1
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Fang Y, Gong Z, You M, Peng K. Identification of a novel caspase cleavage motif AEAD. Virol Sin 2024:S1995-820X(24)00115-9. [PMID: 39098717 DOI: 10.1016/j.virs.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/16/2023] [Indexed: 08/06/2024] Open
Abstract
Infections of many viruses induce caspase activation to regulate multiple cellular pathways, including programmed cell death, immune signaling and etc. Characterizations of caspase cleavage sites and substrates are important for understanding the regulation mechanisms of caspase activation. Here, we identified and analyzed a novel caspase cleavage motif AEAD, and confirmed its caspase dependent cleavage activity in natural substrate, such as nitric oxide-associated protein 1 (NOA1). Fusing the enhanced green fluorescent protein (EGFP) with the mitochondrial marker protein Tom20 through the AEAD motif peptide localized EGFP to the mitochondria. Upon the activation of caspase triggered by Sendai virus (SeV) or herpes simplex virus type 1 (HSV-1) infection, EGFP diffusely localized to the cell due to the caspase-mediated cleavage, thus allowing visual detection of the virus-induced caspase activation. An AEAD peptide-derived inhibitor Z-AEAD-FMK were developed, which significantly inhibited the activities of caspases-1, -3, -6, -7, -8 and -9, exhibiting a broad caspase inhibition effect. The inhibitor further prevented caspases-mediated cleavage of downstream substrates, including BID, PARP1, LMNA, pro-IL-1β, pro-IL-18, GSDMD and GSDME, protecting cells from virus-induced apoptotic and pyroptotic cell death. Together, our findings provide a new perspective for the identification of novel caspase cleavage motifs and the development of new caspase inhibitors and anti-inflammatory drugs.
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Affiliation(s)
- Yujie Fang
- State Key Laboratory of Virology, Center for Antiviral Research, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, 430071, China
| | - Miaomiao You
- State Key Laboratory of Virology, Center for Antiviral Research, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Peng
- State Key Laboratory of Virology, Center for Antiviral Research, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Provincial Key Laboratory of Jiangxia, Wuhan, 430207, China.
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2
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Exconde PM, Bourne CM, Kulkarni M, Discher BM, Taabazuing CY. Inflammatory caspase substrate specificities. mBio 2024; 15:e0297523. [PMID: 38837391 PMCID: PMC11253702 DOI: 10.1128/mbio.02975-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Caspases are a family of cysteine proteases that act as molecular scissors to cleave substrates and regulate biological processes such as programmed cell death and inflammation. Extensive efforts have been made to identify caspase substrates and to determine factors that dictate substrate specificity. Thousands of putative substrates have been identified for caspases that regulate an immunologically silent type of cell death known as apoptosis, but less is known about substrates of the inflammatory caspases that regulate an immunostimulatory type of cell death called pyroptosis. Furthermore, much of our understanding of caspase substrate specificities is derived from work done with peptide substrates, which do not often translate to native protein substrates. Our knowledge of inflammatory caspase biology and substrates has recently expanded and here, we discuss the recent advances in our understanding of caspase substrate specificities, with a focus on inflammatory caspases. We highlight new substrates that have been discovered and discuss the factors that engender specificity. Recent evidence suggests that inflammatory caspases likely utilize two binding interfaces to recognize and process substrates, the active site and a conserved exosite.
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Affiliation(s)
- Patrick M. Exconde
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Christopher M. Bourne
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Madhura Kulkarni
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bohdana M. Discher
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Cornelius Y. Taabazuing
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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3
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Azhar G, Nagano K, Patyal P, Zhang X, Verma A, Wei JY. Deletion of Interleukin-1β Converting Enzyme Alters Mouse Cardiac Structure and Function. BIOLOGY 2024; 13:172. [PMID: 38534442 DOI: 10.3390/biology13030172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024]
Abstract
Interleukin-1β converting enzyme (ICE, caspase-1) is a thiol protease that cleaves the pro-inflammatory cytokine precursors of IL-1β and IL-18 into active forms. Given the association between caspase-1 and cardiovascular pathology, we analyzed the hearts of ICE knockout (ICE KO) mice to test the hypothesis that caspase-1 plays a significant role in cardiac morphology and function. We characterized the histological and functional changes in the hearts of ICE KO mice compared to the Wild type. The cardiomyocytes from the neonatal ICE KO mice showed an impaired response to oxidative stress. Subsequently, the hearts from the ICE KO mice were hypertrophied, with a significant increase in the left ventricular and septal wall thickness and a greater LV mass/body weight ratio. The ICE KO mice hearts exhibited irregular myofibril arrangements and disruption of the cristae in the mitochondrial structure. Proapoptotic proteins that were significantly increased in the hearts of ICE KO versus the Wild type included pErk, pJNK, p53, Fas, Bax, and caspase 3. Further, the antiapoptotic proteins Bag-1 and Bcl-2 are activated in ICE KO hearts. Functionally, there was an increase in the left ventricular epicardial diameter and volume in ICE KO. In conclusion, our findings support the important role of caspase-1 in maintaining cardiac health; specifically, a significant decrease in caspase-1 is detrimental to the cardiovascular system.
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Affiliation(s)
- Gohar Azhar
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Koichiro Nagano
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Pankaj Patyal
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiaomin Zhang
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ambika Verma
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jeanne Y Wei
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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4
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Olesen MA, Quintanilla RA. Pathological Impact of Tau Proteolytical Process on Neuronal and Mitochondrial Function: a Crucial Role in Alzheimer's Disease. Mol Neurobiol 2023; 60:5691-5707. [PMID: 37332018 DOI: 10.1007/s12035-023-03434-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023]
Abstract
Tau protein plays a pivotal role in the central nervous system (CNS), participating in microtubule stability, axonal transport, and synaptic communication. Research interest has focused on studying the role of post-translational tau modifications in mitochondrial failure, oxidative damage, and synaptic impairment in Alzheimer's disease (AD). Soluble tau forms produced by its pathological cleaved induced by caspases could lead to neuronal injury contributing to oxidative damage and cognitive decline in AD. For example, the presence of tau cleaved by caspase-3 has been suggested as a relevant factor in AD and is considered a previous event before neurofibrillary tangles (NFTs) formation.Interestingly, we and others have shown that caspase-cleaved tau in N- or C- terminal sites induce mitochondrial bioenergetics defects, axonal transport impairment, neuronal injury, and cognitive decline in neuronal cells and murine models. All these abnormalities are considered relevant in the early neurodegenerative manifestations such as memory and cognitive failure reported in AD. Therefore, in this review, we will discuss for the first time the importance of truncated tau by caspases activation in the pathogenesis of AD and how its negative actions could impact neuronal function.
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Affiliation(s)
- Margrethe A Olesen
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, 5to Piso, San Miguel, 8910060, Santiago, Chile
| | - Rodrigo A Quintanilla
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, 5to Piso, San Miguel, 8910060, Santiago, Chile.
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5
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Hanna R, Rozenberg A, Saied L, Ben-Yosef D, Lavy T, Kleifeld O. In-Depth Characterization of Apoptosis N-terminome Reveals a Link Between Caspase-3 Cleavage and Post-Translational N-terminal Acetylation. Mol Cell Proteomics 2023:100584. [PMID: 37236440 PMCID: PMC10362333 DOI: 10.1016/j.mcpro.2023.100584] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023] Open
Abstract
The N-termini of proteins contain information about their biochemical properties and functions. These N-termini can be processed by proteases, and can undergo other co- or post-translational modifications. We have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides, in order to improve N-terminome identification in conjunction with other enrichment strategies. We applied LATE alongside another N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This has enabled us to identify many unreported caspase-3 cleavages, some of which cannot be identified by other methods. Moreover, we have found direct evidence that neo-N-termini generated by caspase-3 cleavage can be further modified by Nt-acetylation. Some of these neo-Nt-acetylation events occur in the early phase of the apoptotic process and may have a role in translation inhibition. This has provided a comprehensive overview of the caspase-3 degradome and has uncovered previously unrecognized crosstalk between post-translational Nt-acetylation and caspase proteolytic pathways.
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Affiliation(s)
- Rawad Hanna
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Layla Saied
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Daniel Ben-Yosef
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Tali Lavy
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel.
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6
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Luo SY, Moussa EW, Lopez-Orozco J, Felix-Lopez A, Ishida R, Fayad N, Gomez-Cardona E, Wang H, Wilson JA, Kumar A, Hobman TC, Julien O. Identification of Human Host Substrates of the SARS-CoV-2 M pro and PL pro Using Subtiligase N-Terminomics. ACS Infect Dis 2023; 9:749-761. [PMID: 37011043 PMCID: PMC10081575 DOI: 10.1021/acsinfecdis.2c00458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Indexed: 04/04/2023]
Abstract
The recent emergence of SARS-CoV-2 in the human population has caused a global pandemic. The virus encodes two proteases, Mpro and PLpro, that are thought to play key roles in the suppression of host protein synthesis and immune response evasion during infection. To identify the specific host cell substrates of these proteases, active recombinant SARS-CoV-2 Mpro and PLpro were added to A549 and Jurkat human cell lysates, and subtiligase-mediated N-terminomics was used to capture and enrich protease substrate fragments. The precise location of each cleavage site was identified using mass spectrometry. Here, we report the identification of over 200 human host proteins that are potential substrates for SARS-CoV-2 Mpro and PLpro and provide a global mapping of proteolysis for these two viral proteases in vitro. Modulating proteolysis of these substrates will increase our understanding of SARS-CoV-2 pathobiology and COVID-19.
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Affiliation(s)
- Shu Y. Luo
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joaquin Lopez-Orozco
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Alberto Felix-Lopez
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ray Ishida
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Nawell Fayad
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Erik Gomez-Cardona
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Henry Wang
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joyce A. Wilson
- Department
of Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Anil Kumar
- Department
of Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Tom C. Hobman
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, Edmonton, Alberta T6G
2E1, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, Edmonton, Alberta T6G
2E1, Canada
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7
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Khezri MR, Ghasemnejad-Berenji M. The Role of Caspases in Alzheimer's Disease: Pathophysiology Implications and Pharmacologic Modulation. J Alzheimers Dis 2023; 91:71-90. [PMID: 36442198 DOI: 10.3233/jad-220873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder worldwide. Although the main cause of the onset and development of AD is not known yet, neuronal death due to pathologic changes such as amyloid-β (Aβ) deposition, tau aggregation, neuroinflammation, oxidative stress, and calcium dyshomeostasis are considered to be the main cause. At the present, there is no cure for this insidious disorder. However, accurate identification of molecular changes in AD can help provide new therapeutic goals. Caspases are a group of proteases which are known because of their role in cellular apoptosis. In addition, different caspases are involved in other cellular responses to the environment, such as induction of inflammation. Emerging evidence suggest that these proteases play a central role in AD pathophysiology due to their role in the processing of amyloid-β protein precursor, tau cleavage, and neuroinflammation. Therefore, it seems that targeting caspases may be a suitable therapeutic option to slow the progression of AD. This review focuses on the role of caspases in AD pathophysiology and introduce results from studies targeted caspases in different models of AD.
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Affiliation(s)
| | - Morteza Ghasemnejad-Berenji
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Urmia University of Medical Sciences, Urmia, Iran.,Research Center for Experimental and Applied Pharmaceutical Sciences, Urmia University of Medical Sciences, Urmia, Iran
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8
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Dhage PA, Sharbidre AA, Magdum SM. Interlacing the relevance of caspase activation in the onset and progression of Alzheimer's disease. Brain Res Bull 2023; 192:83-92. [PMID: 36372374 DOI: 10.1016/j.brainresbull.2022.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Caspases, a family of cysteine proteases is a renowned regulator of apoptosis. Members of this family are responsible for the proteolytic dismantling of numerous cellular structures. Apart from apoptosis, caspases remarkably contribute to a diverse range of molecular processes. Being the imperative members of several cellular cascades their abnormal activation/deactivation has severe implications and also leads to various diseased conditions. Similar aberrant activation of caspases is one of the several causes of neuropathologies associated with Alzheimer's disease (AD), a form of dementia severely affecting neuropsychiatric and cognitive functions. Emerging studies are providing deeper insights into the mechanisms of caspase action in the progression of AD. Current article is an attempt to review these studies and present the action mechanisms of different mammalian caspases in the advancement of AD associated neuropathologies.
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Affiliation(s)
- Prajakta A Dhage
- Department of Zoology, K.R.T. Arts, B.H. Commerce and A.M. Science College (KTHM College), Nashik 422002, MS, India.
| | - Archana A Sharbidre
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, MS, India.
| | - Sujata M Magdum
- Department of Zoology, K.R.T. Arts, B.H. Commerce and A.M. Science College (KTHM College), Nashik 422002, MS, India.
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9
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Zhang K, Peng T, Tao X, Tian M, Li Y, Wang Z, Ma S, Hu S, Pan X, Xue J, Luo J, Wu Q, Fu Y, Li S. Structural insights into caspase ADPR deacylization catalyzed by a bacterial effector and host calmodulin. Mol Cell 2022; 82:4712-4726.e7. [PMID: 36423631 DOI: 10.1016/j.molcel.2022.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
Programmed cell death and caspase proteins play a pivotal role in host innate immune response combating pathogen infections. Blocking cell death is employed by many bacterial pathogens as a universal virulence strategy. CopC family type III effectors, including CopC from an environmental pathogen Chromobacterium violaceum, utilize calmodulin (CaM) as a co-factor to inactivate caspases by arginine ADPR deacylization. However, the molecular basis of the catalytic and substrate/co-factor binding mechanism is unknown. Here, we determine successive cryo-EM structures of CaM-CopC-caspase-3 ternary complex in pre-reaction, transition, and post-reaction states, which elucidate a multistep enzymatic mechanism of CopC-catalyzed ADPR deacylization. Moreover, we capture a snapshot of the detachment of modified caspase-3 from CopC. These structural insights are validated by mutagenesis analyses of CopC-mediated ADPR deacylization in vitro and animal infection in vivo. Our study offers a structural framework for understanding the molecular basis of arginine ADPR deacylization catalyzed by the CopC family.
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Affiliation(s)
- Kuo Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Ting Peng
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Xinyuan Tao
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Miao Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yanxin Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Zhao Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Shuaifei Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Shufan Hu
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Xing Pan
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jiwei Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qiulan Wu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Shan Li
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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10
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Weghorst F, Mirzakhanyan Y, Hernandez KL, Gershon PD, Cramer KS. Non-Apoptotic Caspase Activity Preferentially Targets a Novel Consensus Sequence Associated With Cytoskeletal Proteins in the Developing Auditory Brainstem. Front Cell Dev Biol 2022; 10:844844. [PMID: 35330912 PMCID: PMC8940215 DOI: 10.3389/fcell.2022.844844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022] Open
Abstract
The auditory brainstem relies on precise circuitry to facilitate sound source localization. In the chick, the development of this specialized circuitry requires non-apoptotic activity of caspase-3, for which we previously identified several hundred proteolytic substrates. Here we tested whether the sequence of the caspase cleavage site differentially encodes proteolytic preference in apoptotic and non-apoptotic contexts. We constructed a consensus sequence for caspase activity in the non-apoptotic chick auditory brainstem comprising the four residues N-terminal to the cleavage site: IX(G/R)D↓ where X represents no significant enrichment and ↓ represents the cleavage site. We identified GO terms significantly enriched among caspase substrates containing motifs found in the above consensus sequence. (G/R)D↓ was associated with the term “Structural Constituent of Cytoskeleton” (SCoC), suggesting that SCoC proteins may be specifically targeted by caspase activity during non-apoptotic developmental processes. To ascertain whether this consensus sequence was specific to the non-apoptotic auditory brainstem at embryonic day (E) 10, we used protein mass spectrometry of brainstems harvested at a time when auditory brainstem neurons undergo apoptotic cell death (E13). The apoptotic motif VD was significantly enriched among E13 cleavage sites, indicating that motif preference at the P2 subsite had shifted toward the canonical caspase consensus sequence. Additionally, Monte Carlo simulations revealed that only the GD motif was associated with SCoC substrates in the apoptotic auditory brainstem, indicating that GD encodes specificity for SCoC proteins in both non-apoptotic and apoptotic contexts, despite not being preferred in the latter. Finally, to identify candidate human non-apoptotic consensus sequences, we used Monte Carlo analyses to determine motifs and motif pairs associated with SCoC caspase substrates in the Degrabase, a database of cleavage sites in human apoptotic cell lines. We found 11 motifs significantly associated with SCoC proteolysis, including IXXD and GD. We employed a stepwise method to select motif pairs that optimized SCoC specificity for a given coverage of SCoC cleavage events, yielding 11 motif pairs likely to be preferred in SCoC-directed human non-apoptotic caspase consensus sequences. GD + IXXD was among these motif pairs, suggesting a conservation of non-apoptotic consensus sites among vertebrates.
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Affiliation(s)
- Forrest Weghorst
- Department of Neurobiology and Behavior, UC Irvine, Irvine, CA, United States
| | - Yeva Mirzakhanyan
- Department of Molecular Biology and Biochemistry, UC Irvine, Irvine, CA, United States
| | | | - Paul D Gershon
- Department of Molecular Biology and Biochemistry, UC Irvine, Irvine, CA, United States
| | - Karina S Cramer
- Department of Neurobiology and Behavior, UC Irvine, Irvine, CA, United States
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11
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Peng T, Tao X, Xia Z, Hu S, Xue J, Zhu Q, Pan X, Zhang Q, Li S. Pathogen hijacks programmed cell death signaling by arginine ADPR-deacylization of caspases. Mol Cell 2022; 82:1806-1820.e8. [PMID: 35338844 DOI: 10.1016/j.molcel.2022.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/05/2022] [Accepted: 03/03/2022] [Indexed: 12/14/2022]
Abstract
Caspases are evolutionarily conserved cysteine proteases that are essential for regulating cell death and are involved in multiple development and disease processes, including immunity. Here, we show that the bacterial type III secretion system (T3SS) effector CopC (Chromobacterium outer protein C) from the environmental pathogen Chromobacterium violaceum attacks caspase-3/-7/-8/-9 by ADPR-deacylization to dysregulate programmed cell death, including apoptosis, necroptosis, and pyroptosis. This modification involves ADP-ribosylation- and deamination-mediated cyclization on Arg207 of caspase-3 by a mechanism that requires the eukaryote-specific protein calmodulin (CaM), leading to inhibition of caspase activity. The manipulation of cell death signaling by CopC is essential for the virulence of C. violaceum in a mouse infection model. CopC represents a family of enzymes existing in taxonomically diverse bacteria associated with a wide spectrum of eukaryotes ranging from humans to plants. The unique activity of CopC establishes a mechanism by which bacteria counteract host defenses through a previously unrecognized post-translational modification.
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Affiliation(s)
- Ting Peng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xinyuan Tao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhujun Xia
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shufan Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Qiuyu Zhu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xing Pan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qiang Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shan Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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12
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Ross C, Chan AH, von Pein JB, Maddugoda MP, Boucher D, Schroder K. Inflammatory Caspases: Toward a Unified Model for Caspase Activation by Inflammasomes. Annu Rev Immunol 2022; 40:249-269. [PMID: 35080918 DOI: 10.1146/annurev-immunol-101220-030653] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Inflammasomes are inflammatory signaling complexes that provide molecular platforms to activate the protease function of inflammatory caspases. Caspases-1, -4, -5, and -11 are inflammatory caspases activated by inflammasomes to drive lytic cell death and inflammatory mediator production, thereby activating host-protective and pathological immune responses. Here, we comprehensively review the mechanisms that govern the activity of inflammatory caspases. We discuss inflammatory caspase activation and deactivation mechanisms, alongside the physiological importance of caspase activity kinetics. We also examine mechanisms of caspase substrate selection and how inflammasome and cell identities influence caspase activity and resultant inflammatory and pyroptotic cellular programs. Understanding how inflammatory caspases are regulated may offer new strategies for treating infection and inflammasome-driven disease. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Connie Ross
- Institute for Molecular Bioscience and IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Australia; .,Current affiliation: School of Molecular and Chemical Sciences, The University of Queensland, St. Lucia, Australia
| | - Amy H Chan
- Institute for Molecular Bioscience and IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Australia;
| | - Jessica B von Pein
- Institute for Molecular Bioscience and IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Australia;
| | - Madhavi P Maddugoda
- Institute for Molecular Bioscience and IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Australia;
| | - Dave Boucher
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
| | - Kate Schroder
- Institute for Molecular Bioscience and IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Australia;
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13
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Soni IV, Hardy JA. Caspase-9 Activation of Procaspase-3 but Not Procaspase-6 Is Based on the Local Context of Cleavage Site Motifs and on Sequence. Biochemistry 2021; 60:2824-2835. [PMID: 34472839 DOI: 10.1021/acs.biochem.1c00459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Studying the interactions between a protease and its protein substrates at a molecular level is crucial for identifying the factors facilitating selection of particular proteolytic substrates and not others. These selection criteria include both the sequence and the local context of the substrate cleavage site where the active site of the protease initially binds and then performs proteolytic cleavage. Caspase-9, an initiator of the intrinsic apoptotic pathway, mediates activation of executioner procaspase-3 by cleavage of the intersubunit linker (ISL) at site 172IETD↓S. Although procaspase-6, another executioner, possesses two ISL cleavage sites (site 1, 176DVVD↓N; site 2, 190TEVD↓A), neither is directly cut by caspase-9. Thus, caspase-9 directly activates procaspase-3 but not procaspase-6. To elucidate this selectivity of caspase-9, we engineered constructs of procaspase-3 (e.g., swapping the ISL site, 172IETD↓S, with DVVDN and TEVDA) and procaspase-6 (e.g., swapping site 1, 176DVVD↓N, and site 2, 190TEVD↓A, with IETDS). Using the substrate digestion data of these constructs, we show here that the P4-P1' sequence of procaspase-6 ISL site 1 (DVVDN) can be accessed but not cleaved by caspase-9. We also found that caspase-9 can recognize the P4-P1' sequence of procaspase-6 ISL site 2 (TEVDA); however, the local context of this cleavage site is the critical factor that prevents proteolytic cleavage. Overall, our data have demonstrated that both the sequence and the local context of the ISL cleavage sites play a vital role in preventing the activation of procaspase-6 directly by caspase-9.
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Affiliation(s)
- Ishankumar V Soni
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States.,Models to Medicine Center, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
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14
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Kinases leave their mark on caspase substrates. Biochem J 2021; 478:3179-3184. [PMID: 34492095 DOI: 10.1042/bcj20210399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
Apoptosis is a cell death program that is executed by the caspases, a family of cysteine proteases that typically cleave after aspartate residues during a proteolytic cascade that systematically dismantles the dying cell. Extensive signaling crosstalk occurs between caspase-mediated proteolysis and kinase-mediated phosphorylation, enabling integration of signals from multiple pathways into the decision to commit to apoptosis. A new study from Maluch et al. examines how phosphorylation within caspase cleavage sites impacts the efficiency of substrate cleavage. The results demonstrate that while phosphorylation in close proximity to the scissile bond is generally inhibitory, it does not necessarily abrogate substrate cleavage, but instead attenuates the rate. In some cases, this inhibition can be overcome by additional favorable substrate features. These findings suggest potential nuanced physiological roles for phosphorylation of caspase substrates with exciting implications for targeting caspases with chemical probes and therapeutics.
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15
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Abstract
All living organisms depend on tightly regulated cellular networks to control biological functions. Proteolysis is an important irreversible post-translational modification that regulates most, if not all, cellular processes. Proteases are a large family of enzymes that perform hydrolysis of protein substrates, leading to protein activation or degradation. The 473 known and 90 putative human proteases are divided into 5 main mechanistic groups: metalloproteases, serine proteases, cysteine proteases, threonine proteases, and aspartic acid proteases. Proteases are fundamental to all biological systems, and when dysregulated they profoundly influence disease progression. Inhibiting proteases has led to effective therapies for viral infections, cardiovascular disorders, and blood coagulation just to name a few. Between 5 and 10% of all pharmaceutical targets are proteases, despite limited knowledge about their biological roles. More than 50% of all human proteases have no known substrates. We present here a comprehensive list of all current known human proteases. We also present current and novel biochemical tools to characterize protease functions in vitro, in vivo, and ex vivo. These tools make it achievable to define both beneficial and detrimental activities of proteases in health and disease.
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Affiliation(s)
- Longxiang Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kimberly Main
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Henry Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
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16
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Mintoo M, Chakravarty A, Tilvawala R. N-Terminomics Strategies for Protease Substrates Profiling. Molecules 2021; 26:molecules26154699. [PMID: 34361849 PMCID: PMC8348681 DOI: 10.3390/molecules26154699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023] Open
Abstract
Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.
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17
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Evaluation of the effects of phosphorylation of synthetic peptide substrates on their cleavage by caspase-3 and -7. Biochem J 2021; 478:2233-2245. [PMID: 34037204 DOI: 10.1042/bcj20210255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/02/2023]
Abstract
Caspases are a family of enzymes that play roles in cell death and inflammation. It has been suggested that in the execution phase of the apoptotic pathway, caspase-3, -6 and -7 are involved. The substrate specificities of two proteases (caspases 3 and 7) are highly similar, which complicates the design of compounds that selectively interact with a single enzyme exclusively. The recognition of residues other than Asp in the P1 position of the substrate by caspase-3/-7 has been reported, promoting interest in the effects of phosphorylation of amino acids in the direct vicinity of the scissile bond. To evaluate conflicting reports on this subject, we synthesized a series of known caspase-3 and -7 substrates and phosphorylated analogs, performed enzyme kinetic assays and mapped the peptide cleavage sites using internally quenched fluorescent peptide substrates. Caspases 3 and 7 will tolerate pSer at the P1 position but only poorly at the P2' position. Our investigation demonstrates the importance of peptide length and composition in interpreting sequence/activity relationships. Based on the results, we conclude that the relationship between caspase-3/-7 and their substrates containing phosphorylated amino acids might depend on the steric conditions and not be directly connected with ionic interactions. Thus, the precise effect of phospho-amino acid residues located in the vicinity of the cleaved bond on the regulation of the substrate specificity of caspases remains difficult to predict. Our observations allow to predict that natural phosphorylated proteins may be cleaved by caspases, but only when extended substrate binding site interactions are satisfied.
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18
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Great balls of fire: activation and signalling of inflammatory caspases. Biochem Soc Trans 2021; 49:1311-1324. [PMID: 34060593 PMCID: PMC8286819 DOI: 10.1042/bst20200986] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/17/2022]
Abstract
Innate immune responses are tightly regulated by various pathways to control infections and maintain homeostasis. One of these pathways, the inflammasome pathway, activates a family of cysteine proteases called inflammatory caspases. They orchestrate an immune response by cleaving specific cellular substrates. Canonical inflammasomes activate caspase-1, whereas non-canonical inflammasomes activate caspase-4 and -5 in humans and caspase-11 in mice. Caspases are highly specific enzymes that select their substrates through diverse mechanisms. During inflammation, caspase activity is responsible for the secretion of inflammatory cytokines and the execution of a form of lytic and inflammatory cell death called pyroptosis. This review aims to bring together our current knowledge of the biochemical processes behind inflammatory caspase activation, substrate specificity, and substrate signalling.
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19
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Weigand I, Ronchi CL, Vanselow JT, Bathon K, Lenz K, Herterich S, Schlosser A, Kroiss M, Fassnacht M, Calebiro D, Sbiera S. PKA Cα subunit mutation triggers caspase-dependent RIIβ subunit degradation via Ser 114 phosphorylation. SCIENCE ADVANCES 2021; 7:7/8/eabd4176. [PMID: 33608270 PMCID: PMC7895437 DOI: 10.1126/sciadv.abd4176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Mutations in the PRKACA gene are the most frequent cause of cortisol-producing adrenocortical adenomas leading to Cushing's syndrome. PRKACA encodes for the catalytic subunit α of protein kinase A (PKA). We already showed that PRKACA mutations lead to impairment of regulatory (R) subunit binding. Furthermore, PRKACA mutations are associated with reduced RIIβ protein levels; however, the mechanisms leading to reduced RIIβ levels are presently unknown. Here, we investigate the effects of the most frequent PRKACA mutation, L206R, on regulatory subunit stability. We find that Ser114 phosphorylation of RIIβ is required for its degradation, mediated by caspase 16. Last, we show that the resulting reduction in RIIβ protein levels leads to increased cortisol secretion in adrenocortical cells. These findings reveal the molecular mechanisms and pathophysiological relevance of the R subunit degradation caused by PRKACA mutations, adding another dimension to the deregulation of PKA signaling caused by PRKACA mutations in adrenal Cushing's syndrome.
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Affiliation(s)
- Isabel Weigand
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, 97080 Würzburg, Germany
| | - Cristina L Ronchi
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, 97080 Würzburg, Germany
- Institute of Metabolism and System Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Edgbaston, Birmingham B15 2TT, UK
| | - Jens T Vanselow
- Rudolf-Virchow-Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR), 10589 Berlin, Germany
| | - Kerstin Bathon
- Institute of Pharmacology and Toxicology and Bio-Imaging Center, University of Würzburg, 97080 Würzburg, Germany
| | - Kerstin Lenz
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, 97080 Würzburg, Germany
| | - Sabine Herterich
- Central Laboratory, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Matthias Kroiss
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, 97080 Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University of Würzburg, 97080 Würzburg, Germany
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, 97080 Würzburg, Germany.
- Central Laboratory, University Hospital Würzburg, 97080 Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University of Würzburg, 97080 Würzburg, Germany
| | - Davide Calebiro
- Institute of Metabolism and System Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Institute of Pharmacology and Toxicology and Bio-Imaging Center, University of Würzburg, 97080 Würzburg, Germany
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK
| | - Silviu Sbiera
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, 97080 Würzburg, Germany.
- Central Laboratory, University Hospital Würzburg, 97080 Würzburg, Germany
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20
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Yan J, Xie Y, Si J, Gan L, Li H, Sun C, Di C, Zhang J, Huang G, Zhang X, Zhang H. Crosstalk of the Caspase Family and Mammalian Target of Rapamycin Signaling. Int J Mol Sci 2021; 22:E817. [PMID: 33467535 PMCID: PMC7830632 DOI: 10.3390/ijms22020817] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/20/2022] Open
Abstract
Cell can integrate the caspase family and mammalian target of rapamycin (mTOR) signaling in response to cellular stress triggered by environment. It is necessary here to elucidate the direct response and interaction mechanism between the two signaling pathways in regulating cell survival and determining cell fate under cellular stress. Members of the caspase family are crucial regulators of inflammation, endoplasmic reticulum stress response and apoptosis. mTOR signaling is known to mediate cell growth, nutrition and metabolism. For instance, over-nutrition can cause the hyperactivation of mTOR signaling, which is associated with diabetes. Nutrition deprivation can inhibit mTOR signaling via SH3 domain-binding protein 4. It is striking that Ras GTPase-activating protein 1 is found to mediate cell survival in a caspase-dependent manner against increasing cellular stress, which describes a new model of apoptosis. The components of mTOR signaling-raptor can be cleaved by caspases to control cell growth. In addition, mTOR is identified to coordinate the defense process of the immune system by suppressing the vitality of caspase-1 or regulating other interferon regulatory factors. The present review discusses the roles of the caspase family or mTOR pathway against cellular stress and generalizes their interplay mechanism in cell fate determination.
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Affiliation(s)
- Junfang Yan
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yi Xie
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
| | - Lu Gan
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
| | - Hongyan Li
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
| | - Chao Sun
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
| | - Cuixia Di
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
| | - Jinhua Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Guomin Huang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xuetian Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Hong Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; (J.Y.); (J.S.); (L.G.); (H.L.); (C.S.); (C.D.); (J.Z.); (G.H.); (X.Z.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou 730000, China
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21
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Weghorst F, Mirzakhanyan Y, Samimi K, Dhillon M, Barzik M, Cunningham LL, Gershon PD, Cramer KS. Caspase-3 Cleaves Extracellular Vesicle Proteins During Auditory Brainstem Development. Front Cell Neurosci 2020; 14:573345. [PMID: 33281555 PMCID: PMC7689216 DOI: 10.3389/fncel.2020.573345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022] Open
Abstract
Sound localization requires extremely precise development of auditory brainstem circuits, the molecular mechanisms of which are largely unknown. We previously demonstrated a novel requirement for non-apoptotic activity of the protease caspase-3 in chick auditory brainstem development. Here, we used mass spectrometry to identify proteolytic substrates of caspase-3 during chick auditory brainstem development. These auditory brainstem caspase-3 substrates were enriched for proteins previously shown to be cleaved by caspase-3, especially in non-apoptotic contexts. Functional annotation analysis revealed that our caspase-3 substrates were also enriched for proteins associated with several protein categories, including proteins found in extracellular vesicles (EVs), membrane-bound nanoparticles that function in intercellular communication. The proteome of EVs isolated from the auditory brainstem was highly enriched for our caspase-3 substrates. Additionally, we identified two caspase-3 substrates with known functions in axon guidance, namely Neural Cell Adhesion Molecule (NCAM) and Neuronal-glial Cell Adhesion Molecule (Ng-CAM), that were found in auditory brainstem EVs and expressed in the auditory pathway alongside cleaved caspase-3. Taken together, these data suggest a novel developmental mechanism whereby caspase-3 influences auditory brainstem circuit formation through the proteolytic cleavage of extracellular vesicle (EV) proteins.
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Affiliation(s)
- Forrest Weghorst
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, United States
| | - Yeva Mirzakhanyan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Kian Samimi
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, United States
| | - Mehron Dhillon
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, United States
| | - Melanie Barzik
- Section on Sensory Cell Biology, NIDCD, NIH, Bethesda, MD, United States
| | - Lisa L. Cunningham
- Section on Sensory Cell Biology, NIDCD, NIH, Bethesda, MD, United States
| | - Paul D. Gershon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Karina S. Cramer
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, United States
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22
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Wang Y, Chen Y, Zhang H, Chen J, Cao J, Chen Q, Li X, Sun C. Polymethoxyflavones from citrus inhibited gastric cancer cell proliferation through inducing apoptosis by upregulating RARβ, both in vitro and in vivo. Food Chem Toxicol 2020; 146:111811. [PMID: 33058988 DOI: 10.1016/j.fct.2020.111811] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022]
Abstract
In order to discover the active anti-tumor ingredients during the flavonoids separation process of Ougan (Citrus reticulata cv. Suavissima), gastric cancer cell lines including AGS, BGC-823, and SGC-7901 were employed to evaluate the proliferation inhibition abilities of Ougan extracts, flavanone components, polymethoxyflavone components, neohesperidin, nobiletin, tangeretin, and 5-demethylnobiletin. Quantitative real-time PCR was used to detect the expression of three retinoic acid receptor genes, including RARA, RARB, and RARG. Western blot and immunohistochemistry were used to detect protein expressions. The results showed that the polymethoxyflavone components and the PMFs monomers inhibited the proliferation of three gastric cancer cell lines and induced apoptosis. The mechanism exploration found that PMFs up-regulated the expression of the RARB gene selectively and activated the Caspase3, 9, and PARP1 proteins. In addition to 5-demethylnobiletin, other PMFs also upregulated the expression of cleaved Caspase8. The mechanism was preliminarily verified by a RARβ inhibitor AGN 193109. Moreover, a nude mice tumor xenograft model confirmed the tangeretin could exhibit in vivo anti-tumor effect through inducing apoptosis and upregulating RARβ protein. All result suggested that tangeretin may be a potentially novel, safe and effective drugs with less toxicity and lesser side effects for gastric cancer therapeutics.
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Affiliation(s)
- Yue Wang
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Yunyi Chen
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - He Zhang
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Jiebiao Chen
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Jinping Cao
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Qingjun Chen
- Zanyu Tecnology Group Co., LTD, No. 628, Xinggang Road, Qingshan Lake Science and Technology City, Hangzhou, China
| | - Xian Li
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Chongde Sun
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China.
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23
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Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries. Proc Natl Acad Sci U S A 2020; 117:25464-25475. [PMID: 32973096 DOI: 10.1073/pnas.2009279117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Proteolysis is a major posttranslational regulator of biology inside and outside of cells. Broad identification of optimal cleavage sites and natural substrates of proteases is critical for drug discovery and to understand protease biology. Here, we present a method that employs two genetically encoded substrate phage display libraries coupled with next generation sequencing (SPD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical six- to eight-residue protease cleavage sites compared to state-of-the-art synthetic peptide libraries or proteomics. We applied SPD-NGS to two classes of proteases, the intracellular caspases, and the ectodomains of the sheddases, ADAMs 10 and 17. The first library (Lib 10AA) allowed us to identify 104 to 105 unique cleavage sites over a 1,000-fold dynamic range of NGS counts and produced consensus and optimal cleavage motifs based position-specific scoring matrices. A second SPD-NGS library (Lib hP), which displayed virtually the entire human proteome tiled in contiguous 49 amino acid sequences with 25 amino acid overlaps, enabled us to identify candidate human proteome sequences. We identified up to 104 natural linear cut sites, depending on the protease, and captured most of the examples previously identified by proteomics and predicted 10- to 100-fold more. Structural bioinformatics was used to facilitate the identification of candidate natural protein substrates. SPD-NGS is rapid, reproducible, simple to perform and analyze, inexpensive, and renewable, with unprecedented depth of coverage for substrate sequences, and is an important tool for protease biologists interested in protease specificity for specific assays and inhibitors and to facilitate identification of natural protein substrates.
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24
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Poreba M. Protease-activated prodrugs: strategies, challenges, and future directions. FEBS J 2020; 287:1936-1969. [PMID: 31991521 DOI: 10.1111/febs.15227] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/14/2020] [Accepted: 01/23/2020] [Indexed: 02/06/2023]
Abstract
Proteases play critical roles in virtually all biological processes, including proliferation, cell death and survival, protein turnover, and migration. However, when dysregulated, these enzymes contribute to the progression of multiple diseases, with cancer, neurodegenerative disorders, inflammation, and blood disorders being the most prominent examples. For a long time, disease-associated proteases have been used for the activation of various prodrugs due to their well-characterized catalytic activity and ability to selectively cleave only those substrates that strictly correspond with their active site architecture. To date, versatile peptide sequences that are cleaved by proteases in a site-specific manner have been utilized as bioactive linkers for the targeted delivery of multiple types of cargo, including fluorescent dyes, photosensitizers, cytotoxic drugs, antibiotics, and pro-antibodies. This platform is highly adaptive, as multiple protease-labile conjugates have already been developed, some of which are currently in clinical use for cancer treatment. In this review, recent advancements in the development of novel protease-cleavable linkers for selective drug delivery are described. Moreover, the current limitations regarding the selectivity of linkers are discussed, and the future perspectives that rely on the application of unnatural amino acids for the development of highly selective peptide linkers are also presented.
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Affiliation(s)
- Marcin Poreba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Poland
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25
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Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets. Biomolecules 2020; 10:biom10040612. [PMID: 32326640 PMCID: PMC7225963 DOI: 10.3390/biom10040612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/27/2022] Open
Abstract
Caspases are proteases conserved throughout Metazoans and responsible for initiating and executing the apoptotic program. Currently, there are over 1800 known apoptotic caspase substrates, many of them known regulators of cell proliferation and death, which makes them attractive therapeutic targets. However, most caspase substrates are by-standers, and identifying novel apoptotic mediators amongst all caspase substrates remains an unmet need. Here, we conducted an in silico search for significant apoptotic caspase targets across different species within the Vertebrata subphylum, using different criteria of conservation combined with structural features of cleavage sites. We observed that P1 aspartate is highly conserved while the cleavage sites are extensively variable and found that cleavage sites are located primarily in coiled regions composed of hydrophilic amino acids. Using the combination of these criteria, we determined the final list of the 107 most relevant caspase substrates including 30 novel targets previously unknown for their role in apoptosis and cancer. These newly identified substrates can be potential regulators of apoptosis and candidates for anti-tumor therapy.
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26
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Boice A, Bouchier-Hayes L. Targeting apoptotic caspases in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118688. [PMID: 32087180 DOI: 10.1016/j.bbamcr.2020.118688] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/20/2020] [Accepted: 02/15/2020] [Indexed: 12/30/2022]
Abstract
Members of the caspase family of proteases play essential roles in the initiation and execution of apoptosis. These caspases are divided into two groups: the initiator caspases (caspase-2, -8, -9 and -10), which are the first to be activated in response to a signal, and the executioner caspases (caspase-3, -6, and -7) that carry out the demolition phase of apoptosis. Many conventional cancer therapies induce apoptosis to remove the cancer cell by engaging these caspases indirectly. Newer therapeutic applications have been designed, including those that specifically activate individual caspases using gene therapy approaches and small molecules that repress natural inhibitors of caspases already present in the cell. For such approaches to have maximal clinical efficacy, emerging insights into non-apoptotic roles of these caspases need to be considered. This review will discuss the roles of caspases as safeguards against cancer in the context of the advantages and potential limitations of targeting apoptotic caspases for the treatment of cancer.
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Affiliation(s)
- Ashley Boice
- Department of Pediatrics, Division of Hematology-Oncology and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Lisa Bouchier-Hayes
- Department of Pediatrics, Division of Hematology-Oncology and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA.
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27
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Qi E, Wang D, Li Y, Li G, Su Z. Revealing favorable and unfavorable residues in cooperative positions in protease cleavage sites. Biochem Biophys Res Commun 2019; 519:714-720. [PMID: 31543345 DOI: 10.1016/j.bbrc.2019.09.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/14/2019] [Indexed: 11/17/2022]
Abstract
Proteases play critical roles in a wide variety of fundamental biological functions, and numerous protease inhibitors have been developed to treat various diseases including cancer. A wide range of experimental and computational methods have been developed to investigate the specificity and catalytic mechanisms of proteases. However, these methods only focused on the preferences of a single position around a cleavage site in a substrate, rarely on the compositionality of the subsites. We present new methods to quantify the specificity of proteases by considering the combinatorial patterns of amino acid residuals of cleavage sites in substrates. By incorporating the preference at positions, we modeled three types of favorable combinations of residues in cleavage sites. Moreover, by constructing a relationship weight matrix of residues between two positions, we can easily identify unfavorable combinations of residues at the positions. Applying these methods to a set of known cleavage sites of proteases, we revealed numerous favorable and unfavorable residues in cooperative positions in the protease cleavage sites. The results can help understand the specificity and catalytic mechanisms of proteases. To our knowledge, this is the first study that quantifies unfavorable combinations of amino acids between two sites. Furthermore, this method is not limited to the study of proteases and cleavage sites, and can be generalized to uncover the relationships of residues at meaningful sites in other proteins.
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Affiliation(s)
- Enfeng Qi
- School of Mathematics, Shandong University, Jinan, 250100, China; School of Mathematics and Statistics, Guangxi Normal University, Guilin, 541000, China
| | - Dongyu Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Yang Li
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100, China.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, 28223, USA.
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28
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Solania A, González-Páez GE, Wolan DW. Selective and Rapid Cell-Permeable Inhibitor of Human Caspase-3. ACS Chem Biol 2019; 14:2463-2470. [PMID: 31334631 DOI: 10.1021/acschembio.9b00564] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Individual roles and overlapping functionalities of 12 human caspases during apoptosis and other cellular processes remain poorly resolved primarily due to a lack of chemical tools. Here we present a new selective caspase-3 inhibitor, termed Ac-ATS010-KE, with rapid and irreversible binding kinetics. Relative to previously designed caspase-3-selective molecules that have tremendously abated inhibitory rates and thus limited use in biological settings, the improved kinetics of Ac-ATS010-KE permits its use in a cell-based capacity. We demonstrate that Ac-ATS010-KE prevents apoptosis with comparable efficacy to the general caspase inhibitor Ac-DEVD-KE and surprisingly does so without side-chain methylation. This observation is in contrast to the well-established peptide modification strategy typically employed for improving cellular permeability. Ac-ATS010-KE protects against extrinsic apoptosis, which demonstrates the utility of a thiophene carboxylate leaving group in biological settings, challenges the requisite neutralization of free carboxylic acids to improve cell permeability, and provides a tool-like compound to interrogate the role of caspase-3 in a variety of cellular processes.
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Affiliation(s)
- Angelo Solania
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gonzalo E. González-Páez
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis W. Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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29
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Abstract
Proteases are key regulators of vital biological processes, such as apoptosis, cell differentiation, viral infection and neurodegeneration. Proteases are tightly regulated, largely because proteolysis is a unique post-translational modification (PTM) that is essentially irreversible. In order to understand the role of proteases in health and disease, the identification of protease substrates is an important step toward our understanding of their biological functions. Classic approaches for the study of proteolysis in complex mixtures employ gel electrophoresis and mass spectrometry. Such approaches typically identify a few protein substrates at a time but often fail to identify specific cleavage site locations. In contrast, modern proteomic methods using enrichment of proteolytic protein fragments can lead to the identification of hundreds of modified peptides with precise cleavage site determination in a single experiment. In this manuscript, we will review recent advances in N-terminomics methods and highlight key studies that have taken advantage of these technologies to advance our understanding of the role of proteases in cellular physiology.
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Affiliation(s)
- Shu Yue Luo
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
| | - Luam Ellen Araya
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
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30
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Maluch I, Czarna J, Drag M. Applications of Unnatural Amino Acids in Protease Probes. Chem Asian J 2019; 14:4103-4113. [PMID: 31593336 DOI: 10.1002/asia.201901152] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/01/2019] [Indexed: 12/11/2022]
Abstract
Since proteases are involved in a wide range of physiological and disease states, the development of novel tools for imaging proteolytic enzyme activity is attracting increasing interest from scientists. Peptide substrates containing proteinogenic amino acids are often the first line of defining enzyme specificity. This Minireview outlines examples of major recent advances in probing proteases using unnatural amino acid residues, which greatly expands the possibilities for designing substrate probes and inhibitory activity-based probes. This approach already yielded innovative probes that selectively target only one active protease within the group of enzymes exhibiting similar specificity both in cellular assays and in bioimaging research.
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Affiliation(s)
- Izabela Maluch
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Justyna Czarna
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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31
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Ly HGT, Mihaylov TT, Proost P, Pierloot K, Harvey JN, Parac‐Vogt TN. Chemical Mimics of Aspartate‐Directed Proteases: Predictive and Strictly Specific Hydrolysis of a Globular Protein at Asp−X Sequence Promoted by Polyoxometalate Complexes Rationalized by a Combined Experimental and Theoretical Approach. Chemistry 2019; 25:14370-14381. [DOI: 10.1002/chem.201902675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/13/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Hong Giang T. Ly
- Laboratory of Bioinorganic ChemistryDepartment of ChemistryKU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Tzvetan T. Mihaylov
- Laboratory of Computational Coordination ChemistryDepartment of ChemistryKU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Paul Proost
- Laboratory of Molecular ImmunologyRega InstituteDepartment of Microbiology, Immunology, and TransplantationKU Leuven Herestraat 49 3000 Leuven Belgium
| | - Kristine Pierloot
- Laboratory of Computational Coordination ChemistryDepartment of ChemistryKU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Jeremy N. Harvey
- Laboratory of Computational Coordination ChemistryDepartment of ChemistryKU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Tatjana N. Parac‐Vogt
- Laboratory of Bioinorganic ChemistryDepartment of ChemistryKU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
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32
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Pham B, Eron SJ, Hill ME, Li X, Fahie MA, Hardy JA, Chen M. A Nanopore Approach for Analysis of Caspase-7 Activity in Cell Lysates. Biophys J 2019; 117:844-855. [PMID: 31427065 PMCID: PMC6731459 DOI: 10.1016/j.bpj.2019.07.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/02/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
Caspases are an important protease family that coordinate inflammation and programmed cell death. Two closely related caspases, caspase-3 and caspase-7, exhibit largely overlapping substrate specificities. Assessing their proteolytic activities individually has therefore proven extremely challenging. Here, we constructed an outer membrane protein G (OmpG) nanopore with a caspase substrate sequence DEVDG grafted into one of the OmpG loops. Cleavage of the substrate sequence in the nanopore by caspase-7 generated a characteristic signal in the current recording of the OmpG nanopore that allowed the determination of the activity of caspase-7 in Escherichia coli cell lysates. Our approach may provide a framework for the activity-based profiling of proteases that share highly similar substrate specificity spectrums.
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Affiliation(s)
- Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Scott J Eron
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Maureen E Hill
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Xin Li
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Monifa A Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts.
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33
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Martins AM, Latham JA, Martel PJ, Barr I, Iavarone AT, Klinman JP. A two-component protease in Methylorubrum extorquens with high activity toward the peptide precursor of the redox cofactor pyrroloquinoline quinone. J Biol Chem 2019; 294:15025-15036. [PMID: 31427437 DOI: 10.1074/jbc.ra119.009684] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
Pyrroloquinoline quinone is a prominent redox cofactor in many prokaryotes, produced from a ribosomally synthesized and post-translationally modified peptide PqqA via a pathway comprising four conserved proteins PqqB-E. These four proteins are now fairly well-characterized and span radical SAM activity (PqqE), aided by a peptide chaperone (PqqD), a dual hydroxylase (PqqB), and an eight-electron, eight-proton oxidase (PqqC). A full description of this pathway has been hampered by a lack of information regarding a protease/peptidase required for the excision of an early, cross-linked di-amino acid precursor to pyrroloquinoline quinone. Herein, we isolated and characterized a two-component heterodimer protein from the α-proteobacterium Methylobacterium (Methylorubrum) extorquens that can rapidly catalyze cleavage of PqqA into smaller peptides. Using pulldown assays, surface plasmon resonance, and isothermal calorimetry, we demonstrated the formation of a complex PqqF/PqqG, with a KD of 300 nm We created a molecular model of the heterodimer by comparison with the Sphingomonas sp. A1 M16B Sph2681/Sph2682 protease. Analysis of time-dependent patterns for the appearance of proteolysis products indicates high specificity of PqqF/PqqG for serine side chains. We hypothesize that PqqF/PqqG initially cleaves between the PqqE/PqqD-generated cross-linked form of PqqA, with nonspecific cellular proteases completing the release of a suitable substrate for the downstream enzyme PqqB. The finding of a protease that specifically targets serine side chains is rare, and we propose that this activity may be useful in proteomic analyses of the large family of proteins that have undergone post-translational phosphorylation at serine.
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Affiliation(s)
- Ana M Martins
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720
| | - John A Latham
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 8020
| | - Paulo J Martel
- Centre for Biomedical Research, Faculty of Sciences and Technology, University of the Algarve, 8005-139 Faro, Portugal
| | - Ian Barr
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720.,Department of Chemistry, University of California Berkeley, Berkeley, California 94720
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720.,Department of Chemistry, University of California Berkeley, Berkeley, California 94720
| | - Judith P Klinman
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720 .,Department of Chemistry, University of California Berkeley, Berkeley, California 94720.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720
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34
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Willems P, Horne A, Van Parys T, Goormachtig S, De Smet I, Botzki A, Van Breusegem F, Gevaert K. The Plant PTM Viewer, a central resource for exploring plant protein modifications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:752-762. [PMID: 31004550 DOI: 10.1111/tpj.14345] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 05/15/2023]
Abstract
Post-translational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site-specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry-based PTM data to remain at pace with future PTM plant studies.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
| | - Alison Horne
- VIB Bioinformatics Core, VIB, 9052, Ghent, Belgium
| | | | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | | | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
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35
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The prodomain of caspase-3 regulates its own removal and caspase activation. Cell Death Discov 2019; 5:56. [PMID: 30701088 PMCID: PMC6349851 DOI: 10.1038/s41420-019-0142-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/08/2018] [Accepted: 10/16/2018] [Indexed: 12/28/2022] Open
Abstract
Caspase-3 is a cysteine–aspartic acid protease that cleaves cellular targets and executes cell death. Our current understanding is caspase-3 is activated by the cleavage of the interdomain linker and then subsequent cleavage of the N-terminal prodomain. However, previous reports have suggested that removal of the prodomain can result in the constitutive activation of caspase-3, although other studies have not observed this. To address this question in a more physiological setting, we developed an inducible doxycycline system to express a mutant form of caspase-3 that lacks the prodomain (∆28). We found that the removal of the prodomain renders the cells more susceptible to death signals, but the caspase is not constitutively active. To elucidate the regions of the prodomain that regulate activity, we created deletion constructs that remove 10 and 19 N-terminal amino acids. Surprisingly, removal of the first 10 amino acids renders caspase-3 inactive. Following serum withdrawal, the interdomain linker is cleaved, however, the remaining prodomain is not removed. Therefore, there is a specific amino acid or stretch of amino acids within the first 10 that are important for prodomain removal and caspase-3 function. We created different point mutations within the prodomain and found amino acid D9 is vital for caspase-3 function. We hypothesize that an initial cleavage event at D9 is required to allow cleavage at D28 that causes the complete removal of the prodomain allowing for full caspase activation. Together these findings demonstrate a previously unknown role of the prodomain in caspase activation.
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36
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Kasperkiewicz P, Kołt S, Janiszewski T, Groborz K, Poręba M, Snipas SJ, Salvesen GS, Drąg M. Determination of extended substrate specificity of the MALT1 as a strategy for the design of potent substrates and activity-based probes. Sci Rep 2018; 8:15998. [PMID: 30375474 PMCID: PMC6207715 DOI: 10.1038/s41598-018-34476-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/16/2018] [Indexed: 11/10/2022] Open
Abstract
Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) belongs to the CD clan of cysteine proteases. MALT1 is a unique enzyme among this clan because it recognizes the basic amino acid arginine in the P1 pocket. Previous studies carried out with natural amino acids revealed the substrate specificity of the P4-P1 pockets of MALT1 but have provided only limited information about the catalytic preferences of this enzyme. In this study, we exploited Hybrid Combinatorial Substrate Library and Internally Quenched Fluorescence substrate technologies to interrogate the extended substrate specificity profile of the S5-S2' active site pockets using unnatural amino acids. This strategy resulted in the design of a peptide-based fluorogenic substrate, which exhibited significant activity toward MALT1. Subsequently, the substrate sequence was further utilized to develop potent, irreversible activity-based probes.
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Affiliation(s)
- Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Sonia Kołt
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Tomasz Janiszewski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Katarzyna Groborz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Poręba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.,NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Scott J Snipas
- NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Guy S Salvesen
- NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.
| | - Marcin Drąg
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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37
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Bachhawat N. PE-only/PE_PGRS proteins of Mycobacterium tuberculosis contain a conserved tetra-peptide sequence DEVS/DXXS that is a potential caspase-3 cleavage motif. J Biosci 2018; 43:597-604. [PMID: 30207307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mycobacterium tuberculosis H37Rv is an intracellular pathogen responsible for causing tuberculosis in humans. The M. tuberculosis genome has been shown to contain a very large and unique family of PE proteins made of two sub-families: PE-only and PE_PGRS proteins. These two subtypes of proteins play a crucial role in the pathogenesis of the microbe. However, despite numerous investigations, the role of these proteins in disease development remains obscure. In this study, sequence analysis with a search for short conserved motifs revealed a conserved tetra-peptide motif DEVS/DXXS at the PE domain of almost every PE-only and PE_PGRS protein. The motif was found at a distance of 43-46 amino acids from the N-terminal of PE_PGRS proteins, and at a distance of between 35 and 82 amino acids of the PE-only proteins. As phosphorylation of the serine residue of this tetra-peptide could yield a motif similar to the caspase-3 binding recognition sequence DEVD/E, the region from a representative PE_PGRS protein (PE_PGRS45) was docked to human caspase-3. Strong interactions of only the protein containing the phosphorylated motif (DEVpS/DXXpS) to caspase-3 were observed. This suggested that the conserved DEVS/DXXS motif could have evolved for phosphorylation and subsequent recognition by caspase-3. These findings have important implications in unravelling the role of these PE proteins in mycobacterial infection.
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38
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Vizovišek M, Vidmar R, Drag M, Fonović M, Salvesen GS, Turk B. Protease Specificity: Towards In Vivo Imaging Applications and Biomarker Discovery. Trends Biochem Sci 2018; 43:829-844. [PMID: 30097385 DOI: 10.1016/j.tibs.2018.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/05/2018] [Accepted: 07/12/2018] [Indexed: 02/06/2023]
Abstract
Proteases are considered of major importance in biomedical research because of their crucial roles in health and disease. Their ability to hydrolyze their protein and peptide substrates at single or multiple sites, depending on their specificity, makes them unique among the enzymes. Understanding protease specificity is therefore crucial to understand their biology as well as to develop tools and drugs. Recent advancements in the fields of proteomics and chemical biology have improved our understanding of protease biology through extensive specificity profiling and identification of physiological protease substrates. There are growing efforts to transfer this knowledge into clinical modalities, but their success is often limited because of overlapping protease features, protease redundancy, and chemical tools lacking specificity. Herein, we discuss the current trends and challenges in protease research and how to exploit the growing information on protease specificities for understanding protease biology, as well as for development of selective substrates, cleavable linkers, and activity-based probes and for biomarker discovery.
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Affiliation(s)
- Matej Vizovišek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Robert Vidmar
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marko Fonović
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Guy S Salvesen
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
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39
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PE-only/PE_PGRS proteins of Mycobacterium tuberculosis contain a conserved tetra-peptide sequence DEVS/DXXS that is a potential caspase-3 cleavage motif. J Biosci 2018. [DOI: 10.1007/s12038-018-9775-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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40
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Yozwiak CE, Hirschhorn T, Stockwell BR. Toward a Microparticle-Based System for Pooled Assays of Small Molecules in Cellular Contexts. ACS Chem Biol 2018; 13:761-771. [PMID: 29365249 DOI: 10.1021/acschembio.8b00043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Experimental approaches to the discovery of small molecule probes and drug candidates often use biochemical or cell-based screening of large libraries (>105) of small molecules. Small molecules of interest are tested one at a time in individual wells of a microtiter plate, at a significant cost in time and resources. Furthermore, evaluation of large numbers of compounds in such assays requires robust cellular or biochemical screening formats that may not be relevant to the contexts found in human patients. We envision a solution to these issues that involves a pooled system of small molecule screening, which would require development of numerous new technologies, and solutions to several key challenges. We report here that a microparticle-based screening system can allow for screening of small molecules in such a pooled fashion, analogous to the pooled screens of genetic reagents that have been powerfully deployed in recent years. We developed a cleavable linker that can link small molecules of interest to silica microparticle beads, a DNA tag encoding the identity of the small molecule on each bead that was attached to the silica beads through a photocleavable linker to enable its amplification, and a bead-based fluorescent sensor that can report on the activity of small molecules in cells. We suggest that this pooled small molecule screening system could ultimately be useful for drug and probe discovery, allowing rapid and inexpensive screening of small molecules in assays of relevance to human diseases.
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Affiliation(s)
- Carrie E. Yozwiak
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tal Hirschhorn
- Department of Biological Sciences, Columbia University, Northwest Corner Building, MC 4846, 550 West 120th Street, New York, New York 10027, United States
| | - Brent R. Stockwell
- Department of Chemistry, Columbia University, New York, New York 10027, United States
- Department of Biological Sciences, Columbia University, Northwest Corner Building, MC 4846, 550 West 120th Street, New York, New York 10027, United States
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41
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Abstract
The cysteine protease Caspase-6 (Casp6) is a potential therapeutic target of Alzheimer Disease (AD) and age-dependent cognitive impairment. To assess if Casp6 is essential to human health, we investigated the effect of CASP6 variants sequenced from healthy humans on Casp6 activity. Here, we report the effects of two rare Casp6 amino acid polymorphisms, R65W and G66R, on the catalytic function and structure of Casp6. The G66R substitution eliminated and R65W substitution significantly reduced Casp6 catalytic activity through impaired substrate binding. In contrast to wild-type Casp6, both Casp6 variants were unstable and inactive in transfected mammalian cells. In addition, Casp6-G66R acted as a dominant negative inhibitor of wild-type Casp6. The R65W and G66R substitutions caused perturbations in substrate recognition and active site organization as revealed by molecular dynamics simulations. Our results suggest that full Casp6 activity may not be essential for healthy humans and support the use of Casp6 inhibitors against Casp6-dependent neurodegeneration in age-dependent cognitive impairment and AD. Furthermore, this work illustrates that studying natural single amino acid polymorphisms of enzyme drug targets is a promising approach to uncover previously uncharacterized regulatory sites important for enzyme activity.
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42
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Phosphorylation by protein kinase A disassembles the caspase-9 core. Cell Death Differ 2018; 25:1025-1039. [PMID: 29352269 DOI: 10.1038/s41418-017-0052-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 01/04/2023] Open
Abstract
Caspases, the cysteine proteases which facilitate the faithful execution of apoptosis, are tightly regulated by a number of mechanisms including phosphorylation. In response to cAMP, PKA phosphorylates caspase-9 at three sites preventing caspase-9 activation, and suppressing apoptosis progression. Phosphorylation of caspase-9 by PKA at the functionally relevant site Ser-183 acts as an upstream block of the apoptotic cascade, directly inactivating caspase-9 by a two-stage mechanism. First, Ser-183 phosphorylation prevents caspase-9 self-processing and directly blocks substrate binding. In addition, Ser-183 phosphorylation breaks the fundamental interactions within the caspase-9 core, promoting disassembly of the large and small subunits. This occurs despite Ser-183 being a surface residue distal from the interface between the large and small subunits. This phosphorylation-induced disassembly promotes the formation of ordered aggregates around 20 nm in diameter. Similar aggregates of caspase-9 have not been previously reported. This two-stage regulatory mechanism for caspase-9 has likewise not been reported previously but may be conserved across the caspases.
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43
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Serrano BP, Szydlo HS, Alfandari D, Hardy JA. Active site-adjacent phosphorylation at Tyr-397 by c-Abl kinase inactivates caspase-9. J Biol Chem 2017; 292:21352-21365. [PMID: 29066624 DOI: 10.1074/jbc.m117.811976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/11/2017] [Indexed: 12/11/2022] Open
Abstract
Caspase-9 (casp-9) is an initiator caspase and plays a central role in activating apoptotic cell death. Control of all caspases is tightly regulated by a series of phosphorylation events enacted by several different kinases. Caspase-9 is the most heavily phosphorylated of all caspases, with phosphorylation of at least 11 distinct residues in all three caspase-9 domains by nine kinases. Caspase-9 phosphorylation by the non-receptor tyrosine kinase c-Abl at Tyr-153 reportedly leads to caspase-9 activation. All other phosphorylation events on caspases have been shown to block proteolytic function by a number of mechanisms, so we sought to unravel the molecular mechanism of the putative caspase-9 activation by phosphorylation. Surprisingly, we observed no evidence for Tyr-153 phosphorylation of caspase-9 in vitro or in cells, suggesting that Tyr-153 is not phosphorylated by c-Abl. Instead, we identified a new site for c-Abl-mediated phosphorylation, Tyr-397. This residue is adjacent to the caspase-9 active site but, as a member of the second shell, not a residue that directly contacts substrate. Our results further indicate that Tyr-397 is the dominant site of c-Abl phosphorylation both in vitro and upon c-Abl activation in cells. Of note, phosphorylation at this site inhibits caspase-9 activity, and the bulk of the added phosphate moiety appeared to directly block substrate binding. c-Abl plays both proapoptotic and prosurvival roles, and our findings suggest that c-Abl's effects on caspase-9 activity promote the prosurvival mode.
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Affiliation(s)
| | - Hannah S Szydlo
- Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003
| | - Dominique Alfandari
- Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003
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44
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Prolonged seizure activity causes caspase dependent cleavage and dysfunction of G-protein activated inwardly rectifying potassium channels. Sci Rep 2017; 7:12313. [PMID: 28951616 PMCID: PMC5615076 DOI: 10.1038/s41598-017-12508-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/08/2017] [Indexed: 01/09/2023] Open
Abstract
Recurrent high-frequency epileptic seizures cause progressive hippocampal sclerosis, which is associated with caspase-3 activation and NMDA receptor-dependent excitotoxicity. However, the identity of caspase-3 substrates that contribute to seizure-induced hippocampal atrophy remains largely unknown. Here, we show that prolonged high-frequency epileptiform discharges in cultured hippocampal neurons leads to caspase-dependent cleavage of GIRK1 and GIRK2, the major subunits of neuronal G protein-activated inwardly rectifying potassium (GIRK) channels that mediate membrane hyperpolarization and synaptic inhibition in the brain. We have identified caspase-3 cleavage sites in GIRK1 (387ECLD390) and GIRK2 (349YEVD352). The YEVD motif is highly conserved in GIRK2-4, and located within their C-terminal binding sites for Gβγ proteins that mediate membrane-delimited GIRK activation. Indeed, the cleaved GIRK2 displays reduced binding to Gβγ and cannot coassemble with GIRK1. Loss of an ER export motif upon cleavage of GIRK2 abolishes surface and current expression of GIRK2 homotetramic channels. Lastly, kainate-induced status epilepticus causes GIRK1 and GIRK2 cleavage in the hippocampus in vivo. Our findings are the first to show direct cleavage of GIRK1 and GIRK2 subunits by caspase-3, and suggest the possible role of caspase-3 mediated down-regulation of GIRK channel function and expression in hippocampal neuronal injury during prolonged epileptic seizures.
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45
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Vidmar R, Vizovišek M, Turk D, Turk B, Fonović M. Protease cleavage site fingerprinting by label-free in-gel degradomics reveals pH-dependent specificity switch of legumain. EMBO J 2017; 36:2455-2465. [PMID: 28733325 DOI: 10.15252/embj.201796750] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 01/09/2023] Open
Abstract
Determination of protease specificity is of crucial importance for understanding protease function. We have developed the first gel-based label-free proteomic approach (DIPPS-direct in-gel profiling of protease specificity) that enables quick and reliable determination of protease cleavage specificities under large variety of experimental conditions. The methodology is based on in-gel digestion of the gel-separated proteome with the studied protease, enrichment of cleaved peptides by gel extraction, and subsequent mass spectrometry analysis combined with a length-limited unspecific database search. We applied the methodology to profile ten proteases ranging from highly specific (trypsin, endoproteinase GluC, caspase-7, and legumain) to broadly specific (matrix-metalloproteinase-3, thermolysin, and cathepsins K, L, S, and V). Using DIPPS, we were able to perform specificity profiling of thermolysin at its optimal temperature of 75°C, which confirmed the applicability of the method to extreme experimental conditions. Moreover, DIPPS enabled the first global specificity profiling of legumain at pH as low as 4.0, which revealed a pH-dependent change in the specificity of this protease, further supporting its broad applicability.
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Affiliation(s)
- Robert Vidmar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,International Postgraduate School Jožef Stefan, Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,International Postgraduate School Jožef Stefan, Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia .,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia .,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
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46
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Tsapras P, Nezis IP. Caspase involvement in autophagy. Cell Death Differ 2017; 24:1369-1379. [PMID: 28574508 DOI: 10.1038/cdd.2017.43] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/24/2017] [Accepted: 02/28/2017] [Indexed: 12/26/2022] Open
Abstract
Caspases are a family of cysteine proteases widely known as the principal mediators of the apoptotic cell death response, but considerably less so as the contributors to the regulation of pathways outside cellular demise. In regards to autophagy, the modulatory roles of caspases have only recently begun to be adequately described. In contrast to apoptosis, autophagy promotes cell survival by providing energy and nutrients through the lysosomal degradation of cytoplasmic constituents. Under basal conditions autophagy and apoptosis cross-regulate each other through an elaborate network of interconnections which also includes the interplay between autophagy-related proteins (ATGs) and caspases. In this review we focus on the effects of this crosstalk at the cellular level, as we aim to concentrate the main observations from research conducted so far on the fine-tuning of autophagy by caspases. Several members of this protease-family have been found to directly interact with key ATGs involved in different tiers across the autophagic cascade. Therefore, we firstly outline the core mechanism of macroautophagy in brief. In an effort to emphasize the importance of the intricate cross-regulation of ATGs and caspases, we also present examples of autophagy's contribution to apoptotic cell death during development.
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Affiliation(s)
| | - Ioannis P Nezis
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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47
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Caspases and their substrates. Cell Death Differ 2017; 24:1380-1389. [PMID: 28498362 DOI: 10.1038/cdd.2017.44] [Citation(s) in RCA: 506] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 12/14/2022] Open
Abstract
, or for pyroptosis, gasdermin D. For the most part, it appears that cleavage events function cooperatively in the cell death process to generate a proteolytic synthetic lethal outcome. In contrast to apoptosis, far less is known about caspase biology in non-apoptotic cellular processes, such as cellular remodeling, including which caspases are activated, the mechanisms of their activation and deactivation, and the key substrate targets. Here we survey the progress made in global identification of caspase substrates using proteomics and the exciting new avenues these studies have opened for understanding the molecular logic of substrate cleavage in apoptotic and non-apoptotic processes.
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48
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Duclos C, Lavoie C, Denault JB. Caspases rule the intracellular trafficking cartel. FEBS J 2017; 284:1394-1420. [PMID: 28371378 DOI: 10.1111/febs.14071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/17/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022]
Abstract
During apoptosis, caspases feast on several hundreds of cellular proteins to orchestrate rapid cellular demise. Indeed, caspases are known to get a taste of every cellular process in one way or another, activating some, but most often shutting them down. Thus, it is not surprising that caspases proteolyze proteins involved in intracellular trafficking with particularly devastating consequences for this important process. This review article focuses on how caspases target the machinery responsible for smuggling goods within and outside the cell.
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Affiliation(s)
- Catherine Duclos
- Institut de Pharmacologie de Sherbrooke, Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC, Canada
| | - Christine Lavoie
- Institut de Pharmacologie de Sherbrooke, Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC, Canada
| | - Jean-Bernard Denault
- Institut de Pharmacologie de Sherbrooke, Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC, Canada
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49
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Affiliation(s)
- Catherine M Duclos
- Department of Pharmacology-Physiology and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC, Canada J1H 5N4
| | - Audrey Champagne
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC, Canada J1H 5N4
| | - Julie C Carrier
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC, Canada J1H 5N4
| | - Caroline Saucier
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC, Canada J1H 5N4
| | - Christine L Lavoie
- Department of Pharmacology-Physiology and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC, Canada J1H 5N4
| | - Jean-Bernard Denault
- Department of Pharmacology-Physiology and Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC, Canada J1H 5N4
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50
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Highly sensitive and adaptable fluorescence-quenched pair discloses the substrate specificity profiles in diverse protease families. Sci Rep 2017; 7:43135. [PMID: 28230157 PMCID: PMC5322338 DOI: 10.1038/srep43135] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/19/2017] [Indexed: 12/20/2022] Open
Abstract
Internally quenched fluorescent (IQF) peptide substrates originating from FRET (Förster Resonance Energy Transfer) are powerful tool for examining the activity and specificity of proteases, and a variety of donor/acceptor pairs are extensively used to design individual substrates and combinatorial libraries. We developed a highly sensitive and adaptable donor/acceptor pair that can be used to investigate the substrate specificity of cysteine proteases, serine proteases and metalloproteinases. This novel pair comprises 7-amino-4-carbamoylmethylcoumarin (ACC) as the fluorophore and 2,4-dinitrophenyl-lysine (Lys(DNP)) as the quencher. Using caspase-3, caspase-7, caspase-8, neutrophil elastase, legumain, and two matrix metalloproteinases (MMP2 and MMP9), we demonstrated that substrates containing ACC/Lys(DNP) exhibit 7 to 10 times higher sensitivity than conventional 7-methoxy-coumarin-4-yl acetic acid (MCA)/Lys(DNP) substrates; thus, substantially lower amounts of substrate and enzyme can be used for each assay. We therefore propose that the ACC/Lys(DNP) pair can be considered a novel and sensitive scaffold for designing substrates for any group of endopeptidases. We further demonstrate that IQF substrates containing unnatural amino acids can be used to investigate protease activities/specificities for peptides containing post-translationally modified amino acids. Finally, we used IQF substrates to re-investigate the P1-Asp characteristic of caspases, thus demonstrating that some human caspases can also hydrolyze substrates after glutamic acid.
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