1
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Dai Y, Zhou J, Shi C. Inflammasome: structure, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e391. [PMID: 37817895 PMCID: PMC10560975 DOI: 10.1002/mco2.391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 10/12/2023] Open
Abstract
Inflammasomes are a group of protein complex located in cytoplasm and assemble in response to a wide variety of pathogen-associated molecule patterns, damage-associated molecule patterns, and cellular stress. Generally, the activation of inflammasomes will lead to maturation of proinflammatory cytokines and pyroptotic cell death, both associated with inflammatory cascade amplification. A sensor protein, an adaptor, and a procaspase protein interact through their functional domains and compose one subunit of inflammasome complex. Under physiological conditions, inflammasome functions against pathogen infection and endogenous dangers including mtROS, mtDNA, and so on, while dysregulation of its activation can lead to unwanted results. In recent years, advances have been made to clarify the mechanisms of inflammasome activation, the structural details of them and their functions (negative/positive) in multiple disease models in both animal models and human. The wide range of the stimuli makes the function of inflammasome diverse and complex. Here, we review the structure, biological functions, and therapeutic targets of inflammasomes, while highlight NLRP3, NLRC4, and AIM2 inflammasomes, which are the most well studied. In conclusion, this review focuses on the activation process, biological functions, and structure of the most well-studied inflammasomes, summarizing and predicting approaches for disease treatment and prevention with inflammasome as a target. We aim to provide fresh insight into new solutions to the challenges in this field.
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Affiliation(s)
- Yali Dai
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
| | - Jing Zhou
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
- Institute of ImmunologyArmy Medical UniversityChongqingChina
| | - Chunmeng Shi
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
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2
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Maruta N, Burdett H, Lim BYJ, Hu X, Desa S, Manik MK, Kobe B. Structural basis of NLR activation and innate immune signalling in plants. Immunogenetics 2022; 74:5-26. [PMID: 34981187 PMCID: PMC8813719 DOI: 10.1007/s00251-021-01242-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022]
Abstract
Animals and plants have NLRs (nucleotide-binding leucine-rich repeat receptors) that recognize the presence of pathogens and initiate innate immune responses. In plants, there are three types of NLRs distinguished by their N-terminal domain: the CC (coiled-coil) domain NLRs, the TIR (Toll/interleukin-1 receptor) domain NLRs and the RPW8 (resistance to powdery mildew 8)-like coiled-coil domain NLRs. CC-NLRs (CNLs) and TIR-NLRs (TNLs) generally act as sensors of effectors secreted by pathogens, while RPW8-NLRs (RNLs) signal downstream of many sensor NLRs and are called helper NLRs. Recent studies have revealed three dimensional structures of a CNL (ZAR1) including its inactive, intermediate and active oligomeric state, as well as TNLs (RPP1 and ROQ1) in their active oligomeric states. Furthermore, accumulating evidence suggests that members of the family of lipase-like EDS1 (enhanced disease susceptibility 1) proteins, which are uniquely found in seed plants, play a key role in providing a link between sensor NLRs and helper NLRs during innate immune responses. Here, we summarize the implications of the plant NLR structures that provide insights into distinct mechanisms of action by the different sensor NLRs and discuss plant NLR-mediated innate immune signalling pathways involving the EDS1 family proteins and RNLs.
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Affiliation(s)
- Natsumi Maruta
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Hayden Burdett
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Bryan Y J Lim
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiahao Hu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sneha Desa
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mohammad Kawsar Manik
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia.
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3
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Ma S, Lapin D, Liu L, Sun Y, Song W, Zhang X, Logemann E, Yu D, Wang J, Jirschitzka J, Han Z, Schulze-Lefert P, Parker JE, Chai J. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science 2021; 370:370/6521/eabe3069. [PMID: 33273071 DOI: 10.1126/science.abe3069] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Direct or indirect recognition of pathogen-derived effectors by plant nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) initiates innate immune responses. The Hyaloperonospora arabidopsidis effector ATR1 activates the N-terminal Toll-interleukin-1 receptor (TIR) domain of Arabidopsis NLR RPP1. We report a cryo-electron microscopy structure of RPP1 bound by ATR1. The structure reveals a C-terminal jelly roll/Ig-like domain (C-JID) for specific ATR1 recognition. Biochemical and functional analyses show that ATR1 binds to the C-JID and the LRRs to induce an RPP1 tetrameric assembly required for nicotinamide adenine dinucleotide hydrolase (NADase) activity. RPP1 tetramerization creates two potential active sites, each formed by an asymmetric TIR homodimer. Our data define the mechanism of direct effector recognition by a plant NLR leading to formation of a signaling-active holoenzyme.
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Affiliation(s)
- Shoucai Ma
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Dmitry Lapin
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Li Liu
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yue Sun
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Wen Song
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Xiaoxiao Zhang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Elke Logemann
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Dongli Yu
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Jia Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jan Jirschitzka
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Zhifu Han
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. .,Cluster of Excellence in Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. .,Cluster of Excellence in Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Jijie Chai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China. .,Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany.,Cluster of Excellence in Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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4
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Song W, Forderer A, Yu D, Chai J. Structural biology of plant defence. THE NEW PHYTOLOGIST 2021; 229:692-711. [PMID: 32880948 DOI: 10.1111/nph.16906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Plants employ the innate immune system to discriminate between self and invaders through two types of immune receptors, one on the plasma membrane and the other in the intracellular space. The immune receptors on the plasma membrane are pattern recognition receptors (PRRs) that can perceive pathogen-associated molecular patterns (PAMPs) or host-derived damage-associated molecular patterns (DAMPs) leading to pattern-triggered immunity (PTI). Particular pathogens are capable of overcoming PTI by secreting specific effectors into plant cells to perturb different components of PTI signalling through various mechanisms. Most of the immune receptors from the intracellular space are the nucleotide-binding leucine-rich repeat receptors (NLRs), which specifically recognize pathogen-secreted effectors to mediate effector-triggered immunity (ETI). In this review, we will summarize recent progress in structural studies of PRRs, NLRs, and effectors, and discuss how these studies shed light on ligand recognition and activation mechanisms of the two types of immune receptors and the diversified mechanisms used by effectors to manipulate plant immune signalling.
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Affiliation(s)
- Wen Song
- Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Institute of Biochemistry, University of Cologne, Cologne, 50923, Germany
| | - Alexander Forderer
- Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Institute of Biochemistry, University of Cologne, Cologne, 50923, Germany
| | - Dongli Yu
- Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Institute of Biochemistry, University of Cologne, Cologne, 50923, Germany
| | - Jijie Chai
- Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Institute of Biochemistry, University of Cologne, Cologne, 50923, Germany
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5
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Chakraborty J, Ghosh P. Advancement of research on plant NLRs evolution, biochemical activity, structural association, and engineering. PLANTA 2020; 252:101. [PMID: 33180185 DOI: 10.1007/s00425-020-03512-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
In this review, we have included evolution of plant intracellular immune receptors, oligomeric complex formation, enzymatic action, engineering, and mechanisms of immune inspection for appropriate defense outcomes. NLR (Nucleotide binding oligomerization domain containing leucine-rich repeat) proteins are the intracellular immune receptors that recognize pathogen-derived virulence factors to confer effector-triggered immunity (ETI). Activation of plant defense by the NLRs are often conveyed through N-terminal Toll-like/ IL-1 receptor (TIR) or non-TIR (coiled-coils or CC) domains. Homodimerization or self-association property of CC/ TIR domains of plant NLRs contribute to their auto-activity and induction of in planta ectopic cell death. High resolution crystal structures of Arabidopsis thaliana RPS4TIR, L6TIR, SNC1TIR, RPP1TIR and Muscadinia rotundifolia RPV1TIR showed that interaction is mediated through one or two distinct interfaces i.e., αA and αE helices comprise AE interface and αD and αE helices were found to form DE interface. By contrast, conserved helical regions were determined for CC domains of plant NLRs. Evolutionary history of NLRs diversification has shown that paired forms were originated from NLR singletons. Plant TIRs executed NAD+ hydrolysis activity for cell death promotion. Plant NLRs were found to form large oligomeric complexes as observed in animal inflammasomes. We have also discussed different protein engineering methods includes domain shuffling, and decoy modification that increase effector recognition spectrum of plant NLRs. In summary, our review highlights structural basis of perception of the virulence factors by NLRs or NLR pairs to design novel classes of plant immune receptors.
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Affiliation(s)
| | - Prithwi Ghosh
- Department of Botany, Narajole Raj College, Narajole, Paschim Medinipur, 721211, West Bengal, India
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6
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Sandall CF, Ziehr BK, MacDonald JA. ATP-Binding and Hydrolysis in Inflammasome Activation. Molecules 2020; 25:molecules25194572. [PMID: 33036374 PMCID: PMC7583971 DOI: 10.3390/molecules25194572] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023] Open
Abstract
The prototypical model for NOD-like receptor (NLR) inflammasome assembly includes nucleotide-dependent activation of the NLR downstream of pathogen- or danger-associated molecular pattern (PAMP or DAMP) recognition, followed by nucleation of hetero-oligomeric platforms that lie upstream of inflammatory responses associated with innate immunity. As members of the STAND ATPases, the NLRs are generally thought to share a similar model of ATP-dependent activation and effect. However, recent observations have challenged this paradigm to reveal novel and complex biochemical processes to discern NLRs from other STAND proteins. In this review, we highlight past findings that identify the regulatory importance of conserved ATP-binding and hydrolysis motifs within the nucleotide-binding NACHT domain of NLRs and explore recent breakthroughs that generate connections between NLR protein structure and function. Indeed, newly deposited NLR structures for NLRC4 and NLRP3 have provided unique perspectives on the ATP-dependency of inflammasome activation. Novel molecular dynamic simulations of NLRP3 examined the active site of ADP- and ATP-bound models. The findings support distinctions in nucleotide-binding domain topology with occupancy of ATP or ADP that are in turn disseminated on to the global protein structure. Ultimately, studies continue to reveal how the ATP-binding and hydrolysis properties of NACHT domains in different NLRs integrate with signaling modules and binding partners to control innate immune responses at the molecular level.
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7
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Xiong Y, Han Z, Chai J. Resistosome and inflammasome: platforms mediating innate immunity. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:47-55. [PMID: 32554225 DOI: 10.1016/j.pbi.2020.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/12/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
The nucleotide-binding domain (NBD) and leucine-rich repeat (LRR) containing (NLR) proteins are intracellular immune receptors that sense pathogens or stress-associated signals in animals and plants. Direct or indirect binding of these stimuli to NLRs results in formation of higher-order large protein complexes termed inflammasomes in animals and resistosomes in plants to mediate immune signaling. Here we focus on plant NLRs and discuss the activation mechanism of the ZAR1 resistosome from Arabidopsis thaliana. We also outline the analogies and differences between the ZAR1 resistosome and the NLR inflammasomes, and discuss how the structural and biochemical information available on these two large types of protein complexes sheds light on signaling mechanisms of other plant NLRs.
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Affiliation(s)
- Yehui Xiong
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Zhifu Han
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jijie Chai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China; Max Planck Institute for Plant Breeding Research, Cologne, Germany; Institute of Biochemistry, University of Cologne, Zuelpicher Strasse 47, 50674 Cologne, Germany.
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8
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Davenne T, Klintman J, Sharma S, Rigby RE, Blest HTW, Cursi C, Bridgeman A, Dadonaite B, De Keersmaecker K, Hillmen P, Chabes A, Schuh A, Rehwinkel J. SAMHD1 Limits the Efficacy of Forodesine in Leukemia by Protecting Cells against the Cytotoxicity of dGTP. Cell Rep 2020; 31:107640. [PMID: 32402273 PMCID: PMC7225753 DOI: 10.1016/j.celrep.2020.107640] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
The anti-leukemia agent forodesine causes cytotoxic overload of intracellular deoxyguanosine triphosphate (dGTP) but is efficacious only in a subset of patients. We report that SAMHD1, a phosphohydrolase degrading deoxyribonucleoside triphosphate (dNTP), protects cells against the effects of dNTP imbalances. SAMHD1-deficient cells induce intrinsic apoptosis upon provision of deoxyribonucleosides, particularly deoxyguanosine (dG). Moreover, dG and forodesine act synergistically to kill cells lacking SAMHD1. Using mass cytometry, we find that these compounds kill SAMHD1-deficient malignant cells in patients with chronic lymphocytic leukemia (CLL). Normal cells and CLL cells from patients without SAMHD1 mutation are unaffected. We therefore propose to use forodesine as a precision medicine for leukemia, stratifying patients by SAMHD1 genotype or expression.
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Affiliation(s)
- Tamara Davenne
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Jenny Klintman
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Rachel E Rigby
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Henry T W Blest
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Chiara Cursi
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Bernadeta Dadonaite
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Kim De Keersmaecker
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Peter Hillmen
- St James' Institute of Oncology, St James' University Hospital, Leeds LS9 7TF, UK
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Anna Schuh
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Department of Oncology, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK; Department of Haematology, Oxford University Hospitals NHS Trust, Oxford OX3 7JL, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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9
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Wang J, Chai J. Structural Insights into the Plant Immune Receptors PRRs and NLRs. PLANT PHYSIOLOGY 2020; 182:1566-1581. [PMID: 32047048 PMCID: PMC7140948 DOI: 10.1104/pp.19.01252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/20/2020] [Indexed: 05/30/2023]
Abstract
Recent progresses made in structural analysis of plant PRRs and NLRs show the advancements in cryo-EM structural biology.
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Affiliation(s)
- Jizong Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jijie Chai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
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10
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Yadav N, Gogada R, O'Malley J, Gundampati RK, Jayanthi S, Hashmi S, Lella R, Zhang D, Wang J, Kumar R, Suresh Kumar TK, Chandra D. Molecular insights on cytochrome c and nucleotide regulation of apoptosome function and its implication in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118573. [PMID: 31678591 PMCID: PMC7733678 DOI: 10.1016/j.bbamcr.2019.118573] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 10/14/2019] [Accepted: 10/22/2019] [Indexed: 12/20/2022]
Abstract
Cytochrome c (Cyt c) released from mitochondria interacts with Apaf-1 to form the heptameric apoptosome, which initiates the caspase cascade to execute apoptosis. Although lysine residue at 72 (K72) of Cyt c plays an important role in the Cyt c-Apaf-1 interaction, the underlying mechanism of interaction between Cyt c and Apaf-1 is still not clearly defined. Here we identified multiple lysine residues including K72, which are also known to interact with ATP, to play a key role in Cyt c-Apaf-1 interaction. Mutation of these lysine residues abrogates the apoptosome formation causing inhibition of caspase activation. Using in-silico molecular docking, we have identified Cyt c-binding interface on Apaf-1. Although mutant Cyt c shows higher affinity for Apaf-1, the presence of Cyt c-WT restores the apoptosome activity. ATP addition modulates only mutant Cyt c binding to Apaf-1 but not WT Cyt c binding to Apaf-1. Using TCGA and cBioPortal, we identified multiple mutations in both Apaf-1 and Cyt c that are predicted to interfere with apoptosome assembly. We also demonstrate that transcript levels of various enzymes involved with dATP or ATP synthesis are increased in various cancers. Silencing of nucleotide metabolizing enzymes such as ribonucleotide reductase subunit M1 (RRM1) and ATP-producing glycolytic enzymes PKM2 attenuated ATP production and enhanced caspase activation. These findings suggest important role for lysine residues of Cyt c and nucleotides in the regulation of apoptosome-dependent apoptotic cell death as well as demonstrate how these mutations and nucleotides may have a pivotal role in human diseases such as cancer.
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Affiliation(s)
- Neelu Yadav
- The Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America
| | - Raghu Gogada
- The Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America
| | - Jordan O'Malley
- The Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America
| | - Ravi Kumar Gundampati
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America
| | - Srinivas Jayanthi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America
| | - Sana Hashmi
- The Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America
| | - Ravi Lella
- The Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America
| | - Dianmu Zhang
- The Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America
| | - Jianmin Wang
- The Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America
| | - Rahul Kumar
- The Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America
| | | | - Dhyan Chandra
- The Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, United States of America.
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11
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Burdett H, Bentham AR, Williams SJ, Dodds PN, Anderson PA, Banfield MJ, Kobe B. The Plant "Resistosome": Structural Insights into Immune Signaling. Cell Host Microbe 2019; 26:193-201. [PMID: 31415752 DOI: 10.1016/j.chom.2019.07.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plant innate immunity is triggered via direct or indirect recognition of pathogen effectors by the NLR family immune receptors. Mechanistic understanding of plant NLR function has relied on structural information from individual NLR domains and inferences from studies on animal NLRs. Recent reports of the cryo-EM structures of the Arabidopsis plant immune receptor ZAR1 in monomeric inactive and transition states, as well as the active oligomeric state or the "resistosome," have afforded a quantum leap in our understanding of how plant NLRs function. In this Review, we outline the recent structural findings and examine their implications for the activation of plant immune receptors more broadly. We also discuss how NLR signaling in plants, as illustrated by the ZAR1 structure, is analogous to innate immune receptor signaling mechanisms across kingdoms, drawing particular attention to the concept of signaling by cooperative assembly formation.
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Affiliation(s)
- Hayden Burdett
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Adam R Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra 2601, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Peter A Anderson
- College of Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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12
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α-Hederin Induces Apoptosis of Esophageal Squamous Cell Carcinoma via an Oxidative and Mitochondrial-Dependent Pathway. Dig Dis Sci 2019; 64:3528-3538. [PMID: 31273592 DOI: 10.1007/s10620-019-05689-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 05/30/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND α-Hederin has been shown promising anti-tumor potential against various cancer cell lines. However, reports about effects of α-hederin on esophageal squamous cell carcinoma (ESCC) are still unavailable. AIM To investigate the inhibitory effects of α-hederin on ESCC and explore the underlying mechanism. METHODS Human esophageal carcinoma cell line (Eca-109) was used for the experiment. Cell Counting Kit-8, flow cytometry, Hoechst 33258 staining, enhanced ATP assay kit, 2',7'-dichlorofluorescin diacetate, JC-1 kit, and Western bolt were used to assess the cell viability, cycle, apoptosis, cellular ATP content, reactive oxygen species (ROS) level, mitochondrial membrane potential (MMP), and protein expression, respectively, in vitro. Xenografted tumor model was constructed to evaluate the in vivo anti-tumor effects of α-hederin. RESULTS Compared with control group, α-hederin significantly inhibited the proliferation, induced apoptosis of ESCC, and arrested the cell cycle in G1 phase (P < 0.05). α-Hederin induced the accumulation of ROS, decrement of ATP levels, and disruption of MMP (P < 0.05). The detection of mitochondrial and cytosol proteins showed that AIF, Apaf-1, and Cyt C were released and increased in cytoplasm, and then, caspase-3, caspase-9, and Bax were involved and increased, while Bcl-2 level was decreased (P < 0.05). Furthermore, the above changes were amplified in the group pretreated with L-buthionine sulfoximine, while N-acetyl-L-cysteine plays an opposite role (P < 0.05). Meanwhile, α-hederin significantly inhibited the growth of xenografted tumors with favorable safety. CONCLUSION α-Hederin could inhibit the proliferation and induce apoptosis of ESCC via dissipation of the MMP with simultaneous ROS generation and activation of the mitochondrial pathway.
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Animal NLRs continue to inform plant NLR structure and function. Arch Biochem Biophys 2019; 670:58-68. [PMID: 31071301 DOI: 10.1016/j.abb.2019.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/10/2019] [Accepted: 05/01/2019] [Indexed: 12/22/2022]
Abstract
Plant NLRs share many of the structural hallmarks of their animal counterparts. At a functional level, the central nucleotide-binding pocket appears to have binding and hydrolysis activities, similar to that of animal NLRs. The TIR domains of plant NLRs have been shown to self-associate, and there is emerging evidence that full-length plant NLRs may do so as well. It is therefore tempting to speculate that plant NLRs may form higher-order complexes similar to those of the mammalian inflammasome. Here we review the available knowledge on structure-function relationships in plant NLRs, focusing on how the information available on animal NLRs informs the mechanism of plant NLR function, and highlight the evidence that innate immunity signalling pathways in multicellular organisms often require the formation of higher-order protein complexes.
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14
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Lima TS, Lodoen MB. Mechanisms of Human Innate Immune Evasion by Toxoplasma gondii. Front Cell Infect Microbiol 2019; 9:103. [PMID: 31041194 PMCID: PMC6476913 DOI: 10.3389/fcimb.2019.00103] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Toxoplasma gondii is an intracellular protozoan parasite of global importance that can remarkably infect, survive, and replicate in nearly all mammalian cells. Notably, 110 years after its discovery, Toxoplasmosis is still a neglected parasitic infection. Although most human infections with T. gondii are mild or asymptomatic, T. gondii infection can result in life-threatening disease in immunocompromised individuals and in the developing fetus due to congenital infection, underscoring the role of the host immune system in controlling the parasite. Recent evidence indicates that T. gondii elicits a robust innate immune response during infection. Interestingly, however, T. gondii has evolved strategies to successfully bypass or manipulate the immune system and establish a life-long infection in infected hosts. In particular, T. gondii manipulates host immunity through the control of host gene transcription and dysregulation of signaling pathways that result in modulation of cell adhesion and migration, secretion of immunoregulatory cytokines, production of microbicidal molecules, and apoptosis. Many of these host-pathogen interactions are governed by parasite effector proteins secreted from the apical secretory organelles, including the rhoptries and dense granules. Here, we review recent findings on mechanisms by which T. gondii evades host innate immunity, with a focus on parasite evasion of the human innate immune system.
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Affiliation(s)
- Tatiane S Lima
- Department of Molecular Biology and Biochemistry and the Institute for Immunology, University of California, Irvine, Irvine, CA, United States
| | - Melissa B Lodoen
- Department of Molecular Biology and Biochemistry and the Institute for Immunology, University of California, Irvine, Irvine, CA, United States
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15
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Structural Biology of NOD-Like Receptors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1172:119-141. [DOI: 10.1007/978-981-13-9367-9_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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16
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Dorstyn L, Akey CW, Kumar S. New insights into apoptosome structure and function. Cell Death Differ 2018; 25:1194-1208. [PMID: 29765111 DOI: 10.1038/s41418-017-0025-z] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 02/08/2023] Open
Abstract
The apoptosome is a platform that activates apical procaspases in response to intrinsic cell death signals. Biochemical and structural studies in the past two decades have extended our understanding of apoptosome composition and structure, while illuminating the requirements for initiator procaspase activation. A number of studies have now provided high-resolution structures for apoptosomes from C. elegans (CED-4), D. melanogaster (Dark), and H. sapiens (Apaf-1), which define critical protein interfaces, including intra and interdomain interactions. This work also reveals interactions of apoptosomes with their respective initiator caspases, CED-3, Dronc and procaspase-9. Structures of the human apoptosome have defined the requirements for cytochrome c binding, which triggers the conversion of inactive Apaf-1 molecules to an extended, assembly competent state. While recent data have provided a detailed understanding of apoptosome formation and procaspase activation, they also highlight important evolutionary differences with functional implications for caspase activation. Comparison of the CARD/CARD disks and apoptosomes formed by CED-4, Dark and Apaf-1. Cartoons of the active states of the CARD-CARD disks, illustrating the two CED-4 CARD tetrameric ring layers (CED4a and CED4b; top row) and the binding of 8 Dronc CARDs and between 3-4 pc-9 CARDs, to the Dark and Apaf-1 CARD disk respectively (middle and lower rows). Ribbon diagrams of the active CED-4, Dark and Apaf-1 apoptosomes are shown (right column).
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Affiliation(s)
- Loretta Dorstyn
- Center for Cancer Biology, University of South Australia and SA Pathology, Frome Road, Adelaide, SA, 5001, Australia.
| | - Christopher W Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Sharad Kumar
- Center for Cancer Biology, University of South Australia and SA Pathology, Frome Road, Adelaide, SA, 5001, Australia.
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Abstract
The first plant disease resistance (R) genes were identified and cloned more than two decades ago. Since then, many more R genes have been identified and characterized in numerous plant pathosystems. Most of these encode members of the large family of intracellular NLRs (NOD-like receptors), which also includes animal immune receptors. New discoveries in this expanding field of research provide new elements for our understanding of plant NLR function. But what do we know about plant NLR function today? Genetic, structural, and functional analyses have uncovered a number of commonalities and differences in pathogen recognition strategies as well as how NLRs are regulated and activate defense signaling, but many unknowns remain. This review gives an update on the latest discoveries and breakthroughs in this field, with an emphasis on structural findings and some comparison to animal NLRs, which can provide additional insights and paradigms in plant NLR function.
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Affiliation(s)
- Xiaoxiao Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
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18
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Lai X, Friedman A. Exosomal microRNA concentrations in colorectal cancer: A mathematical model. J Theor Biol 2017; 415:70-83. [DOI: 10.1016/j.jtbi.2016.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/06/2016] [Accepted: 12/10/2016] [Indexed: 12/19/2022]
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19
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Sergeeva TF, Shirmanova MV, Zlobovskaya OA, Gavrina AI, Dudenkova VV, Lukina MM, Lukyanov KA, Zagaynova EV. Relationship between intracellular pH, metabolic co-factors and caspase-3 activation in cancer cells during apoptosis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:604-611. [PMID: 28063999 DOI: 10.1016/j.bbamcr.2016.12.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 12/21/2022]
Abstract
A complex cascade of molecular events occurs in apoptotic cells but cell-to-cell variability significantly complicates determination of the order and interconnections between different processes. For better understanding of the mechanisms of programmed cell death, dynamic simultaneous registration of several parameters is required. In this paper we used multiparameter fluorescence microscopy to analyze energy metabolism, intracellular pH and caspase-3 activation in living cancer cells in vitro during staurosporine-induced apoptosis. We performed metabolic imaging of two co-factors, NAD(P)H and FAD, and used the genetically encoded pH-indicator SypHer1 and the FRET-based sensor for caspase-3 activity, mKate2-DEVD-iRFP, to visualize these parameters by confocal fluorescence microscopy and two-photon fluorescence lifetime imaging microscopy. The correlation between energy metabolism, intracellular pH and caspase-3 activation and their dynamic changes were studied in CT26 cancer cells during apoptosis. Induction of apoptosis was accompanied by a switch to oxidative phosphorylation, cytosol acidification and caspase-3 activation. We showed that alterations in cytosolic pH and the activation of oxidative phosphorylation are relatively early events associated with the induction of apoptosis.
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Affiliation(s)
- Tatiana F Sergeeva
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia.
| | - Marina V Shirmanova
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia.
| | - Olga A Zlobovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.
| | - Alena I Gavrina
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia; Nizhny Novgorod State University, Gagarin Ave., 23, 603950 Nizhny Novgorod, Russia.
| | - Varvara V Dudenkova
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia; Nizhny Novgorod State University, Gagarin Ave., 23, 603950 Nizhny Novgorod, Russia.
| | - Maria M Lukina
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia; Nizhny Novgorod State University, Gagarin Ave., 23, 603950 Nizhny Novgorod, Russia.
| | - Konstantin A Lukyanov
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.
| | - Elena V Zagaynova
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia.
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20
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Zumbrägel FK, Machtens DA, Curth U, Lüder CG, Reubold TF, Eschenburg S. Survivin does not influence the anti-apoptotic action of XIAP on caspase-9. Biochem Biophys Res Commun 2017; 482:530-535. [DOI: 10.1016/j.bbrc.2016.11.094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 10/20/2022]
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21
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Lai X, Friedman A. Exosomal miRs in Lung Cancer: A Mathematical Model. PLoS One 2016; 11:e0167706. [PMID: 28002496 PMCID: PMC5176278 DOI: 10.1371/journal.pone.0167706] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 11/18/2016] [Indexed: 01/11/2023] Open
Abstract
Lung cancer, primarily non-small-cell lung cancer (NSCLC), is the leading cause of cancer deaths in the United States and worldwide. While early detection significantly improves five-year survival, there are no reliable diagnostic tools for early detection. Several exosomal microRNAs (miRs) are overexpressed in NSCLC, and have been suggested as potential biomarkers for early detection. The present paper develops a mathematical model for early stage of NSCLC with emphasis on the role of the three highest overexpressed miRs, namely miR-21, miR-205 and miR-155. Simulations of the model provide quantitative relationships between the tumor volume and the total mass of each of the above miRs in the tumor. Because of the positive correlation between these miRs in the tumor tissue and in the blood, the results of the paper may be viewed as a first step toward establishing a combination of miRs 21, 205, 155 and possibly other miRs as serum biomarkers for early detection of NSCLC.
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Affiliation(s)
- Xiulan Lai
- Institute for Mathematical Sciences, Renmin University of China, Beijing, P. R. China
| | - Avner Friedman
- Mathematical Bioscience Institute & Department of Mathematics, Ohio State University, Columbus, OH, United States of America
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22
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Cheng TC, Akey IV, Yuan S, Yu Z, Ludtke SJ, Akey CW. A Near-Atomic Structure of the Dark Apoptosome Provides Insight into Assembly and Activation. Structure 2016; 25:40-52. [PMID: 27916517 DOI: 10.1016/j.str.2016.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/11/2016] [Accepted: 10/27/2016] [Indexed: 11/19/2022]
Abstract
In Drosophila, the Apaf-1-related killer (Dark) forms an apoptosome that activates procaspases. To investigate function, we have determined a near-atomic structure of Dark double rings using cryo-electron microscopy. We then built a nearly complete model of the apoptosome that includes 7- and 8-blade β-propellers. We find that the preference for dATP during Dark assembly may be governed by Ser325, which is in close proximity to the 2' carbon of the deoxyribose ring. Interestingly, β-propellers in V-shaped domains of the Dark apoptosome are more widely separated, relative to these features in the Apaf-1 apoptosome. This wider spacing may be responsible for the lack of cytochrome c binding to β-propellers in the Dark apoptosome. Our structure also highlights the roles of two loss-of-function mutations that may block Dark assembly. Finally, the improved model provides a framework to understand apical procaspase activation in the intrinsic cell death pathway.
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Affiliation(s)
- Tat Cheung Cheng
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
| | - Ildikó V Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
| | - Shujun Yuan
- Department of Biologics Research - Protein Sciences, U.S. Innovation Center, Bayer Healthcare, 455 Mission Bay Boulevard South, San Francisco, CA 94158, USA
| | - Zhiheng Yu
- Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christopher W Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
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23
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Cheng TC, Hong C, Akey IV, Yuan S, Akey CW. A near atomic structure of the active human apoptosome. eLife 2016; 5. [PMID: 27697150 PMCID: PMC5050015 DOI: 10.7554/elife.17755] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/12/2016] [Indexed: 01/19/2023] Open
Abstract
In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease. DOI:http://dx.doi.org/10.7554/eLife.17755.001 An adult human loses around 50–70 billion cells every day via a process termed apoptosis. The term arises from the Greek word that describes leaves “falling off” a tree, and the process entails damaged or unwanted cells essentially committing suicide in a controlled manner. As such, apoptosis keeps the number of cells in tissues and organs in check. It also allows components of old cells to be recycled to make new ones. In cells that are targeted to die, a protein called cytochrome c interacts with another protein, named Apaf-1, together with a nucleotide triphosphate molecule. These steps work in concert to trigger the assembly of the apoptosome: a large wheel-like complex that contains seven copies each of Apaf-1 and cytochrome c. The central hub of the wheel then recruits a specific protein-cutting enzyme, which once activated sets in motion a cascade of events that dismantle the cell from the inside out. Cheng et al. now use an electron microscope to reveal the three-dimensional structure of the active human apoptosome, in enough detail to determine the positions of many of the amino acids that make up the complex. The three dimensional model provides new insights into how Apaf-1 changes shape as the complex assembles in the presence of cytochrome c and nucleotide triphosphate. Cheng et al. went on to reveal a disk-like structure made from the parts of four Apaf-1 proteins that interact with the protein-cutting enzymes. This disk forms a spiral that sits atop the central hub of the wheel-like apoptosome. Finally, the findings suggest that, although the wheel like complex has seven spokes, at any one time the active apoptosome may only need two (or at most four) copies of the protein-cutting enzyme to trigger the cascade of events that lead to cell death In the future, emerging technologies may provide high enough resolution to visualize fine details of the interactions between cytochrome c and Apaf-1, and reveal more about the disk-like spiral as well. This in turn will give a better understanding of how the apoptosome assembles and how the protein-cutting enzyme becomes activated. DOI:http://dx.doi.org/10.7554/eLife.17755.002
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Affiliation(s)
- Tat Cheung Cheng
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, United States
| | - Chuan Hong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Ildikó V Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, United States
| | - Shujun Yuan
- Department of Biologics Research - Protein Sciences, U.S. Innovation Center, Bayer Healthcare, San Franciso, United States
| | - Christopher W Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, United States
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24
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Bernoux M, Burdett H, Williams SJ, Zhang X, Chen C, Newell K, Lawrence GJ, Kobe B, Ellis JG, Anderson PA, Dodds PN. Comparative Analysis of the Flax Immune Receptors L6 and L7 Suggests an Equilibrium-Based Switch Activation Model. THE PLANT CELL 2016; 28:146-59. [PMID: 26744216 PMCID: PMC4746675 DOI: 10.1105/tpc.15.00303] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 12/10/2015] [Accepted: 01/06/2016] [Indexed: 05/18/2023]
Abstract
NOD-like receptors (NLRs) are central components of the plant immune system. L6 is a Toll/interleukin-1 receptor (TIR) domain-containing NLR from flax (Linum usitatissimum) conferring immunity to the flax rust fungus. Comparison of L6 to the weaker allele L7 identified two polymorphic regions in the TIR and the nucleotide binding (NB) domains that regulate both effector ligand-dependent and -independent cell death signaling as well as nucleotide binding to the receptor. This suggests that a negative functional interaction between the TIR and NB domains holds L7 in an inactive/ADP-bound state more tightly than L6, hence decreasing its capacity to adopt the active/ATP-bound state and explaining its weaker activity in planta. L6 and L7 variants with a more stable ADP-bound state failed to bind to AvrL567 in yeast two-hybrid assays, while binding was detected to the signaling active variants. This contrasts with current models predicting that effectors bind to inactive receptors to trigger activation. Based on the correlation between nucleotide binding, effector interaction, and immune signaling properties of L6/L7 variants, we propose that NLRs exist in an equilibrium between ON and OFF states and that effector binding to the ON state stabilizes this conformation, thereby shifting the equilibrium toward the active form of the receptor to trigger defense signaling.
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Affiliation(s)
| | - Hayden Burdett
- School of Biological Sciences, Flinders University, Adelaide SA 5001, Australia
| | - Simon J Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane QLD 4072, Australia
| | | | | | - Kim Newell
- CSIRO Agriculture, Canberra ACT 2601, Australia
| | | | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane QLD 4072, Australia
| | | | - Peter A Anderson
- School of Biological Sciences, Flinders University, Adelaide SA 5001, Australia
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Zhang L, Chen S, Ruan J, Wu J, Tong AB, Yin Q, Li Y, David L, Lu A, Wang WL, Marks C, Ouyang Q, Zhang X, Mao Y, Wu H. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization. Science 2015; 350:404-9. [PMID: 26449474 DOI: 10.1126/science.aac5789] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/14/2015] [Indexed: 12/15/2022]
Abstract
The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the inflammasome adapter to activate innate immunity. We found that the PrgJ-NAIP2-NLRC4 inflammasome is assembled into multisubunit disk-like structures through a unidirectional adenosine triphosphatase polymerization, primed with a single PrgJ-activated NAIP2 per disk. Cryo-electron microscopy (cryo-EM) reconstruction at subnanometer resolution revealed a ~90° hinge rotation accompanying NLRC4 activation. Unlike in the related heptameric Apaf-1 apoptosome, in which each subunit needs to be conformationally activated by its ligand before assembly, a single PrgJ-activated NAIP2 initiates NLRC4 polymerization in a domino-like reaction to promote the disk assembly. These insights reveal the mechanism of signal amplification in NAIP-NLRC4 inflammasomes.
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Affiliation(s)
- Liman Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Shuobing Chen
- Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China. Department of Cancer Immunology and Virology, Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jianbin Ruan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jiayi Wu
- Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China. Department of Cancer Immunology and Virology, Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander B Tong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Qian Yin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yang Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alvin Lu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Wei Li Wang
- Department of Cancer Immunology and Virology, Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Carolyn Marks
- Center for Nanoscale Systems, Harvard University, Cambridge, MA 02138, USA
| | - Qi Ouyang
- Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Youdong Mao
- Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China. Department of Cancer Immunology and Virology, Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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Kondrikov D, Fulton D, Dong Z, Su Y. Heat Shock Protein 70 Prevents Hyperoxia-Induced Disruption of Lung Endothelial Barrier via Caspase-Dependent and AIF-Dependent Pathways. PLoS One 2015; 10:e0129343. [PMID: 26066050 PMCID: PMC4465980 DOI: 10.1371/journal.pone.0129343] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/07/2015] [Indexed: 12/03/2022] Open
Abstract
Exposure of pulmonary artery endothelial cells (PAECs) to hyperoxia results in a compromise in endothelial monolayer integrity, an increase in caspase-3 activity, and nuclear translocation of apoptosis-inducing factor (AIF), a marker of caspase-independent apoptosis. In an endeavor to identify proteins involved in hyperoxic endothelial injury, we found that the protein expression of heat-shock protein 70 (Hsp70) was increased in hyperoxic PAECs. The hyperoxia-induced Hsp70 protein expression is from hspA1B gene. Neither inhibition nor overexpression of Hsp70 affected the first phase barrier disruption of endothelial monolayer. Nevertheless, inhibition of Hsp70 by using the Hsp70 inhibitor KNK437 or knock down Hsp70 using siRNA exaggerated and overexpression of Hsp70 prevented the second phase disruption of lung endothelial integrity. Moreover, inhibition of Hsp70 exacerbated and overexpression of Hsp70 prevented hyperoxia-induced apoptosis, caspase-3 activation, and increase in nuclear AIF protein level in PAECs. Furthermore, we found that Hsp70 interacted with AIF in the cytosol in hyperoxic PAECs. Inhibition of Hsp70/AIF association by KNK437 correlated with increased nuclear AIF level and apoptosis in KNK437-treated PAECs. Finally, the ROS scavenger NAC prevented the hyperoxia-induced increase in Hsp70 expression and reduced the interaction of Hsp70 with AIF in hyperoxic PAECs. Together, these data indicate that increased expression of Hsp70 plays a protective role against hyperoxia-induced lung endothelial barrier disruption through caspase-dependent and AIF-dependent apoptotic pathways. Association of Hsp70 with AIF prevents AIF nuclear translocation, contributing to the protective effect of Hsp70 on hyperoxia-induced endothelial apoptosis. The hyperoxia-induced increase in Hsp70 expression and Hsp70/AIF interaction is contributed to ROS formation.
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Affiliation(s)
- Dmitry Kondrikov
- Department of Pharmacology & Toxicology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States of America
| | - David Fulton
- Department of Pharmacology & Toxicology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States of America
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States of America
| | - Zheng Dong
- Department of Cell Biology and Anatomy, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States of America
- Research Service, Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia 30912, United States of America
| | - Yunchao Su
- Department of Pharmacology & Toxicology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States of America
- Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States of America
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States of America
- Research Service, Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia 30912, United States of America
- * E-mail:
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Graumann K, Schaumburg F, Reubold TF, Hippe D, Eschenburg S, Lüder CGK. Toxoplasma gondii inhibits cytochrome c-induced caspase activation in its host cell by interference with holo-apoptosome assembly. MICROBIAL CELL 2015; 2:150-162. [PMID: 28357287 PMCID: PMC5349237 DOI: 10.15698/mic2015.05.201] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Inhibition of programmed cell death pathways of mammalian cells often facilitates the sustained survival of intracellular microorganisms. The apicomplexan parasite Toxoplasma gondii is a master regulator of host cell apoptotic pathways. Here, we have characterized a novel anti-apoptotic activity of T. gondii. Using a cell-free cytosolic extract model, we show that T. gondii interferes with the activities of caspase 9 and caspase 3/7 which have been induced by exogenous cytochrome c and dATP. Proteolytic cleavage of caspases 9 and 3 is also diminished suggesting inhibition of holo-apoptosome function. Parasite infection of Jurkat T cells and subsequent triggering of apoptosome formation by exogenous cytochrome cin vitro and in vivo indicated that T. gondii also interferes with caspase activation in infected cells. Importantly, parasite inhibition of cytochrome c-induced caspase activation considerably contributes to the overall anti-apoptotic activity of T. gondii as observed in staurosporine-treated cells. Co-immunoprecipitation showed that T. gondii abolishes binding of caspase 9 to Apaf-1 whereas the interaction of cytochrome c with Apaf-1 remains unchanged. Finally, T. gondii lysate mimics the effect of viable parasites and prevents holo-apoptosome functionality in a reconstituted in vitro system comprising recombinant Apaf-1 and caspase 9. Beside inhibition of cytochrome c release from host cell mitochondria, T. gondii thus also targets the holo-apoptosome assembly as a second mean to efficiently inhibit the caspase-dependent intrinsic cell death pathway.
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Affiliation(s)
- Kristin Graumann
- Institute for Medical Microbiology, Georg-August-University, Göttingen, Germany. ; Present address: In den Brühlwiesen 12, 61352 Bad Homburg, Germany
| | - Frieder Schaumburg
- Institute for Medical Microbiology, Georg-August-University, Göttingen, Germany. ; Present address: Institute for Medical Microbiology, University Hospital Münster, Domagkstraße 10, 48149 Münster, Germany
| | - Thomas F Reubold
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Diana Hippe
- Institute for Medical Microbiology, Georg-August-University, Göttingen, Germany
| | - Susanne Eschenburg
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Carsten G K Lüder
- Institute for Medical Microbiology, Georg-August-University, Göttingen, Germany
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28
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Danot O. How 'arm-twisting' by the inducer triggers activation of the MalT transcription factor, a typical signal transduction ATPase with numerous domains (STAND). Nucleic Acids Res 2015; 43:3089-99. [PMID: 25740650 PMCID: PMC4381067 DOI: 10.1093/nar/gkv158] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/11/2015] [Indexed: 11/14/2022] Open
Abstract
Signal transduction ATPases with numerous domains (STAND) get activated through inducer-dependent assembly into multimeric platforms. This switch relies on the conversion of their nucleotide-binding oligomerization domain (NOD) from a closed, ADP-bound form to an open, ATP-bound form. The NOD closed form is stabilized by contacts with the arm, a domain that connects the NOD to the inducer-binding domain called the sensor. How the inducer triggers NOD opening remains unclear. Here, I pinpointed the NOD-arm interface of the MalT STAND transcription factor, and I generated a MalT variant in which this interface can be covalently locked on demand, thereby trapping the NOD in the closed state. By characterizing this locked variant, I found that the inducer is recognized in two steps: it first binds to the sole sensor with low affinity, which then triggers the recruitment of the arm to form a high-affinity arm-sensor inducer-binding site. Strikingly, this high-affinity binding step was incompatible with arm-NOD contacts maintaining the NOD closed. Through this toggling between two mutually exclusive states reminiscent of a single-pole double-throw switch, the arm couples inducer binding to NOD opening, shown here to precede nucleotide exchange. This scenario likely holds for other STANDs like mammalian NLR innate immunity receptors.
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Affiliation(s)
- Olivier Danot
- Institut Pasteur, Molecular Genetics Unit, Microbiology Department, F-75015 Paris, France CNRS, ERL3526, F-75015 Paris, France
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29
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Würstle ML, Rehm M. A systems biology analysis of apoptosome formation and apoptosis execution supports allosteric procaspase-9 activation. J Biol Chem 2014; 289:26277-26289. [PMID: 25107908 DOI: 10.1074/jbc.m114.590034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protease caspase-9 is activated on the apoptosome, a multiprotein signal transduction platform that assembles in response to mitochondria-dependent apoptosis initiation. Despite extensive molecular research, the assembly of the holo-apoptosome and the process of caspase-9 activation remain incompletely understood. Here, we therefore integrated quantitative data on the molecular interactions and proteolytic processes during apoptosome formation and apoptosis execution and conducted mathematical simulations to investigate the resulting biochemical signaling, quantitatively and kinetically. Interestingly, when implementing the homodimerization of procaspase-9 as a prerequisite for activation, the calculated kinetics of apoptosis execution and the efficacy of caspase-3 activation failed to replicate experimental data. In contrast, assuming a scenario in which procaspase-9 is activated allosterically upon binding to the apoptosome backbone, the mathematical simulations quantitatively and kinetically reproduced all experimental data. These data included a XIAP threshold concentration at which apoptosis execution is suppressed in HeLa cervical cancer cells, half-times of procaspase-9 processing, as well as the molecular timer function of the apoptosome. Our study therefore provides novel mechanistic insight into apoptosome-dependent apoptosis execution and suggests that caspase-9 is activated allosterically by binding to the apoptosome backbone. Our findings challenge the currently prevailing dogma that all initiator procaspases require homodimerization for activation.
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Affiliation(s)
- Maximilian L Würstle
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Markus Rehm
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
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30
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Singer H, Biswas A, Zimmer N, Messaed C, Oldenburg J, Slim R, El-Maarri O. NLRP7 inter-domain interactions: the NACHT-associated domain is the physical mediator for oligomeric assembly. Mol Hum Reprod 2014; 20:990-1001. [PMID: 25082979 DOI: 10.1093/molehr/gau060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mutations in NLRP7 (NOD-like-receptor family, pyrin domain containing 7) are responsible for a type of recurrent pregnancy loss known as recurrent hydatidiform mole (HYDM1). This condition is characterized by abnormal growth of the placenta, a lack of proper embryonic development and abnormal methylation patterns at multiple imprinted loci in diploid biparental molar tissues. The role of NLRP7 protein in the disease manifestation is currently not clear. In order to better understand how the effects of HYDM1 are associated with mutations on the structure of NLRP7, we performed an inter-domain interaction screen using a yeast two-hybrid system. Additionally, we generated in silico structural models of NLRP7 in its non-activated and activated forms. Our observations from the yeast two-hybrid screen and modeling suggest that the NACHT-associated domain (NAD) of the NLRP7 protein is central to its oligomeric assembly. Upon activation, the NAD and a small part of the leucine rich repeat (LRR) of one molecule emerged out of the protective LRR domain and interact with the NACHT domain of the second molecule to form an oligomer. Furthermore, we investigated the molecular basis for the pathophysiological effect of four missense mutations, three HYDM1-causing and one rare non-synonymous variant, on the protein using confocal microscopy of transiently transfected NLRP7 in HEK293T cells and in silico structural analysis. We found that with the two clinically severe missense mutations, L398R and R693W, the normal molecule to molecule interaction was apparently affected thus decreasing their oligomerization potential while aggresome formation was increased; these changes could disturb the normal downstream functions of NLRP7 and therefore be a possible molecular effect underlying their pathophysiological impact.
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Affiliation(s)
- Heike Singer
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Arijit Biswas
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Nicole Zimmer
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Christiane Messaed
- Department of Human Genetics, McGill University Health Centre Research Institute, Montreal, Canada Department of Obstetrics and Gynecology, McGill University Health Centre Research Institute, Montreal, Canada
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Rima Slim
- Department of Human Genetics, McGill University Health Centre Research Institute, Montreal, Canada Department of Obstetrics and Gynecology, McGill University Health Centre Research Institute, Montreal, Canada
| | - Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
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31
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Chai J, Shi Y. Apoptosome and inflammasome: conserved machineries for caspase activation. Natl Sci Rev 2014. [DOI: 10.1093/nsr/nwt025] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Apoptosome and inflammasome are multimeric protein complexes that mediate the activation of specific caspases at the onset of apoptosis and inflammation. The central component of apoptosome or inflammasome is a tripartite scaffold protein, exemplified by Apaf-1 and NLRC4, which contains an amino-terminal homotypic interaction motif, a central nucleotide-binding oligomerization domain and a carboxyl-terminal ligand-sensing domain. In the absence of death cue or an inflammatory signal, Apaf-1 or NLRC4 exists in an auto-inhibited, monomeric state, which is stabilized by adenosine diphosphate (ADP). Binding to an apoptosis- or inflammation-inducing ligand, together with replacement of ADP by adenosine triphosphate (ATP), results in the formation of a multimeric apoptosome or inflammasome. The assembled apoptosome and inflammasome serve as dedicated machineries to facilitate the activation of specific caspases. In this review, we describe the structure and functional mechanisms of mammalian inflammasome and apoptosomes from three representative organisms. Emphasis is placed on the molecular mechanism of caspase activation and the shared features of apoptosomes and inflammasomes.
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Affiliation(s)
- Jijie Chai
- Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
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32
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Yadav N, Chandra D. Mitochondrial and postmitochondrial survival signaling in cancer. Mitochondrion 2013; 16:18-25. [PMID: 24333692 DOI: 10.1016/j.mito.2013.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 11/23/2013] [Accepted: 11/26/2013] [Indexed: 12/11/2022]
Abstract
Cancer cells are resistant to conventional chemotherapy and radiotherapy, however, the molecular mechanisms of resistance to therapy remain unclear. Cellular survival machinery protects mitochondrial integrity against endogenous or exogenous stresses. Prodeath molecules orchestrate around mitochondria to initiate and execute cell death in cancer, and also play an underappreciated role in survival of cancer cells. Prosurvival mechanisms can operate at mitochondrial and postmitochondrial levels to attenuate core apoptotic death program. It is intriguing to explore how prosurvival and prodeath molecules crosstalk to regulate mitochondrial functions leading to increased cancer cell survival. This review describes some putative survival mechanisms at mitochondria, which may play a role in designing effective agents for cancer prevention and therapy. These survival pathways may also have significance in understanding other human pathophysiological conditions including diabetes, cardiovascular, autoimmune, and neurodegenerative diseases.
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Affiliation(s)
- Neelu Yadav
- Department of Pharmacology Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - Dhyan Chandra
- Department of Pharmacology Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, United States.
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33
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Hossain A, Radwan FFY, Doonan BP, God JM, Zhang L, Bell PD, Haque A. A possible cross-talk between autophagy and apoptosis in generating an immune response in melanoma. Apoptosis 2013; 17:1066-78. [PMID: 22847295 DOI: 10.1007/s10495-012-0745-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Melanoma is the most aggressive form of skin cancer, responsible for the majority of skin cancer related deaths. Thus, the search for natural molecules which can effectively destroy tumors while promoting immune activation is essential for designing novel therapies against metastatic melanoma. Here, we report for the first time that a natural triterpenoid, Ganoderic acid DM (GA-DM), induces an orchestrated autophagic and apoptotic cell death, as well as enhanced immunological responses via increased HLA class II presentation in melanoma cells. Annexin V staining and flow cytometry showed that GA-DM treatment induced apoptosis of melanoma cells, which was supported by a detection of increased Bax proteins, co-localization and elevation of Apaf-1 and cytochrome c, and a subsequent cleavage of caspases 9 and 3. Furthermore, GA-DM treatment initiated a possible cross-talk between autophagy and apoptosis as evidenced by increased levels of Beclin-1 and LC3 proteins, and their timely interplay with apoptotic and/or anti-apoptotic molecules in melanoma cells. Despite GA-DM's moderate cytotoxicity, viable cells expressed high levels of HLA class II proteins with improved antigen presentation and CD4+ T cell recognition. The antitumor efficacy of GA-DM was also investigated in vivo in murine B16 melanoma model, where GA-DM treatment slowed tumor formation with a significant reduction in tumor volume. Taken together, these findings demonstrate the potential of GA-DM as a natural chemo-immunotherapeutic capable of inducing a possible cross-talk between autophagy and apoptosis, as well as improved immune recognition for sustained melanoma tumor clearance.
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Affiliation(s)
- Azim Hossain
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue, BSB-201, Charleston, SC 29425, USA
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34
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Hu Z, Yan C, Liu P, Huang Z, Ma R, Zhang C, Wang R, Zhang Y, Martinon F, Miao D, Deng H, Wang J, Chang J, Chai J. Crystal structure of NLRC4 reveals its autoinhibition mechanism. Science 2013; 341:172-5. [PMID: 23765277 DOI: 10.1126/science.1236381] [Citation(s) in RCA: 287] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nucleotide-binding and oligomerization domain-like receptor (NLR) proteins oligomerize into multiprotein complexes termed inflammasomes when activated. Their autoinhibition mechanism remains poorly defined. Here, we report the crystal structure of mouse NLRC4 in a closed form. The adenosine diphosphate-mediated interaction between the central nucleotide-binding domain (NBD) and the winged-helix domain (WHD) was critical for stabilizing the closed conformation of NLRC4. The helical domain HD2 repressively contacted a conserved and functionally important α-helix of the NBD. The C-terminal leucine-rich repeat (LRR) domain is positioned to sterically occlude one side of the NBD domain and consequently sequester NLRC4 in a monomeric state. Disruption of ADP-mediated NBD-WHD or NBD-HD2/NBD-LRR interactions resulted in constitutive activation of NLRC4. Together, our data reveal the NBD-organized cooperative autoinhibition mechanism of NLRC4 and provide insight into its activation.
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Affiliation(s)
- Zehan Hu
- School of Life Sciences, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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35
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Yuan S, Akey CW. Apoptosome structure, assembly, and procaspase activation. Structure 2013; 21:501-15. [PMID: 23561633 PMCID: PMC3644875 DOI: 10.1016/j.str.2013.02.024] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 02/04/2013] [Accepted: 02/11/2013] [Indexed: 11/22/2022]
Abstract
Apaf-1-like molecules assemble into a ring-like platform known as the apoptosome. This cell death platform then activates procaspases in the intrinsic cell death pathway. In this review, crystal structures of Apaf-1 monomers and CED-4 dimers have been combined with apoptosome structures to provide insights into the assembly of cell death platforms in humans, nematodes, and flies. In humans, the caspase recognition domains (CARDs) of procaspase-9 and Apaf-1 interact with each other to form a CARD-CARD disk, which interacts with the platform to create an asymmetric proteolysis machine. The disk tethers multiple pc-9 catalytic domains to the platform to raise their local concentration, and this leads to zymogen activation. These findings have now set the stage for further studies of this critical activation process on the apoptosome.
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Affiliation(s)
- Shujun Yuan
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
| | - Christopher W. Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
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36
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Yuan S, Topf M, Reubold TF, Eschenburg S, Akey CW. Changes in Apaf-1 conformation that drive apoptosome assembly. Biochemistry 2013. [PMID: 23521171 DOI: 10.1021/bi 301721g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apoptosome assembly is highly regulated in the intrinsic cell death pathway. To better understand this step, we created an improved model of the human apoptosome using a crystal structure of full length Apaf-1 and a single particle, electron density map at ~9.5 Å resolution. The apoptosome model includes N-terminal domains of Apaf-1, cognate β-propellers, and cytochrome c. A direct comparison of Apaf-1 in the apoptosome and as a monomer reveals conformational changes that occur during the first two steps of assembly. This includes an induced-fit mechanism for cytochrome c binding to regulatory β-propellers, which is dependent on shape and charge complementarity, and a large rotation of the nucleotide binding module during nucleotide exchange. These linked conformational changes create an extended Apaf-1 monomer and drive apoptosome assembly. Moreover, the N-terminal CARD in the inactive Apaf-1 monomer is not shielded from other proteins by β-propellers. Hence, the Apaf-1 CARD may be free to interact with a procaspase-9 CARD either before or during apoptosome assembly. Irrespective of the timing, the end product of assembly is a holo-apoptosome with an acentric CARD-CARD disk and tethered pc-9 catalytic domains. Subsequent activation of pc-9 leads to a proteolytic cascade and cell death.
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Affiliation(s)
- Shujun Yuan
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
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37
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Yuan S, Topf M, Reubold TF, Eschenburg S, Akey CW. Changes in Apaf-1 conformation that drive apoptosome assembly. Biochemistry 2013; 52:2319-27. [PMID: 23521171 DOI: 10.1021/bi301721g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Apoptosome assembly is highly regulated in the intrinsic cell death pathway. To better understand this step, we created an improved model of the human apoptosome using a crystal structure of full length Apaf-1 and a single particle, electron density map at ~9.5 Å resolution. The apoptosome model includes N-terminal domains of Apaf-1, cognate β-propellers, and cytochrome c. A direct comparison of Apaf-1 in the apoptosome and as a monomer reveals conformational changes that occur during the first two steps of assembly. This includes an induced-fit mechanism for cytochrome c binding to regulatory β-propellers, which is dependent on shape and charge complementarity, and a large rotation of the nucleotide binding module during nucleotide exchange. These linked conformational changes create an extended Apaf-1 monomer and drive apoptosome assembly. Moreover, the N-terminal CARD in the inactive Apaf-1 monomer is not shielded from other proteins by β-propellers. Hence, the Apaf-1 CARD may be free to interact with a procaspase-9 CARD either before or during apoptosome assembly. Irrespective of the timing, the end product of assembly is a holo-apoptosome with an acentric CARD-CARD disk and tethered pc-9 catalytic domains. Subsequent activation of pc-9 leads to a proteolytic cascade and cell death.
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Affiliation(s)
- Shujun Yuan
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
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38
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Lee EF, Fairlie WD. Structural biology of the intrinsic cell death pathway: what do we know and what is missing? Comput Struct Biotechnol J 2012; 1:e201204007. [PMID: 24688636 PMCID: PMC3962096 DOI: 10.5936/csbj.201204007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 04/01/2012] [Accepted: 04/05/2012] [Indexed: 11/22/2022] Open
Affiliation(s)
- Erinna F Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia and Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - W Douglas Fairlie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia and Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
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39
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Health and cellular impacts of air pollutants: from cytoprotection to cytotoxicity. Biochem Res Int 2012; 2012:493894. [PMID: 22550588 PMCID: PMC3328890 DOI: 10.1155/2012/493894] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/17/2012] [Accepted: 01/18/2012] [Indexed: 12/11/2022] Open
Abstract
Air pollution as one of the ravages of our modern societies is primarily linked to urban centers, industrial activities, or road traffic. These atmospheric pollutants have been incriminated in deleterious health effects by numerous epidemiological and in vitro studies. Environmental air pollutants are a heterogeneous mixture of particles suspended into a liquid and gaseous phase which trigger the disruption of redox homeostasis—known under the term of cellular oxidative stress—in relation with the establishment of inflammation and cell death via necrosis, apoptosis, or autophagy. Activation or repression of the apoptotic process as an adaptative response to xenobiotics might lead to either acute or chronic toxicity. The purpose of this paper is to highlight the central role of oxidative stress induced by air pollutants and to focus on the subsequent cellular impacts ranging from cytoprotection to cytotoxicity by decreasing or stimulating apoptosis, respectively.
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40
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Reubold TF, Eschenburg S. A molecular view on signal transduction by the apoptosome. Cell Signal 2012; 24:1420-5. [PMID: 22446004 DOI: 10.1016/j.cellsig.2012.03.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/05/2012] [Indexed: 12/22/2022]
Abstract
Apoptosomes are signaling platforms that initiate the dismantling of a cell during apoptosis. In mammals, assembly of the apoptosome is the pivotal point in the mitochondrial pathway of apoptosis, and is prompted by binding of cytochrome c to the apoptotic protease-activating factor 1 (Apaf-1) in the presence of ATP. The resulting wheel-like heptamer of seven molecules Apaf-1 and seven molecules cytochrome c binds and activates the initiator caspase-9, which in turn ignites the downstream caspase cascade. In this review we discuss the molecular determinants for the formation of the mammalian apoptosome and caspase activation and describe the related signaling platforms in flies and nematodes.
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Affiliation(s)
- Thomas F Reubold
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
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41
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Prudnikov IM, Smirnov AN. Short peptide tools for monitoring caspase and proteasome activities in embryonal and adult rat brain lysates: an approach for the differential identification of proteases. J Biochem 2012; 151:299-316. [PMID: 22228904 DOI: 10.1093/jb/mvs001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The numerous caspase-like activities present in nervous tissue can be investigated with labelled peptides. However, the cross-reactivities of peptides with both proteasomes and caspases complicate the analysis of protease activity. The pharmacological features of substrates and inhibitors specific for either caspases or proteasome caspase-like proteases in rat brain lysates were similar or identical to the profiles of commercially purified proteasome preparations. Caspase inhibitors bind directly to active proteasome centres, thus competing with selective antagonists of proteasomes. Separation of lysates by molecular weight does not separate active caspases from proteasomes because these enzymes co-localize under native electrophoresis. The addition of ATP or its analogues is associated with the differential modulation of proteasomal activity, which also leads to ambiguity in the data. However, induced caspase activity could be successfully differentiated from proteasome activity in embryonal brain lysates with the non-selective caspase inhibitors Z-VAD-FMK and Q-VD-OPh and the proteasome inhibitor AdaAhx(3)L(3)VS that are not cross-reactive. This strategy is proposed for the simultaneous examination of caspases and proteasomes using proteolysis experiments. The present study reveals that all of the caspase-like activities in the tissue lysates of non-injured adult rat brains were related to proteasomal caspase-like activities.
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Affiliation(s)
- Igor M Prudnikov
- Laboratory of stem cell biology, A. Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Bogomoletz str., 4, 01024, Kiev, Ukraine.
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Lin NC, Lin JC, Chen SH, Ho CT, Yeh AI. Effect of Goji (Lycium barbarum) on expression of genes related to cell survival. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:10088-10096. [PMID: 21846086 DOI: 10.1021/jf2021754] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This study investigated the interrelationship between Lycium barbarum (goji) and gene expression in mouse spleen. Oligomicroarray technology was employed to explore the comprehensive response of gene expression and to screen candidate marker genes in the spleens of mice fed a goji suspension. Goji was micronized by media milling and then used to evaluate the effect of size reduction. The average diameter of nano/submicrometer goji was about 100 nm, which exhibited no cytotoxicity to cell lines IEC-6 (rat normal small intestinal cell line) and Caco-2 (human colon adenocarcinoma cell line). It was found that three genes, TNF, Nfkb1, and Bcl-2, were up-regulated and two genes, APAF-1 and caspase-3, were down-regulated by goji. This phenomenon could be helpful for cytoprotection when cells undergo stress or damage that induces the apoptotic pathway. Size reduction into nano/submicrometer scale enhanced bioactivity.
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Affiliation(s)
- Nien-Chen Lin
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
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Reubold T, Wohlgemuth S, Eschenburg S. Crystal Structure of Full-Length Apaf-1: How the Death Signal Is Relayed in the Mitochondrial Pathway of Apoptosis. Structure 2011; 19:1074-83. [DOI: 10.1016/j.str.2011.05.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 05/30/2011] [Accepted: 05/31/2011] [Indexed: 10/17/2022]
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Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW. Structure of the Drosophila apoptosome at 6.9 å resolution. Structure 2011; 19:128-40. [PMID: 21220123 DOI: 10.1016/j.str.2010.10.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 09/26/2010] [Accepted: 10/01/2010] [Indexed: 11/19/2022]
Abstract
The Drosophila Apaf-1 related killer forms an apoptosome in the intrinsic cell death pathway. In this study we show that Dark forms a single ring when initiator procaspases are bound. This Dark-Dronc complex cleaves DrICE efficiently; hence, a single ring represents the Drosophila apoptosome. We then determined the 3D structure of a double ring at ∼6.9 Å resolution and created a model of the apoptosome. Subunit interactions in the Dark complex are similar to those in Apaf-1 and CED-4 apoptosomes, but there are significant differences. In particular, Dark has "lost" a loop in the nucleotide-binding pocket, which opens a path for possible dATP exchange in the apoptosome. In addition, caspase recruitment domains (CARDs) form a crown on the central hub of the Dark apoptosome. This CARD geometry suggests that conformational changes will be required to form active Dark-Dronc complexes. When taken together, these data provide insights into apoptosome structure, function, and evolution.
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Affiliation(s)
- Shujun Yuan
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
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Mace PD, Riedl SJ. Molecular cell death platforms and assemblies. Curr Opin Cell Biol 2011; 22:828-36. [PMID: 20817427 DOI: 10.1016/j.ceb.2010.08.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2010] [Revised: 08/01/2010] [Accepted: 08/05/2010] [Indexed: 10/19/2022]
Abstract
Multi-cellular animals have evolved a variety of mechanisms to respond to diverse apoptotic stimuli. In general these proceed through activation of apical caspases and culminate in executioner caspase activation and cell death. Because of the breadth of possible initiators, various molecular platforms are used to trigger different apical caspases. Although some common protein domains are used to assemble the apoptosome, the PIDDosome and death receptor complexes, an array of checks-and-balances are employed to ensure appropriate activation. Notwithstanding, these pathways share the underlying principle of proximity-dependent activation and post-translational modification. Here we will describe our current structural understanding of assembly and regulation of these signaling platforms.
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Affiliation(s)
- Peter D Mace
- Program in Apoptosis and Cell Death Research, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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De Zio D, Bordi M, Tino E, Lanzuolo C, Ferraro E, Mora E, Ciccosanti F, Fimia GM, Orlando V, Cecconi F. The DNA repair complex Ku70/86 modulates Apaf1 expression upon DNA damage. Cell Death Differ 2010; 18:516-27. [PMID: 20966962 DOI: 10.1038/cdd.2010.125] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Apaf1 is a key regulator of the mitochondrial intrinsic pathway of apoptosis, as it activates executioner caspases by forming the apoptotic machinery apoptosome. Its genetic regulation and its post-translational modification are crucial under the various conditions where apoptosis occurs. Here we describe Ku70/86, a mediator of non-homologous end-joining pathway of DNA repair, as a novel regulator of Apaf1 transcription. Through analysing different Apaf1 promoter mutants, we identified an element repressing the Apaf1 promoter. We demonstrated that Ku70/86 is a nuclear factor able to bind this repressing element and downregulating Apaf1 transcription. We also found that Ku70/86 interaction with Apaf1 promoter is dynamically modulated upon DNA damage. The effect of this binding is a downregulation of Apaf1 expression immediately following the damage to DNA; conversely, we observed Apaf1 upregulation and apoptosis activation when Ku70/86 unleashes the Apaf1-repressing element. Therefore, besides regulating DNA repair, our results suggest that Ku70/86 binds to the Apaf1 promoter and represses its activity. This may help to inhibit the apoptosome pathway of cell death and contribute to regulate cell survival.
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Affiliation(s)
- D De Zio
- Department of Biology, Dulbecco Telethon Institute, University of Rome Tor Vergata, 00133 Rome, Italy
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Conserved motifs involved in ATP hydrolysis by MalT, a signal transduction ATPase with numerous domains from Escherichia coli. J Bacteriol 2010; 192:5181-91. [PMID: 20693326 DOI: 10.1128/jb.00522-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The signal transduction ATPases with numerous domains (STAND) are sophisticated signaling proteins that are related to AAA+ proteins and control various biological processes, including apoptosis, gene expression, and innate immunity. They function as tightly regulated switches, with the off and on positions corresponding to an ADP-bound, monomeric form and an ATP-bound, multimeric form, respectively. Protein activation is triggered by inducer binding to the sensor domain. ATP hydrolysis by the nucleotide-binding oligomerization domain (NOD) ensures the generation of the ADP-bound form. Here, we use MalT, an Escherichia coli transcription activator, as a model system to identify STAND conserved motifs involved in ATP hydrolysis besides the catalytic acidic residue. Alanine substitution of the conserved polar residue (H131) that is located two residues downstream from the catalytic residue (D129) blocks ATP hydrolysis and traps MalT in an active, ATP-bound, multimeric form. This polar residue is also conserved in AAA+. Based on AAA+ X-ray structures, we proposed that it is responsible for the proper positioning of the catalytic and the sensor I residues for the hydrolytic attack. Alanine substitution of the putative STAND sensor I (R160) abolished MalT activity. Substitutions of R171 impaired both ATP hydrolysis and multimerization, which is consistent with an arginine finger function and provides further evidence that ATP hydrolysis is primarily catalyzed by MalT multimers.
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Yuan S, Yu X, Topf M, Ludtke SJ, Wang X, Akey CW. Structure of an apoptosome-procaspase-9 CARD complex. Structure 2010; 18:571-83. [PMID: 20462491 PMCID: PMC2874686 DOI: 10.1016/j.str.2010.04.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 04/07/2010] [Accepted: 04/16/2010] [Indexed: 10/19/2022]
Abstract
Apaf-1 coassembles with cytochrome c to form the apoptosome, which then binds and activates procaspase-9 (pc-9). We removed pc-9 catalytic domains from the holoapoptosome by site-directed thrombinolysis. A structure of the resulting apoptosome-pc-9 CARD complex was then determined at approximately 9.5 A resolution. In our model, the central hub is constructed like other AAA+ protein rings but also contains novel features. At higher radius, the regulatory region of each Apaf-1 is comprised of tandem seven and eight blade beta-propellers with cytochrome c docked between them. Remarkably, Apaf-1 CARDs are disordered in the ground state. During activation, each Apaf-1 CARD interacts with a pc-9 CARD and these heterodimers form a flexibly tethered "disk" that sits above the central hub. When taken together, the data reveal conformational changes during Apaf-1 assembly that allow pc-9 activation. The model also provides a plausible explanation for the effects of NOD mutations that have been mapped onto the central hub.
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Affiliation(s)
- Shujun Yuan
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St. Boston, Massachusetts 02118-2526, USA
| | - Xinchao Yu
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St. Boston, Massachusetts 02118-2526, USA
| | - Maya Topf
- Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX
| | - Steven J. Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Xiaodong Wang
- National Institute of Biological Sciences, Zhongguancun Life Sciences Park, Beijing, China
| | - Christopher W. Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St. Boston, Massachusetts 02118-2526, USA
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