Identification Of Heat Shock Proteins Research Articles

Genome-wide identification of heat shock proteins in harpacticoid, cyclopoid, and calanoid copepods: Potential application in marine ecotoxicology

Constant evolution of omics-technologies has provided access to identification of various important gene families. Recently, genome assemblies on widely used ecotoxicological model species, including rotifers and copepods have been completed and representative detoxification-related gene families have been discovered for biomarker genes. However, despite ubiquitous presence of stress-response proteins, limited information on full genome-wide report on heat shock proteins (Hsps) is available. Various studies have demonstrated multiple cellular functions of Hsps in living organisms as an important biomarker in response to abiotic and biotic stressors, however, full genome-wide identification of Hsps, particularly in aquatic invertebrates, has not been reported. This is the first study to report the entire Hsps and basal gene expression levels in three regional-specific copepods: Tigriopus japonicus and kingsejongensis, Paracyclopina nana, and Eurytemora affnis, and how each Hsp family gene is regulated at a basal level.

Computational genome-wide identification of heat shock protein genes in the bovine genome

Background: Heat shock proteins (HSPs) are molecular chaperones known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, we carried out a computational genome-wide survey of the bovine genome. For this, HSP sequences from each subfamily (sHSP, HSP40, HSP70 and HSP90) were used to search the Pfam (Protein family) database, for identifying exact HSP domain sequences based on the hidden Markov model. ProtParam tool was used to compute potential physico-chemical parameters detectable from a protein sequence. Evolutionary trace (ET) method was used to extract evolutionarily functional residues of a homologous protein family. Results: We computationally identified 67 genes made up of 10, 43, 10 and 4 genes belonging to small HSP, HSP40, HSP70 and HSP90 families respectively. These genes were widely dispersed across the bovine genome, except in chromosomes 24, 26 and 27, which lack bovine HSP genes. We found an uncharacterized outer dense fiber ( ODF1) gene in cattle with an intact alpha crystallin domain, like other small HSPs. Physico-chemical characteristic of aliphatic index was higher in HSP70 and HSP90 gene families, compared to small HSP and HSP40. Grand average hydropathy showed that small HSP (sHSP), HSP40, HSP70 and HSP90 genes had negative values except for DNAJC22, a member of HSP40 gene family. The uniqueness of DNAJA3 and DNAJB13 among HSP40 members, based on multiple sequence alignment, evolutionary trace analysis and sequence identity dendrograms, suggests evolutionary distinct structural and functional features, with unique roles in substrate recognition and chaperone functions. The monophyletic pattern of the sequence identity dendrograms of cattle, human and mouse HSP sequences suggests functional similarities. Conclusions: Our computational results demonstrate the first-pass in-silico identification of heat shock proteins and calls for further investigation to better understand their functional roles and mechanisms in Bovidae.

Computational genome-wide identification of heat shock protein genes in the bovine genome.

Background: Heat shock proteins (HSPs) are molecular chaperones known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, we carried out a computational genome-wide survey of the bovine genome. For this, HSP sequences from each subfamily (sHSP, HSP40, HSP70 and HSP90) were used to search the Pfam (Protein family) database, for identifying exact HSP domain sequences based on the hidden Markov model. ProtParam tool was used to compute potential physico-chemical parameters detectable from a protein sequence. Evolutionary trace (ET) method was used to extract evolutionarily functional residues of a homologous protein family. Results: We computationally identified 67 genes made up of 10, 43, 10 and 4 genes belonging to small HSP, HSP40, HSP70 and HSP90 families respectively. These genes were widely dispersed across the bovine genome, except in chromosomes 24, 26 and 27, which lack bovine HSP genes. We found an uncharacterized outer dense fiber ( ODF1) gene in cattle with an intact alpha crystallin domain, like other small HSPs. Physico-chemical characteristic of aliphatic index was higher in HSP70 and HSP90 gene families, compared to small HSP and HSP40. Grand average hydropathy showed that small HSP (sHSP), HSP40, HSP70 and HSP90 genes had negative values except for DNAJC22, a member of HSP40 gene family. The uniqueness of DNAJA3 and DNAJB13 among HSP40 members, based on multiple sequence alignment, evolutionary trace analysis and sequence identity dendrograms, suggests evolutionary distinct structural and functional features, with unique roles in substrate recognition and chaperone functions. The monophyletic pattern of the sequence identity dendrograms of cattle, human and mouse HSP sequences suggests functional similarities. Conclusions: Our computational results demonstrate the first-pass in-silico identification of heat shock proteins and calls for further investigation to better understand their functional roles and mechanisms in Bovidae.

Rethinking HSF1 in Stress, Development, and Organismal Health.

The heat shock response (HSR) was originally discovered as a transcriptional response to elevated temperature shock and led to the identification of heat shock proteins and heat shock factor 1 (HSF1). Since then HSF1 has been shown to be important for combating other forms of environmental perturbations as well as genetic variations that cause proteotoxic stress. The HSR has long been thought to be an absolute response to conditions of cell stress and the primary mechanism by which HSF1 promotes organismal health by preventing protein aggregation and subsequent proteome imbalance. Accumulating evidence now shows that HSF1, the central player in the HSR, is regulated according to specific cellular requirements through cell-autonomous and non-autonomous signals, and directs transcriptional programs distinct from the HSR during development and in carcinogenesis. We discuss here these 'non-canonical' roles of HSF1, its regulation in diverse conditions of development, reproduction, metabolism, and aging, and posit that HSF1 serves to integrate diverse biological and pathological responses.

A transplant “immunome” screening platform defines a targetable epitope fingerprint of multiple myeloma

AbstractMultiple myeloma (MM) is a hematological cancer for which immune-based treatments are currently in development. Many of these rely on the identification of highly disease-specific, strongly and stably expressed antigens. Here, we profiled the myeloma B-cell immunome both to explore its predictive role in the context of autologous and allogeneic hematopoietic stem cell transplantation (HSCT) and to identify novel immunotherapeutic targets. We used random peptide phage display, reverse immunization, and next-generation sequencing–assisted antibody phage display to establish a highly myeloma-specific epitope fingerprint targeted by B-cell responses of 18 patients in clinical remission. We found that allogeneic HSCT more efficiently allowed production of myeloma-specific antibodies compared with autologous HSCT and that a highly reactive epitope recognition signature correlated with superior response to treatment. Next, we performed myeloma cell surface screenings of phage-displayed patient transplant immunomes. Although some of the screenings yielded clear-cut surface binders, the majority of screenings did not, suggesting that many of the targeted antigens may in fact not be accessible to the B-cell immune system in untreated myeloma cells. This fit well with the identification of heat-shock proteins as a class of antigens that showed overall the broadest reactivity with myeloma patient sera after allogeneic HSCT and that may be significantly translocated to the cell surface upon treatment as a result of immunogenic cell death. Our data reveal a disease-specific epitope signature of MM that is predictive for response to treatment. Mining of transplant immunomes for strong myeloma surface binders may open up avenues for myeloma immunotherapy.

Brassinosteroid-induced de novo protein synthesis in Zea mays under salinity and bioinformatic approach for identification of heat shock proteins

Using radioactive labeling technique it was analyzed proteins profiles of maize plants after treatment (12 h) with salt and brassinosteroids (BRs). Among separated proteins 66 and 67 proteins were observed specifically upregulated by salt treatment or BRs under salinity, respectively. Brassinazole—inhibitor of BRs biosynthesis—lowered BR-induced accumulation of proteins that confirm their BR-mediated synthesis. Data on 200 heat shock proteins (HSPs) from Arabidopsis thaliana and 42 HSPs from Zea mays have been used for polypeptide identification with bioinformatic approach. Protein bands separated on SDS-PAGE were compared with gene expression profile of HSPs from Genevestigator database in response to salinity and hormone treatment. In result, eight correlative matches were found between levels of polypeptide accumulation and activation of HSPs genes’ expression. It was suggested involvement of BRs in regulation of synthesis of mitochondrial chaperones under salinity.

Identification of heat shock proteins via transcriptome profiling of tree peony leaf exposed to high temperature.

The tree peony leaf is an important vegetative organ that is sensitive to abiotic stress and particularly to high temperature. This sensitivity affects plant growth and restricts tree peony distribution. However, the transcriptomic information currently available on the peony leaf in public databases is limited. In this study, we sequenced the transcriptomes of peony leaves subjected to high temperature using the Illumina HiSeq TM 2000 platform. We performed de novo assembly of 93,714 unigenes (average length of 639.7 bp). By searching the public databases, 22,323 unigenes and 13,107 unigenes showed significant similarities with proteins in the NCBI non-redundant protein database and SWISS-PROT database (E-value < 1e-5), respectively. We assigned 17,340 unigenes to Gene Ontology categories, and we assigned 7618 unigenes to clusters of orthologous groups for eukaryotic complete genomes. By searching the Kyoto Encyclopedia of Genes and Genomes Pathway database, 8014 unigenes were assigned to 6 main categories, including 290 KEGG pathways. To advance research on improving thermotolerance, we identified 24 potential heat shock protein genes with complete open reading frames from the transcriptomic sequences. This is the first study to characterize the leaf transcriptome of tree peony leaf using high-throughput sequencing. The information obtained from the tree peony leaf is valuable for gene discovery, and the identified heat shock protein genes can be used to improve plant stress-tolerance.

Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study.

BackgroundHeat shock proteins (Hsps) perform a fundamental role in protecting plants against abiotic stresses. Although researchers have made great efforts on the functional analysis of individual family members, Hsps have not been fully characterized in rice (Oryza sativa L.) and little is known about their interactors.ResultsIn this study, we combined orthology-based approach with expression association data to screen rice Hsps for the expression patterns of which strongly correlated with that of heat responsive probe-sets. Twenty-seven Hsp candidates were identified, including 12 small Hsps, six Hsp70s, three Hsp60s, three Hsp90s, and three clpB/Hsp100s. Then, using a combination of interolog and expression profile-based methods, we inferred 430 interactors of Hsp70s in rice, and validated the interactions by co-localization and function-based methods. Subsequent analysis showed 13 interacting domains and 28 target motifs were over-represented in Hsp70s interactors. Twenty-four GO terms of biological processes and five GO terms of molecular functions were enriched in the positive interactors, whose expression levels were positively associated with Hsp70s. Hsp70s interaction network implied that Hsp70s were involved in macromolecular translocation, carbohydrate metabolism, innate immunity, photosystem II repair and regulation of kinase activities.ConclusionsTwenty-seven Hsps in rice were identified and 430 interactors of Hsp70s were inferred and validated, then the interacting network of Hsp70s was induced and the function of Hsp70s was analyzed. Furthermore, two databases named Rice Heat Shock Proteins (RiceHsps) and Rice Gene Expression Profile (RGEP), and one online tool named Protein-Protein Interaction Predictor (PPIP), were constructed and could be accessed at http://bioinformatics.fafu.edu.cn/.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-344) contains supplementary material, which is available to authorized users.

Ferruccio Ritossa’s scientific legacy 50 years after his discovery of the heat shock response: a new view of biology, a new society, and a new journal

The pioneering discovery of the heat shock response by the Italian scientist Ferruccio Ritossa reached maturity this year, 2012. It was 50 years ago that Professor Ritossa, through an extraordinary combination of serendipity, curiosity, knowledge and inspiration, published the first observation that cells could mount very strong transcriptional activity when exposed to elevated temperatures, which was coined the heat shock response. This discovery led to the identification of heat shock proteins, which impact many areas of current biology and medicine, and has created a new avenue for more exciting discoveries. In recognition of the discovery of the heat shock response, Cell Stress Society International (CSSI) awarded Professor Ritossa with the CSSI medallion in October 2010 in Dozza, Italy. This article is based on a session of the Fifth CSSI Congress held in Québec commemorating Professor Ritossa and his discovery.

Identification of heat shock proteins from bacteria by electrophoretic separation and nanoflow LC-MS/MS

Examination of heat shock and PR (“pathogenesis-related”) proteins is of special interest in food science. Many food allergens have a similar or the same structure as PR proteins, which are produce...

Detection and identification of heat-shock proteins

Detection and identification of heat-shock proteins

Identification of heat shock proteins binding to an immunodominant uveitopathogenic peptide of IRBP.

Intracellular binding proteins have been identified and isolated from B cells by their ability to bind to the synthetic peptide (1169-1191), the major immunodominant epitope of bovine interphotoreceptor retinoid-binding protein (IRBP) coupled to cyanogen bromide activated Sepharose 4B. After SDS-PAGE, two discrete protein bands of approximately 72 and 74 kDa, were found to be present in B cells of naive Lewis rats as well as in EBV transformed B cells from a human patient with ocular Behçet's disease. Enhanced expression of these peptide-binding proteins was achieved by incubating the cells with Lipopolysaccharide (LPS) from S. typhimurium. The approximately 72 and 74 kDa peptide-binding proteins reacted in western blot with monoclonal antibodies specific for both constitutively expressed and inducible 72/74 kDa hsp 70 proteins. The demonstration that these proteins bind to the immunodominant epitope of IRBP indicates that they may play a role in the processing and presentation of antigens by antigen-presenting cell (APC).

Identification of heat shock proteins binding to an immunodominant uveitopathogenic peptide of IRBP: ERRATUM

Identification of heat shock proteins binding to an immunodominant uveitopathogenic peptide of IRBP: ERRATUM