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Lee J, Ryu B, Kim T, Kim KK. Cryo-EM structure of a 16.5-kDa small heat-shock protein from Methanocaldococcus jannaschii. Int J Biol Macromol 2024; 258:128763. [PMID: 38103675 DOI: 10.1016/j.ijbiomac.2023.128763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
The small heat-shock protein (sHSP) from the archaea Methanocaldococcus jannaschii, MjsHSP16.5, functions as a broad substrate ATP-independent holding chaperone protecting misfolded proteins from aggregation under stress conditions. This protein is the first sHSP characterized by X-ray crystallography, thereby contributing significantly to our understanding of sHSPs. However, despite numerous studies assessing its functions and structures, the precise arrangement of the N-terminal domains (NTDs) within this sHSP cage remains elusive. Here we present the cryo-electron microscopy (cryo-EM) structure of MjsHSP16.5 at 2.49-Å resolution. The subunits of MjsHSP16.5 in the cryo-EM structure exhibit lesser compaction compared to their counterparts in the crystal structure. This structural feature holds particular significance in relation to the biophysical properties of MjsHSP16.5, suggesting a close resemblance to this sHSP native state. Additionally, our cryo-EM structure unveils the density of residues 24-33 within the NTD of MjsHSP16.5, a feature that typically remains invisible in the majority of its crystal structures. Notably, these residues show a propensity to adopt a β-strand conformation and engage in antiparallel interactions with strand β1, both intra- and inter-subunit modes. These structural insights are corroborated by structural predictions, disulfide bond cross-linking studies of Cys-substitution mutants, and protein disaggregation assays. A comprehensive understanding of the structural features of MjsHSP16.5 expectedly holds the potential to inspire a wide range of interdisciplinary applications, owing to the renowned versatility of this sHSP as a nanoscale protein platform.
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Affiliation(s)
- Joohyun Lee
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bumhan Ryu
- Research Solution Center, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Truc Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.
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de la Fuente M, Novo M. Understanding Diversity, Evolution, and Structure of Small Heat Shock Proteins in Annelida Through in Silico Analyses. Front Physiol 2022; 13:817272. [PMID: 35530508 PMCID: PMC9075518 DOI: 10.3389/fphys.2022.817272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/22/2022] [Indexed: 12/04/2022] Open
Abstract
Small heat shock proteins (sHsps) are oligomeric stress proteins characterized by an α-crystallin domain (ACD). These proteins are localized in different subcellular compartments and play critical roles in the stress physiology of tissues, organs, and whole multicellular eukaryotes. They are ubiquitous proteins found in all living organisms, from bacteria to mammals, but they have never been studied in annelids. Here, a data set of 23 species spanning the annelid tree of life, including mostly transcriptomes but also two genomes, was interrogated and 228 novel putative sHsps were identified and manually curated. The analysis revealed very high protein diversity and showed that a significant number of sHsps have a particular dimeric architecture consisting of two tandemly repeated ACDs. The phylogenetic analysis distinguished three main clusters, two of them containing both monomeric sHsps, and ACDs located downstream in the dimeric sHsps, and the other one comprising the upstream ACDs from those dimeric forms. Our results support an evolutionary history of these proteins based on duplication events prior to the Spiralia split. Monomeric sHsps 76) were further divided into five subclusters. Physicochemical properties, subcellular location predictions, and sequence conservation analyses provided insights into the differentiating elements of these putative functional groups. Strikingly, three of those subclusters included sHsps with features typical of metazoans, while the other two presented characteristics resembling non-metazoan proteins. This study provides a solid background for further research on the diversity, evolution, and function in the family of the sHsps. The characterized annelid sHsps are disclosed as essential for improving our understanding of this important family of proteins and their pleotropic functions. The features and the great diversity of annelid sHsps position them as potential powerful molecular biomarkers of environmental stress for acting as prognostic tool in a diverse range of environments.
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Affiliation(s)
- Mercedes de la Fuente
- Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), Las Rozas, Spain
- *Correspondence: Mercedes de la Fuente,
| | - Marta Novo
- Faculty of Biology, Biodiversity, Ecology and Evolution Department, Complutense University of Madrid, Madrid, Spain
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Singh P, Unik B, Puri A, Nagpal G, Singh B, Gautam A, Sharma D. HSPMdb: a computational repository of heat shock protein modulators. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5743069. [PMID: 32090260 PMCID: PMC7043294 DOI: 10.1093/database/baaa003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 12/27/2022]
Abstract
Heat shock proteins (Hsp) are among highly conserved proteins across all domains of life. Though originally discovered as a cellular response to stress, these proteins are also involved in a wide range of cellular functions such as protein refolding, protein trafficking and cellular signalling. A large number of potential Hsp modulators are under clinical trials against various human diseases. As the number of modulators targeting Hsps is growing, there is a need to develop a comprehensive knowledge repository of these findings which is largely scattered. We have thus developed a web-accessible database, HSPMdb, which is a first of its kind manually curated repository of experimentally validated Hsp modulators (activators and inhibitors). The data was collected from 176 research articles and current version of HSPMdb holds 10 223 entries of compounds that are known to modulate activities of five major Hsps (Hsp100, Hsp90, Hsp70, Hsp60 and Hsp40) originated from 15 different organisms (i.e. human, yeast, bacteria, virus, mouse, rat, bovine, porcine, canine, chicken, Trypanosoma brucei and Plasmodium falciparum). HSPMdb provides comprehensive information on biological activities as well as the chemical properties of Hsp modulators. The biological activities of modulators are presented as enzymatic activity and cellular activity. Under the enzymatic activity field, parameters such as IC50, EC50, DC50, Ki and KD have been provided. In the cellular activity field, complete information on cellular activities (percentage cell growth inhibition, EC50 and GI50), type of cell viability assays and cell line used has been provided. One of the important features of HSPMdb is that it allows users to screen whether or not their compound of interest has any similarity with the previously known Hsp modulators. We anticipate that HSPMdb would become a valuable resource for the broader scientific community working in the area of chaperone biology and protein misfolding diseases. HSPMdb is freely accessible at http://bioinfo.imtech.res.in/bvs/hspmdb/index.php.
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Affiliation(s)
- Prashant Singh
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Breezy Unik
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Anuradhika Puri
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Gandharva Nagpal
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Balvinder Singh
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Ankur Gautam
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
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Feng P, Liu W, Huang C, Tang Z. Classifying the superfamily of small heat shock proteins by using g-gap dipeptide compositions. Int J Biol Macromol 2020; 167:1575-1578. [PMID: 33212104 DOI: 10.1016/j.ijbiomac.2020.11.111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 01/16/2023]
Abstract
Small heat shock protein (sHSP) is a superfamily of molecular chaperone and is found from archaea to human. Recent researches have demonstrated that sHSPs participate in a series of biological processes and are even closely associated with serious diseases. Since sHSP is a very large superfamily and members from different superfamilies exhibit distinct functions, accurate classification of the subfamily of sHSP will be helpful for unrevealing its functions. In the present work, a support vector machine-based method was proposed to classify the subfamily of sHSPs. In the 10-fold cross validation test, an overall accuracy of 93.25% was obtained for classifying the subfamily of sHSPs. The superiority of the proposed method was also demonstrated by comparing it with the other methods. It is anticipated that the proposed method will become a useful tool for classifying the subfamily of sHSPs.
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Affiliation(s)
- Pengmian Feng
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China.
| | - Weiwei Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Cong Huang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Zhaohui Tang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
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Nava Ramírez T, Hansberg W. Características comunes de las chaperonas pequeñas y diméricas. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2020. [DOI: 10.22201/fesz.23958723e.2020.0.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Las chaperonas moleculares constituyen un mecanismo importante para evitar la muerte celular provocada por la agregación de proteínas. Las chaperonas independientes del ATP son un grupo de proteínas de bajo peso molecular que pueden proteger y ayudar a alcanzar la estructura nativa de las proteínas desplegadas o mal plegadas sin necesidad de un gasto energético. Hemos encontrado que el dominio C-terminal de las catalasas de subunidad grande tiene actividad de chaperona. Por ello, en esta revisión analizamos las características más comunes de las chaperonas pequeñas y más estudiadas como: αB-cristalina, Hsp20, Spy, Hsp33 y Hsp31. En particular, se examina la participación de los aminoácidos hidrofóbicos y de los aminoácidos con carga en el reconocimiento de las proteínas sustrato, así como el papel que tiene la forma dimérica y su oligomerización en la actividad de chaperona. En cada una de esas chaperonas revisaremos la estructura de la proteína, su función, localización celular e importancia para la célula.
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Cappetta E, Andolfo G, Di Matteo A, Ercolano MR. Empowering crop resilience to environmental multiple stress through the modulation of key response components. JOURNAL OF PLANT PHYSIOLOGY 2020; 246-247:153134. [PMID: 32070802 DOI: 10.1016/j.jplph.2020.153134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/13/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Crop plants have developed a multitude of defense and adaptation responses to protect themselves against invading pathogens and challenging environmental stresses, mostly operating jointly. The plant perception of overall stress induces a coordinated response mediated by complex signaling networks. Experimental evidences proved that plant response to combined biotic and abiotic stresses substantially diverge from the responses to individual stresses. Moreover, the cross-talk of signaling pathways involved in responding to biotic and abiotic stresses is pivoted on several converging elements able to simultaneously modulate the timing and amplitude of the overall plant response. Comprehensively, the interaction between biotic and abiotic stresses can dramatically changes the plant response to the individual stress and the phenotypical outcome of each stress factor. System biology and data mining can synergistically help biologists in finding out regulative mechanisms and key genes controlling the response to biotic and abiotic stresses. Deploying new genetic engineering solutions can rely on the modification of genes involved in resistance/tolerance processes and/or in the modulation of regulatory elements. Finally, a model of the engineered crop for enhanced tolerance to pressures resulting from invasive pathogens and abiotic constraints in semiarid and warm environment is discussed.
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Affiliation(s)
- E Cappetta
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055 Portici (Naples), Italy.
| | - G Andolfo
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055 Portici (Naples), Italy.
| | - A Di Matteo
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055 Portici (Naples), Italy.
| | - M R Ercolano
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055 Portici (Naples), Italy.
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Expression of Heat Shock Proteins in Thermally Challenged Pacific Abalone Haliotis discus hannai. Genes (Basel) 2019; 11:genes11010022. [PMID: 31878084 PMCID: PMC7016835 DOI: 10.3390/genes11010022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022] Open
Abstract
Summer mortality, caused by thermal conditions, is the biggest threat to abalone aquaculture production industries. Various measures have been taken to mitigate this issue by adjusting the environment; however, the cellular processes of Pacific abalone (Haliotis discus hannai) have been overlooked due to the paucity of genetic information. The draft genome of H. discus hannai has recently been reported, prompting exploration of the genes responsible for thermal regulation in Pacific abalone. In this study, 413 proteins were systematically annotated as members of the heat shock protein (HSP) super families, and among them 26 HSP genes from four Pacific abalone tissues (hemocytes, gill, mantle, and muscle) were differentially expressed under cold and heat stress conditions. The co-expression network revealed that HSP expression patterns were tissue-specific and similar to those of other shellfish inhabiting intertidal zones. Finally, representative HSPs were selected at random and their expression patterns were identified by RNA sequencing and validated by qRT-PCR to assess expression significance. The HSPs expressed in hemocytes were highly similar in both analyses, suggesting that hemocytes could be more reliable samples for validating thermal condition markers compared to other tissues.
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Avelange-Macherel MH, Rolland A, Hinault MP, Tolleter D, Macherel D. The Mitochondrial Small Heat Shock Protein HSP22 from Pea is a Thermosoluble Chaperone Prone to Co-Precipitate with Unfolding Client Proteins. Int J Mol Sci 2019; 21:E97. [PMID: 31877784 PMCID: PMC6981728 DOI: 10.3390/ijms21010097] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
The small heat shock proteins (sHSPs) are molecular chaperones that share an alpha-crystallin domain but display a high diversity of sequence, expression, and localization. They are especially prominent in plants, populating most cellular compartments. In pea, mitochondrial HSP22 is induced by heat or oxidative stress in leaves but also strongly accumulates during seed development. The molecular function of HSP22 was addressed by studying the effect of temperature on its structural properties and chaperone effects using a recombinant or native protein. Overexpression of HSP22 significantly increased bacterial thermotolerance. The secondary structure of the recombinant protein was not affected by temperature in contrast with its quaternary structure. The purified protein formed large polydisperse oligomers that dissociated upon heating (42 °C) into smaller species (mainly monomers). The recombinant protein appeared thermosoluble but precipitated with thermosensitive proteins upon heat stress in assays either with single protein clients or within complex extracts. As shown by in vitro protection assays, HSP22 at high molar ratio could partly prevent the heat aggregation of rhodanese but not of malate dehydrogenase. HSP22 appears as a holdase that could possibly prevent the aggregation of some proteins while co-precipitating with others to facilitate their subsequent refolding by disaggregases or clearance by proteases.
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Affiliation(s)
| | | | | | | | - David Macherel
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 Quasav, 42 rue George Morel, 49071 Beaucouzé, France; (M.-H.A.-M.)
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Chen W, Feng P, Liu T, Jin D. Recent Advances in Machine Learning Methods for Predicting Heat Shock Proteins. Curr Drug Metab 2019; 20:224-228. [DOI: 10.2174/1389200219666181031105916] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/21/2018] [Accepted: 08/02/2018] [Indexed: 02/08/2023]
Abstract
Background:As molecular chaperones, Heat Shock Proteins (HSPs) not only play key roles in protein folding and maintaining protein stabilities, but are also linked with multiple kinds of diseases. Therefore, HSPs have been regarded as the focus of drug design. Since HSPs from different families play distinct functions, accurately classifying the families of HSPs is the key step to clearly understand their biological functions. In contrast to laborintensive and cost-ineffective experimental methods, computational classification of HSP families has emerged to be an alternative approach.Methods:We reviewed the paper that described the existing datasets of HSPs and the representative computational approaches developed for the identification and classification of HSPs.Results:The two benchmark datasets of HSPs, namely HSPIR and sHSPdb were introduced, which provided invaluable resources for computationally identifying HSPs. The gold standard dataset and sequence encoding schemes for building computational methods of classifying HSPs were also introduced. The three representative web-servers for identifying HSPs and their families were described.Conclusion:The existing machine learning methods for identifying the different families of HSPs indeed yielded quite encouraging results and did play a role in promoting the research on HSPs. However, the number of HSPs with known structures is very limited. Therefore, determining the structure of the HSPs is also urgent, which will be helpful in revealing their functions.
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Affiliation(s)
- Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Pengmian Feng
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063000, China
| | - Tao Liu
- School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China
| | - Dianchuan Jin
- School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China
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Regulation of Antimicrobial Pathways by Endogenous Heat Shock Proteins in Gastrointestinal Disorders. GASTROINTESTINAL DISORDERS 2018. [DOI: 10.3390/gidisord1010005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Heat shock proteins (HSPs) are essential mediators of cellular homeostasis by maintaining protein functionality and stability, and activating appropriate immune cells. HSP activity is influenced by a variety of factors including diet, microbial stimuli, environment and host immunity. The overexpression and down-regulation of HSPs is associated with various disease phenotypes, including the inflammatory bowel diseases (IBD) such as Crohn’s disease (CD). While the precise etiology of CD remains unclear, many of the putative triggers also influence HSP activity. The development of different CD phenotypes therefore may be a result of the disease-modifying behavior of the environmentally-regulated HSPs. Understanding the role of bacterial and endogenous HSPs in host homeostasis and disease will help elucidate the complex interplay of factors. Furthermore, discerning the function of HSPs in CD may lead to therapeutic developments that better reflect and respond to the gut environment.
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Petitjean C, Makarova KS, Wolf YI, Koonin EV. Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families. Genome Biol Evol 2018; 9:2791-2811. [PMID: 28985292 PMCID: PMC5737733 DOI: 10.1093/gbe/evx189] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2017] [Indexed: 02/07/2023] Open
Abstract
Origin of new biological functions is a complex phenomenon ranging from single-nucleotide substitutions to the gain of new genes via horizontal gene transfer or duplication. Neofunctionalization and subfunctionalization of proteins is often attributed to the emergence of paralogs that are subject to relaxed purifying selection or positive selection and thus evolve at accelerated rates. Such phenomena potentially could be detected as anomalies in the phylogenies of the respective gene families. We developed a computational pipeline to search for such anomalies in 1,834 orthologous clusters of archaeal genes, focusing on lineage-specific subfamilies that significantly deviate from the expected rate of evolution. Multiple potential cases of neofunctionalization and subfunctionalization were identified, including some ancient, house-keeping gene families, such as ribosomal protein S10, general transcription factor TFIIB and chaperone Hsp20. As expected, many cases of apparent acceleration of evolution are associated with lineage-specific gene duplication. On other occasions, long branches in phylogenetic trees correspond to horizontal gene transfer across long evolutionary distances. Significant deceleration of evolution is less common than acceleration, and the underlying causes are not well understood; functional shifts accompanied by increased constraints could be involved. Many gene families appear to be “highly evolvable,” that is, include both long and short branches. Even in the absence of precise functional predictions, this approach allows one to select targets for experimentation in search of new biology.
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Affiliation(s)
- Celine Petitjean
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
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Ju Y, Tian H, Zhang R, Zuo L, Jin G, Xu Q, Ding X, Li X, Chu Z. Overexpression of OsHSP18.0-CI Enhances Resistance to Bacterial Leaf Streak in Rice. RICE (NEW YORK, N.Y.) 2017; 10:12. [PMID: 28417425 PMCID: PMC5393982 DOI: 10.1186/s12284-017-0153-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 04/07/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The small heat shock proteins represent a large family of proteins that respond to a wide range of abiotic and biotic stresses. OsHsp18.0-CI confers tolerance to salt and cadmium and interacts with viral RNA-dependent RNA polymerase (RdRp). However, the direct function of OsHsp18.0-CI in resistance against biotic stresses remains unclear in rice. RESULTS Here, we report that the expression of OsHsp18.0-CI was up-regulated upon inoculation with RS105, a strain of Xanthomonas oryzae pv. oryzicola (Xoc) that causes bacterial leaf streak in rice. In comparison with wild-type, OsHsp18.0-CI overexpression (OE) lines exhibited enhanced resistance to RS105, whereas repression lines exhibited compromised resistance to RS105. In addition, the transcriptional profiles of wild type and OE lines were compared with and without inoculation with RS105. After inoculation with RS105, most of the genes with up-regulated expression were commonly stimulated in the wild type and OE lines, with stronger induction in the OE lines than in wild type. CONCLUSION Our study reveals that OsHsp18.0-CI positively regulates resistance to Xoc by mediating an enhanced version of the basal defense response in rice.
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Affiliation(s)
- Yanhu Ju
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018 Shandong People’s Republic of China
| | - Hongjuan Tian
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018 Shandong People’s Republic of China
- Present address: Haoyunjiao Resort Party Committee Government Office, Rongcheng, Shandong People’s Republic of China
| | - Ruihua Zhang
- Rice Research Institute, Linyi Academy of Agricultural Science, Linyi, 276012 Shandong People’s Republic of China
| | - Liping Zuo
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018 Shandong People’s Republic of China
| | - Guixiu Jin
- Rice Research Institute, Linyi Academy of Agricultural Science, Linyi, 276012 Shandong People’s Republic of China
| | - Qian Xu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018 Shandong People’s Republic of China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018 Shandong People’s Republic of China
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 China
| | - Xiangkui Li
- Rice Research Institute, Linyi Academy of Agricultural Science, Linyi, 276012 Shandong People’s Republic of China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018 Shandong People’s Republic of China
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 China
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13
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Structural and functional studies of SAV0551 from Staphylococcus aureus as a chaperone and glyoxalase III. Biosci Rep 2017; 37:BSR20171106. [PMID: 29046369 PMCID: PMC5691139 DOI: 10.1042/bsr20171106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/10/2017] [Accepted: 12/10/2017] [Indexed: 11/17/2022] Open
Abstract
The DJ-1/ThiJ/PfpI superfamily of proteins is highly conserved across all biological kingdoms showing divergent multifunctions, such as chaperone, catalase, protease, and kinase. The common theme of these functions is responding to and managing various cellular stresses. DJ-1/ThiJ/PfpI superfamily members are classified into three subfamilies according to their quaternary structure (DJ-1-, YhbO-, and Hsp-types). The Hsp-type subfamily includes Hsp31, a chaperone and glyoxalase III. SAV0551, an Hsp-type subfamily member from Staphylococcus aureus, is a hypothetical protein that is predicted as Hsp31. Thus, to reveal the function and reaction mechanism of SAV0551, the crystal structure of SAV0551 was determined. The overall folds in SAV0551 are similar to other members of the Hsp-type subfamily. We have shown that SAV0551 functions as a chaperone and that the surface structure is crucial for holding unfolded substrates. As many DJ-1/ThiJ/PfpI superfamily proteins have been characterized as glyoxalase III, our study also demonstrates SAV0551 as a glyoxalase III that is independent of any cofactors. The reaction mechanism was evaluated via a glyoxylate-bound structure that mimics the hemithioacetal reaction intermediate. We have confirmed that the components required for reaction are present in the structure, including a catalytic triad for a catalytic action, His78 as a base, and a water molecule for hydrolysis. Our functional studies based on the crystal structures of native and glyoxylate-bound SAV0551 will provide a better understanding of the reaction mechanism of a chaperone and glyoxalase III.
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Rutsdottir G, I Rasmussen M, Hojrup P, Bernfur K, Emanuelsson C, Söderberg CAG. Chaperone-client interactions between Hsp21 and client proteins monitored in solution by small angle X-ray scattering and captured by crosslinking mass spectrometry. Proteins 2017; 86:110-123. [PMID: 29082555 DOI: 10.1002/prot.25413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 10/13/2017] [Accepted: 10/27/2017] [Indexed: 11/07/2022]
Abstract
The small heat shock protein (sHsp) chaperones are important for stress survival, yet the molecular details of how they interact with client proteins are not understood. All sHsps share a folded middle domain to which is appended flexible N- and C-terminal regions varying in length and sequence between different sHsps which, in different ways for different sHsps, mediate recognition of client proteins. In plants there is a chloroplast-localized sHsp, Hsp21, and a structural model suggests that Hsp21 has a dodecameric arrangement with six N-terminal arms located on the outside of the dodecamer and six inwardly-facing. Here, we investigated the interactions between Hsp21 and thermosensitive model substrate client proteins in solution, by small-angle X-ray scattering (SAXS) and crosslinking mass spectrometry. The chaperone-client complexes were monitored and the Rg -values were found to increase continuously during 20 min at 45°, which could reflect binding of partially unfolded clients to the flexible N-terminal arms of the Hsp21 dodecamer. No such increase in Rg -values was observed with a mutational variant of Hsp21, which is mainly dimeric and has reduced chaperone activity. Crosslinking data suggest that the chaperone-client interactions involve the N-terminal region in Hsp21 and only certain parts in the client proteins. These parts are peripheral structural elements presumably the first to unfold under destabilizing conditions. We propose that the flexible and hydrophobic N-terminal arms of Hsp21 can trap and refold early-unfolding intermediates with or without dodecamer dissociation.
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Affiliation(s)
- Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Morten I Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Hojrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Lund University, Sweden
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15
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Ning F, Wu X, Zhang H, Wu Z, Niu L, Yang H, Wang W. Accumulation Profiles of Embryonic Salt-Soluble Proteins in Maize Hybrids and Parental Lines Indicate Matroclinous Inheritance: A Proteomic Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:1824. [PMID: 29118775 PMCID: PMC5661082 DOI: 10.3389/fpls.2017.01824] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/10/2017] [Indexed: 05/29/2023]
Abstract
Maize is one of the most widely cultivated crops. It accumulates a large quantity of seed storage proteins, which are important for seed development and germination, and contribute to the nutritional quality of seeds. Based on solubility, the storage proteins are divided into albumins (water-soluble), globulins (salt-soluble), prolamins (alcohol-soluble), and glutelins (acid- or alkali-soluble). Maize hybrids are cultivated due to the superior performance of F1 hybrids than that of their parents, a phenomenon known as heterosis. However, the accumulation patterns of seed storage proteins in maize embryos between the hybrids and their parental inbred lines have not been compared. In the present study, two elite inbred lines of China, Zheng 58 and Chang 7-2, and their reciprocal hybrids (Zheng 58 × Chang 7-2 and Chang 7-2 × Zheng 58) were used to explore parental influences on the accumulation patterns of seed storage proteins in maize embryos. For this purpose, we focused on seed salt-soluble proteins (SSPs) in our experiments. The SSPs were selectively extracted from maize mature embryos after extensive removal of water-soluble albumin and separated using two-dimensional gel electrophoresis (2-DE), followed by mass spectrometry analysis. Our results indicated that the 2-DE SSP profiles of hybrids closely resembled those of their maternal parent rather than the paternal parent. In other words, 2-DE SSP profiles of Zheng 58 × Chang 7-2 were more similar those of Zheng 58 whereas such profiles of Chang 7-2 × Zheng 58 were more similar to those of Chang 7-2 although the 2-DE profiles of all four maize types were quite similar. In total, 12 relatively abundant SSPs spots representing five kinds of proteins were identified, of which nine protein spots displayed non-additive accumulation in at least one hybrid. This study provided additional data on dominance and partial dominance effects on maize hybrids embryos. Besides, earlier studies on accumulation profiles of globulin-1 (also known as vicilin), which is one of the most abundant globulins in maize embryos, also support the above results. This study would be helpful in revealing the mechanisms underlying SSPs accumulation patterns in the hybrids.
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16
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Carra S, Alberti S, Arrigo PA, Benesch JL, Benjamin IJ, Boelens W, Bartelt-Kirbach B, Brundel BJJM, Buchner J, Bukau B, Carver JA, Ecroyd H, Emanuelsson C, Finet S, Golenhofen N, Goloubinoff P, Gusev N, Haslbeck M, Hightower LE, Kampinga HH, Klevit RE, Liberek K, Mchaourab HS, McMenimen KA, Poletti A, Quinlan R, Strelkov SV, Toth ME, Vierling E, Tanguay RM. The growing world of small heat shock proteins: from structure to functions. Cell Stress Chaperones 2017; 22:601-611. [PMID: 28364346 PMCID: PMC5465036 DOI: 10.1007/s12192-017-0787-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2017] [Indexed: 12/21/2022] Open
Abstract
Small heat shock proteins (sHSPs) are present in all kingdoms of life and play fundamental roles in cell biology. sHSPs are key components of the cellular protein quality control system, acting as the first line of defense against conditions that affect protein homeostasis and proteome stability, from bacteria to plants to humans. sHSPs have the ability to bind to a large subset of substrates and to maintain them in a state competent for refolding or clearance with the assistance of the HSP70 machinery. sHSPs participate in a number of biological processes, from the cell cycle, to cell differentiation, from adaptation to stressful conditions, to apoptosis, and, even, to the transformation of a cell into a malignant state. As a consequence, sHSP malfunction has been implicated in abnormal placental development and preterm deliveries, in the prognosis of several types of cancer, and in the development of neurological diseases. Moreover, mutations in the genes encoding several mammalian sHSPs result in neurological, muscular, or cardiac age-related diseases in humans. Loss of protein homeostasis due to protein aggregation is typical of many age-related neurodegenerative and neuromuscular diseases. In light of the role of sHSPs in the clearance of un/misfolded aggregation-prone substrates, pharmacological modulation of sHSP expression or function and rescue of defective sHSPs represent possible routes to alleviate or cure protein conformation diseases. Here, we report the latest news and views on sHSPs discussed by many of the world's experts in the sHSP field during a dedicated workshop organized in Italy (Bertinoro, CEUB, October 12-15, 2016).
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Affiliation(s)
- Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, and Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via G. Campi 287, 41125 Modena, Italy
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Patrick A. Arrigo
- Université de Lyon, 69622 Lyon, France
- CNRS, UMR 5310, INSERM U1217, Institut NeuroMyoGène, Université Lyon 1, 69100 Villeurbanne, France
| | | | - Ivor J. Benjamin
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650 USA
| | - Wilbert Boelens
- Biomolecular Chemistry, 284, Radboud University, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | | | - Bianca J. J. M. Brundel
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - John A. Carver
- The Research School of Chemistry, The Australian National University, Acton, ACT 2601 Australia
| | - Heath Ecroyd
- Illawara Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522 Australia
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Stephanie Finet
- IMPMC UMR7590, CNRS, UPMC Paris 6, 4 place Jussieu, Paris, France
| | - Nikola Golenhofen
- Institute of Anatomy and Cell Biology, University of Ulm, 89081 Ulm, Germany
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nikolai Gusev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, 119991 Russia
| | | | - Lawrence E. Hightower
- Department of Molecular & Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125 USA
| | - Harm H. Kampinga
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Rachel E. Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Krzysztof Liberek
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232 USA
| | - Kathryn A. McMenimen
- Departments of Pathology, Biological Chemistry, and Medicinal Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, MI USA
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Milan, Italy
| | - Roy Quinlan
- Department of Biosciences and the Biophysical Sciences Institute, University of Durham, Durham, UK
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Melinda E. Toth
- Laboratory of Animal Genetics and Molecular Neurobiology, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Elizabeth Vierling
- Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003 USA
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721 USA
| | - Robert M. Tanguay
- Laboratory of Cell & Developmental Genetics, IBIS, and Department of Molecular Biology, Medical Biochemistry and Pathology, Medical School, Université Laval, Québec (Qc), G1V 0A6 Canada
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17
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Rutsdottir G, Härmark J, Weide Y, Hebert H, Rasmussen MI, Wernersson S, Respondek M, Akke M, Højrup P, Koeck PJB, Söderberg CAG, Emanuelsson C. Structural model of dodecameric heat-shock protein Hsp21: Flexible N-terminal arms interact with client proteins while C-terminal tails maintain the dodecamer and chaperone activity. J Biol Chem 2017; 292:8103-8121. [PMID: 28325834 PMCID: PMC5427286 DOI: 10.1074/jbc.m116.766816] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/16/2017] [Indexed: 01/14/2023] Open
Abstract
Small heat-shock proteins (sHsps) prevent aggregation of thermosensitive client proteins in a first line of defense against cellular stress. The mechanisms by which they perform this function have been hard to define due to limited structural information; currently, there is only one high-resolution structure of a plant sHsp published, that of the cytosolic Hsp16.9. We took interest in Hsp21, a chloroplast-localized sHsp crucial for plant stress resistance, which has even longer N-terminal arms than Hsp16.9, with a functionally important and conserved methionine-rich motif. To provide a framework for investigating structure-function relationships of Hsp21 and understanding these sequence variations, we developed a structural model of Hsp21 based on homology modeling, cryo-EM, cross-linking mass spectrometry, NMR, and small-angle X-ray scattering. Our data suggest a dodecameric arrangement of two trimer-of-dimer discs stabilized by the C-terminal tails, possibly through tail-to-tail interactions between the discs, mediated through extended IXVXI motifs. Our model further suggests that six N-terminal arms are located on the outside of the dodecamer, accessible for interaction with client proteins, and distinct from previous undefined or inwardly facing arms. To test the importance of the IXVXI motif, we created the point mutant V181A, which, as expected, disrupts the Hsp21 dodecamer and decreases chaperone activity. Finally, our data emphasize that sHsp chaperone efficiency depends on oligomerization and that client interactions can occur both with and without oligomer dissociation. These results provide a generalizable workflow to explore sHsps, expand our understanding of sHsp structural motifs, and provide a testable Hsp21 structure model to inform future investigations.
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Affiliation(s)
| | - Johan Härmark
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | - Yoran Weide
- From the Departments of Biochemistry and Structural Biology and
| | - Hans Hebert
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | - Morten I Rasmussen
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | | | | | | | - Peter Højrup
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Philip J B Koeck
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
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