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Pinheiro GMS, Amorim GC, Matos CO, Ramos CHI, Almeida FCL. Backbone NMR resonance assignment of Sis1, a type B J-domain protein from Saccharomyces cerevisiae. BIOMOLECULAR NMR ASSIGNMENTS 2025; 19:29-34. [PMID: 39738939 DOI: 10.1007/s12104-024-10212-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Accepted: 12/10/2024] [Indexed: 01/02/2025]
Abstract
J-domain proteins (JDPs) are essential cochaperones of heat shock protein 70 (Hsp70), as they bind and deliver misfolded polypeptides while also stimulating ATPase activity, thereby mediating the refolding process and assisting Hsp70 in maintaining cellular proteostasis. Despite their importance, detailed structural information about JDP‒Hsp70 complexes is still being explored due to various technical challenges. One major challenge is the lack of more detailed structural data on full-length JDPs. Class A and B JDPs, the most extensively studied, are typically dimers of 300-400 residue polypeptides with central intrinsically disordered regions. These features complicate structural analysis via NMR and X-ray crystallography techniques. This work presents the 1H, 15N, and 13C backbone resonance assignments of the full-length (352 residues long) Sis1, a dimeric class B JDP from S. cerevisiae. Our study achieved 70.5% residue assignment distributed across the entire protein, providing probes in all Sis1 domains for the first time. To overcome this challenging task, strategies such as deuteration and 3D BEST-TROSY correlation experiments were used. The methods and results are detailed within the text. We are confident that this achievement will significantly benefit both the structural biology and the proteostasis scientific communities.
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Affiliation(s)
| | - Gisele C Amorim
- Numpex-Bio, Federal University of Rio de Janeiro, Duque de Caxias, RJ, Brazil
- National Center of Nuclear Magnetic Resonance (CNRMN), National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carolina O Matos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas, SP, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas, SP, Brazil.
- National Center of Nuclear Magnetic Resonance (CNRMN), National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fabio C L Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
- National Center of Nuclear Magnetic Resonance (CNRMN), National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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2
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Tai MDS, Ochoa L, Flydal MI, Velasco-Carneros L, Muntaner J, Santiago C, Gamiz-Arco G, Moro F, Jung-Kc K, Gil-Cantero D, Marcilla M, Kallio JP, Muga A, Valpuesta JM, Cuéllar J, Martinez A. Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12. Nat Commun 2025; 16:2755. [PMID: 40113792 PMCID: PMC11926245 DOI: 10.1038/s41467-025-57733-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/28/2025] [Indexed: 03/22/2025] Open
Abstract
Pathogenic variants of the J-domain protein DNAJC12 cause parkinsonism, which is associated with a defective interaction of DNAJC12 with tyrosine hydroxylase (TH), the rate-limiting enzyme in dopamine biosynthesis. In this work, we characterize the formation of the TH:DNAJC12 complex, showing that DNAJC12 binding stabilizes both TH and the variant TH-p.R202H, associated with TH deficiency. This binding delays their time-dependent aggregation in an Hsp70-independent manner, while preserving TH activity and feedback regulatory inhibition by dopamine. DNAJC12 alone barely activates Hsc70 but synergistically stimulates Hsc70 ATPase activity when complexed with TH. Cryo-electron microscopy supported by crosslinking-mass spectroscopy reveals two DNAJC12 monomers bound per TH tetramer, each embracing one of the two regulatory domain dimers, leaving the active sites available for substrate, cofactor and inhibitory dopamine interaction. Our results also reveal the key role of the C-terminal region of DNAJC12 in TH binding, explaining the pathogenic mechanism of the DNAJC12 disease variant p.W175Ter.
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Affiliation(s)
- Mary Dayne S Tai
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Lissette Ochoa
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Marte I Flydal
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Lorea Velasco-Carneros
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena, Leioa, Spain
| | | | - César Santiago
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gloria Gamiz-Arco
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Fernando Moro
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena, Leioa, Spain
| | - Kunwar Jung-Kc
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
| | | | | | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Arturo Muga
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena, Leioa, Spain
| | - José María Valpuesta
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
- Unidad de Nanobiotecnología, CNB-CSIC-IMDEA Nanociencia Associated Unit, Madrid, Spain.
| | - Jorge Cuéllar
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway.
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3
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Zhang Y, Du B, Zou M, Peng B, Rao Y. Neuronal Ceroid Lipofuscinosis-Concepts, Classification, and Avenues for Therapy. CNS Neurosci Ther 2025; 31:e70261. [PMID: 39925015 PMCID: PMC11808193 DOI: 10.1111/cns.70261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 01/26/2025] [Accepted: 01/28/2025] [Indexed: 02/11/2025] Open
Abstract
Neuronal ceroid lipofuscinosis (NCL) is a group of neurodegenerative lysosomal storage disorders characterized by excessive accumulation of lysosomal lipofuscin. Thirteen subtypes of NCL have been identified, each associated with distinct genes encoding various transmembrane proteins, secretory proteins, or lysosomal enzymes. Clinically, NCL manifests in infants through vision impairment, motor and cognitive dysfunctions, epilepsy, and premature death. The pathological complexity of NCL has hindered the development of effective clinical protocols. Current treatment modalities, including enzyme replacement therapy, pharmacological approaches, gene therapy, and stem cell therapy, have demonstrated limited efficacy. However, emerging evidence suggests a significant relationship between NCL and microglial cells, highlighting the potential of novel microglial cell replacement therapies. This review comprehensively examines the pathogenic genes associated with various NCL subtypes, elucidating their roles, clinical presentations, and corresponding mouse models. Especially, we thoroughly discuss the advances in the clinical study of potential therapeutics, which crucially calls for early diagnosis and treatment more than ever.
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Affiliation(s)
- Yuheng Zhang
- Department of Neurology, Zhongshan Hospital, Laboratory Animal CenterFudan UniversityShanghaiChina
- Children’s Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, MOE Innovative Center for New Drug Development of Immune Inflammatory DiseasesFudan UniversityShanghaiChina
| | - Bingying Du
- Children’s Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, MOE Innovative Center for New Drug Development of Immune Inflammatory DiseasesFudan UniversityShanghaiChina
- Department of NeurologyThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Miaozhan Zou
- Department of Neurology, Zhongshan Hospital, Laboratory Animal CenterFudan UniversityShanghaiChina
- Children’s Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, MOE Innovative Center for New Drug Development of Immune Inflammatory DiseasesFudan UniversityShanghaiChina
| | - Bo Peng
- Children’s Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, MOE Innovative Center for New Drug Development of Immune Inflammatory DiseasesFudan UniversityShanghaiChina
| | - Yanxia Rao
- Department of Neurology, Zhongshan Hospital, Laboratory Animal CenterFudan UniversityShanghaiChina
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Zheng Y, Peng L, Jiang G, Zhou J, Yang S, Bai L, Li X, He M. Activation of chaperone-mediated autophagy exerting neuroprotection effect on intracerebral hemorrhage-induced neuronal injury by targeting Lamp2a. Exp Neurol 2024; 382:114986. [PMID: 39368534 DOI: 10.1016/j.expneurol.2024.114986] [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: 07/09/2024] [Revised: 09/27/2024] [Accepted: 10/02/2024] [Indexed: 10/07/2024]
Abstract
Intracerebral hemorrhage (ICH) is a common and devastating type of stroke, marked by significant morbidity and a grim prognosis. The inflammation cascade triggered by astrocytes plays a critical role in secondary brain injury (SBI) following ICH, leading to detrimental effects such as cell death. However, effective intervention strategies are currently lacking. This study aims to investigate the role of the astrocyte cascade reaction following ICH and identify potential intervention targets. Utilizing the GSE216607 and GSE206971 databases for analysis, we established a mouse autologous blood model. Firstly, our research revealed a significant activation of the autophagy pathway following intracerebral hemorrhage (ICH), with a notable upregulation of Lamp2a, a key factor in chaperone-mediated autophagy (CMA), primarily localized in astrocytes. Additionally, the downregulation of Lamp2a resulted in a significant augmentation of A1 reactive astrocytes, concomitant with a reduction in myelin coverage area, heightened neuronal injury, exacerbated motor and sensory deficits, and diminished neurological scores after ICH in mice. Conversely, CA77.1, an activator of CMA, could reverse ICH-induced augmentation of A1 reactive astrocytes, myelin damage, neuronal death, and neurobehavioral disorders. In conclusion, the activation of astrocyte CMA following ICH can exert neuroprotective effects. Lamp2a represents a promising therapeutic target for post-ICH treatment.
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Affiliation(s)
- Yun Zheng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China; Department of Geriatrics, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China
| | - Lu Peng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China; Institute of Stroke Research, Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China
| | - Guannan Jiang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China; Institute of Stroke Research, Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China
| | - Jialei Zhou
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China; Institute of Stroke Research, Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China
| | - Siyuan Yang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China; Institute of Stroke Research, Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China
| | - Lei Bai
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China; Institute of Stroke Research, Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China; Institute of Stroke Research, Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China.
| | - Mingqing He
- Department of Geriatrics, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, Jiangsu Province, China.
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5
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Daniyan MO, Singh H, Blatch GL. The J Domain Proteins of Plasmodium knowlesi, a Zoonotic Malaria Parasite of Humans. Int J Mol Sci 2024; 25:12302. [PMID: 39596368 PMCID: PMC11594657 DOI: 10.3390/ijms252212302] [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: 10/12/2024] [Revised: 11/07/2024] [Accepted: 11/08/2024] [Indexed: 11/28/2024] Open
Abstract
Plasmodium knowlesi is a zoonotic form of human malaria, the pathology of which is poorly understood. While the J domain protein (JDP) family has been extensively studied in Plasmodium falciparum, and shown to contribute to malaria pathology, there is currently very limited information on the P. knowlesi JDPs (PkJDPs). This review provides a critical analysis of the literature and publicly available data on PkJDPs. Interestingly, the P. knowlesi genome encodes at least 31 PkJDPs, with well over half belonging to the most diverse types which contain only the signature J domain (type IIIs, 19) or a corrupted version of the J domain (type IVs, 2) as evidence of their membership. The more typical PkJDPs containing other domains typical of JDPs in addition to the J domain are much fewer in number (type IIs, 8; type Is, 2). This study indentifies PkJDPs that are potentially involved in: folding of newly synthesized or misfolded proteins within the P. knowlesi cytosol (a canonical type I and certain typical type IIs); protein translocation (a type III) and folding (a type II) in the ER; and protein import into mitochondria (a type III). Interestingly, a type II PkJDP is potentially exported to the host cell cytosol where it may recruit human HSP70 for the trafficking and folding of other exported P. knowlesi proteins. Experimental studies are required on this fascinating family of proteins, not only to validate their role in the pathology of knowlesi malaria, but also because they represent potential anti-malarial drug targets.
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Affiliation(s)
- Michael O Daniyan
- Department of Pharmacology, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife 220005, Nigeria
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008, India
| | - Gregory L Blatch
- Biomedical Biotechnology Research Unit, Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda 6140, South Africa
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
- The Vice Chancellery, The University of Notre Dame Australia, Fremantle, WA 6959, Australia
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6
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Duranti E, Villa C. Insights into Dysregulated Neurological Biomarkers in Cancer. Cancers (Basel) 2024; 16:2680. [PMID: 39123408 PMCID: PMC11312413 DOI: 10.3390/cancers16152680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
The link between neurodegenerative diseases (NDs) and cancer has generated greater interest in biomedical research, with decades of global studies investigating neurodegenerative biomarkers in cancer to better understand possible connections. Tau, amyloid-β, α-synuclein, SOD1, TDP-43, and other proteins associated with nervous system diseases have also been identified in various types of solid and malignant tumors, suggesting a potential overlap in pathological processes. In this review, we aim to provide an overview of current evidence on the role of these proteins in cancer, specifically examining their effects on cell proliferation, apoptosis, chemoresistance, and tumor progression. Additionally, we discuss the diagnostic and therapeutic implications of this interconnection, emphasizing the importance of further research to completely comprehend the clinical implications of these proteins in tumors. Finally, we explore the challenges and opportunities in targeting these proteins for the development of new targeted anticancer therapies, providing insight into how to integrate knowledge of NDs in oncology research.
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Affiliation(s)
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
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7
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Coto ALDS, Pereira AA, Oliveira SD, Moritz MNDO, Franco da Rocha AM, Dores-Silva PR, da Silva NSM, de Araújo Nogueira AR, Gava LM, Seraphim TV, Borges JC. Structural characterization of the human DjC20/HscB cochaperone in solution. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140970. [PMID: 37871810 DOI: 10.1016/j.bbapap.2023.140970] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/27/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Abstract
J-domain proteins (JDPs) form a very large molecular chaperone family involved in proteostasis processes, such as protein folding, trafficking through membranes and degradation/disaggregation. JDPs are Hsp70 co-chaperones capable of stimulating ATPase activity as well as selecting and presenting client proteins to Hsp70. In mitochondria, human DjC20/HscB (a type III JDP that possesses only the conserved J-domain in some region of the protein) is involved in [FeS] protein biogenesis and assists human mitochondrial Hsp70 (HSPA9). Human DjC20 possesses a zinc-finger domain in its N-terminus, which closely contacts the J-domain and appears to be essential for its function. Here, we investigated the hDjC20 structure in solution as well as the importance of Zn+2 for its stability. The recombinant hDjC20 was pure, folded and capable of stimulating HSPA9 ATPase activity. It behaved as a slightly elongated monomer, as attested by small-angle X-ray scattering and SEC-MALS. The presence of Zn2+ in the hDjC20 samples was verified, a stoichiometry of 1:1 was observed, and its removal by high concentrations of EDTA and DTPA was unfeasible. However, thermal and chemical denaturation in the presence of EDTA led to a reduction in protein stability, suggesting a synergistic action between the chelating agent and denaturators that facilitate protein unfolding depending on metal removal. These data suggest that the affinity of Zn+2 for the protein is very high, evidencing its importance for the hDjC20 structure.
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Affiliation(s)
| | - Arthur Alexandre Pereira
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Sabrina Dorta Oliveira
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | | | | | | | | | | | | | - Thiago Vagas Seraphim
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Júlio César Borges
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil.
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8
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Nelson B, Soper N, Lupoli TJ. Bacterial J-Domains with C-Terminal Tags Contact the Substrate Binding Domain of DnaK and Sequester Chaperone Activity. Chembiochem 2023; 24:e202300261. [PMID: 37556312 DOI: 10.1002/cbic.202300261] [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: 03/31/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023]
Abstract
Functional interactions between the molecular chaperone DnaK and cofactor J-proteins (DnaJs), as well as their homologs, are crucial to the maintenance of proteostasis across cell types. In the bacterial pathogen Mycobacterium tuberculosis, DnaK-DnaJ interactions are essential for cell growth and represent potential targets for antibiotic or adjuvant development. While the N-terminal J-domains of J-proteins are known to form important contacts with DnaK, C-terminal domains have varied roles. Here, we have studied the effect of adding C-terminal tags to N-terminal J-domain truncations of mycobacterial DnaJ1 and DnaJ2 to promote additional interactions with DnaK. We found that His6 tags uniquely promote binding to additional sites in the substrate binding domain at the C-terminus of DnaK. Other C-terminal tags attached to J-domains, even peptides known to interact with DnaK, do not produce the same effects. Expression of C-terminally modified DnaJ1 or DnaJ2 J-domains in mycobacterial cells suppresses chaperone activity following proteotoxic stress, which is exaggerated in the presence of a small-molecule DnaK inhibitor. Hence, this work uncovers genetically encodable J-protein variants that may be used to study chaperone-cofactor interactions in other organisms.
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Affiliation(s)
- Brock Nelson
- Department of Chemistry, New York University, New York, 10003, USA
| | - Nathan Soper
- Department of Chemistry, New York University, New York, 10003, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, 10003, USA
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9
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Singh H, Almaazmi SY, Dutta T, Keyzers RA, Blatch GL. In silico identification of modulators of J domain protein-Hsp70 interactions in Plasmodium falciparum: a drug repurposing strategy against malaria. Front Mol Biosci 2023; 10:1158912. [PMID: 37621993 PMCID: PMC10445141 DOI: 10.3389/fmolb.2023.1158912] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Plasmodium falciparum is a unicellular, intracellular protozoan parasite, and the causative agent of malaria in humans, a deadly vector borne infectious disease. A key phase of malaria pathology, is the invasion of human erythrocytes, resulting in drastic remodeling by exported parasite proteins, including molecular chaperones and co-chaperones. The survival of the parasite within the human host is mediated by P. falciparum heat shock protein 70s (PfHsp70s) and J domain proteins (PfJDPs), functioning as chaperones-co-chaperones partnerships. Two complexes have been shown to be important for survival and pathology of the malaria parasite: PfHsp70-x-PFE0055c (exported); and PfHsp70-2-PfSec63 (endoplasmic reticulum). Virtual screening was conducted on the drug repurposing library, the Pandemic Response Box, to identify small-molecules that could specifically disrupt these chaperone complexes. Five top ranked compounds possessing preferential binding affinity for the malarial chaperone system compared to the human system, were identified; three top PfHsp70-PfJDP binders, MBX 1641, zoliflodacin and itraconazole; and two top J domain binders, ezetimibe and a benzo-diazepinone. These compounds were validated by repeat molecular dockings and molecular dynamics simulation, resulting in all the compounds, except for MBX 1461, being confirmed to bind preferentially to the malarial chaperone system. A detailed contact analysis of the PfHsp70-PfJDP binders identified two different types of modulators, those that potentially inhibit complex formation (MBX 1461), and those that potentially stabilize the complex (zoliflodacin and itraconazole). These data suggested that zoliflodacin and itraconazole are potential novel modulators specific to the malarial system. A detailed contact analysis of the J domain binders (ezetimibe and the benzo-diazepinone), revealed that they bound with not only greater affinity but also a better pose to the malarial J domain compared to that of the human system. These data suggested that ezetimibe and the benzo-diazepinone are potential specific inhibitors of the malarial chaperone system. Both itraconazole and ezetimibe are FDA-approved drugs, possess anti-malarial activity and have recently been repurposed for the treatment of cancer. This is the first time that such drug-like compounds have been identified as potential modulators of PfHsp70-PfJDP complexes, and they represent novel candidates for validation and development into anti-malarial drugs.
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Affiliation(s)
- Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Shaikha Y. Almaazmi
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Tanima Dutta
- Department of Diagnostic Genomics, Path West Nedlands, QEII Medical Centre, Nedlands, WA, Australia
| | - Robert A. Keyzers
- Centre for Biodiscovery & School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory L. Blatch
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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10
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Malinverni D, Zamuner S, Rebeaud ME, Barducci A, Nillegoda NB, De Los Rios P. Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins. Proc Natl Acad Sci U S A 2023; 120:e2218217120. [PMID: 37523524 PMCID: PMC10410713 DOI: 10.1073/pnas.2218217120] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/23/2023] [Indexed: 08/02/2023] Open
Abstract
The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J-domain protein (JDP) co-chaperone family carrying the small namesake J-domain, required to interact and drive the ATPase cycle of Hsp70s. Besides the J-domain, prokaryotic and eukaryotic JDPs display a staggering diversity in domain architecture, function, and cellular localization. Very little is known about the overall JDP family, despite their essential role in cellular proteostasis, development, and its link to a broad range of human diseases. In this work, we leverage the exponentially increasing number of JDP gene sequences identified across all kingdoms owing to the advancements in sequencing technology and provide a broad overview of the JDP repertoire. Using an automated classification scheme based on artificial neural networks (ANNs), we demonstrate that the sequences of J-domains carry sufficient discriminatory information to reliably recover the phylogeny, localization, and domain composition of the corresponding full-length JDP. By harnessing the interpretability of the ANNs, we find that many of the discriminatory sequence positions match residues that form the interaction interface between the J-domain and Hsp70. This reveals that key residues within the J-domains have coevolved with their obligatory Hsp70 partners to build chaperone circuits for specific functions in cells.
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Affiliation(s)
- Duccio Malinverni
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN38105
| | - Stefano Zamuner
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Mathieu E. Rebeaud
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Alessandro Barducci
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Nadinath B. Nillegoda
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC3800, Australia
- Centre for Dementia and Brain Repair at the Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC3800, Australia
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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11
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Fathinejad F, Ghafouri H, Barzegari E, Sarikhan S, Alizadeh A, Howard N. Gene cloning and characterization of a novel recombinant 40-kDa heat shock protein from Mesobacillus persicus B48. World J Microbiol Biotechnol 2023; 39:248. [PMID: 37436487 DOI: 10.1007/s11274-023-03693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
The present study reports the recognition and characterization of the gene encoding the co-chaperone DnaJ in the halophilic strain Mesobacillus persicus B48. The new extracted gene was sequenced and cloned in E. coli, followed by protein purification using a C-terminal His-tag. The stability and function of the recombinant DnaJ protein under salt and pH stress conditions were evaluated. SDS-PAGE revealed a band on nearly 40-kDa region. The homology model structure of new DnaJ demonstrated 56% similarity to the same protein from Streptococcus pneumonia. Fluorescence spectra indicated several hydrophobic residues located on the protein surface, which is consistent with the misfolded polypeptide recognition function of DnaJ. Spectroscopic results showed 56% higher carbonic anhydrase activity in the presence of the recombinant DnaJ homolog compared to its absence. In addition, salt resistance experiments showed that the survival of recombinant E. coli+DnaJ was 2.1 times more than control cells in 0.5 M NaCl. Furthermore, the number of recombinant E. coli BL21+DnaJ colonies was 7.7 times that of the control colonies in pH 8.5. Based on the results, DnaJ from the M. persicus can potentially be employed for improving the functional features of enzymes and other proteins in various applications.
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Affiliation(s)
- Fatemeh Fathinejad
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Hossein Ghafouri
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran.
- Department of Marine Sciences, The Caspian Sea Basin Research Center, University of Guilan, Rasht, Iran.
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajjad Sarikhan
- Molecular Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Arghavan Alizadeh
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Newton Howard
- Nuffield Department of Surgical Science, University of Oxford, Oxford, UK
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12
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Mamun MAA, Cao W, Nakamura S, Maruyama JI. Large-scale identification of genes involved in septal pore plugging in multicellular fungi. Nat Commun 2023; 14:1418. [PMID: 36932089 PMCID: PMC10023807 DOI: 10.1038/s41467-023-36925-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Multicellular filamentous fungi have septal pores that allow cytoplasmic exchange, and thus connectivity, between neighboring cells in the filament. Hyphal wounding and other stress conditions induce septal pore closure to minimize cytoplasmic loss. However, the composition of the septal pore and the mechanisms underlying its function are not well understood. Here, we set out to identify new septal components by determining the subcellular localization of 776 uncharacterized proteins in a multicellular ascomycete, Aspergillus oryzae. The set of 776 uncharacterized proteins was selected on the basis that their genes were present in the genomes of multicellular, septal pore-bearing ascomycetes (three Aspergillus species, in subdivision Pezizomycotina) and absent/divergent in the genomes of septal pore-lacking ascomycetes (yeasts). Upon determining their subcellular localization, 62 proteins were found to localize to the septum or septal pore. Deletion of the encoding genes revealed that 23 proteins are involved in regulating septal pore plugging upon hyphal wounding. Thus, this study determines the subcellular localization of many uncharacterized proteins in A. oryzae and, in particular, identifies a set of proteins involved in septal pore function.
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Affiliation(s)
| | - Wei Cao
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shugo Nakamura
- Department of Information Networking for Innovation and Design, Faculty of Information Networking for Innovation and Design, Toyo University, Tokyo, Japan
| | - Jun-Ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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13
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Kiemel K, Gurke M, Paraskevopoulou S, Havenstein K, Weithoff G, Tiedemann R. Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species. Sci Rep 2022; 12:22626. [PMID: 36587065 PMCID: PMC9805463 DOI: 10.1038/s41598-022-27137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
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Affiliation(s)
- K. Kiemel
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
| | - M. Gurke
- grid.422371.10000 0001 2293 9957Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany ,grid.7468.d0000 0001 2248 7639Department of Biology, Humboldt-University, Invalidenstraße 42, 10115 Berlin, Germany
| | - S. Paraskevopoulou
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Microbiology Group, Sölvegatan 35, 223 62 Lund, Sweden
| | - K. Havenstein
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
| | - G. Weithoff
- grid.11348.3f0000 0001 0942 1117Unit of Ecology and Ecosystem Modelling, Institute for Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany
| | - R. Tiedemann
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
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14
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Zhang Z, Zhang X, Wu X, Zhang Y, Lu J, Li D. Sirt1 attenuates astrocyte activation via modulating Dnajb1 and chaperone-mediated autophagy after closed head injury. Cereb Cortex 2022; 32:5191-5205. [PMID: 35106540 DOI: 10.1093/cercor/bhac007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 12/27/2022] Open
Abstract
Our previous study indicates that Silent information regulator 1 (Sirt1) is involved in macroautophagy by upregulating light chain 3 (LC3) expression in astrocyte to exert a neuroprotective effect. Chaperon-mediated autophagy (CMA), another form of autophagy, is also upregulated after brain injury. However, little is known about the role of Sirt1 in regulation of the CMA. In the present study, an in vivo model of closed head injury (CHI) and an in vitro model of primary cortical astrocyte stimulated with interleukin-1β were employed to mimic the astrocyte activation induced by traumatic brain injury. Lentivirus carrying target complementary DNA (cDNA) or short hairpin RNA (shRNA) sequence was used to overexpress Sirt1 or knockdown DnaJ heat shock protein family member B1 (Dnajb1) (a molecular chaperone). We found that Sirt1 overexpression ameliorated neurological deficits, reduced tissue loss, and attenuated astrocyte activation after CHI, which was reversed by Dnajb1-shRNA administration. The upregulation of CMA activity induced by CHI in vivo and in vitro was inhibited after Dnajb1 knockdown. Sirt1 potently promoted CMA activity via upregulating Dnajb1 expression. Mechanically, Sirt1 could interact with Dnajb1 and modulate the deacetylation and ubiquitination of Dnajb1. These findings collectively suggest that Sirt1 plays a protective role against astrocyte activation, which may be associated with the regulation of the CMA activity via modulating the deacetylation and ubiquitination of Dnajb1 after CHI.
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Affiliation(s)
- Zhuo Zhang
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, Liaoning Province, P.R. China
| | - Xu Zhang
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, Liaoning Province, P.R. China
| | - Xin Wu
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, Liaoning Province, P.R. China
| | - Yan Zhang
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, Liaoning Province, P.R. China
| | - Jie Lu
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, Liaoning Province, P.R. China
| | - Dan Li
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, Liaoning Province, P.R. China
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15
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Roth HE, De Lima Leite A, Palermo NY, Powers R. Leveraging the Structure of DNAJA1 to Discover Novel Potential Pancreatic Cancer Therapies. Biomolecules 2022; 12:1391. [PMID: 36291603 PMCID: PMC9599757 DOI: 10.3390/biom12101391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic cancer remains one of the deadliest forms of cancer with a 5-year survival rate of only 11%. Difficult diagnosis and limited treatment options are the major causes of the poor outcome for pancreatic cancer. The human protein DNAJA1 has been proposed as a potential therapeutic target for pancreatic cancer, but its cellular and biological functions remain unclear. Previous studies have suggested that DNAJA1's cellular activity may be dependent upon its protein binding partners. To further investigate this assertion, the first 107 amino acid structures of DNAJA1 were solved by NMR, which includes the classical J-domain and its associated linker region that is proposed to be vital to DNAJA1 functionality. The DNAJA1 NMR structure was then used to identify both protein and ligand binding sites and potential binding partners that may suggest the intracellular roles of DNAJA1. Virtual drug screenings followed by NMR and isothermal titration calorimetry identified 5 drug-like compounds that bind to two different sites on DNAJA1. A pull-down assay identified 8 potentially novel protein binding partners of DNAJA1. These proteins in conjunction with our previously published metabolomics study support a vital role for DNAJA1 in cellular oncogenesis and pancreatic cancer.
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Affiliation(s)
- Heidi E. Roth
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Aline De Lima Leite
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Nicolas Y. Palermo
- Computational Chemistry Core Facility, VCR Cores, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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16
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Johnson OT, Gestwicki JE. Multivalent protein-protein interactions are pivotal regulators of eukaryotic Hsp70 complexes. Cell Stress Chaperones 2022; 27:397-415. [PMID: 35670950 PMCID: PMC9346034 DOI: 10.1007/s12192-022-01281-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
Heat shock protein 70 (Hsp70) is a molecular chaperone and central regulator of protein homeostasis (proteostasis). Paramount to this role is Hsp70's binding to client proteins and co-chaperones to produce distinct complexes, such that understanding the protein-protein interactions (PPIs) of Hsp70 is foundational to describing its function and dysfunction in disease. Mounting evidence suggests that these PPIs include both "canonical" interactions, which are universally conserved, and "non-canonical" (or "secondary") contacts that seem to have emerged in eukaryotes. These two categories of interactions involve discrete binding surfaces, such that some clients and co-chaperones engage Hsp70 with at least two points of contact. While the contributions of canonical interactions to chaperone function are becoming increasingly clear, it can be challenging to deconvolute the roles of secondary interactions. Here, we review what is known about non-canonical contacts and highlight examples where their contributions have been parsed, giving rise to a model in which Hsp70's secondary contacts are not simply sites of additional avidity but are necessary and sufficient to impart unique functions. From this perspective, we propose that further exploration of non-canonical contacts will generate important insights into the evolution of Hsp70 systems and inspire new approaches for developing small molecules that tune Hsp70-mediated proteostasis.
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Affiliation(s)
- Oleta T Johnson
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, 94158, USA.
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17
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Nelson B, Hong SH, Lupoli TJ. Protein Cofactor Mimics Disrupt Essential Chaperone Function in Stressed Mycobacteria. ACS Infect Dis 2022; 8:901-910. [PMID: 35412813 DOI: 10.1021/acsinfecdis.1c00651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial DnaK is an ATP-dependent molecular chaperone important for maintaining cellular proteostasis in concert with cofactor proteins. The cofactor DnaJ delivers non-native client proteins to DnaK and activates its ATPase activity, which is required for protein folding. In the bacterial pathogen Mycobacterium tuberculosis, DnaK is assisted by two DnaJs, DnaJ1 and DnaJ2. Functional protein-protein interactions (PPIs) between DnaK and at least one DnaJ are essential for survival of mycobacteria; hence, these PPIs represent untapped antibacterial targets. Here, we synthesize peptide-based mimetics of DnaJ1 and DnaJ2 N-terminal domains as rational inhibitors of DnaK-cofactor interactions. We find that covalently stabilized DnaJ mimetics are capable of disrupting DnaK-cofactor activity in vitro and prevent mycobacterial recovery from proteotoxic stress in vivo, leading to cell death. Since chaperones and cofactors are highly conserved, we anticipate these results will inform the design of other mimetics to modulate chaperone function across cell types.
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Affiliation(s)
- Brock Nelson
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Seong Ho Hong
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, New York 10003, United States
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18
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DnaJC7 in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2022; 23:ijms23084076. [PMID: 35456894 PMCID: PMC9025444 DOI: 10.3390/ijms23084076] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
Protein misfolding is a common basis of many neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Misfolded proteins, such as TDP-43, FUS, Matrin3, and SOD1, mislocalize and form the hallmark cytoplasmic and nuclear inclusions in neurons of ALS patients. Cellular protein quality control prevents protein misfolding under normal conditions and, particularly, when cells experience protein folding stress due to the fact of increased levels of reactive oxygen species, genetic mutations, or aging. Molecular chaperones can prevent protein misfolding, refold misfolded proteins, or triage misfolded proteins for degradation by the ubiquitin–proteasome system or autophagy. DnaJC7 is an evolutionarily conserved molecular chaperone that contains both a J-domain for the interaction with Hsp70s and tetratricopeptide domains for interaction with Hsp90, thus joining these two major chaperones’ machines. Genetic analyses reveal that pathogenic variants in the gene encoding DnaJC7 cause familial and sporadic ALS. Yet, the underlying ALS-associated molecular pathophysiology and many basic features of DnaJC7 function remain largely unexplored. Here, we review aspects of DnaJC7 expression, interaction, and function to propose a loss-of-function mechanism by which pathogenic variants in DNAJC7 contribute to defects in DnaJC7-mediated chaperoning that might ultimately contribute to neurodegeneration in ALS.
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19
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Johnson OT, Nadel CM, Carroll EC, Arhar T, Gestwicki JE. Two distinct classes of cochaperones compete for the EEVD motif in heat shock protein 70 to tune its chaperone activities. J Biol Chem 2022; 298:101697. [PMID: 35148989 PMCID: PMC8913300 DOI: 10.1016/j.jbc.2022.101697] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/30/2022] Open
Abstract
Chaperones of the heat shock protein 70 (Hsp70) family engage in protein-protein interactions with many cochaperones. One "hotspot" for cochaperone binding is the EEVD motif, found at the extreme C terminus of cytoplasmic Hsp70s. This motif is known to bind tetratricopeptide repeat domain cochaperones, such as the E3 ubiquitin ligase CHIP. In addition, the EEVD motif also interacts with a structurally distinct domain that is present in class B J-domain proteins, such as DnaJB4. These observations suggest that CHIP and DnaJB4 might compete for binding to Hsp70's EEVD motif; however, the molecular determinants of such competition are not clear. Using a collection of EEVD-derived peptides, including mutations and truncations, we explored which residues are critical for binding to both CHIP and DnaJB4. These results revealed that some features, such as the C-terminal carboxylate, are important for both interactions. However, CHIP and DnaJB4 also had unique preferences, especially at the isoleucine position immediately adjacent to the EEVD. Finally, we show that competition between these cochaperones is important in vitro, as DnaJB4 limits the ubiquitination activity of the Hsp70-CHIP complex, whereas CHIP suppresses the client refolding activity of the Hsp70-DnaJB4 complex. Together, these data suggest that the EEVD motif has evolved to support diverse protein-protein interactions, such that competition between cochaperones may help guide whether Hsp70-bound proteins are folded or degraded.
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Affiliation(s)
- Oleta T Johnson
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Cory M Nadel
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Emma C Carroll
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Taylor Arhar
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA; Department of Chemistry, Beloit College, Beloit, Wisconsin, USA.
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.
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20
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Huang X, Huang L, Zhao X, Jia J, Zhang G, Zhang M, Jiang M. A J-Protein OsDjC46 Interacts with ZFP36 to Participate in ABA-Mediated Antioxidant Defense in Rice. Antioxidants (Basel) 2022; 11:antiox11020207. [PMID: 35204090 PMCID: PMC8868554 DOI: 10.3390/antiox11020207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
ZFP36 has been shown to be involved in ABA-induced antioxidant defense and enhance rice tolerance to drought, salt stress and oxidative stress. Using ZFP36 as bait, a yeast two-hybrid system was used to obtain the interacting protein OsDjC46, which belongs to heat shock protein and usually exists in the form of molecular chaperone, was identified. Further Co-IP (co-immunoprecipitation), BiFC (bimolecular fluorescence complement) and GST (glutathione-S-transferase) pull-down experiments verified that ZFP36 interacted with OsDjC46 in vivo and in vitro. Heat shock protein has been shown to increase plant resistance to stresses, but whether OsDjC46 was a key factor in plant response to various stresses has not been reported. Here, various stimuli, such as abscisic acid (ABA), hydrogen peroxidase (H2O2), polyethylene (PEG) and sodium chloride (NaCl) markedly induced the expression of OsDjC46 in the seedlings. Overexpression of OsDjC46 in rice can enhance the tolerance to salinity and drought; in contrast, knockout of OsDjC46 rice plants was more sensitive to salt stress and drought. Further investigation revealed that OsDjC46 could participate in regulating the expression and activities of antioxidant of SOD and CAT under drought and salt stress. Taken together, these findings reveal a novel function of OsDjC46 in adjusting ABA-induced antioxidant defense.
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Affiliation(s)
- Xingxiu Huang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.H.); (L.H.); (X.Z.); (J.J.); (G.Z.); (M.Z.)
| | - Liping Huang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.H.); (L.H.); (X.Z.); (J.J.); (G.Z.); (M.Z.)
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Xixi Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.H.); (L.H.); (X.Z.); (J.J.); (G.Z.); (M.Z.)
| | - Jing Jia
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.H.); (L.H.); (X.Z.); (J.J.); (G.Z.); (M.Z.)
| | - Gang Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.H.); (L.H.); (X.Z.); (J.J.); (G.Z.); (M.Z.)
| | - Mengyao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.H.); (L.H.); (X.Z.); (J.J.); (G.Z.); (M.Z.)
| | - Mingyi Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.H.); (L.H.); (X.Z.); (J.J.); (G.Z.); (M.Z.)
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: ; Tel.: +86-025-84396372
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21
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Karamanos TK, Clore GM. Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy. Annu Rev Biophys 2022; 51:223-246. [PMID: 35044800 DOI: 10.1146/annurev-biophys-090921-120150] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular chaperones are the guardians of the proteome inside the cell. Chaperones recognize and bind unfolded or misfolded substrates, thereby preventing further aggregation; promoting correct protein folding; and, in some instances, even disaggregating already formed aggregates. Chaperones perform their function by means of an array of weak protein-protein interactions that take place over a wide range of timescales and are therefore invisible to structural techniques dependent upon the availability of highly homogeneous samples. Nuclear magnetic resonance (NMR) spectroscopy, however, is ideally suited to study dynamic, rapidly interconverting conformational states and protein-protein interactions in solution, even if these involve a high-molecular-weight component. In this review, we give a brief overview of the principles used by chaperones to bind their client proteins and describe NMR methods that have emerged as valuable tools to probe chaperone-substrate and chaperone-chaperone interactions. We then focus on a few systems for which the application of these methods has greatly increased our understanding of the mechanisms underlying chaperone functions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom;
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA;
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22
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Clathrin: the molecular shape shifter. Biochem J 2021; 478:3099-3123. [PMID: 34436540 DOI: 10.1042/bcj20200740] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/19/2021] [Accepted: 08/04/2021] [Indexed: 12/11/2022]
Abstract
Clathrin is best known for its contribution to clathrin-mediated endocytosis yet it also participates to a diverse range of cellular functions. Key to this is clathrin's ability to assemble into polyhedral lattices that include curved football or basket shapes, flat lattices or even tubular structures. In this review, we discuss clathrin structure and coated vesicle formation, how clathrin is utilised within different cellular processes including synaptic vesicle recycling, hormone desensitisation, spermiogenesis, cell migration and mitosis, and how clathrin's remarkable 'shapeshifting' ability to form diverse lattice structures might contribute to its multiple cellular functions.
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23
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Park JC, Lee JS. Genome-wide identification of heat shock proteins in harpacticoid, cyclopoid, and calanoid copepods: Potential application in marine ecotoxicology. MARINE POLLUTION BULLETIN 2021; 169:112545. [PMID: 34111604 DOI: 10.1016/j.marpolbul.2021.112545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
- Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Ba M, Paillat M, Tronche N, Vigneron-Bouquet A, Latifi A. [Role of chaperons in bacterial adaptive mechanisms]. Med Sci (Paris) 2021; 37:293-297. [PMID: 33739279 DOI: 10.1051/medsci/2021020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Moly Ba
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
| | - Maëlle Paillat
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
| | - Nolan Tronche
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
| | - Amélie Vigneron-Bouquet
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
| | - Amel Latifi
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
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Li C, Xu Y, Fu S, Liu Y, Li Z, Zhang T, Wu J, Zhou X. The unfolded protein response plays dual roles in rice stripe virus infection through fine-tuning the movement protein accumulation. PLoS Pathog 2021; 17:e1009370. [PMID: 33662041 PMCID: PMC8075255 DOI: 10.1371/journal.ppat.1009370] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/26/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
The movement of plant viruses is a complex process that requires support by the virus-encoded movement protein and multiple host factors. The unfolded protein response (UPR) plays important roles in plant virus infection, while how UPR regulates viral infection remains to be elucidated. Here, we show that rice stripe virus (RSV) elicits the UPR in Nicotiana benthamiana. The RSV-induced UPR activates the host autophagy pathway by which the RSV-encoded movement protein, NSvc4, is targeted for autophagic degradation. As a counteract, we revealed that NSvc4 hijacks UPR-activated type-I J-domain proteins, NbMIP1s, to protect itself from autophagic degradation. Unexpectedly, we found NbMIP1 stabilizes NSvc4 in a non-canonical HSP70-independent manner. Silencing NbMIP1 family genes in N. benthamiana, delays RSV infection, while over-expressing NbMIP1.4b promotes viral cell-to-cell movement. Moreover, OsDjA5, the homologue of NbMIP1 family in rice, behaves in a similar manner toward facilitating RSV infection. This study exemplifies an arms race between RSV and the host plant, and reveals the dual roles of the UPR in RSV infection though fine-tuning the accumulation of viral movement protein.
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Affiliation(s)
- Chenyang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yi Xu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zongdi Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Tianze Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Insights from a vertebrate model organism on the molecular mechanisms of whole-body dehydration tolerance. Mol Cell Biochem 2021; 476:2381-2392. [PMID: 33595794 DOI: 10.1007/s11010-021-04072-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/16/2021] [Indexed: 10/25/2022]
Abstract
Studies on the molecular mechanisms of dehydration tolerance have been largely limited to plants and invertebrates. Currently, research in whole body dehydration of complex animals is limited to cognitive and behavioral effects in humans, leaving the molecular mechanisms of vertebrate dehydration relatively unexplored. The present review summarizes studies to date on the African clawed frog (Xenopus laevis) and examines whole-body dehydration on physiological, cellular and molecular levels. This aquatic frog is exposed to seasonal droughts in its native habitat and can endure a loss of over 30% of its total body water. When coping with dehydration, osmoregulatory processes prioritize water retention in skeletal tissues and vital organs over plasma volume. Although systemic blood circulation is maintained in the vital organs and even elevated in the brain during dehydration, it is done so at the expense of reduced circulation to the skeletal muscles. Increased hemoglobin affinity for oxygen helps to counteract impaired blood circulation and metabolic enzymes show altered kinetic and regulatory parameters that support the use of anaerobic glycolysis. Recent studies with X. laevis also show that pro-survival pathways such as antioxidant defenses and heat shock proteins are activated in an organ-specific manner during dehydration. These pathways are tightly coordinated at the post-transcriptional level by non-coding RNAs, and at the post-translational level by reversible protein phosphorylation. Paired with ongoing research on the X. laevis genome, the African clawed frog is poised to be an ideal animal model with which to investigate the molecular adaptations for dehydration tolerance much more deeply.
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Edkins AL, Boshoff A. General Structural and Functional Features of Molecular Chaperones. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1340:11-73. [PMID: 34569020 DOI: 10.1007/978-3-030-78397-6_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular chaperones are a group of structurally diverse and highly conserved ubiquitous proteins. They play crucial roles in facilitating the correct folding of proteins in vivo by preventing protein aggregation or facilitating the appropriate folding and assembly of proteins. Heat shock proteins form the major class of molecular chaperones that are responsible for protein folding events in the cell. This is achieved by ATP-dependent (folding machines) or ATP-independent mechanisms (holders). Heat shock proteins are induced by a variety of stresses, besides heat shock. The large and varied heat shock protein class is categorised into several subfamilies based on their sizes in kDa namely, small Hsps (HSPB), J domain proteins (Hsp40/DNAJ), Hsp60 (HSPD/E; Chaperonins), Hsp70 (HSPA), Hsp90 (HSPC), and Hsp100. Heat shock proteins are localised to different compartments in the cell to carry out tasks specific to their environment. Most heat shock proteins form large oligomeric structures, and their functions are usually regulated by a variety of cochaperones and cofactors. Heat shock proteins do not function in isolation but are rather part of the chaperone network in the cell. The general structural and functional features of the major heat shock protein families are discussed, including their roles in human disease. Their function is particularly important in disease due to increased stress in the cell. Vector-borne parasites affecting human health encounter stress during transmission between invertebrate vectors and mammalian hosts. Members of the main classes of heat shock proteins are all represented in Plasmodium falciparum, the causative agent of cerebral malaria, and they play specific functions in differentiation, cytoprotection, signal transduction, and virulence.
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Affiliation(s)
- Adrienne Lesley Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown, South Africa.
- Rhodes University, Makhanda/Grahamstown, South Africa.
| | - Aileen Boshoff
- Rhodes University, Makhanda/Grahamstown, South Africa.
- Biotechnology Innovation Centre, Rhodes University, Makhanda/Grahamstown, South Africa.
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Hsp40 proteins phase separate to chaperone the assembly and maintenance of membraneless organelles. Proc Natl Acad Sci U S A 2020; 117:31123-31133. [PMID: 33229560 DOI: 10.1073/pnas.2002437117] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Membraneless organelles contain a wide spectrum of molecular chaperones, indicating their important roles in modulating the metastable conformation and biological function of membraneless organelles. Here we report that class I and II Hsp40 (DNAJ) proteins possess a high ability of phase separation rendered by the flexible G/F-rich region. Different Hsp40 proteins localize in different membraneless organelles. Specifically, human Hdj1 (DNAJB1), a class II Hsp40 protein, condenses in ubiquitin (Ub)-rich nuclear bodies, while Hdj2 (DNAJA1), a class I Hsp40 protein, condenses in nucleoli. Upon stress, both Hsp40 proteins incorporate into stress granules (SGs). Mutations of the G/F-rich region not only markedly impaired Hdj1 phase separation and SG involvement and disrupted the synergistic phase separation and colocalization of Hdj1 and fused in sarcoma (FUS) in cells. Being cophase separated with FUS, Hdj1 stabilized the liquid phase of FUS against proceeding into amyloid aggregation in vitro and alleviated abnormal FUS aggregation in cells. Moreover, Hdj1 uses different domains to chaperone FUS phase separation and amyloid aggregation. This paper suggests that phase separation is an intrinsic property of Hsp40 proteins, which enables efficient incorporation and function of Hsp40 in membraneless organelles and may further mediate the buildup of chaperone network in membraneless organelles.
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Kohler V, Andréasson C. Hsp70-mediated quality control: should I stay or should I go? Biol Chem 2020; 401:1233-1248. [PMID: 32745066 DOI: 10.1515/hsz-2020-0187] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/11/2020] [Indexed: 12/30/2022]
Abstract
Chaperones of the 70 kDa heat shock protein (Hsp70) superfamily are key components of the cellular proteostasis system. Together with its co-chaperones, Hsp70 forms proteostasis subsystems that antagonize protein damage during physiological and stress conditions. This function stems from highly regulated binding and release cycles of protein substrates, which results in a flow of unfolded, partially folded and misfolded species through the Hsp70 subsystem. Specific factors control how Hsp70 makes decisions regarding folding and degradation fates of the substrate proteins. In this review, we summarize how the flow of Hsp70 substrates is controlled in the cell with special emphasis on recent advances regarding substrate release mechanisms.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
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Park JC, Kim DH, Lee Y, Lee MC, Kim TK, Yim JH, Lee JS. Genome-wide identification and structural analysis of heat shock protein gene families in the marine rotifer Brachionus spp.: Potential application in molecular ecotoxicology. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100749. [PMID: 33065474 DOI: 10.1016/j.cbd.2020.100749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 01/07/2023]
Abstract
Heat shock proteins (Hsp) are class of conserved and ubiquitous stress proteins present in all living organisms from primitive to higher level. Various studies have demonstrated multiple cellular functions of Hsp in living organisms as an important biomarker in response to abiotic and biotic stressors including temperature, salinity, pH, hypoxia, environmental pollutants, and pathogens. However, full understanding on the mechanism and pathway involved in the induction of Hsp still remains challenging, especially in aquatic invertebrates. In this study, the entire Hsp family and subfamily members in the marine rotifers Brachionus spp., one of the cosmopolitan ecotoxicological model organisms, have been genome-widely identified. In Brachionus spp. Hsp family was comprised of Hsp10, small hsp (sHsp), Hsp40, Hsp60, Hsp70/105, and Hsp90, with highest number of genes found within Hsp40 DnaJ homolog subfamily C members. Also, the differences in the orientation of the conserved motifs within Hsp family may have induced differences in transcriptional gene modulation in response to thermal stress in Brachionus koreanus. Overall, Hsp family-specific domains were highly conserved in all three Brachionus spp., relative to Homo sapiens and across other animal taxa and these findings will be helpful for future ecotoxicological studies focusing on Hsps.
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Affiliation(s)
- Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Yoseop Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Tai Kyoung Kim
- Division of Polar Life Science, Korea Polar Research Institute, Incheon 21990, South Korea
| | - Joung Han Yim
- Division of Polar Life Science, Korea Polar Research Institute, Incheon 21990, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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31
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Sun H, Zou HY, Cai XY, Zhou HF, Li XQ, Xie WJ, Xie WM, Du ZP, Xu LY, Li EM, Wu BL. Network Analyses of the Differential Expression of Heat Shock Proteins in Glioma. DNA Cell Biol 2020; 39:1228-1242. [PMID: 32429692 DOI: 10.1089/dna.2020.5425] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Heat shock protein (HSP) is a family of highly conserved protein, which exists widely in various organisms and has a variety of important physiological functions. Currently, there is no systematic analysis of HSPs in human glioma. The aim of this study was to investigate the characteristics of HSPs through constructing protein-protein interaction network (PPIN) considering the expression level of HSPs in glioma. After the identification of the differentially expressed HSPs in glioma tissues, a specific PPIN was constructed and found that there were many interactions between the differentially expressed HSPs in glioma. Subcellular localization analysis shows that HSPs and their interacting proteins distribute from the cell membrane to the nucleus in a multilayer structure. By functional enrichment analysis, gene ontology analysis, and Kyoto Encyclopedia of Genes and Genomes pathway analysis, the potential function of HSPs and two meaningful enrichment pathways was revealed. In addition, nine HSPs (DNAJA4, DNAJC6, DNAJC12, HSPA6, HSP90B1, DNAJB1, DNAJB6, DNAJC10, and SERPINH1) are prognostic markers for human brain glioma. These analyses provide a full view of HSPs about their expression, biological process, as well as clinical significance in glioma.
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Affiliation(s)
- Hong Sun
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Hai-Ying Zou
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Xin-Yi Cai
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Hao-Feng Zhou
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Xiao-Qi Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Wei-Jie Xie
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Wen-Ming Xie
- Network and Information Center, Shantou University Medical College, Shantou, China
| | - Ze-Peng Du
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, China
| | - En-Min Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Bing-Li Wu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
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32
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Barriot R, Latour J, Castanié-Cornet MP, Fichant G, Genevaux P. J-Domain Proteins in Bacteria and Their Viruses. J Mol Biol 2020; 432:3771-3789. [DOI: 10.1016/j.jmb.2020.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023]
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Kao CH, Ryu SW, Kim MJ, Wen X, Wimalarathne O, Paull TT. Growth-Regulated Hsp70 Phosphorylation Regulates Stress Responses and Prion Maintenance. Mol Cell Biol 2020; 40:e00628-19. [PMID: 32205407 PMCID: PMC7261718 DOI: 10.1128/mcb.00628-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/05/2020] [Accepted: 03/18/2020] [Indexed: 11/20/2022] Open
Abstract
Maintenance of protein homeostasis in eukaryotes under normal growth and stress conditions requires the functions of Hsp70 chaperones and associated cochaperones. Here, we investigate an evolutionarily conserved serine phosphorylation that occurs at the site of communication between the nucleotide-binding and substrate-binding domains of Hsp70. Ser151 phosphorylation in yeast Hsp70 (Ssa1) is promoted by cyclin-dependent kinase (Cdk1) during normal growth. Phosphomimetic substitutions at this site (S151D) dramatically downregulate heat shock responses, a result conserved with HSC70 S153 in human cells. Phosphomimetic forms of Ssa1 also fail to relocalize in response to starvation conditions, do not associate in vivo with Hsp40 cochaperones Ydj1 and Sis1, and do not catalyze refolding of denatured proteins in vitro in cooperation with Ydj1 and Hsp104. Despite these negative effects on HSC70/HSP70 function, the S151D phosphomimetic allele promotes survival of heavy metal exposure and suppresses the Sup35-dependent [PSI+ ] prion phenotype, consistent with proposed roles for Ssa1 and Hsp104 in generating self-nucleating seeds of misfolded proteins. Taken together, these results suggest that Cdk1 can downregulate Hsp70 function through phosphorylation of this site, with potential costs to overall chaperone efficiency but also advantages with respect to reduction of metal-induced and prion-dependent protein aggregate production.
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Affiliation(s)
- Chung-Hsuan Kao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Seung W Ryu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Min J Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Oshadi Wimalarathne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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34
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The Role of Secretory Pathways in Candida albicans Pathogenesis. J Fungi (Basel) 2020; 6:jof6010026. [PMID: 32102426 PMCID: PMC7151058 DOI: 10.3390/jof6010026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Candida albicans is a fungus that is a commensal organism and a member of the normal human microbiota. It has the ability to transition into an opportunistic invasive pathogen. Attributes that support pathogenesis include secretion of virulence-associated proteins, hyphal formation, and biofilm formation. These processes are supported by secretion, as defined in the broad context of membrane trafficking. In this review, we examine the role of secretory pathways in Candida virulence, with a focus on the model opportunistic fungal pathogen, Candida albicans.
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35
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A History of Molecular Chaperone Structures in the Protein Data Bank. Int J Mol Sci 2019; 20:ijms20246195. [PMID: 31817979 PMCID: PMC6940948 DOI: 10.3390/ijms20246195] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
Thirty years ago a class of proteins was found to prevent the aggregation of Rubisco. These proteins’ ability to prevent unwanted associations led to their being called chaperones. These chaperone proteins also increased in expression as a response to heat shock, hence their label as heat shock proteins (Hsps). However, neither label encompasses the breadth of these proteins’ functional capabilities. The term “unfoldases” has been proposed, as this basic function is shared by most members of this protein family. Onto this is added specializations that allow the different family members to perform various cellular functions. This current article focuses on the resolved structural bases for these functions. It reviews the currently available molecular structures in the Protein Data Bank for several classes of Hsps (Hsp60, Hsp70, Hsp90, and Hsp104). When possible, it discusses the complete structures for these proteins, and the types of molecular machines to which they have been assigned. The structures of domains and the associated functions are discussed in order to illustrate the rationale for the proposed unfoldase function.
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36
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Liu Q, Liang C, Zhou L. Structural and functional analysis of the Hsp70/Hsp40 chaperone system. Protein Sci 2019; 29:378-390. [PMID: 31509306 DOI: 10.1002/pro.3725] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/22/2022]
Abstract
As one of the most abundant and highly conserved molecular chaperones, the 70-kDa heat shock proteins (Hsp70s) play a key role in maintaining cellular protein homeostasis (proteostasis), one of the most fundamental tasks for every living organism. In this role, Hsp70s are inextricably linked to many human diseases, most notably cancers and neurodegenerative diseases, and are increasingly recognized as important drug targets for developing novel therapeutics for these diseases. Hsp40s are a class of essential and universal partners for Hsp70s in almost all aspects of proteostasis. Thus, Hsp70s and Hsp40s together constitute one of the most important chaperone systems across all kingdoms of life. In recent years, we have witnessed significant progress in understanding the molecular mechanism of this chaperone system through structural and functional analysis. This review will focus on this recent progress, mainly from a structural perspective.
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Affiliation(s)
- Qinglian Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
| | - Ce Liang
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
| | - Lei Zhou
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
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37
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Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis. Proc Natl Acad Sci U S A 2019; 116:21529-21538. [PMID: 31591220 DOI: 10.1073/pnas.1914999116] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
J-domain chaperones are involved in the efficient handover of misfolded/partially folded proteins to Hsp70 but also function independently to protect against cell death. Due to their high flexibility, the mechanism by which they regulate the Hsp70 cycle and how specific substrate recognition is performed remains unknown. Here we focus on DNAJB6b, which has been implicated in various human diseases and represents a key player in protection against neurodegeneration and protein aggregation. Using a variant that exists mainly in a monomeric form, we report the solution structure of an Hsp40 containing not only the J and C-terminal substrate binding (CTD) domains but also the functionally important linkers. The structure reveals a highly dynamic protein in which part of the linker region masks the Hsp70 binding site. Transient interdomain interactions via regions crucial for Hsp70 binding create a closed, autoinhibited state and help retain the monomeric form of the protein. Detailed NMR analysis shows that the CTD (but not the J domain) self-associates to form an oligomer comprising ∼35 monomeric units, revealing an intricate balance between intramolecular and intermolecular interactions. The results shed light on the mechanism of autoregulation of the Hsp70 cycle via conserved parts of the linker region and reveal the mechanism of DNAJB6b oligomerization and potentially antiaggregation.
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38
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Zhang X, Li G, Yang X, Wang L, Wang Y, Guo X, Li H, Xu B. Identification of a DnaJC3 gene in Apis cerana cerana and its involvement in various stress responses. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 160:171-180. [PMID: 31519252 DOI: 10.1016/j.pestbp.2019.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 08/23/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
As molecular chaperones, DnaJs play critical roles in maintaining cytoplasmic structure and resisting various stresses. However, the functions of DnaJs in insects are poorly understood. In this study, we identified a DnaJC3 from Apis cerana cerana (AccDnaJC3) and investigated its roles in adverse conditions. Real-time quantitative PCR analysis showed that AccDnaJC3 was highly expressed in muscle and epidermis. In addition, AccDnaJC3 was induced by a variety of stresses, such as 4 °C, 24 °C, 44 °C, H2O2, HgCl2, VC, UV, cyhalothrin, abamectin and emamectin benzoate treatments, whereas it was inhibited by CdCl2 and paraquat treatments. Disc diffusion experiments indicated that overexpression of recombinant AccDnaJC3 enhanced Escherichia coli tolerance to some stress conditions. In contrast to the control group, when AccDnaJC3 was knocked down with RNAi technology, several other antioxidant genes were downregulated, suggesting that AccDnaJC3 may play important roles in stress response. Furthermore, we found that the enzyme activities of superoxide dismutase, peroxidase and catalase were lower in AccDnaJC3-knockdown bees than in control bees. Taken together, these results suggest that AccDnaJC3 may be involved in various stress responses in Apis cerana cerana.
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Affiliation(s)
- Xuemei Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Guilin Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Xinxin Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Lijun Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Han Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China.
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China.
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39
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Griffith AA, Holmes W. Fine Tuning: Effects of Post-Translational Modification on Hsp70 Chaperones. Int J Mol Sci 2019; 20:ijms20174207. [PMID: 31466231 PMCID: PMC6747426 DOI: 10.3390/ijms20174207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 02/07/2023] Open
Abstract
The discovery of heat shock proteins shaped our view of protein folding in the cell. Since their initial discovery, chaperone proteins were identified in all domains of life, demonstrating their vital and conserved functional roles in protein homeostasis. Chaperone proteins maintain proper protein folding in the cell by utilizing a variety of distinct, characteristic mechanisms to prevent aberrant intermolecular interactions, prevent protein aggregation, and lower entropic costs to allow for protein refolding. Continued study has found that chaperones may exhibit alternative functions, including maintaining protein folding during endoplasmic reticulum (ER) import and chaperone-mediated degradation, among others. Alternative chaperone functions are frequently controlled by post-translational modification, in which a given chaperone can switch between functions through covalent modification. This review will focus on the Hsp70 class chaperones and their Hsp40 co-chaperones, specifically highlighting the importance of post-translational control of chaperones. These modifications may serve as a target for therapeutic intervention in the treatment of diseases of protein misfolding and aggregation.
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Affiliation(s)
| | - William Holmes
- Rhode Island College, Biology Department, Providence, RI 02908, USA.
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40
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Roosen DA, Blauwendraat C, Cookson MR, Lewis PA. DNAJC
proteins and pathways to parkinsonism. FEBS J 2019; 286:3080-3094. [DOI: 10.1111/febs.14936] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/21/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Dorien A. Roosen
- Laboratory of Neurogenetics National Institute on AgingNational Institutes of Health Bethesda MD USA
- School of Pharmacy University of Reading UK
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics National Institute on AgingNational Institutes of Health Bethesda MD USA
| | - Mark R. Cookson
- Laboratory of Neurogenetics National Institute on AgingNational Institutes of Health Bethesda MD USA
| | - Patrick A. Lewis
- School of Pharmacy University of Reading UK
- Department of Neurodegenerative Disease UCL Institute of Neurology London UK
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41
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Pinheiro GMS, Amorim GC, Iqbal A, Almeida FCL, Ramos CHI. Solution NMR investigation on the structure and function of the isolated J-domain from Sis1: Evidence of transient inter-domain interactions in the full-length protein. Arch Biochem Biophys 2019; 669:71-79. [PMID: 31141701 DOI: 10.1016/j.abb.2019.05.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 11/25/2022]
Abstract
J-domain/Hsp40 proteins cooperate in aiding with folding in the cell by binding partially folded client proteins and delivering them to be folded by Hsp70. The delivery occurs concomitantly to the stimulation of the ATPase activity of Hsp70 via the N-terminally located J-domain. Although several lines of investigation have been used to study J-domain proteins, the presence of highly flexible domains (G/F- and G/M-rich) hold up obtaining a detailed full-length structure. In this work, we present the high-resolution structure of the J-domain and the N-terminal part of the G/F domain of Sis1, solved by NMR, and used chemical-shift perturbation approaches to further study the structure/function relationship of the Sis1/Hsp70 interaction. When the J-domain was compared to the full-length protein and to a G/M domain deletion mutant, an internal interaction patch formed by hydrophobic and positively charged residues (V2, D9, R27, T39, F52 and R73) was identified. Curiously, the same patch is protected by internal contacts in the full-length protein and, in combination with the loop containing the conserved HPD motif, participates in the interaction with Hsp70. Combined, these results suggest that the J-domain in the full-length Sis1 is in a transient intermediate conformation, in which its interacting patch is protected and, at the same time, also in a favorable condition to bind Hsp70, facilitating the interaction between the two proteins. Finally, 1D NMR experiments showed that the addition of ATP is followed by the disruption of the J-domain/Hsp70 complex, a necessary step for aiding the folding of the client protein.
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Affiliation(s)
| | - Gisele C Amorim
- Institute of Medical Biochemistry and Nucleus for Structural Biology and Bioimaging (CENABIO) - Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Federal University of Rio de Janeiro, Núcleo Multidisciplinar de Pesquisa em Biologia, Campus Duque de Caxias, RJ, Brazil
| | - Anwar Iqbal
- Institute of Medical Biochemistry and Nucleus for Structural Biology and Bioimaging (CENABIO) - Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry and Nucleus for Structural Biology and Bioimaging (CENABIO) - Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e tecnologia em Biologia Estrutural e Bioimagem INBEB, Brazil.
| | - C H I Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas, SP, Brazil; Instituto Nacional de Ciência e tecnologia em Biologia Estrutural e Bioimagem INBEB, Brazil.
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42
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Yan Y, Rato C, Rohland L, Preissler S, Ron D. MANF antagonizes nucleotide exchange by the endoplasmic reticulum chaperone BiP. Nat Commun 2019; 10:541. [PMID: 30710085 PMCID: PMC6358605 DOI: 10.1038/s41467-019-08450-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/11/2019] [Indexed: 12/24/2022] Open
Abstract
Despite its known role as a secreted neuroprotectant, much of the mesencephalic astrocyte-derived neurotrophic factor (MANF) is retained in the endoplasmic reticulum (ER) of producer cells. There, by unknown mechanisms, MANF plays a role in protein folding homeostasis in complex with the ER-localized Hsp70 chaperone BiP. Here we report that the SAF-A/B, Acinus, and PIAS (SAP) domain of MANF selectively associates with the nucleotide binding domain (NBD) of ADP-bound BiP. In crystal structures the SAP domain engages the cleft between NBD subdomains Ia and IIa, stabilizing the ADP-bound conformation and clashing with the interdomain linker that occupies this site in ATP-bound BiP. MANF inhibits both ADP release from BiP and ATP binding to BiP, and thereby client release. Cells lacking MANF have fewer ER stress-induced BiP-containing high molecular weight complexes. These findings suggest that MANF contributes to protein folding homeostasis as a nucleotide exchange inhibitor that stabilizes certain BiP-client complexes.
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Affiliation(s)
- Yahui Yan
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Claudia Rato
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Lukas Rohland
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.,Center for Molecular Biology (ZMBH) of Heidelberg University, Heidelberg, Germany
| | - Steffen Preissler
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - David Ron
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
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43
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Pinheiro GMS, Amorim GC, Iqbal A, Ramos CHI, Almeida FCL. 1H, 15N and 13C resonance assignments of the J-domain of co-chaperone Sis1 from Saccharomyces cerevisiae. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:279-281. [PMID: 29713947 DOI: 10.1007/s12104-018-9823-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
Protein folding in the cell is usually aided by molecular chaperones, from which the Hsp70 (Hsp = heat shock protein) family has many important roles, such as aiding nascent folding and participating in translocation. Hsp70 has ATPase activity which is stimulated by binding to the J-domain present in co-chaperones from the Hsp40 family. Hsp40s have many functions, as for instance the binding to partially folded proteins to be delivered to Hsp70. However, the presence of the J-domain characterizes Hsp40s or, by this reason, as J-proteins. The J-domain alone can stimulate Hsp70 ATPase activity. Apparently, it also maintains the same conformation as in the whole protein although structural information on full J-proteins is still missing. This work reports the 1H, 15N and 13C resonance assignments of the J-domain of a Hsp40 from Saccharomyces cerevisiae, named Sis1. Secondary structure and order parameter prediction from chemical shifts are also reported. Altogether, the data show that Sis1 J-domain is highly structured and predominantly formed by α-helices, results that are in very good agreement with those previously reported for the crystallographic structure.
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Affiliation(s)
| | - Gisele C Amorim
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Numpex-Bio - Federal University of Rio de Janeiro, Duque de Caxias, RJ, Brazil
| | - Anwar Iqbal
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - C H I Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas, SP, Brazil.
| | - Fabio C L Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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44
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Ajayi OO, Peters SO, De Donato M, Sowande SO, Mujibi FDN, Morenikeji OB, Thomas BN, Adeleke MA, Imumorin IG. Computational genome-wide identification of heat shock protein genes in the bovine genome. F1000Res 2018; 7:1504. [PMID: 30542619 PMCID: PMC6259560 DOI: 10.12688/f1000research.16058.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 11/20/2022] Open
Abstract
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.
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Affiliation(s)
- Oyeyemi O Ajayi
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria.,International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA
| | - Marcos De Donato
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Departamento Regional de Bioingenierias, Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Sunday O Sowande
- Department of Animal Production and Health, Federal University of Agriculture, Abeokuta, Nigeria
| | | | - Olanrewaju B Morenikeji
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Matthew A Adeleke
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Ikhide G Imumorin
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30032, USA.,African Institute of Bioscience Research and Training, Ibadan, Nigeria
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45
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Uchida T, Kanemori M. Two J domains ensure high cochaperone activity of DnaJ, Escherichia coli heat shock protein 40. J Biochem 2018; 164:153-163. [PMID: 29635480 DOI: 10.1093/jb/mvy038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/26/2018] [Indexed: 11/13/2022] Open
Abstract
Heat shock protein 70 (Hsp70) chaperone systems consist of Hsp70, Hsp40 and a nucleotide-exchange factor and function to help unfolded proteins achieve their native conformations. Typical Hsp40s assume a homodimeric structure and have both chaperone and cochaperone activity. The dimeric structure is critical for chaperone function, whereas the relationship between the dimeric structure and cochaperone function is hardly known. Here, we examined whether two intact protomers are required for cochaperone activity of Hsp40 using an Escherichia coli Hsp70 chaperone system consisting of DnaK, DnaJ and GrpE. The expression systems were generated and two heterodimeric DnaJs that included a mutated protomer lacking cochaperone activity were purified. Normal chaperone activity was demonstrated by assessing aggregation prevention activity using urea-denatured luciferase. The heterodimeric DnaJs were investigated for cochaperone activity by measuring DnaK ATPase activity and the heat-denatured glucose-6-phosphate dehydrogenase refolding activity of the DnaK chaperone system, and they showed reduced cochaperone activity. These results indicate that two intact protomers are required for high cochaperone activity of DnaJ, suggesting that one homodimeric DnaJ molecule promotes the simultaneous binding of multiple DnaK molecules to one substrate molecule, and that this binding mode is required for the efficient folding of denatured proteins.
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Affiliation(s)
- Tomoya Uchida
- School of Natural System, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Masaaki Kanemori
- School of Natural System, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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46
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Dong-Po X, Di-An F, Chang-Sheng Z, Shu-Lun J, Hao-Yuan H. Effect of tributyltin chloride (TBT-Cl) exposure on expression of HSP90β1 in the river pufferfish (Takifugu obscurus): Evidences for its immunologic function involving in exploring process. Gene 2018; 666:9-17. [PMID: 29723535 DOI: 10.1016/j.gene.2018.04.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 01/27/2023]
Abstract
HSP90β1 (known as glyco-protein 96, GP96) is a vital endoplasmic reticulum (ER) depended chaperonin among the HSPs (heat shock proteins) family. Furthermore, it always processes and presents antigen of the tumor and keeps balance for the intracellular environment. In the present study, we explored the effect of tributyltin chloride (TBT-Cl) exposure on HSP90β1 expression in river pufferfish, Takifugu obscurus. The full length of To-HSP90β1 was gained with 2775 bp in length, with an ORF (open reading frame) encoding an 803 aa polypeptide. A phylogenetic tree was constructed and showed the close relationship to other fish species. The HSP90β1 mRNA transcript was expressed in all tissues investigated with higher level in the gill and liver. After the acute and chronic exposure of TBT-Cl, the To-HSP90β1 mRNA transcript significantly was up-regulated in gills. Moreover, the histology study indicated the different injury degree of TBT-Cl in liver and gill. Immunohistochemistry (IHC) staining results implied the cytoplasm reorganization after TBT-Cl stress and the function of immunoregulation for To-HSP90β1 to TBT-Cl exposure. All the results indicated that HSP90β1 may be involved in the resistance to the invasion of TBT-Cl for keeping autoimmune homeostasis.
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Affiliation(s)
- Xu Dong-Po
- Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Fang Di-An
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Zhao Chang-Sheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Jiang Shu-Lun
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Hu Hao-Yuan
- Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China.
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47
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Wang G, Zhou S, Luo Y, Ma C, Gong Y, Zhou Y, Gao S, Huang Z, Yan L, Hu Y, Bian Y. The heat shock protein 40 LeDnaJ regulates stress resistance and indole-3-acetic acid biosynthesis in Lentinula edodes. Fungal Genet Biol 2018; 118:37-44. [PMID: 30003956 DOI: 10.1016/j.fgb.2018.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/05/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022]
Abstract
DnaJ proteins, termed heat shock proteins based on their molecular weight, function as molecular chaperones that play critical roles in regulating organism growth and development as well as adaptation to the environment. However, little has been reported on their gene function in higher basidiomycetes. Here, the heat shock protein 40 (LeDnaJ) gene was cloned and characterized from Lentinula edodes. RNA interference was used to explore the function of LeDnaJ in response to heat stress and Trichoderma atroviride. Integration of the target gene into the L. edodes genome was confirmed by Southern blot analysis, and the silence efficiency of LeDnaJ was analyzed by qRT-PCR. The results revealed that LeDnaJ silence caused defects in mycelial growth and resistance to heat stress and T. atroviride, but increased the mycelial density compared with the wild type (WT) strain S606. Additionally, the IAA content showed a more than 10-fold increase in the WT after heat stress, but an about two-fold increase in the two LeDnaJ RNAi transfortants (LeDnaJ-i-6 and LeDnaJ-i-8). Previous study has shown that enhanced IAA (indole-3-acetic acid) content enhanced the thermotolerance of the heat-sensitive strain YS3357. In this study, it was documented that IAA amendments could partly restore the resistance to T. atroviride and thermotolerance of the two LeDnaJ RNAi transformants. Overall, LeDnaJ is nvolved in fungal growth, T. atroviride resistance, and thermotolerance by regulating the IAA biosynthesis in L. edodes.
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Affiliation(s)
- Gangzheng Wang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - ShaSha Zhou
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yi Luo
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chaojun Ma
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuhua Gong
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yan Zhou
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shuangshuang Gao
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhicheng Huang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lianlian Yan
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yue Hu
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yinbing Bian
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China.
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48
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Ranek MJ, Stachowski MJ, Kirk JA, Willis MS. The role of heat shock proteins and co-chaperones in heart failure. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2016.0530. [PMID: 29203715 DOI: 10.1098/rstb.2016.0530] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2017] [Indexed: 12/18/2022] Open
Abstract
The ongoing contractile and metabolic demands of the heart require a tight control over protein quality control, including the maintenance of protein folding, turnover and synthesis. In heart disease, increases in mechanical and oxidative stresses, post-translational modifications (e.g., phosphorylation), for example, decrease protein stability to favour misfolding in myocardial infarction, heart failure or ageing. These misfolded proteins are toxic to cardiomyocytes, directly contributing to the common accumulation found in human heart failure. One of the critical class of proteins involved in protecting the heart against these threats are molecular chaperones, including the heat shock protein70 (HSP70), HSP90 and co-chaperones CHIP (carboxy terminus of Hsp70-interacting protein, encoded by the Stub1 gene) and BAG-3 (BCL2-associated athanogene 3). Here, we review their emerging roles in the maintenance of cardiomyocytes in human and experimental models of heart failure, including their roles in facilitating the removal of misfolded and degraded proteins, inhibiting apoptosis and maintaining the structural integrity of the sarcomere and regulation of nuclear receptors. Furthermore, we discuss emerging evidence of increased expression of extracellular HSP70, HSP90 and BAG-3 in heart failure, with complementary independent roles from intracellular functions with important therapeutic and diagnostic considerations. While our understanding of these major HSPs in heart failure is incomplete, there is a clear potential role for therapeutic modulation of HSPs in heart failure with important contextual considerations to counteract the imbalance of protein damage and endogenous protein quality control systems.This article is part of the theme issue 'Heat shock proteins as modulators and therapeutic targets of chronic disease: an integrated perspective'.
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Affiliation(s)
- Mark J Ranek
- Division of Cardiology, Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Marisa J Stachowski
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University, Chicago, IL 60302, USA
| | - Jonathan A Kirk
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University, Chicago, IL 60302, USA
| | - Monte S Willis
- Department of Pathology and Laboratory Medicine, McAllister Heart Institute, CB#7525, Chapel Hill, NC 27599-7525, USA
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49
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Sun H, Cai X, Zhou H, Li X, Du Z, Zou H, Wu J, Xie L, Cheng Y, Xie W, Lu X, Xu L, Chen L, Li E, Wu B. The protein-protein interaction network and clinical significance of heat-shock proteins in esophageal squamous cell carcinoma. Amino Acids 2018; 50:685-697. [PMID: 29700654 DOI: 10.1007/s00726-018-2569-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/09/2018] [Indexed: 02/06/2023]
Abstract
Heat-shock proteins (HSPs), one of the evolutionarily conserved protein families, are widely found in various organisms, and play important physiological functions. Nevertheless, HSPs have not been systematically analyzed in esophageal squamous cell carcinoma (ESCC). In this study, we applied the protein-protein interaction (PPI) network methodology to explore the characteristics of HSPs, and integrate their expression in ESCC. First, differentially expressed HSPs in ESCC were identified from our previous RNA-seq data. By constructing a specific PPI network, we found differentially expressed HSPs interacted with hundreds of neighboring proteins. Subcellular localization analyses demonstrated that HSPs and their interacting proteins distributed in multiple layers, from membrane to nucleus. Functional enrichment annotation analyses revealed known and potential functions for HSPs. KEGG pathway analyses identified four significant enrichment pathways. Moreover, three HSPs (DNAJC5B, HSPA1B, and HSPH1) could serve as promising targets for prognostic prediction in ESCC, suggesting these HSPs might play a significant role in the development of ESCC. These multiple bioinformatics analyses have provided a comprehensive view of the roles of heat-shock proteins in esophageal squamous cell carcinoma.
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Affiliation(s)
- Hong Sun
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Xinyi Cai
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Haofeng Zhou
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Xiaoqi Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Zepeng Du
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, 515041, China
| | - Haiying Zou
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Jianyi Wu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Lei Xie
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Yinwei Cheng
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, 515041, China
| | - Wenming Xie
- Network and Information Center, Shantou University Medical College, Shantou, 515041, China
| | - Xiaomei Lu
- Tumor Hospital Affiliated to Xinjiang Medical University, Ürümqi, 830054, Xinjiang Uygur Autonomous Region, China
| | - Liyan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, 515041, China
| | - Longqi Chen
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Sichuan, 610041, China
| | - Enmin Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China.
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China.
| | - Bingli Wu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, 515041, China.
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China.
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50
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Wu H, Shi N, An X, Liu C, Fu H, Cao L, Feng Y, Sun D, Zhang L. Candidate Genes for Yellow Leaf Color in Common Wheat ( Triticum aestivum L.) and Major Related Metabolic Pathways according to Transcriptome Profiling. Int J Mol Sci 2018; 19:ijms19061594. [PMID: 29843474 PMCID: PMC6032196 DOI: 10.3390/ijms19061594] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/05/2023] Open
Abstract
The photosynthetic capacity and efficiency of a crop depends on the biosynthesis of photosynthetic pigments and chloroplast development. However, little is known about the molecular mechanisms of chloroplast development and chlorophyll (Chl) biosynthesis in common wheat because of its huge and complex genome. Ygm, a spontaneous yellow-green leaf color mutant of winter wheat, exhibits reduced Chl contents and abnormal chloroplast development. Thus, we searched for candidate genes associated with this phenotype. Comparative transcriptome profiling was performed using leaves from the yellow leaf color type (Y) and normal green color type (G) of the Ygm mutant progeny. We identified 1227 differentially expressed genes (DEGs) in Y compared with G (i.e., 689 upregulated genes and 538 downregulated genes). Gene ontology and pathway enrichment analyses indicated that the DEGs were involved in Chl biosynthesis (i.e., magnesium chelatase subunit H (CHLH) and protochlorophyllide oxidoreductase (POR) genes), carotenoid biosynthesis (i.e., β-carotene hydroxylase (BCH) genes), photosynthesis, and carbon fixation in photosynthetic organisms. We also identified heat shock protein (HSP) genes (sHSP, HSP70, HSP90, and DnaJ) and heat shock transcription factor genes that might have vital roles in chloroplast development. Quantitative RT-PCR analysis of the relevant DEGs confirmed the RNA-Seq results. Moreover, measurements of seven intermediate products involved in Chl biosynthesis and five carotenoid compounds involved in carotenoid-xanthophyll biosynthesis confirmed that CHLH and BCH are vital enzymes for the unusual leaf color phenotype in Y type. These results provide insights into leaf color variation in wheat at the transcriptional level.
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Affiliation(s)
- Huiyu Wu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Narong Shi
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Xuyao An
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Cong Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Hongfei Fu
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
| | - Li Cao
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Yi Feng
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Daojie Sun
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
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