacity with reduced relative electrolyte leakage and malondialdehyde content. Gene expression analysis revealed that DcHsp17.8 modulated the expression of genes involved in antioxidant enzyme synthesis. Our data provided a solid foundation for the further detailed study of DcHsp20 genes.

Functional characterization of the Pinellia ternata cytoplasmic class II small heat shock protein gene PtsHSP17.2 via promoter analysis and overexpression in tobacco

High temperature is one of the main abiotic factors limiting agricultural production, particularly for heat-sensitive plant species. Small heat-shock proteins contribute substantially to alleviating damage to plants caused by heat stress. In the present study, the heat shock protein gene PtsHSP17.2 from Pinellia ternata was functionally characterized through promoter analysis and its overexpression in tobacco. Respectively, relative expression using real-time RT-PCR and ex situ promoter activity assay indicated that PtsHSP17.2 is strongly inducible under heat stress, and in silico promoter analysis discovered multiple stress-related cis elements including heat shock element. When overexpressing PtsHSP17.2 in tobacco, the thermotolerance of transgenic plants was markedly enhanced. Furthermore, the transgenic tobacco plants exhibited less variation in chlorophyll content, relative electrolyte leakage, and malondialdehyde content under heat stress compared with wild-type (WT) plants. The activities of antioxidant enzymes and content of proline were significantly enhanced under heat stress in transgenic plants relative to WT plants. Transgenic plants also had enhanced water retention and increased antioxidative capacity. Further, the expression levels of genes encoding antioxidant enzymes were more highly induced by heat stress in transgenic lines than WT. These results enrich the current understanding of thermal adaptation of heat-sensitive plant species and encourage further genetic improvement.

Comparative Transcriptomics of the Northern Quahog Mercenaria mercenaria and Southern Quahog Mercenaria campechiensis in Response to Chronic Heat Stress

The northern quahog (Mercenaria mercenaria) supports lucrative aquaculture industries in the USA. In the southeastern USA, aquacultured M. mercenaria faces increasing risks of summer die-offs from prolonged heat waves. We used a comparative transcriptomic approach to investigate the molecular responses of M. mercenaria and its southern congener, Mercenaria campechiensis, to controlled incremental heat stress over a 4-week period. Mercenaria were exposed to temperatures from 24 to 34 °C with 2.5 °C/week, after which, gill transcriptomes were de novo assembled and annotated. During the 4 weeks of chronic heat exposure, both species had the same survival rate (96%); M. mercenaria experienced body weight gain/loss depending on the originated hatcheries while M. campechiensis experienced an average net weight loss. The upregulated genes in both species included those in chaperone-mediated protein folding and regulation of cell death pathways, while the downregulated genes in both species involved in mRNA processing and splicing pathways. Compared to M. mercenaria, M. campechiensis appears to be more sensitive to prolonged heat stress as indicated by upregulating significantly more genes in coping with oxidative stress and in the protein degradation pathways, while downregulating some inhibitors of apoptosis. We discussed this finding within their ecological and evolutionary context. Our findings highlighted the potential vulnerability of the two quahogs, especially the southern quahog, to continued ocean warming.

Genomic and Transcriptomic Landscape and Evolutionary Dynamics of Heat Shock Proteins in Spotted Sea Bass (Lateolabrax maculatus) under Salinity Change and Alkalinity Stress

Simple Summary

Heat shock proteins (Hsps) are ubiquitous and conserved in almost all living organisms and are involved in a wide spectrum of cellular responses against diverse environmental stresses. However, our knowledge about the coordinated Hsp co-chaperon interaction is still limited, especially in aquatic animals facing dynamic water environments. In this study, we provided the systematic analysis of 95 Hsp genes (LmHsps) in spotted sea bass (Lateolabrax maculatus), an important aquaculture species in China, under salinity change and alkalinity stress through in silico analysis. The coordinated expression of LmHsps in response to salinity change and alkalinity stress in the gills was determined. Our results confirmed the diverse regulated expression of Hsps in L. maculatus, and that the responses to alkalinity stress may have arisen through the adaptive recruitment of LmHsp40-70-90 co-chaperons. Our results provide vital insights into the function and adaptation of aquatic animal Hsps in response to salinity-alkalinity stress.

Abstract

The heat shock protein (Hsp) superfamily has received accumulated attention because it is ubiquitous and conserved in almost all living organisms and is involved in a wide spectrum of cellular responses against diverse environmental stresses. However, our knowledge about the Hsp co-chaperon network is still limited in non-model organisms. In this study, we provided the systematic analysis of 95 Hsp genes (LmHsps) in the genome of spotted sea bass (Lateolabrax maculatus), an important aquaculture species in China that can widely adapt to diverse salinities from fresh to sea water, and moderately adapt to high alkaline water. Through in silico analysis using transcriptome and genome database, we determined the expression profiles of LmHsps in response to salinity change and alkalinity stress in L. maculatus gills. The results revealed that LmHsps were sensitive in response to alkalinity stress, and the LmHsp40-70-90 members were more actively regulated than other LmHsps and may also be coordinately interacted as co-chaperons. This was in accordance with the fact that members of LmHsp40, LmHsp70, and LmHsp90 evolved more rapidly in L. maculatus than other teleost lineages with positively selected sites detected in their functional domains. Our results revealed the diverse and cooperated regulation of LmHsps under alkaline stress, which may have arisen through the functional divergence and adaptive recruitment of the Hsp40-70-90 co-chaperons and will provide vital insights for the development of L. maculatus cultivation in alkaline water.

Combining enhanced sampling and deep learning dimensionality reduction for the study of the heat shock protein B8 and its pathological mutant K141E

The biological functions of proteins closely depend on their conformational dynamics. This aspect is especially relevant for intrinsically disordered proteins (IDP) for which structural ensembles often offer more useful representations than individual conformations. Here we employ extensive enhanced sampling temperature replica-exchange atomistic simulations (TREMD) and deep learning dimensionality reduction to study the conformational ensembles of the human heat shock protein B8 and its pathological mutant K141E, for which no experimental 3D structures are available. First, we combined homology modelling with TREMD to generate high-dimensional data sets of 3D structures. Then, we employed a recently developed machine learning based post-processing algorithm, EncoderMap, to project the large conformational data sets into meaningful two-dimensional maps that helped us interpret the data and extract the most significant conformations adopted by both proteins during TREMD. These studies provide the first 3D structural characterization of HSPB8 and reveal the effects of the pathogenic K141E mutation on its conformational ensembles. In particular, this missense mutation appears to increase the compactness of the protein and its structural variability, at the same time rearranging the hydrophobic patches exposed on the protein surface. These results offer the possibility of rationalizing the pathogenic effects of the K141E mutation in terms of conformational changes.

The study provides the first 3D structural characterization of HSPB8 and its K141E mutant: extensive TREMD are combined with a deep learning algorithm to rationalize the disordered ensemble of structures adopted by each variant.

The HSP/co-chaperone network in environmental cold adaptation of Chilo suppressalis

Winter cold is one of the major environmental stresses for ectotherm species. Chilo suppressalis, a notorious lepidopteran pest of rice, has a wide geographic region that includes temperate zones with severe environmental conditions. Although C. suppressalis exhibits remarkable cold tolerance, its cold-adaptation mechanisms remain unclear. Here, we used bioinformatics approaches to evaluate transcript levels of genes comprising the C. suppressalis heat shock protein (HSP)/co-chaperone network in response to cold-induced stress. Using all such genes identified in the C. suppressalis genome, we experimentally examined the corresponding transcript levels under cold-acclimation or intermittent cold-shock stresses in diapause and non-diapausing larvae. In total, we identified 19 HSPs and 8 HSP co-chaperones in the C. suppressalis genome. Nine (hsp90, hsp75, hsp70, hsp40, small hsp, activator of 90 kDa heat shock protein ATPase-like, heat shock factor, heat shock factor binding protein 1-like and HSPB1-associated protein 1) were highly cold-inducible and likely comprise the principal cold-response HSP/co-chaperone network in C. suppressalis. We also found that transcriptional regulation of the HSP/co-chaperone networks response differs between cold-acclimation and short-term cold-shock. Moreover, activation of the HSP/co-chaperone network depends on the diapause state of overwintering larvae and cold acclimation may further increase larval cold tolerance. These results provide key new insights in the cold-adaptation mechanisms in C. suppressalis.

At elevated temperatures, heat shock protein genes show altered ratios of different RNAs and expression of new RNAs, including several novel HSPB1 mRNAs encoding HSP27 protein isoforms

Heat shock proteins (HSP) serve as chaperones to maintain the physiological conformation and function of numerous cellular proteins when the ambient temperature is increased. To determine how accurate the general assumption that HSP gene expression is increased in febrile situations is, the RNA levels of the HSF1 (heat shock transcription factor 1) gene and certain HSP genes were determined in three cell lines cultured at 37˚C or 39˚C for three days. At 39˚C, the expression of HSF1, HSPB1, HSP90AA1 and HSP70A1L genes demonstrated complex changes in the ratios of expression levels between different RNA variants of the same gene. Several older versions of the RNAs of certain HSP genes that have been replaced by a newer version in the National Center for Biotechnology Information database were also detected, indicating that the older versions are actually RNA variants of these genes. The present study cloned four new RNA variants of the HSP27-encoding HSPB1 gene, which together encode three short HSP27 peptides. Reanalysis of the proteomics data from our previous studies also demonstrated that proteins from certain HSP genes could be detected simultaneously at multiple positions using SDS-PAGE, suggesting that these genes may engender multiple protein isoforms. These results collectively suggested that, besides increasing their expression, certain HSP and associated genes also use alternative transcription start sites to produce multiple RNA transcripts and use alternative splicing of a transcript to produce multiple mature RNAs, as important mechanisms for responding to an increased ambient temperature in vitro.

Small Heat Shock Proteins in Cancers: Functions and Therapeutic Potential for Cancer Therapy

Small heat shock proteins (sHSPs) are ubiquitous ATP-independent chaperones that play essential roles in response to cellular stresses and protein homeostasis. Investigations of sHSPs reveal that sHSPs are ubiquitously expressed in numerous types of tumors, and their expression is closely associated with cancer progression. sHSPs have been suggested to control a diverse range of cancer functions, including tumorigenesis, cell growth, apoptosis, metastasis, and chemoresistance, as well as regulation of cancer stem cell properties. Recent advances in the field indicate that some sHSPs have been validated as a powerful target in cancer therapy. In this review, we present and highlight current understanding, recent progress, and future challenges of sHSPs in cancer development and therapy.