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Zou Y, Sabljić I, Horbach N, Dauphinee AN, Åsman A, Sancho Temino L, Minina EA, Drag M, Stael S, Poreba M, Ståhlberg J, Bozhkov PV. Thermoprotection by a cell membrane-localized metacaspase in a green alga. Plant Cell 2024; 36:665-687. [PMID: 37971931 PMCID: PMC10896300 DOI: 10.1093/plcell/koad289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/10/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Caspases are restricted to animals, while other organisms, including plants, possess metacaspases (MCAs), a more ancient and broader class of structurally related yet biochemically distinct proteases. Our current understanding of plant MCAs is derived from studies in streptophytes, and mostly in Arabidopsis (Arabidopsis thaliana) with 9 MCAs with partially redundant activities. In contrast to streptophytes, most chlorophytes contain only 1 or 2 uncharacterized MCAs, providing an excellent platform for MCA research. Here we investigated CrMCA-II, the single type-II MCA from the model chlorophyte Chlamydomonas (Chlamydomonas reinhardtii). Surprisingly, unlike other studied MCAs and similar to caspases, CrMCA-II dimerizes both in vitro and in vivo. Furthermore, activation of CrMCA-II in vivo correlated with its dimerization. Most of CrMCA-II in the cell was present as a proenzyme (zymogen) attached to the plasma membrane (PM). Deletion of CrMCA-II by genome editing compromised thermotolerance, leading to increased cell death under heat stress. Adding back either wild-type or catalytically dead CrMCA-II restored thermoprotection, suggesting that its proteolytic activity is dispensable for this effect. Finally, we connected the non-proteolytic role of CrMCA-II in thermotolerance to the ability to modulate PM fluidity. Our study reveals an ancient, MCA-dependent thermotolerance mechanism retained by Chlamydomonas and probably lost during the evolution of multicellularity.
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Affiliation(s)
- Yong Zou
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Natalia Horbach
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Anna Åsman
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Lucia Sancho Temino
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Simon Stael
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Marcin Poreba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
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Steens JA, Bravo JPK, Salazar CRP, Yildiz C, Amieiro AM, Köstlbacher S, Prinsen SHP, Andres AS, Patinios C, Bardis A, Barendregt A, Scheltema RA, Ettema TJG, van der Oost J, Taylor DW, Staals RHJ. Type III-B CRISPR-Cas cascade of proteolytic cleavages. Science 2024; 383:512-519. [PMID: 38301007 DOI: 10.1126/science.adk0378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from Haliangium ochraceum that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide-based antiphage signaling system (CBASS). Cyclic tri-adenosine monophosphate (AMP)-induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Escherichia coli. Taken together, our findings reveal how a CRISPR-Cas-based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities.
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Affiliation(s)
- Jurre A Steens
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
- Scope Biosciences B.V., Wageningen, Netherlands
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Caglar Yildiz
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Afonso M Amieiro
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Stephan Köstlbacher
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Ane S Andres
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Constantinos Patinios
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Andreas Bardis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, University of Utrecht, Utrecht, Netherlands
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, University of Utrecht, Utrecht, Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
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3
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Stael S, Sabljić I, Audenaert D, Andersson T, Tsiatsiani L, Kumpf RP, Vidal-Albalat A, Lindgren C, Vercammen D, Jacques S, Nguyen L, Njo M, Fernández-Fernández ÁD, Beunens T, Timmerman E, Gevaert K, Van Montagu M, Ståhlberg J, Bozhkov PV, Linusson A, Beeckman T, Van Breusegem F. Structure-function study of a Ca 2+-independent metacaspase involved in lateral root emergence. Proc Natl Acad Sci U S A 2023; 120:e2303480120. [PMID: 37216519 PMCID: PMC10235996 DOI: 10.1073/pnas.2303480120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Metacaspases are part of an evolutionarily broad family of multifunctional cysteine proteases, involved in disease and normal development. As the structure-function relationship of metacaspases remains poorly understood, we solved the X-ray crystal structure of an Arabidopsis thaliana type II metacaspase (AtMCA-IIf) belonging to a particular subgroup not requiring calcium ions for activation. To study metacaspase activity in plants, we developed an in vitro chemical screen to identify small molecule metacaspase inhibitors and found several hits with a minimal thioxodihydropyrimidine-dione structure, of which some are specific AtMCA-IIf inhibitors. We provide mechanistic insight into the basis of inhibition by the TDP-containing compounds through molecular docking onto the AtMCA-IIf crystal structure. Finally, a TDP-containing compound (TDP6) effectively hampered lateral root emergence in vivo, probably through inhibition of metacaspases specifically expressed in the endodermal cells overlying developing lateral root primordia. In the future, the small compound inhibitors and crystal structure of AtMCA-IIf can be used to study metacaspases in other species, such as important human pathogens, including those causing neglected diseases.
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Affiliation(s)
- Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Dominique Audenaert
- VIB Screening Core, VIB,9052Ghent, Belgium
- Centre for Bioassay Development and Screening, Ghent University,9000Ghent, Belgium
| | | | - Liana Tsiatsiani
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | | | | | | | - Dominique Vercammen
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Silke Jacques
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Long Nguyen
- VIB Screening Core, VIB,9052Ghent, Belgium
- Centre for Bioassay Development and Screening, Ghent University,9000Ghent, Belgium
| | - Maria Njo
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Álvaro D. Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Tine Beunens
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Evy Timmerman
- Department of Biomolecular Medicine, Ghent University,9052Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University,9052Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052Ghent, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Anna Linusson
- Department of Chemistry, Umeå University,90187Umeå, Sweden
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
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Hu C, van Beljouw SPB, Nam KH, Schuler G, Ding F, Cui Y, Rodríguez-Molina A, Haagsma AC, Valk M, Pabst M, Brouns SJ, Ke A. Craspase is a CRISPR RNA-guided, RNA-activated protease. Science 2022; 377:1278-1285. [PMID: 36007061 PMCID: PMC10041820 DOI: 10.1126/science.add5064] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo-electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5' region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain-binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA-activated protease with self-regulatory capacity.
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Affiliation(s)
- Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Sam P. B. van Beljouw
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Gabriel Schuler
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Fran Ding
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Yanru Cui
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Alicia Rodríguez-Molina
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Anna C Haagsma
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Menno Valk
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Martin Pabst
- Department of Environmental Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
| | - Stan J.J. Brouns
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
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5
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Yu H, Hou Z, Xiang M, Yang F, Ma J, Yang L, Ma X, Zhou L, He F, Miao M, Liu X, Wang Y. Arsenic trioxide activates yes-associated protein by lysophosphatidic acid metabolism to selectively induce apoptosis of vascular smooth muscle cells. Biochim Biophys Acta Mol Cell Res 2022; 1869:119211. [PMID: 35041860 DOI: 10.1016/j.bbamcr.2022.119211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/24/2021] [Accepted: 12/31/2021] [Indexed: 02/06/2023]
Abstract
Inhibition of vascular smooth muscle cells (VSMCs) proliferation without dysregulating endothelial cells (ECs) may provide an ideal therapy for in-stent restenosis. Due to its anti-proliferation effect on VSMCs and pro-endothelium effect, arsenic trioxide (ATO) has been used in a drug-eluting stent in a recent clinical trial. However, the underlying mechanism by which ATO achieves this effect has not been determined. In the present work, we showed that ATO induced apoptosis in VSMCs but not in ECs. Mechanistically, ATO achieved this through modulation of cellular metabolism to increase lysophosphatidic acid (LPA) in VSMCs, while LPA concentration was stable in ECs. The elevated LPA facilitated the nuclear accumulation and initiated the transcriptional function of Yes-associated protein (YAP) in VSMCs. YAP regulated the transcription of N6-Methyladenosine (m6A) modulators (Mettl14 and Wtap) to increase the m6A methylation levels of apoptosis-related genes to induce their high expression and exacerbate VSMCs apoptosis. On the other hand, YAP nuclear accumulation in ECs was not observed. Collectively, our data exhibited the molecular process involved in selective apoptosis of VSMCs induced by ATO.
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Affiliation(s)
- Hongchi Yu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China; Institute of Biomedical Engineering, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zhe Hou
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Maolong Xiang
- College of Life Sciences, Sichuan University, 610064 Chengdu, China
| | - Fan Yang
- Institute of Biomedical Engineering, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jia Ma
- Institute of Biomedical Engineering, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Li Yang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Xiaoyi Ma
- Beijing Key Laboratory of Cardiac Drug Device Technology and Evidence Based Medicine, Beijing 100021, China
| | - Lifeng Zhou
- Beijing Key Laboratory of Cardiac Drug Device Technology and Evidence Based Medicine, Beijing 100021, China
| | - Fugui He
- Beijing Key Laboratory of Cardiac Drug Device Technology and Evidence Based Medicine, Beijing 100021, China
| | - Michael Miao
- Division of Oral & Craniofacial Health Sciences, University of North Carolina Adams School of Dentistry, Chapel Hill, NC 27599, USA
| | - Xiaoheng Liu
- Institute of Biomedical Engineering, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yunbing Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China.
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Hippe K, Lilley C, William Berkenpas J, Chandana Pocha C, Kishaba K, Ding H, Hou J, Si D, Cao R. ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features. Brief Bioinform 2022; 23:bbab384. [PMID: 34553747 PMCID: PMC8499977 DOI: 10.1093/bib/bbab384] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/02/2021] [Accepted: 08/28/2021] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION The Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. As of CASP14, there are 79 global QA methods, and a minority of 39 residue-level QA methods with very few of them working on protein complexes. Here, we introduce ZoomQA, a novel, single-model method for assessing the accuracy of a tertiary protein structure/complex prediction at residue level, which have many applications such as drug discovery. ZoomQA differs from others by considering the change in chemical and physical features of a fragment structure (a portion of a protein within a radius $r$ of the target amino acid) as the radius of contact increases. Fourteen physical and chemical properties of amino acids are used to build a comprehensive representation of every residue within a protein and grade their placement within the protein as a whole. Moreover, we have shown the potential of ZoomQA to identify problematic regions of the SARS-CoV-2 protein complex. RESULTS We benchmark ZoomQA on CASP14, and it outperforms other state-of-the-art local QA methods and rivals state of the art QA methods in global prediction metrics. Our experiment shows the efficacy of these new features and shows that our method is able to match the performance of other state-of-the-art methods without the use of homology searching against databases or PSSM matrices. AVAILABILITY http://zoomQA.renzhitech.com.
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Affiliation(s)
- Kyle Hippe
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA 98447, USA
| | - Cade Lilley
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA 98447, USA
| | | | | | - Kiyomi Kishaba
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA 98447, USA
| | - Hui Ding
- Center for Informational Biology at University of Electronic Science and Technology of China
| | | | - Dong Si
- University of Washington Bothell, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA 98447, USA
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7
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Yu H, Li ZQ, Ou-Yang YY, Huang GH. Identification of four caspase genes from Spodoptera exigua (Lepidoptera: Noctuidae) and their regulations toward different apoptotic stimulations. Insect Sci 2020; 27:1158-1172. [PMID: 31793737 DOI: 10.1111/1744-7917.12741] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/09/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Apoptosis plays critical roles in multiple biological processes in multicellular organisms. Caspases are known as important participators and regulators of apoptosis. Here, four novel caspase genes of Spodoptera exigua were cloned and characterized, which were designated as SeCasp-1, SeCasp-6, SeCasp-7 and SeCasp-8. Analysis of the putative encoded protein sequences of these SeCasps indicated that SeCasp-1 and SeCasp-7 were possible homologs of executor caspases; SeCasp-8 was a possible homolog of initiator caspases; and SeCasp-6 was a unique caspase of S. exigua that shares low similarity with all the identified insect caspases. Based on baculovirus expression system analyses, SeCasp-1 exhibited similar caspase activity to human caspase-1, -3, -4, -6, -8 and -9; SeCasp-6 presented similar caspase activity to human caspase-2, -3, -4, -6, -8 and -9; SeCasp-7 exhibited similar caspase activity to human caspase-2, -3 and -6; and SeCasp-8 presented similar caspase activity only to human caspase-8. Induction with different chemicals revealed that SeCasp-1 showed extreme upregulation after 24 h in the treated fat body cell line (IOZCAS-Spex-II) of S. exigua. Developmental expression analysis revealed that SeCasp-1 was highly transcribed in the larval stages, while SeCasp-6, SeCasp-7, SeCasp-8 were down-regulated. The in vivo detection of the relative expression levels of SeCasps in S. eixgua larvae inoculated with different pathogens suggested that SeCasp-1 was sensitive to Bacillus thuringiensis infection and that SeCasp-6 was sensitive to baculovirus infection. SeCasp-7 and SeCasp-8 showed slight changes under either in vitro chemical apoptosis induction or in vivo pathogen infection.
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Affiliation(s)
- Huan Yu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zi-Qi Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Yi-Yi Ou-Yang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Guo-Hua Huang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
- College of Plant Protection, Hunan Agricultural University, Changsha, China
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8
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Fu S, Ding M, Wang J, Yin X, Zhou E, Kong L, Tu X, Guo Z, Wang A, Huang Y, Ye J. Identification and functional characterization of three caspases in Takifugu obscurus in response to bacterial infection. Fish Shellfish Immunol 2020; 106:252-262. [PMID: 32735858 DOI: 10.1016/j.fsi.2020.07.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Caspases are evolutionarily conserved proteases, which are inextricably linked with the apoptosis and immune system in mammals. However, the expression pattern and function of some caspases remain largely unknown in pufferfish. In this study, three different pufferfish caspases (caspase-2 (Pfcasp-2), caspase-3 (Pfcasp-3), and caspase-8 (Pfcasp-8)) were characterized, and their expression patterns and functions were determined following Aeromonas hydrophila infection. The open reading frames of Pfcasp-2, -3, and -8 are 1,320, 846, and 1455 bp, respectively. Analyses of sequence alignment and phylogenetic tree showed that casp-2, -3, and -8 share 52%-65%, 33%-40%, 63%-78% overall sequence identities with those of other vertebrates, respectively. 3D structures of Pfcasp-2, -3, and -8 enjoy conservation in core area together, while each owns a distinctive profile. Comparisons of deduced amino acid sequences indicated that Pfcaspases possessed the caspase domain and conserved active sites like 'HG' and 'QACXG' (X for R or G). qRT-PCR results revealed that Pfcasp-2, -3, and -8 were expressed constitutively in a wide range of organs, especially in immune-related organs including whole blood and kidney. In vitro, the expressions of the three caspases (Pfcasp-2, 3, and -8) and immune-related genes (IgM and IL-8) were significantly up-regulated in kidney leukocytes after A. Hydrophila challenge and inhibitors treatment. The expressions of Pfcasp-2 and Pfcasp-3 were successfully inhibited in the kidney leukocytes by Ac-DEVD-CHO (an inhibitor to caspase-3), but the expression of Pfcasp-8 was not affected. Cellular localization analysis showed that the distribution of Pfcasp-2, -3, and -8 was in cytoplasm. Further, overexpression of Pfcasp-2, -3, or -8 was found to cause DNA damage and apoptosis, suggesting that three caspases may be related to apoptosis and mediate different apoptosis pathways in pufferfish. Moreover, the expressions of these caspases were also up-regulated in whole blood and kidney after A. hydrophila challenge, indicating their possible involvement in the immune response against A. hydrophia stimulation. Taken together, the results of this study suggest that the caspase-2,-3, and -8 may play an important role in the apoptosis and immune response in pufferfish.
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Affiliation(s)
- Shengli Fu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China; Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Mingmei Ding
- School of medicine, Sun Yat-Sen University, Guangzhou, 510006, PR China
| | - Junru Wang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiaoxue Yin
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Enxu Zhou
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Linghe Kong
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiao Tu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Zheng Guo
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Anli Wang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Yu Huang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Jianmin Ye
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
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9
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Li J, Dong L, Zhu D, Zhang M, Wang K, Chen F. An effector caspase Sp-caspase first identified in mud crab Scylla paramamosain exhibiting immune response and cell apoptosis. Fish Shellfish Immunol 2020; 103:442-453. [PMID: 32446967 DOI: 10.1016/j.fsi.2020.05.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
Apoptosis plays a key role in the immune defense against pathogen infection, and caspase is one of the most important protease enzyme families, which could initiate and execute apoptosis. Among crustaceans, several caspase genes have been reported. However, caspase in mud crab Scylla paramamosain, have not been identified yet. Here, in the present study, we characterized a new caspase, named as Sp-caspase, from S. paramamosain. The full-length cDNA sequence of Sp-caspase contained 966 bp open reading frame, encoding 322 amino acids, and its molecular weight was 36 kDa. This gene has three conserved domains of the caspase family, a prodomain, a large subunit P20 and a small subunit P10. Phylogenetic analysis showed that Sp-caspase was clustered into an effector caspase group. Sp-caspase mainly distributed in midgut, hepatopancreas, hemocytes and female ovaries, and the transcript was significantly regulated in different tissues after being challenged with Vibrio parahaemolyticus, Vibrio alginolyticus or LPS. After infection with V. alginolyticus, the apoptosis rate of hemocytes notably increased, while the mRNA level of Sp-caspase and hydrolysis activity of caspase 3/7 significantly decreased. Furthermore, in vitro assays showed that the recombinant protein tSp-caspase (deletion of Sp-caspase prodomain) could efficiently recognize and cleave human caspase 3/7 substrate Ac-DEVD-pNA, functioning as an effector caspase. Meanwhile, heterologous expression of Sp-caspase in several cell lines (HEK293T cells, HeLa cells and HighFive cells) could specifically induce cell apoptosis. Taken together, these data demonstrated that Sp-caspase could perform apoptosis as an effector caspase. In addition, it might be a negative regulator of hemocytes apoptosis under pathogen infection, which would contribute to homeostasis and immune defense of hemocytes in S. paramamosain.
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Affiliation(s)
- Jishan Li
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Lixia Dong
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Depeng Zhu
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Min Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Kejian Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, China
| | - Fangyi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, China.
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10
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Hou J, Adhikari B, Tanner JJ, Cheng J. SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering data. Proteins 2020; 88:775-787. [PMID: 31860156 PMCID: PMC7230021 DOI: 10.1002/prot.25865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/18/2019] [Accepted: 12/14/2019] [Indexed: 12/27/2022]
Abstract
Many proteins are composed of several domains that pack together into a complex tertiary structure. Multidomain proteins can be challenging for protein structure modeling, particularly those for which templates can be found for individual domains but not for the entire sequence. In such cases, homology modeling can generate high quality models of the domains but not for the orientations between domains. Small-angle X-ray scattering (SAXS) reports the structural properties of entire proteins and has the potential for guiding homology modeling of multidomain proteins. In this article, we describe a novel multidomain protein assembly modeling method, SAXSDom that integrates experimental knowledge from SAXS with probabilistic Input-Output Hidden Markov model to assemble the structures of individual domains together. Four SAXS-based scoring functions were developed and tested, and the method was evaluated on multidomain proteins from two public datasets. Incorporation of SAXS information improved the accuracy of domain assembly for 40 out of 46 critical assessment of protein structure prediction multidomain protein targets and 45 out of 73 multidomain protein targets from the ab initio domain assembly dataset. The results demonstrate that SAXS data can provide useful information to improve the accuracy of domain-domain assembly. The source code and tool packages are available at https://github.com/jianlin-cheng/SAXSDom.
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Affiliation(s)
- Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, 63103, USA
| | - Badri Adhikari
- Department of Computer Science, University of Missouri-St. Louis, Saint Louis, MO 63121, USA
| | - John J. Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
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11
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Saavedra E, Estévez-Sarmiento F, Said M, Eiroa JL, Rubio S, Quintana J, Estévez F. Cytotoxicity of the Sesquiterpene Lactone Spiciformin and Its Acetyl Derivative against the Human Leukemia Cell Lines U-937 and HL-60. Int J Mol Sci 2020; 21:ijms21082782. [PMID: 32316340 PMCID: PMC7215469 DOI: 10.3390/ijms21082782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 12/03/2022] Open
Abstract
Spiciformin (1) is a sesquiterpene lactone with a germacrane skeleton that is found in two Tanacetum species endemic to the Canary Islands. In this study, the cytotoxicities of 1 and its acetyl derivative (2) were evaluated against human tumor cells. These sesquiterpene lactones were cytotoxic against human acute myeloid leukemia (U-937 and HL-60) cells, even in cells over-expressing the pro-survival protein Bcl-2, but melanoma (SK-MEL-1) and human mononuclear cells isolated from blood of healthy donors were more resistant. Both compounds are apoptotic inducers in human leukemia U-937 cells. Cell death was mediated by the processing and activation of initiator and effector caspases and the cleavage of poly(ADP-ribose) polymerase, and it was blocked by a broad-spectrum caspase inhibitor and (in the case of sesquiterpene lactone 2) by the selective caspase-3/7, -8, and -9 inhibitors. In addition, certainly in the case of compound 2, this was found to be associated with a decrease in mitochondrial membrane potential, downregulation of the anti-apoptotic protein Bcl-2, activation of the mitogen-activated protein kinases signaling pathway, and generation of reactive oxygen species. It will, therefore, be relevant to continue characterization of this class of compounds.
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Affiliation(s)
- Ester Saavedra
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain; (E.S.); (F.E.-S.); (M.S.); (S.R.); (J.Q.)
| | - Francisco Estévez-Sarmiento
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain; (E.S.); (F.E.-S.); (M.S.); (S.R.); (J.Q.)
| | - Mercedes Said
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain; (E.S.); (F.E.-S.); (M.S.); (S.R.); (J.Q.)
| | - José Luis Eiroa
- Departamento de Química, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas de Gran Canaria, Spain;
| | - Sara Rubio
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain; (E.S.); (F.E.-S.); (M.S.); (S.R.); (J.Q.)
| | - José Quintana
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain; (E.S.); (F.E.-S.); (M.S.); (S.R.); (J.Q.)
| | - Francisco Estévez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain; (E.S.); (F.E.-S.); (M.S.); (S.R.); (J.Q.)
- Correspondence: ; Tel.: +34-928-451443
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12
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Ding Y, Wei K, Yang X, Jing F, Shen B, Zhang J. Molecular characterization of three caspases from Bostrychus sinensis and their transcriptional responses to bacteria and viruses. J Fish Dis 2020; 43:431-443. [PMID: 32056240 DOI: 10.1111/jfd.13140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
The caspase family proteins are aspartate-specific cysteine proteases that transmit extracellular signals to cells, ultimately cause apoptosis and therefore play a key role in cellular immunity. In this study, we cloned and characterized three caspases from Chinese black sleeper (Bostrychus sinensis), Bscasp-1, Bscasp-8 and Bscasp-9. Real-time PCR analysis showed that Bscasp-1, Bscasp-8 and Bscasp-9 were universally expressed in all tested tissues of B. sinensis. Expression analyses showed that after poly(I:C) stimulation and bacterial (Vibrio parahaemolyticus) infection, the three caspases were significantly upregulated. After poly(I:C) stimulation, the change of Bscasp-1 expression in the head kidney was the most obvious; peak expression was about 80.78-fold more than that of the control. In addition, the expression of Bscasp-8 and Bscasp-9 in the peripheral blood and liver was 167.99- and 17.98-fold higher than that in the control group, respectively. After V. parahaemolyticus infection, the expression peaks of Bscasp-1 and Bscasp-8 in the peripheral blood and spleen were 85.82-fold and 280.83-fold that of the control. However, the expression of Bscasp-9 in the peripheral blood was upregulated only 8.33-fold higher than that in the control group. These results indicate that Bscasp-1, Bscasp-8 and Bscasp-9 are likely involved in response to viral and bacterial infection.
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Affiliation(s)
- Yuehan Ding
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Ke Wei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Xiao Yang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Fei Jing
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Bin Shen
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Jianshe Zhang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, China
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13
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Anaya-Eugenio GD, Addo EM, Ezzone N, Henkin JM, Ninh TN, Ren Y, Soejarto DD, Kinghorn AD, Carcache de Blanco EJ. Caspase-Dependent Apoptosis in Prostate Cancer Cells and Zebrafish by Corchorusoside C from Streptocaulon juventas. J Nat Prod 2019; 82:1645-1655. [PMID: 31120251 PMCID: PMC6615048 DOI: 10.1021/acs.jnatprod.9b00140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Corchorusoside C (1), isolated from Streptocaulon juventas collected in Vietnam, was found to be nontoxic in a zebrafish ( Danio rerio) model and to induce cytotoxicity in several cancer cell lines with notable selective activity against prostate DU-145 cancer cells (IC50 0.08 μM). Moreover, corchorusoside C induced DU-145 cell shrinkage and cell detachment. In CCD-112CoN colon normal cells, 1 showed significantly reduced cytotoxic activity (IC50 2.3 μM). A preliminary mechanistic study indicated that 1 inhibits activity and protein expression of NF-κB (p50 and p65), IKK (α and β), and ICAM-1 in DU-145 cells. ROS concentrations increased at 5 h post-treatment, and MTP decreased in a dose-dependent manner. Moreover, decreased protein expression of Bcl-2 and increased expression of PARP-1 was observed. Furthermore, corchorusoside C increased both the activity and protein levels of caspases 3 and 7. Additionally, 1 induced sub-G1 population increase of DU-145 cells and modulated caspases in zebrafish with nondifferential morphological effects. Therefore, corchorusoside C (1) induces apoptosis in DU-145 cells and targets the same pathways both in vitro and in vivo in zebrafish. Thus, the use of zebrafish assays seems worthy of wider application than is currently employed for the evaluation of potential anticancer agents of natural origin.
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Affiliation(s)
- Gerardo D. Anaya-Eugenio
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ermias Mekuria Addo
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nathan Ezzone
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Joshua M. Henkin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Tran Ngoc Ninh
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Yulin Ren
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Djaja D. Soejarto
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - A. Douglas Kinghorn
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Esperanza J. Carcache de Blanco
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Corresponding Author Tel (E. J. Carcache de Blanco): +1 (614)-247-7815, Fax: +1 (614)-292-1335.
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14
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Abstract
Effective cancer therapy largely depends on inducing apoptosis in cancer cells via chemotherapy and/or radiation. Monitoring apoptosis in real-time provides invaluable information for evaluating cancer therapy response and screening preclinical anticancer drugs. In this work, we describe the design, synthesis, characterization, and in vitro evaluation of caspase probe 1 (CP1), a bimodal fluorescence-magnetic resonance (FL-MR) probe that exhibits simultaneous FL-MR turn-on response to caspase-3/7. Both caspases exist as inactive zymogens in normal cells but are activated during apoptosis and are unique biomarkers for this process. CP1 has three distinct components: a DOTA-Gd(III) chelate that provides the MR signal enhancement, tetraphenylethylene as the aggregation induced emission luminogen (AIEgen), and DEVD peptide which is a substrate for caspase-3/7. In response to caspase-3/7, the water-soluble peptide DEVD is cleaved and the remaining Gd(III)-AIEgen (Gad-AIE) conjugate aggregates leading to increased FL-MR signals. CP1 exhibited sensitive and selective dual FL-MR turn-on response to caspase-3/7 in vitro and was successfully tested by fluorescence imaging of apoptotic cells. Remarkably, we were able to use the FL response of CP1 to quantify the exact concentrations of inactive and active agents and accurately predict the MR signal in vitro. We have demonstrated that the aggregation-driven FL-MR probe design is a unique method for MR signal quantification. This probe design platform can be adapted for a variety of different imaging targets, opening new and exciting avenues for multimodal molecular imaging.
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Affiliation(s)
- Hao Li
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology , Northwestern University , Evanston , Illinois 60208 , United States
| | - Giacomo Parigi
- Department of Chemistry and Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Claudio Luchinat
- Department of Chemistry and Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Thomas J Meade
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology , Northwestern University , Evanston , Illinois 60208 , United States
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15
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Fortin J, Lam E. Domain swap between two type-II metacaspases defines key elements for their biochemical properties. Plant J 2018; 96:921-936. [PMID: 30176090 DOI: 10.1111/tpj.14079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
Type-II metacaspases are conserved cysteine proteases found in eukaryotes with oxygenic photosynthesis, including green plants and some algae, such as Chlamydomonas and Volvox. Genetic and biochemical studies showed that some members in this protease family could be involved in oxidative stress-induced cell death in higher plants, but their regulatory mechanisms remain unclear. Biochemically, two distinct classes of type-II metacaspases are exemplified by AtMC4 and AtMC9 from Arabidopsis, with AtMC4 activation dependent on calcium under neutral pH, whereas AtMC9 is active only under mildly acidic pH, regardless of the availability of calcium. Here, we constructed all six possible combinations between the p20, linker, and p10 domains from AtMC4 and AtMC9. Our results show that calcium stimulation of AtMC4 activity is associated with essential amino acids located in its p20 domain. In contrast, the acidic pH optimum trait is lost from AtMC9 if one or two of its domains are replaced by that from AtMC4, suggesting that multiple interactions between domains in AtMC9 may be responsible for this property. Consistent with this, we found conserved 'signature' residues in each of the three domains that distinguish AtMC4- and AtMC9-like classes of metacaspases. Tracing the origin of the AtMC9 class, we found evidence for its appearance between lycophytes and gymnosperms, coincident with the evolution of more complex root archetypes in terrestrial plants. Our work suggests that the distinctive properties of the AtMC9-like protease could be associated with special cellular physiology in the roots of gymnosperms and angiosperms that are distinct from lycophytes.
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Affiliation(s)
- Jianqiao Fortin
- Department of Plant Biology, Rutgers,The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers,The State University of New Jersey, New Brunswick, NJ, 08901, USA
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16
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Grinshpon RD, Williford A, Titus‐McQuillan J, Clay Clark A. The CaspBase: a curated database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Protein Sci 2018; 27:1857-1870. [PMID: 30076665 PMCID: PMC6199153 DOI: 10.1002/pro.3494] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/22/2022]
Abstract
Sequence databases are powerful tools for the contemporary scientists' toolkit. However, most functional annotations in public databases are determined computationally and are not verified by a human expert. While hypotheses generated from computational studies are now amenable to experimentation, the quality of the results relies on the quality of input data. We developed the CaspBase to expedite high-quality dataset compilation of annotated caspase sequences, to maximize phylogenetic signal, and to reduce the noise contributed from public databanks. We describe our methods of curation for the CaspBase and how researchers can acquire sequences from CaspBase.org. Our immediate goal for developing the CaspBase was to optimize the ancestral protein reconstruction (APR) of caspases, and we demonstrate the utility of the CaspBase in APR studies. We also developed the Common Position (CP) system for comparing human caspase family paralogs and suggest the CP system as an update to current reporting methods of caspase amino acid positions. We present a standardized multiple sequence alignment (MSA) for the CP system and show the advantage of using large databases such as the CaspBase in defining structural positions in proteins. Although the results described here pertain to caspase evolution and structure-function studies, the methods can be adapted to any gene family.
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Affiliation(s)
- Robert D. Grinshpon
- Department of Molecular and Structural BiochemistryNC State UniversityRaleighNorth Carolina27608
| | - Anna Williford
- Department of BiologyUniversity of Texas at ArlingtonArlingtonTexas76019
| | | | - A. Clay Clark
- Department of BiologyUniversity of Texas at ArlingtonArlingtonTexas76019
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17
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Karami Y, Guyon F, De Vries S, Tufféry P. DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. Sci Rep 2018; 8:13673. [PMID: 30209260 PMCID: PMC6135855 DOI: 10.1038/s41598-018-32079-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/31/2018] [Indexed: 11/08/2022] Open
Abstract
Despite efforts during the past decades, loop modeling remains a difficult part of protein structure modeling. Several approaches have been developed in the framework of crystal structures. However, for homology models, the modeling of loops is still far from being solved. We propose DaReUS-Loop, a data-based approach that identifies loop candidates mining the complete set of experimental structures available in the Protein Data Bank. Candidate filtering relies on local conformation profile-profile comparison, together with physico-chemical scoring. Applied to three different template-based test sets, DaReUS-Loop shows significant increase in the number of high-accuracy loops, and significant enhancement for modeling long loops. A special advantage is that our method proposes a prediction confidence score that correlates well with the expected accuracy of the loops. Strikingly, over 50% of successful loop models are derived from unrelated proteins, indicating that fragments under similar constraints tend to adopt similar structure, beyond mere homology.
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Affiliation(s)
- Yasaman Karami
- Molécules Thérapeutiques in silico, UMR-S973, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot, Sorbonne Paris Cité, RPBS, 75013, Paris, France
| | - Frédéric Guyon
- Molécules Thérapeutiques in silico, UMR-S973, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot, Sorbonne Paris Cité, RPBS, 75013, Paris, France
| | - Sjoerd De Vries
- Molécules Thérapeutiques in silico, UMR-S973, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot, Sorbonne Paris Cité, RPBS, 75013, Paris, France.
| | - Pierre Tufféry
- Molécules Thérapeutiques in silico, UMR-S973, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot, Sorbonne Paris Cité, RPBS, 75013, Paris, France.
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18
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Wang F, Yu Z, Wang W, Li Y, Lu G, Qu C, Wang H, Lu M, Wang L, Song L. A novel caspase-associated recruitment domain (CARD) containing protein (CgCARDCP-1) involved in LPS recognition and NF-κB activation in oyster (Crassostrea gigas). Fish Shellfish Immunol 2018; 79:120-129. [PMID: 29751033 DOI: 10.1016/j.fsi.2018.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Caspase-associated recruitment domain (CARD) containing proteins play critical roles in molecular interaction and regulation of various signaling pathways, such as the activation of caspase and NF-κB singling pathway in the process of apoptosis or inflammation. In the present study, a novel CARD containing protein (designed CgCARDCP-1) was identified and characterized from oyster Crassostrea gigas. Molecular feature analysis revealed that, the open reading frame (ORF) of CgCARDCP-1 gene was 759 bp encoding a polypeptide of 253 amino acids with a conserved N-terminal CARD domain and two transcriptional coactivator p15 (PC4) domains in C-terminus. Homologous alignment showed that the amino acid sequence of CgCARDCP-1 shared 30%-46% identity with that of caspase-2. By RT-PCR detection, the mRNA transcripts of CgCARDCP-1 were found to be widely distributed in various tissues of oyster with the highest expression level in hemocytes and mantle. And CgCARDCP-1 protein was mostly distributed in the cytoplasm of oyster hemocytes as shown by immunohistochemistry. Moreover, the CgCARDCP-1 mRNA expression level in hemocytes was significantly up-regulated after lipopolysaccharide (LPS) and Vibrio splendidus stimulations. The recombinant CgCARDCP-1 displayed strong binding activity with LPS in vitro. In addition, after transfected into the HEK-293T cell with luciferase reporter system, CgCARDCP-1 could significantly promote the NF-κB activation (1.29-fold, p < 0.05) compared to that in the control group. These results collectively demonstrated that the CgCARDCP-1 might serve as a recognition molecule for LPS and a regulator of NF-κB activation in the immune response of oyster.
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Affiliation(s)
- Feifei Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Zichao Yu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Yiqun Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Guangxia Lu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Chen Qu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Hui Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Mengmeng Lu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Disease Prevention and Control for Aquaculture Animals, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
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19
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Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep 2018; 8:9939. [PMID: 29967418 PMCID: PMC6028396 DOI: 10.1038/s41598-018-26812-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/17/2018] [Indexed: 01/14/2023] Open
Abstract
Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.
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Affiliation(s)
- Chen Keasar
- Department of Computer Science, Ben Gurion University of the Negev, Be'er sheva, Israel
| | - Liam J McGuffin
- Biomedical Sciences Division, School of Biological Sciences, University of Reading, Reading, RG6 6AS, UK
| | - Björn Wallner
- Division of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden
| | - Gaurav Chopra
- Department of Chemistry, College of Science, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Badri Adhikari
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Debswapna Bhattacharya
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Lauren Blake
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Leandro Oliveira Bortot
- Laboratory of Biological Physics, Faculty of Pharmaceutical Sciences at Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Renzhi Cao
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - B K Dhanasekaran
- Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India
| | - Itzhel Dimas
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Eshel Faraggi
- Research and Information Systems, LLC, Carmel, IN, USA
- Department of Biochemistry and Molecular Biology, IU School of Medicine, Indianapolis, IN, USA
- Batelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Sambit Ghosh
- Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India
| | - Soma Ghosh
- Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Lukasz Golon
- Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Yi He
- School of Engineering, University of California, Merced, CA, USA
| | - Lim Heo
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Main Khan
- Department of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA
| | - Firas Khatib
- Department of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA
| | - George A Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Chris Kieslich
- Texas A&M Energy Institute, Texas A&M University, College Station, TX, USA
| | - David E Kim
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Pawel Krupa
- Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Gyu Rie Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hongbo Li
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- School of Computer Science and Information Technology, NorthEast Normal University, Changchun, China
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jilong Li
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Ali Hassan A Maghrabi
- Biomedical Sciences Division, School of Biological Sciences, University of Reading, Reading, RG6 6AS, UK
| | - Milot Mirdita
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Shokoufeh Mirzaei
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California State Polytechnic University, Pomona, CA, USA
| | | | - Melis Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Anand Shah
- Department of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA
| | - Utkarsh Shah
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Tomer Sidi
- Department of Computer Science, Ben Gurion University of the Negev, Be'er sheva, Israel
| | | | | | - Rafal Ślusarz
- Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Phanourios Tamamis
- Texas A&M Energy Institute, Texas A&M University, College Station, TX, USA
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Nicholas Trieber
- Department of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA
| | - Tomasz Wirecki
- Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Yanping Yin
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jaume Bacardit
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing, Newcastle University, Newcastle-upon-Tyne, UK
| | - Maciej Baranowski
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Nicholas Chapman
- Center for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Seth Cooper
- College of Computer and Information Science, Northeastern University, Boston, MA, USA
| | - Alexandre Defelicibus
- Institute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil
| | - Jeff Flatten
- Center for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Brian Koepnick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Zoran Popović
- Center for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | | | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Center for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | | | | | | | - Stanislaw Ołdziej
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Michael Levitt
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Harold Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Johannes Söding
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Saraswathi Vishveshwara
- Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Silvia N Crivelli
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Computer Science, University of California, Davis, CA, USA.
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20
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Abstract
First discovered for their role in mediating programmed cell death and inflammatory responses, caspases have now emerged as crucial regulators of other cellular and physiological processes including cell proliferation, differentiation, migration, and survival. In the developing nervous system, for instance, the non-apoptotic functions of caspases have been shown to play critical roles in the formation of neuronal circuits by regulating axon outgrowth, guidance and pruning. How caspase activity is spatially and temporally maintained at sub-lethal levels within cells remains however poorly understood, especially in vivo. Thanks to its transparency and accessibility, the zebrafish offers the unique ability to directly visualize caspase activation in vivo. Yet, detailed information about the caspase family in zebrafish is lacking. Here, we report the identification and characterization of 19 different caspase genes in zebrafish, and show that caspases have diverse expression profiles from cleavage to larval stages, suggesting highly specialized and/or redundant functions during embryonic development.
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Affiliation(s)
- Olivia Spead
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Tine Verreet
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Cory J. Donelson
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Fabienne E. Poulain
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
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21
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Lema Asqui S, Vercammen D, Serrano I, Valls M, Rivas S, Van Breusegem F, Conlon FL, Dangl JL, Coll NS. AtSERPIN1 is an inhibitor of the metacaspase AtMC1-mediated cell death and autocatalytic processing in planta. New Phytol 2018; 218:1156-1166. [PMID: 28157265 DOI: 10.1111/nph.14446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 12/16/2016] [Indexed: 05/10/2023]
Abstract
The hypersensitive response (HR) is a localized programmed cell death phenomenon that occurs in response to pathogen recognition at the site of attempted invasion. Despite more than a century of research on HR, little is known about how it is so tightly regulated and how it can be contained spatially to a few cells. AtMC1 is an Arabidopsis thaliana plant metacaspase that positively regulates the HR. Here, we used an unbiased approach to identify new AtMC1 regulators. Immunoaffinity purification of AtMC1-containing complexes led us to the identification of the protease inhibitor AtSerpin1. Our data clearly showed that coimmunoprecipitation between AtMC1 and AtSerpin1 and formation of a complex between them was lost upon mutation of the AtMC1 catalytic site, and that the AtMC1 prodomain was not required for the interaction. AtSerpin1 blocked AtMC1 self-processing and inhibited AtMC1-mediated cell death. Our results constitute an in vivo example of a Serpin acting as a suicide inhibitor in plants, reminiscent of the activity of animal or viral serpins on immune/cell death regulators, including caspase-1. These results indicate a conserved function of a protease inhibitor on cell death regulators from different kingdoms with unrelated modes of action (i.e. caspases vs metacaspases).
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Affiliation(s)
- Saul Lema Asqui
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Dominique Vercammen
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
| | - Irene Serrano
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Marc Valls
- Department of Genetics, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, Catalonia, 08193, Spain
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Department of Medical Protein Research, VIB, Ghent, 9000, Belgium
- Department of Biochemistry, Ghent University, Ghent, 9000, Belgium
| | - Frank L Conlon
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
| | - Núria S Coll
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
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22
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Heo L, Feig M. PREFMD: a web server for protein structure refinement via molecular dynamics simulations. Bioinformatics 2018; 34:1063-1065. [PMID: 29126101 PMCID: PMC5860225 DOI: 10.1093/bioinformatics/btx726] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/04/2017] [Accepted: 11/07/2017] [Indexed: 11/13/2022] Open
Abstract
Summary Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. Availability and implementation PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. Contact feig@msu.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lim Heo
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Michael Feig
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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23
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Vakamullu S, Arepalli SK, Velatooru LR, J VR, P KK, B N. In vitro apoptotic mechanism of a novel synthetic Quinazolinyl derivative: Induces caspase-dependent intrinsic pathway on THP-1, leukemia cell line. Chem Biol Interact 2017; 280:117-127. [PMID: 29225136 DOI: 10.1016/j.cbi.2017.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/04/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Several quinazoline derivatives have been found to possess a broad spectrum of biological activities. Previously our research group has synthesized and studied the anti-proliferative effects of N-Decyl-N-(2-Methyl-4-Quinazolinyl) Amine (DMQA). The current study evaluated the cytotoxic and apoptotic properties of DMQA in THP-1 cells. The cytotoxic potential of DMQA was assessed using MTT assay on a panel of cancer cell lines which include HeLa, Mia PaCa-2, A 375, B16-F10, A 549,A 431, U937, THP-1, HL-60 and peripheral blood mononuclear cells (PBMC's). Preliminary data revealed that the highest cytotoxic activity was against THP-1 leukemia cell line (IC50=0.66 μg/ml). The apoptotic properties of DMQA on THP-1 cells were characterized by change in nuclear morphology, DNA fragmentation, reduction of pro-caspases-3, 9, Bax/Bcl-2 levels, cleavage of poly (ADP-ribose) polymerase and cytosolic release of cytochrome c. Further investigation revealed a sub-G1 peak, phosphatidyl serine exposure and loss of mitochondrial membrane potential (MMP) in THP-1 cells. The role of caspases was crucial and was demonstrated by the inhibitors Z-VAD-FMK and Z-DEVD-FMK. Moreover DMQA was markedly less effective in inhibiting the growth of normal cells (PBMC's, IC50 =62.17 μg/ml). Based on the results we suggest that DMQA induced apoptosis via intrinsic pathway and could be a promising anticancer agent.
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Affiliation(s)
- Sridhar Vakamullu
- Toxicology Unit, Biology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 607, India; MNR Foundation for Research and Innovation, MNR Medical College, Sangareddy, Telangana, 502294, India
| | - S K Arepalli
- Toxicology Unit, Biology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 607, India
| | - L R Velatooru
- Toxicology Unit, Biology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 607, India
| | - Venkateswara Rao J
- Toxicology Unit, Biology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 607, India.
| | - Kavin Kennedy P
- Flow-cytometry Facility, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500 607, India
| | - Narsaiah B
- Fluoro Organic Division, CSIR- Indian Institute of Chemical Technology, Hyderabad, 500 607, India
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24
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Meininger I, Krappmann D. Lymphocyte signaling and activation by the CARMA1-BCL10-MALT1 signalosome. Biol Chem 2017; 397:1315-1333. [PMID: 27420898 DOI: 10.1515/hsz-2016-0216] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/10/2016] [Indexed: 12/16/2022]
Abstract
The CARMA1-BCL10-MALT1 (CBM) signalosome triggers canonical NF-κB signaling and lymphocyte activation upon antigen-receptor stimulation. Genetic studies in mice and the analysis of human immune pathologies unveiled a critical role of the CBM complex in adaptive immune responses. Great progress has been made in elucidating the fundamental mechanisms that dictate CBM assembly and disassembly. By bridging proximal antigen-receptor signaling to downstream signaling pathways, the CBM complex exerts a crucial scaffolding function. Moreover, the MALT1 subunit confers a unique proteolytic activity that is key for lymphocyte activation. Deregulated 'chronic' CBM signaling drives constitutive NF-κB signaling and MALT1 activation, which contribute to the development of autoimmune and inflammatory diseases as well as lymphomagenesis. Thus, the processes that govern CBM activation and function are promising targets for the treatment of immune disorders. Here, we summarize the current knowledge on the functions and mechanisms of CBM signaling in lymphocytes and how CBM deregulations contribute to aberrant signaling in malignant lymphomas.
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25
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Ren X, Yu X, Gao B, Liu P, Li J. Characterization of three caspases and their pathogen-induced expression pattern in Portunus trituberculatus. Fish Shellfish Immunol 2017; 66:189-197. [PMID: 28478258 DOI: 10.1016/j.fsi.2017.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/21/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Caspases are a family of proteases involved in many important biological processes including apoptosis and inflammation. In this study, we analyzed the expression patterns and effects on immune response in various tissues of the edible crab Portunus trituberculatus. PtCas 2, PtCas 3 and PtCas 4 share overall sequence identities of 55.88%-74.86%, 8.47%-46.54% and 20.11%-50.87%, respectively, with their other crustacean species. PtCas 2, PtCas 3 and PtCas 4 have the same caspase domain and catalytic site found in known caspases. The expression levels of the three caspases differed between tissues. Following bacterial and viral infection, the expression levels of the three caspases reached a maximum level at 24 h post-infection (hpi) in case of bacteria, whereas it was 48 hpi in virus. Moreover, the WSSV, Vibrio alginolyticus or V. parahaemolyticus induced the activities of PtCas 2-4 in a time-dependent manner. These results indicate an involvement of caspases in bacterial and viral induced immune response and demonstrate for the first time that PtCas 2, PtCas 3 and PtCas 4 are essential for optimal response to bacterial and virus infection in crabs.
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Affiliation(s)
- Xianyun Ren
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Xuan Yu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Baoquan Gao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Ping Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China.
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26
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da Silva DC, Andrade PB, Valentão P, Pereira DM. Neurotoxicity of the steroidal alkaloids tomatine and tomatidine is RIP1 kinase- and caspase-independent and involves the eIF2α branch of the endoplasmic reticulum. J Steroid Biochem Mol Biol 2017; 171:178-186. [PMID: 28300624 DOI: 10.1016/j.jsbmb.2017.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/18/2017] [Accepted: 03/09/2017] [Indexed: 12/29/2022]
Abstract
Steroidal alkaloids are a class of natural products that occur in several species of the Solanaceae family. In the case of the tomato plant (Lycopersicon esculentum Mill.), tomatine and its aglycone, tomatidine, are the most representative molecules. These steroidal alkaloids have already shown several potentially useful biological activities, from anticancer to anti-inflammatory or antibacterial. In this work, the toxicity of these molecules in neuronal cells, namely in the neuroblastoma cell line SH-SY5Y, was assessed, emphasis being given to the cellular mechanisms underlying the effects observed. The results show that tomatine/tomatidine-induced cell death is caspase- and RIP1 kinase-independent, as cell death is not prevented by the pan-caspase inhibitor Z-VAD.fmk or by RIP1 inhibitor necrostatin-1. Analysis of Ca2+ levels using the fluorescent probe Fura-2/AM indicates that both tomatine and tomatidine have a marked effect upon Ca2+ homeostasis by increasing cytosolic Ca2+, an event that might be associated with their effect upon the endoplasmic reticulum. We show that the toxicity of these molecules require the PERK/eIF2α branch of the unfolded protein response, but not the IRE1α branch. Given the role of the endoplasmic reticulum in proteostasis, the ability of these molecules to inhibit the proteasome was also evaluated. Tomatine was able to inhibit the chymotrypsin-like catalytic core of purified human 20S proteasome, as shown by its ability to prevent degradation of the fluorogenic substrate Suc-Leu-Leu-Val-Tyr-AMC, thus suggesting that interference with proteostasis can be responsible for the toxicity of these steroidal alkaloids. This study is relevant as it sheds a light regarding the toxicity of molecules present in one of the most consumed plants worldwide.
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Affiliation(s)
- Daniela Correia da Silva
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, N° 228, 4050-213 Porto, Portugal
| | - Paula B Andrade
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, N° 228, 4050-213 Porto, Portugal
| | - Patrícia Valentão
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, N° 228, 4050-213 Porto, Portugal
| | - David M Pereira
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, N° 228, 4050-213 Porto, Portugal.
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Stephan M, Edelmann B, Winoto-Morbach S, Janssen O, Bertsch U, Perrotta C, Schütze S, Fritsch J. Role of caspases in CD95-induced biphasic activation of acid sphingomyelinase. Oncotarget 2017; 8:20067-20085. [PMID: 28223543 PMCID: PMC5386744 DOI: 10.18632/oncotarget.15379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/24/2017] [Indexed: 12/04/2022] Open
Abstract
Acid sphingomyelinase (A-SMase) plays an important role in the initiation of CD95 signaling by forming ceramide-enriched membrane domains that enable clustering and activation of the death receptors. In TNF-R1 and TRAIL-R1/R2 signaling, A-SMase also contributes to the lysosomal apoptosis pathway triggered by receptor internalization. Here, we investigated the molecular mechanism of CD95-mediated A-SMase activation, demonstrating that A-SMase is located in internalized CD95-receptosomes and is activated by the CD95/CD95L complex in a biphasic manner.Since several caspases have been described to be involved in the activation of A-SMase, we evaluated expression levels of caspase-8, caspase-7 and caspase-3 in CD95-receptosomes. The occurrence of cleaved caspase-8 correlated with the first peak of A-SMase activity and translocation of the A-SMase to the cell surface which could be blocked by the caspase-8 inhibitor IETD.Inhibition of CD95-internalization selectively reduced the second phase of A-SMase activity, suggesting a fusion between internalized CD95-receptosomes and an intracellular vesicular pool of A-SMase. Further analysis demonstrated that caspase-7 activity correlates with the second phase of the A-SMase activity, whereas active caspase-3 is present at early and late internalization time points. Blocking caspases-7/ -3 by DEVD reduced the second phase of A-SMase activation in CD95-receptosomes suggesting the potential role of caspase-7 or -3 for late A-SMase activation.In summary, we describe a biphasic A-SMase activation in CD95-receptosomes indicating (I.) a caspase-8 dependent translocation of A-SMase to plasma membrane and (II.) a caspase-7 and/or -3 dependent fusion of internalized CD95-receptosomes with intracellular A-SMase-containing vesicles.
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Affiliation(s)
- Mario Stephan
- Institute of Immunology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Bärbel Edelmann
- Department of Hematology and Oncology, University Hospital Magdeburg, Magdeburg, Germany
| | | | - Ottmar Janssen
- Institute of Immunology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Uwe Bertsch
- Institute of Immunology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Cristiana Perrotta
- Department of Biomedical and Clinical Sciences “Luigi Sacco” (DIBIC), Università degli Studi di Milano, Milano, Italy
| | - Stefan Schütze
- Institute of Immunology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jürgen Fritsch
- Institute of Immunology, Christian-Albrechts-University of Kiel, Kiel, Germany
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Smith CE, Soti S, Jones TA, Nakagawa A, Xue D, Yin H. Non-steroidal Anti-inflammatory Drugs Are Caspase Inhibitors. Cell Chem Biol 2017; 24:281-292. [PMID: 28238723 PMCID: PMC5357154 DOI: 10.1016/j.chembiol.2017.02.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/07/2017] [Accepted: 01/31/2017] [Indexed: 01/07/2023]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are among the most commonly used drugs in the world. While the role of NSAIDs as cyclooxygenase (COX) inhibitors is well established, other targets may contribute to anti-inflammation. Here we report caspases as a new pharmacological target for NSAID family drugs such as ibuprofen, naproxen, and ketorolac at physiologic concentrations both in vitro and in vivo. We characterize caspase activity in both in vitro and in cell culture, and combine computational modeling and biophysical analysis to determine the mechanism of action. We observe that inhibition of caspase catalysis reduces cell death and the generation of pro-inflammatory cytokines. Further, NSAID inhibition of caspases is COX independent, representing a new anti-inflammatory mechanism. This finding expands upon existing NSAID anti-inflammatory behaviors, with implications for patient safety and next-generation drug design.
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Affiliation(s)
- Christina E Smith
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Subada Soti
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Torey A Jones
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Akihisa Nakagawa
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Ding Xue
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA.
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29
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Narayanan S, Sanpui P, Sahoo L, Ghosh SS. Heterologous expression and functional characterization of phytaspase, a caspase-like plant protease. Int J Biol Macromol 2017; 95:288-293. [PMID: 27867055 DOI: 10.1016/j.ijbiomac.2016.11.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/16/2016] [Accepted: 11/16/2016] [Indexed: 01/24/2023]
Abstract
Following the cloning and expression of tobacco (Nicotiana tabacum) phytaspase gene in Escherichia coli BL21, the recombinant protease was purified by affinity chromatography for further characterization. Circular dichroism (CD) spectroscopy and in silico analysis revealed structural similarities of recombinant phytaspase with other plant serine-proteases. Molecular docking studies showed favourable binding of synthetic peptide substrate for caspase 8 (Ac-VETD-AMC) to the reactive pocket of recombinant phytaspase indicating its potential in assessing functional activity of recombinant phytaspase. In silico findings were supported by caspase 8-like activity of purified phytaspase demonstrated in vitro. The Michaelis constant (KM) and specificity constant (kcat/KM) of phytaspase for hydrolyzing Ac-VETD-AMC were found to be 1.587μM and 4.67×103M-1min-1, respectively. Transient expression of phytaspase in lung epithelial adenocarcinoma cells (A549) resulted in reduced IC50 value of doxorubicin. This is the first report of functional expression of mature phytaspase in bacterial system as well as its transfection to sensitize A549 cells at lower doxorubicin concentration.
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Affiliation(s)
- Sharmila Narayanan
- Department of Biosciences & Bioengineering, Indian Institute of Technology Guwahati, Guwahati-39, Assam, India
| | - Pallab Sanpui
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati-39, Assam, India
| | - Lingaraj Sahoo
- Department of Biosciences & Bioengineering, Indian Institute of Technology Guwahati, Guwahati-39, Assam, India
| | - Siddhartha Sankar Ghosh
- Department of Biosciences & Bioengineering, Indian Institute of Technology Guwahati, Guwahati-39, Assam, India; Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati-39, Assam, India.
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30
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Darzynkiewicz Z, Zhao H, Dorota Halicka H, Pozarowski P, Lee B. Fluorochrome-Labeled Inhibitors of Caspases: Expedient In Vitro and In Vivo Markers of Apoptotic Cells for Rapid Cytometric Analysis. Methods Mol Biol 2017; 1644:61-73. [PMID: 28710753 DOI: 10.1007/978-1-4939-7187-9_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Activation of caspases is a characteristic event of apoptosis. Various cytometric methods distinguishing this event have been developed to serve as specific apoptotic markers for the assessment of apoptotic frequency within different cell populations. The method described in this chapter utilizes fluorochrome labeled inhibitors of caspases (FLICA) and is applicable to fluorescence microscopy, flow- and imaging-cytometry as well as to confocal imaging. Cell-permeant FLICA reagents tagged with carboxyfluorescein or sulforhodamine, when applied to live cells in vitro or in vivo, exclusively label the cells that are undergoing apoptosis. The FLICA labeling methodology is rapid, simple, robust, and can be combined with other markers of cell death for multiplexed analysis. Examples are presented on FLICA use in combination with a vital stain (propidium iodide), detection of the loss of mitochondrial electrochemical potential, and exposure of phosphatidylserine on the outer surface of plasma cell membrane using Annexin V fluorochrome conjugates. FLICA staining followed by cell fixation and stoichiometric staining of cellular DNA demonstrate that FLICA binding can be correlated with the concurrent analysis of DNA ploidy, cell cycle phase, DNA fragmentation, and other apoptotic events whose detection requires cell permeabilization. The "time window" for the detection of apoptosis with FLICA is wider compared to the Annexin V binding, making FLICA a preferable marker for the detection of early phase apoptosis and therefore more accurate for quantification of apoptotic cells. Unlike many other biomarkers of apoptotic cells, FLICAs can be used to detect apoptosis ex vivo and in vivo in different tissues.
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Affiliation(s)
- Zbigniew Darzynkiewicz
- Department of Pathology and Brander Cancer Research Institute, New York Medical College, Basic Sciences Building, 15 Dana Road, Valhalla, N.Y, 10595, USA.
| | - Hong Zhao
- Department of Pathology and Brander Cancer Research Institute, New York Medical College, Basic Sciences Building, 15 Dana Road, Valhalla, N.Y, 10595, USA
| | - H Dorota Halicka
- Department of Pathology and Brander Cancer Research Institute, New York Medical College, Basic Sciences Building, 15 Dana Road, Valhalla, N.Y, 10595, USA
| | | | - Brian Lee
- Immunochemistry Technologies, Bloomington, MN, 55431, USA
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31
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Kent CR, Bryja M, Gustafson HA, Kawarski MY, Lenti G, Pierce EN, Knopp RC, Ceja V, Pati B, Walters DE, Karver CE. Variation of the aryl substituent on the piperazine ring within the 4-(piperazin-1-yl)-2,6-di(pyrrolidin-1-yl)pyrimidine scaffold unveils potent, non-competitive inhibitors of the inflammatory caspases. Bioorg Med Chem Lett 2016; 26:5476-5480. [PMID: 27777011 DOI: 10.1016/j.bmcl.2016.10.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/10/2016] [Indexed: 11/19/2022]
Abstract
The inflammatory caspases (caspase-1, -4 and -5) are potential therapeutic targets for autoimmune and inflammatory diseases due to their involvement in the immune response upon inflammasome formation. A series of small molecules based on the 4-(piperazin-1-yl)-2,6-di(pyrrolidin-1-yl)pyrimidine scaffold were synthesized with varying substituents on the piperazine ring. Several compounds were pan-selective inhibitors of the inflammatory caspases, caspase-1, -4 and -5, with the ethylbenzene derivative CK-1-41 displaying low nanomolar Ki values across this family of caspases. Three analogs were nearly 10 fold selective for caspase-5 over caspase-1 and -4. The compounds display non-competitive, time dependent inhibition profiles. To our knowledge, this series is the first example of small molecule inhibitors of all three inflammatory caspases.
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Affiliation(s)
- Courtney R Kent
- Department of Chemistry, DePaul University, 1110 W Belden Ave, Chicago, IL 60614, United States
| | - Magdalena Bryja
- Department of Chemistry, DePaul University, 1110 W Belden Ave, Chicago, IL 60614, United States
| | - Helen A Gustafson
- Department of Chemistry, DePaul University, 1110 W Belden Ave, Chicago, IL 60614, United States
| | - Margaret Y Kawarski
- Department of Chemistry, DePaul University, 1110 W Belden Ave, Chicago, IL 60614, United States
| | - Gena Lenti
- Department of Chemistry, DePaul University, 1110 W Belden Ave, Chicago, IL 60614, United States
| | - Emily N Pierce
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612, United States
| | - Rachel C Knopp
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612, United States
| | - Victor Ceja
- Department of Pharmaceutical Sciences, College of Pharmacy, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Rd, North Chicago, IL 60064, United States
| | - Bhabna Pati
- Department of Pharmaceutical Sciences, College of Pharmacy, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Rd, North Chicago, IL 60064, United States
| | - D Eric Walters
- Department of Pharmaceutical Sciences, College of Pharmacy, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Rd, North Chicago, IL 60064, United States
| | - Caitlin E Karver
- Department of Chemistry, DePaul University, 1110 W Belden Ave, Chicago, IL 60614, United States.
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32
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Chen RT, Jiao P, Lu Y, Xin HH, Zhang DP, Wang MX, Liang S, Miao YG. BMDREDD REGULATES THE APOPTOSIS COORDINATING WITH BMDAXX, BMCIDE-B, BMFADD, AND BMCREB IN BMN CELLS. Arch Insect Biochem Physiol 2016; 93:160-173. [PMID: 27558456 DOI: 10.1002/arch.21349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The apoptosis mechanisms in mammals were investigated relatively clearly. However, little is known about how apoptosis is achieved at a molecular level in silkworm cells. We cloned a caspase homologous gene named BmDredd (where Bm is Bombyx mori and Dredd is death-related ced-3/Nedd2-like caspase) in BmN cells from the ovary of Bm and analyzed its biological information. We constructed the N-terminal, C-terminal, and overexpression vector of BmDredd, respectively. Our results showed that the transcriptional expression level of BmDredd was increased in the apoptotic BmN cells. Furthermore, overexpression of BmDredd increased the caspase-3/7 activity. Simultaneously, RNAi of BmDredd could save BmN cells from apoptosis. The immunofluorescence study showed that BmDredd located at the cytoplasm in normal cell otherwise is found at the nucleus when cells undergo apoptosis. Moreover, we quantified the transcriptional expressions of apoptosis-related genes including BmDredd, BmDaxx (where Daxx is death-domain associated protein), BmCide-b (where Cide-b is cell death inducing DFF45-like effector), BmFadd (Fadd is fas-associated via death domain), and BmCreb (where Creb is cAMP-response element binding protein) in BmN cells with dsRNA interferences to detect the molecular mechanism of apoptosis. In conclusion, BmDredd may function for promoting apoptosis and there are various regulatory interactions among these apoptosis-related genes.
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Affiliation(s)
- Rui-Ting Chen
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Peng Jiao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Yan Lu
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Hu-Hu Xin
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Deng-Pan Zhang
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Mei-Xian Wang
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Shuang Liang
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Yun-Gen Miao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China.
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33
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Long H, Sun L. Molecular characterization reveals involvement of four caspases in the antibacterial immunity of tongue sole (Cynoglossus semilaevis). Fish Shellfish Immunol 2016; 57:340-349. [PMID: 27566101 DOI: 10.1016/j.fsi.2016.08.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Caspases are a family of proteases involved in many important biological processes including apoptosis and inflammation. In this study, we analyzed in a comparative manner the expression patterns and immune effects of four different types of caspases, i.e. caspase-1 (CsCas1), caspase-2 (CsCas2), caspase-3 (CsCas3), and caspase-9 (CsCas9), from the teleost fish tongue sole (Cynoglossus semilaevis). CsCas1, CsCas2, CsCas3, and CsCas9 share 35.4%-58.5%, 61.2%-75.3%, 52.3%-65.6%, and 63.0%-76.2% overall sequence identities, respectively, with their counterparts in teleost species. CsCas1, CsCas2, CsCas3, and CsCas9 possess the caspase domain and catalytic site conserved in known caspases. The expressions of the four caspases were detected in a wide range of tissues, however, the expression levels varied between different tissues and caspases. Following bacterial infection, the expressions of the four caspases were upregulated or downregulated to significant extents in a time- and tissue-dependent manner. In vivo analysis showed that overexpression of each of the caspases in tongue sole significantly enhanced the ability of the fish to resist bacterial dissemination in and colonization of tissues. These results indicate an involvement of fish caspases in bacteria-induced immune response and demonstrate for the first time that caspase-1, 2, 3, and 9 are essential to the optimal defense against bacterial infection in fish.
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Affiliation(s)
- Hao Long
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Liu H, Deng Z, Chen J, Wang S, Hao L, Li D. Genome-wide identification and expression analysis of the metacaspase gene family in Hevea brasiliensis. Plant Physiol Biochem 2016; 105:90-101. [PMID: 27085600 DOI: 10.1016/j.plaphy.2016.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/05/2016] [Accepted: 04/05/2016] [Indexed: 05/13/2023]
Abstract
Metacaspases, a family of cysteine proteases, have been suggested to play important roles in programmed cell death (PCD) during plant development and stress responses. To date, no systematic characterization of this gene family has been reported in rubber tree (Hevea brasiliensis). In the present study, nine metacaspase genes, designated as HbMC1 to HbMC9, were identified from whole-genome sequence of rubber tree. Multiple sequence alignment and phylogenetic analyses suggested that these genes were divided into two types: type I (HbMC1-HBMC7) and type II (HbMC8 and HbMC9). Gene structure analysis demonstrated that type I and type II HbMCs separately contained four and two introns, indicating the conserved exon-intron organization of HbMCs. Quantitative real-time PCR analysis revealed that HbMCs showed distinct expression patterns in different tissues, suggesting the functional diversity of HbMCs in various tissues during development. Most of the HbMCs were regulated by drought, cold, and salt stress, implying their possible functions in regulating abiotic stress-induced cell death. Of the nine HbMCs, HbMC1, HbMC2, HbMC5, and HbMC8 displayed a significantly higher relative transcript accumulation in barks of tapping panel dryness (TPD) trees compared with healthy trees. In addition, the four genes were up-regulated by ethephon (ET) and methyl jasmonate (MeJA), indicating their potential involvement in TPD resulting from ET- or JA-induced PCD. In summary, this work provides valuable information for further functional characterization of HbMC genes in rubber tree.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China.
| | - Zhi Deng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China.
| | - Jiangshu Chen
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Sen Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Lili Hao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dejun Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China.
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Shao Y, Li C, Zhang W, Duan X, Li Y, Jin C, Xiong J, Qiu Q. Molecular cloning and characterization of four caspases members in Apostichopus japonicus. Fish Shellfish Immunol 2016; 55:203-211. [PMID: 27245866 DOI: 10.1016/j.fsi.2016.05.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 06/05/2023]
Abstract
The caspase family representing aspartate-specific cysteine proteases have been demonstrated to possess key roles in apoptosis and immune response. We previously demonstrated that LPS challenged Apostichopus japonicus coelomocyte could significantly induced apoptosis in vitro. However, apoptosis related molecules were scarcely investigated in this economic species. In the present work, we cloned and characterized four members caspase family from A. japonicus (designated as Ajcaspase-2, Ajcaspase-3, Ajcaspase-6, and Ajcaspase-8, respectively) by RACE. Multiple sequence alignment and structural analysis revealed that all Ajcaspases contained the conservative CASC domain at C terminal, in which some unique features for each Ajcaspase made them different from each other. These specific domains together with phylogenetic analysis supported that all these four identified proteins belonged to novel members of apoptotic signaling pathway in sea cucumber. Tissue distribution analysis revealed that four Ajcaspase genes were constitutively expressed in all examined tissues. The expression of Ajcaspase-2 was tightly correlated with that of Ajcaspase-8 in each detected tissues. Ajcaspase-3 and Ajcaspase-6 transcripts were both highly expressed in immune tissue of coelomocytes. Furthermore, the Vibrio splendidus challenged sea cucumber coelomocytes could significantly up-regulate the mRNA expressions of four genes. The expression levels of Ajcaspase-2 and Ajcaspase-8 were relative earlier than those of Ajcaspase-6 and Ajcaspase-3, respectively, which could be inferred that Ajcapase-2 might directly modulate Ajcaspase-6, and Ajcaspase-8 initiate the expression of Ajcaspase-3. The induce expressions differed among each Ajcaspase depending upon their roles such as initiator or effector caspase. All our results demonstrated that four Ajcaspases present diversified functions in apoptotic cascade signaling pathway of sea cucumber under immune response.
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Affiliation(s)
- Yina Shao
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Xuemei Duan
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Ye Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chunhua Jin
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
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36
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Li Z, Wang C, Jiang F, Huan P, Liu B. Characterization and expression of a novel caspase gene: Evidence of the expansion of caspases in Crassostrea gigas. Comp Biochem Physiol B Biochem Mol Biol 2016; 201:37-45. [PMID: 27393814 DOI: 10.1016/j.cbpb.2016.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 07/04/2016] [Accepted: 07/04/2016] [Indexed: 11/18/2022]
Abstract
Caspases are a group of cysteine-aspartate proteases involved in apoptosis and a variety of non-apoptotic processes. In this study, a novel caspase gene was cloned and its potential role in apoptosis was investigated. The caspase gene (CgCasp 3/7) has an open reading frame of 1626bp encoding 541 amino acids containing the conserved functional domains and motifs of effector caspases. Its amino acid sequence shows low identity with the other effector caspases of Crassostrea gigas and contains a unique long intersubunit linker (IL). The CgCasp 3/7 mRNA was expressed highly in oocytes and then decreased gradually after fertilization, indicating CgCasp 3/7 could function in oocyte apoptosis. In adult tissues, it is located primarily in the gills and hepatopancreas. We examined the mRNA expression of CgCasp 3/7 in gills of oysters immersed in ambient (17°C) or heated (27°C) seawater. The thermal stress stimulated mRNA expression of CgCasp 3/7 by 2.5- and 4.1-fold at 2h and 6h post-treatment, respectively, indicating CgCasp3/7 was involved in the early response to thermal stress. To examine the function of the IL, CgCasp 3/7 and CgCasp 3/7-T (with a truncated IL) were expressed using an in vitro translation system and their DEVDase activity was measured. Both proteins showed a significantly higher level of DEVDase activity than control, but CgCasp3/7-T had lower DEVDase activity than CgCasp3/7, indicating CgCasp3/7 had DEVDase activity and the IL was required for maximal DEVDase activity. Our study adds to the complexity of caspases in C. gigas.
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Affiliation(s)
- Zhongxiao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Chao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fengjuan Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Pin Huan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Baozhong Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266000 Qingdao, China.
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Yang Z, Zhou K, Liu H, Wu A, Mei L, Liu Q. SfDredd, a Novel Initiator Caspase Possessing Activity on Effector Caspase Substrates in Spodoptera frugiperda. PLoS One 2016; 11:e0151016. [PMID: 26977926 PMCID: PMC4792459 DOI: 10.1371/journal.pone.0151016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/23/2016] [Indexed: 01/11/2023] Open
Abstract
Sf9, a cell line derived from Spodoptera frugiperda, is an ideal model organism for studying insect apoptosis. The first notable study that attempted to identify the apoptotic pathway in Sf9 was performed in 1997 and included the discovery of Sf-caspase-1, an effector caspase of Sf9. However, it was not until 2013 that the first initiator caspase in Sf9, SfDronc, was discovered, and the apoptotic pathway in Sf9 became clearer. In this study, we report another caspase of Sf9, SfDredd. SfDredd is highly similar to insect initiator caspase Dredd homologs. Experimentally, recombinant SfDredd underwent autocleavage and exhibited different efficiencies in cleavage of synthetic caspase substrates. This was attributed to its caspase activity for the predicted active site mutation blocked the above autocleavage and synthetic caspase substrates cleavage activity. SfDredd was capable of not only cleaving Sf-caspase-1 in vitro but also cleaving Sf-caspase-1 and inducing apoptosis when it was co-expressed with Sf-caspase-1 in Sf9 cells. The protein level of SfDredd was increased when Sf9 cells were treated by Actinomycin D, whereas silencing of SfDredd reduced apoptosis and Sf-caspase-1 cleavage induced by Actinomycin D treatment. These results clearly indicate that SfDredd functioned as an apoptotic initiator caspase. Apoptosis induced in Sf9 cells by overexpression of SfDredd alone was not as obvious as that induced by SfDronc alone, and the cleavage sites of Sf-caspase-1 for SfDredd and SfDronc are different. In addition, despite sharing a sequence homology with initiator caspases and possessing weak activity on initiator caspase substrates, SfDredd showed strong activity on effector caspase substrates, making it the only insect caspase reported so far functioning similar to human caspase-2 in this aspect. We believe that the discovery of SfDredd, and its different properties from SfDronc, will improve the understanding of apoptosis pathway in Sf9 cells.
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Affiliation(s)
- Zhouning Yang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Ke Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Hao Liu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Andong Wu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Long Mei
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Qingzhen Liu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
- * E-mail:
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Unnerståle S, Nowakowski M, Baraznenok V, Stenberg G, Lindberg J, Mayzel M, Orekhov V, Agback T. Backbone Assignment of the MALT1 Paracaspase by Solution NMR. PLoS One 2016; 11:e0146496. [PMID: 26788853 PMCID: PMC4720288 DOI: 10.1371/journal.pone.0146496] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/17/2015] [Indexed: 11/18/2022] Open
Abstract
Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a unique paracaspase protein whose protease activity mediates oncogenic NF-κB signalling in activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs). ABC-DLBCLs are aggressive lymphomas with high resistance to current chemotherapies. Low survival rate among patients emphasizes the urgent need for alternative treatment options. The characterization of the MALT1 will be an essential tool for developing new target-directed drugs against MALT1 dependent disorders. As the first step in the atomic-level NMR studies of the system, here we report, the (15)N/(13)C/(1)H backbone assignment of the apo form of the MALT1 paracaspase region together with the third immunoglobulin-like (Ig3) domain, 44 kDa, by high resolution NMR. In addition, the non-uniform sampling (NUS) based targeted acquisition procedure is evaluated as a mean of decreasing acquisition and analysis time for larger proteins.
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Affiliation(s)
| | - Michal Nowakowski
- Swedish NMR Centre, University of Gothenburg, PO Box 465, SE-40530, Gothenburg, Sweden
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02–097, Warsaw, Poland
| | | | - Gun Stenberg
- Medivir AB, PO Box 1086, SE-141 22, Huddinge, Sweden
| | | | - Maxim Mayzel
- Swedish NMR Centre, University of Gothenburg, PO Box 465, SE-40530, Gothenburg, Sweden
| | - Vladislav Orekhov
- Swedish NMR Centre, University of Gothenburg, PO Box 465, SE-40530, Gothenburg, Sweden
| | - Tatiana Agback
- Medivir AB, PO Box 1086, SE-141 22, Huddinge, Sweden
- * E-mail:
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Abstract
Caspases are proteases that are essential components of apoptotic cell death pathways. There are approximately one dozen apoptotic caspases found in organisms where cells die via apoptosis. These caspases are responsible for initiation or execution of apoptosis through the proteolytic cleavage of specific substrates. These substrates contain specific motifs that are recognized and cleaved by caspases that result in alterations of substrate function that promotes the apoptotic phenotype. Analysis of caspase involvement, much like any other protease, can be followed using peptides corresponding to cleavage motifs of these substrates, which can be used as substrates, inhibitors, or affinity-based probes.Different caspases have different substrates and therefore different motifs are recognized by each different caspase. However, these different caspases have a common amino acid recognition pattern containing an aspartic acid residue at the amino-side of the cleavage site. Therefore, caspase substrates have a certain overlap in the cleavage motif as this aspartic acid is found in almost every one. This means that certain peptide motifs are not exclusively cleaved by one single caspase. This lack of exclusive cleavage has brought the use of these motif-based probes into question and spurred the development of truly caspase-specific motifs. This chapter describes the use of peptide-based probes to measure caspase activity while highlighting the limitations of these reagents.
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Affiliation(s)
- Gavin P McStay
- Department of Life Sciences, New York Institute of Technology, 432 Theobald Science Center, Northern Boulevard, Old Westbury, NY, 11568, USA.
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40
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Winter A, Schmid R, Bayliss R. Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains. PLoS Comput Biol 2015; 11:e1004548. [PMID: 26513470 PMCID: PMC4626109 DOI: 10.1371/journal.pcbi.1004548] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/31/2015] [Indexed: 11/18/2022] Open
Abstract
Separases are large proteins that mediate sister chromatid disjunction in all eukaryotes. They belong to clan CD of cysteine peptidases and contain a well-conserved C-terminal catalytic protease domain similar to caspases and gingipains. However, unlike other well-characterized groups of clan CD peptidases, there are no high-resolution structures of separases and the details of their regulation and substrate recognition are poorly understood. Here we undertook an in-depth bioinformatical analysis of separases from different species with respect to their similarity in amino acid sequence and protein fold in comparison to caspases, MALT-1 proteins (mucosa-associated lymphoidtissue lymphoma translocation protein 1) and gingipain-R. A comparative model of the single C-terminal caspase-like domain in separase from C. elegans suggests similar binding modes of substrate peptides between these protein subfamilies, and enables differences in substrate specificity of separase proteins to be rationalised. We also modelled a newly identified putative death domain, located N-terminal to the caspase-like domain. The surface features of this domain identify potential sites of protein-protein interactions. Notably, we identified a novel conserved region with the consensus sequence WWxxRxxLD predicted to be exposed on the surface of the death domain, which we termed the WR motif. We envisage that findings from our study will guide structural and functional studies of this important protein family. The separation of sister chromatids is a crucial step in cell division and is triggered by the activation of separase, a protease that cleaves the proteins that maintain the cohesion between sister chromatids. Knowledge of the molecular structure and activation mechanism of separase is limited by the difficulty of obtaining structural information on this large and flexible protein. Sequence conservation between separase homologues from diverse species is limited to the C-terminal region that contains the catalytically active protease domain. We conducted an in-depth bioinformatical analysis of separase and generated structural models of the two conserved domains that comprise the C-terminal region: a caspase-like domain and a putative death domain. This analysis provided insights into substrate recognition and identified potential sites of protein-protein interactions. Both the death domain and caspase-like domain are well-conserved in separases, which suggests an evolutionary pressure to keep these two domains together, perhaps to enable separase activity and/or provide stability. Insights into the molecular structures of separase gained in this study may provide a starting point for experimental structural studies on this protein and may aid therapeutic development against cancers where chromosomes are improperly segregated.
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Affiliation(s)
- Anja Winter
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Ralf Schmid
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Richard Bayliss
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Kamada S. Inhibitor of apoptosis proteins as E3 ligases for ubiquitin and NEDD8. Biomol Concepts 2015; 4:161-71. [PMID: 25436573 DOI: 10.1515/bmc-2012-0036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/30/2012] [Indexed: 11/15/2022] Open
Abstract
The inhibitors of apoptosis proteins (IAPs) are endogenous inhibitors for apoptosis. Apoptosis is carried out by caspases, which are the family of cystein proteases. IAPs regulate caspases through two conserved regions, the baculovirus IAP repeats (BIRs) and the really interesting new gene (RING) domains. Although the BIRs are responsible for binding to caspases, the RING domain can act as a ubiquitin-E3 ligase, leading to ubiquitylation of IAPs themselves and their pro-apoptotic IAP counterparts such as caspases. Recently, it is reported that another ubiquitin-like protein, neuronal precursor cell-expressed developmentally downregulated protein 8 (NEDD8), is also involved in the regulation of apoptosis through neddylation of caspases mediated by IAPs. On the contrary, the results against the function of IAPs as a NEDD8-E3 ligase are also suggested. This review presents the summary of IAPs, caspases, and the ubiquitin-proteasome system and how their interactions influence the regulation of apoptosis.
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Chichkova NV, Galiullina RA, Beloshistov RE, Balakireva AV, Vartapetian AB. [Phytaspases: aspartate-specific proteases involved in plant cell death]. Bioorg Khim 2015; 40:658-64. [PMID: 25895361 DOI: 10.1134/s1068162014060065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structure and properties of the recently discovered aspartate-specific cell death-related plant proteases named phytaspases are reviewed and compared to those of animal apoptotic proteases, caspases. Caspases (cysteine-dependent proteases) and phytaspases (serine-dependent proteases) are structurally very different, yet they share cleavage specificity and a role in programmed cell death. We demonstrate here that the distinctions in structural organization of animal and plant death proteases define differences in the strategies to regulate functioning of these proteolytic enzymes in the two kingdoms.
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Avanzi MP, Izak M, Oluwadara OE, Mitchell WB. Actin inhibition increases megakaryocyte proplatelet formation through an apoptosis-dependent mechanism. PLoS One 2015; 10:e0125057. [PMID: 25875470 PMCID: PMC4397066 DOI: 10.1371/journal.pone.0125057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/14/2015] [Indexed: 12/25/2022] Open
Abstract
Background Megakaryocytes assemble and release platelets through the extension of proplatelet processes, which are cytoplasmic extensions that extrude from the megakaryocyte and form platelets at their tips. Proplatelet formation and platelet release are complex processes that require a combination of structural rearrangements. While the signals that trigger the initiation of proplatelet formation process are not completely understood, it has been shown that inhibition of cytoskeletal signaling in mature megakaryocytes induces proplatelet formation. Megakaryocyte apoptosis may also be involved in initiation of proplatelet extension, although this is controversial. This study inquires whether the proplatelet production induced by cytoskeletal signaling inhibition is dependent on activation of apoptosis. Methods Megakaryocytes derived from human umbilical cord blood CD34+ cells were treated with the actin polymerization inhibitor latrunculin and their ploidy and proplatelet formation were quantitated. Apoptosis activation was analyzed by flow cytometry and luminescence assays. Caspase activity was inhibited by two compounds, ZVAD and QVD. Expression levels of pro-survival and pro-apoptosis genes were measured by quantitative RT-PCR. Protein levels of Bcl-XL, Bax and Bak were measured by western blot. Cell ultrastructure was analyzed by electron microscopy. Results Actin inhibition resulted in increased ploidy and increased proplatelet formation in cultured umbilical cord blood-derived megakaryocytes. Actin inhibition activated apoptosis in the cultured cells. The effects of actin inhibition on proplatelet formation were blocked by caspase inhibition. Increased expression of both pro-apoptotic and pro-survival genes was observed. Pro-survival protein (Bcl-xL) levels were increased compared to levels of pro-apoptotic proteins Bak and Bax. Despite apoptosis being activated, the megakaryocytes underwent minimal ultrastructural changes during actin inhibition. Conclusions We report a correlation between increased proplatelet formation and activation of apoptosis, and that the increase in proplatelet formation in response to actin inhibition is caspase dependent. These findings support a role for apoptosis in proplatelet formation in this model.
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Affiliation(s)
- Mauro P. Avanzi
- Platelet Biology Laboratory, New York Blood Center, New York, New York, United States of America
| | - Marina Izak
- Platelet Biology Laboratory, New York Blood Center, New York, New York, United States of America
| | | | - William Beau Mitchell
- Platelet Biology Laboratory, New York Blood Center, New York, New York, United States of America
- * E-mail:
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McLuskey K, Mottram J. Comparative structural analysis of the caspase family with other clan CD cysteine peptidases. Biochem J 2015; 466:219-32. [PMID: 25697094 PMCID: PMC4357240 DOI: 10.1042/bj20141324] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/19/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
Abstract
Clan CD forms a structural group of cysteine peptidases, containing seven individual families and two subfamilies of structurally related enzymes. Historically, it is most notable for containing the mammalian caspases, on which the structures of the clan were founded. Interestingly, the caspase family is split into two subfamilies: the caspases, and a second subfamily containing both the paracaspases and the metacaspases. Structural data are now available for both the paracaspases and the metacaspases, allowing a comprehensive structural analysis of the entire caspase family. In addition, a relative plethora of structural data has recently become available for many of the other families in the clan, allowing both the structures and the structure-function relationships of clan CD to be fully explored. The present review compares the enzymes in the caspase subfamilies with each other, together with a comprehensive comparison of all the structural families in clan CD. This reveals a diverse group of structures with highly conserved structural elements that provide the peptidases with a variety of substrate specificities and activation mechanisms. It also reveals conserved structural elements involved in substrate binding, and potential autoinhibitory functions, throughout the clan, and confirms that the metacaspases are structurally diverse from the caspases (and paracaspases), suggesting that they should form a distinct family of clan CD peptidases.
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Key Words
- caspase
- clan cd
- crystallography
- metacaspase
- peptidase
- protein structure
- ap, activation peptide
- card, caspase recruitment domain
- chf, caspase/haemoglobinase fold
- cpd, cysteine peptidase domain
- csd, c-terminal subdomain
- dd, death domain
- ded, death effector domain
- insp6, myo-inositol hexakisphosphate
- lsam, legumain stabilization and activity modulation
- lsd1, lesion-simulating disease 1
- malt1, mucosa-associated lymphoid tissue translocation protein 1
- martx, multi-functional, autoprocessing repeat in toxin
- rmsd, root-mean-square deviation
- sse, secondary structural element
- xiap, x-linked inhibitor of apoptosis
- z-vrpr-fmk, benzoxycarbonyl-val-arg-pro-arg-fluoromethylketone
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Affiliation(s)
- Karen McLuskey
- *Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Jeremy C. Mottram
- *Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
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Shubin AV, Demidyuk IV, Lunina NA, Komissarov AA, Roschina MP, Leonova OG, Kostrov SV. Protease 3C of hepatitis A virus induces vacuolization of lysosomal/endosomal organelles and caspase-independent cell death. BMC Cell Biol 2015; 16:4. [PMID: 25886889 PMCID: PMC4355371 DOI: 10.1186/s12860-015-0050-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 01/26/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND 3C proteases, the main proteases of picornaviruses, play the key role in viral life cycle by processing polyproteins. In addition, 3C proteases digest certain host cell proteins to suppress antiviral defense, transcription, and translation. The activity of 3C proteases per se induces host cell death, which makes them critical factors of viral cytotoxicity. To date, cytotoxic effects have been studied for several 3C proteases, all of which induce apoptosis. This study for the first time describes the cytotoxic effect of 3C protease of human hepatitis A virus (3Cpro), the only proteolytic enzyme of the virus. RESULTS Individual expression of 3Cpro induced catalytic activity-dependent cell death, which was not abrogated by the pan-caspase inhibitor (z-VAD-fmk) and was not accompanied by phosphatidylserine externalization in contrast to other picornaviral 3C proteases. The cell survival was also not affected by the inhibitors of cysteine proteases (z-FA-fmk) and RIP1 kinase (necrostatin-1), critical enzymes involved in non-apoptotic cell death. A substantial fraction of dying cells demonstrated numerous non-acidic cytoplasmic vacuoles with not previously described features and originating from several types of endosomal/lysosomal organelles. The lysosomal protein Lamp1 and GTPases Rab5, Rab7, Rab9, and Rab11 were associated with the vacuolar membranes. The vacuolization was completely blocked by the vacuolar ATPase inhibitor (bafilomycin A1) and did not depend on the activity of the principal factors of endosomal transport, GTPases Rab5 and Rab7, as well as on autophagy and macropinocytosis. CONCLUSIONS 3Cpro, apart from other picornaviral 3C proteases, induces caspase-independent cell death, accompanying by cytoplasmic vacuolization. 3Cpro-induced vacuoles have unique properties and are formed from several organelle types of the endosomal/lysosomal compartment. The data obtained demonstrate previously undocumented morphological characters of the 3Cpro-induced cell death, which can reflect unknown aspects of the human hepatitis A virus-host cell interaction.
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Affiliation(s)
- Andrey V Shubin
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Ilya V Demidyuk
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Nataliya A Lunina
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Alexey A Komissarov
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Marina P Roschina
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Olga G Leonova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119992, Russia.
| | - Sergey V Kostrov
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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Shan H, Yan R, Diao J, Lin L, Wang S, Zhang M, Zhang R, Wei J. Involvement of caspases and their upstream regulators in myocardial apoptosis in a rat model of selenium deficiency-induced dilated cardiomyopathy. J Trace Elem Med Biol 2015; 31:85-91. [PMID: 26004897 DOI: 10.1016/j.jtemb.2015.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/24/2015] [Accepted: 03/24/2015] [Indexed: 12/19/2022]
Abstract
Keshan disease is an endemic dilated cardiomyopathy (DCM) which is closely related with selenium-deficient diet in China. In the previous study, we reported that the low selenium status plays a pivotal role in the myocardial apoptosis in the DCM rats, however, the underlying mechanism remains unclear. The present study aimed to determine whether the intrinsic, extrinsic pathways and the upstream regulators were involved in the myocardial apoptosis of selenium deficiency-induced DCM rats. Therefore, the rat model of endemic DCM was induced by a selenium-deficient diet for 12 weeks. Accompanied with significant dilation and impaired systolic function of left ventricle, an enhanced myocardial apoptosis was detected by TUNEL assay. Western blot analysis showed remarkably increased protein levels of cleaved caspase-3, caspase-8, caspase-9, and cytosolic cytochrome c released from the mitochondria. In addition, the immunoreactivities of p53 and Bax were significantly up-regulated, while the anti-apoptotic Bcl-2 family members Bcl-2 and Bcl-X(L) were down-regulated. Furthermore, appropriate selenium supplement for another 4 weeks could partially reverse all the above changes. In conclusion, the intrinsic, extrinsic pathways and the upstream regulators such as p53, Bax, Bcl-2, and Bcl-X(L )were all involved in selenium deficiency-induced myocardial apoptosis.
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Affiliation(s)
- Hu Shan
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China; Department of Endemic Disease, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China
| | - Rui Yan
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China; Department of Endemic Disease, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China
| | - Jiayu Diao
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China
| | - Lin Lin
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China
| | - Suqin Wang
- Department of Cardiology, Henan Provincial People's Hospital, 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Ming Zhang
- Key Laboratory of Trace Elements and Endemic Disease of Ministry of Health, Xi'an Jiaotong University School of Medicine, 76 Yantaxi Road, Xi'an, Shaanxi 710061, China
| | - Rong Zhang
- Key Laboratory of Trace Elements and Endemic Disease of Ministry of Health, Xi'an Jiaotong University School of Medicine, 76 Yantaxi Road, Xi'an, Shaanxi 710061, China
| | - Jin Wei
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China; Department of Endemic Disease, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China.
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Park S, Park JA, Kim YE, Song S, Kwon HJ, Lee Y. Suberoylanilide hydroxamic acid induces ROS-mediated cleavage of HSP90 in leukemia cells. Cell Stress Chaperones 2015; 20:149-57. [PMID: 25119188 PMCID: PMC4255254 DOI: 10.1007/s12192-014-0533-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 07/03/2014] [Accepted: 07/29/2014] [Indexed: 12/20/2022] Open
Abstract
Heat shock protein 90 (HSP90) is a molecular chaperone that supports stability of client proteins. We found that HSP90 was cleaved to 55 kDa protein after treatment with histone deacetylase (HDAC) inhibitors including suberoylanilide hydroxamic acid (SAHA) in several leukemia cell lines. We further analyzed molecular changes induced by SAHA in K562 cells. The SAHA-induced cleavage of HSP90 was blocked by a pan-caspase inhibitor, z-VAD-fmk, implying that the process is dependent on caspase activity. However, the experiments using antagonistic and agonistic Fas antibodies revealed that the cleavage of HSP90 was not dependent on Fas signaling. SAHA induced generation of reactive oxygen species (ROS), and the cleavage of HSP90 was blocked by a ROS scavenger N-acetylcystein (NAC). We also confirmed that hydrogen peroxide (H2O2) induced cleavage of HSP90 in a similar manner. Caspase 2, 3, 4, 6, 8, and 10 were activated by treatment with SAHA, and the activities were reduced by the pretreatment of NAC. Treatment of the cells with caspase 10 inhihitor, but not other inhibitors of caspases activated by SAHA, prevented cleavage of HSP90 by SAHA. SAHA-induced ROS generation and HSP90 cleavage were dependent on newly synthesized unknown proteins. Taken together, our results suggest that the cleavage of HSP90 by SAHA is mediated by ROS generation and caspase 10 activation. HSP90 cleavage may provide an additional mechanism involved in anti-cancer effects of HDAC inhibitors.
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Affiliation(s)
- Sangkyu Park
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Jeong-A Park
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Young-Eun Kim
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
- />Biotechnology Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Sukgil Song
- />College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Hyung-Joo Kwon
- />Center for Medical Science Research, Hallym University, Chuncheon, 200-720 Republic of Korea
- />Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 200-720 Republic of Korea
| | - Younghee Lee
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
- />Biotechnology Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, 52 Naesudong-Ro, Heungduk-Gu, Cheongju, Chungbuk 361-763 Republic of Korea
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48
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Ren L, Wang R, Xu T. Three representative subtypes of caspase in miiuy croaker: genomic organization, evolution and immune responses to bacterial challenge. Fish Shellfish Immunol 2014; 40:61-68. [PMID: 24973513 DOI: 10.1016/j.fsi.2014.06.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 06/03/2023]
Abstract
Caspase proteins are intracellular proteases which function as initiators and effectors of apoptosis. According their difference of functions, the caspases can be divided into apoptosis related caspases and inflammatory mediator, and the former included apoptosis activator and apoptosis executioner. In this study, three different subtype caspases (caspase1, caspase3 and caspase9) from Miichthys miiuy miiuy croaker were analyzed. The caspase1 belongs to the inflammatory mediator, caspase3 belongs to apoptosis executioner, and caspase9 belongs to apoptosis activator. Miichthys miiuy caspase1 (Mmcaspase1) and Mmcaspase9 exhibited three conserved domains including a CARD, a large subunit p20 and a small subunit p10. The Mmcaspase3 encoded two conserved domains including a large subunit p20 and a small subunit p10. Mmcaspase3 and Mmcaspase9 contained a histidine active sequence and a cysteine active sequence. However, Mmcaspase1 only contained the cysteine active sequence. The real-time PCR (RT-PCR) analysis showed these three caspases were expressed constitutively in all examined tissues in miiuy croaker, although the expression levels varied from tissue to tissue. Expression analysis showed that Mmcaspase1 was up-regulated obviously in liver, spleen and kidney, and indicated its positive role in response to Vibrio anguillarum infection, but Mmcaspase3 and Mmcaspase9 showed different expression pattern in liver, spleen and kidney, its showed that different subtypes of caspase having different immune response mechanisms. These results revealed that the organs adjusted the expressions of these three genes with the infected of pathogens, suggesting the immunoprotection of these genes.
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Affiliation(s)
- Liping Ren
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China
| | - Rixin Wang
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China.
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Abstract
Delineation of the natural substrate scope of proteases is important for understanding the functions of proteolytic pathways in physiology and disease. Herein we describe the protocol for PROTOMAP, a technique that combines SDS-PAGE with tandem mass spectrometry to globally identify shifts in protein migration indicative of proteolytic processing. When applied to cells undergoing apoptosis, this unbiased global method provides a snapshot of the topography and magnitude of proteolytic events associated with programmed cell death.
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Affiliation(s)
- Melissa M Dix
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
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50
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Zaĭkova II, Kulichkova VA, Mitenkova KA, Tsimokha AS. [Extracellular proteasomes purification methods and the evaluation of proteasomal peptidase activities]. Tsitologiia 2014; 56:427-432. [PMID: 25696979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this paper, we present a comparative analysis of different methods of purification of proteasomes from the culture medium in which proerithroleukemia human K562 cells were grown. The results obtained allowed us to purify proteasomes from samples of conditioned cell culture medium and control the quality of the proteasome preparations at all stages of their separation. Extracellular proteasomes purified via different approaches possess all the three types of peptidase activity described for intracellular counterparts.
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