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Zhra M, Qasem RJ, Aldossari F, Saleem R, Aljada A. A Comprehensive Exploration of Caspase Detection Methods: From Classical Approaches to Cutting-Edge Innovations. Int J Mol Sci 2024; 25:5460. [PMID: 38791499 PMCID: PMC11121653 DOI: 10.3390/ijms25105460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The activation of caspases is a crucial event and an indicator of programmed cell death, also known as apoptosis. These enzymes play a central role in cancer biology and are considered one promising target for current and future advancements in therapeutic interventions. Traditional methods of measuring caspase activity such as antibody-based methods provide fundamental insights into their biological functions, and are considered essential tools in the fields of cell and cancer biology, pharmacology and toxicology, and drug discovery. However, traditional methods, though extensively used, are now recognized as having various shortcomings. In addition, these methods fall short of providing solutions to and matching the needs of the rapid and expansive progress achieved in studying caspases. For these reasons, there has been a continuous improvement in detection methods for caspases and the network of pathways involved in their activation and downstream signaling. Over the past decade, newer methods based on cutting-edge state-of-the-art technologies have been introduced to the biomedical community. These methods enable both the temporal and spatial monitoring of the activity of caspases and their downstream substrates, and with enhanced accuracy and precision. These include fluorescent-labeled inhibitors (FLIs) for live imaging, single-cell live imaging, fluorescence resonance energy transfer (FRET) sensors, and activatable multifunctional probes for in vivo imaging. Recently, the recruitment of mass spectrometry (MS) techniques in the investigation of these enzymes expanded the repertoire of tools available for the identification and quantification of caspase substrates, cleavage products, and post-translational modifications in addition to unveiling the complex regulatory networks implicated. Collectively, these methods are enabling researchers to unravel much of the complex cellular processes involved in apoptosis, and are helping generate a clearer and comprehensive understanding of caspase-mediated proteolysis during apoptosis. Herein, we provide a comprehensive review of various assays and detection methods as they have evolved over the years, so to encourage further exploration of these enzymes, which should have direct implications for the advancement of therapeutics for cancer and other diseases.
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Affiliation(s)
- Mahmoud Zhra
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Rani J. Qasem
- Department of Pharmacology and Pharmacy Practice, College of Pharmacy, Middle East University, Amman 11831, Jordan
| | - Fai Aldossari
- Zoology Department, College of Science, King Saud University, Riyadh 12372, Saudi Arabia
| | - Rimah Saleem
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ahmad Aljada
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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2
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Damnjanović J, Odake N, Fan J, Camagna M, Jia B, Kojima T, Nemoto N, Hitomi K, Nakano H. Comprehensive analysis of transglutaminase substrate preference by cDNA display coupled with next-generation sequencing and bioinformatics. Sci Rep 2022; 12:13578. [PMID: 35945258 PMCID: PMC9363462 DOI: 10.1038/s41598-022-17494-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
cDNA display is an in vitro display technology based on a covalent linkage between a protein and its corresponding mRNA/cDNA, widely used for the selection of proteins and peptides from large libraries (1012) in a high throughput manner, based on their binding affinity. Here, we developed a platform using cDNA display and next-generation sequencing (NGS) for rapid and comprehensive substrate profiling of transglutaminase 2 (TG2), an enzyme crosslinking glutamine and lysine residues in proteins. After screening and selection of the control peptide library randomized at the reactive glutamine, a combinatorial library of displayed peptides randomized at positions - 1, + 1, + 2, and + 3 from the reactive glutamine was screened followed by NGS and bioinformatic analysis, which indicated a strong preference of TG2 towards peptides with glutamine at position - 1 (Gln-Gln motif), and isoleucine or valine at position + 3. The highly enriched peptides indeed contained the indicated sequence and showed a higher reactivity as TG2 substrates than the peptide previously selected by phage display, thus representing the novel candidate peptide probes for TG2 research. Furthermore, the obtained information on substrate profiling can be used to identify potential TG2 protein targets. This platform will be further used for the substrate profiling of other TG isozymes, as well as for the selection and evolution of larger biomolecules.
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Affiliation(s)
- Jasmina Damnjanović
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Nana Odake
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Jicheng Fan
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Tigermed, Hangzhou, China
| | - Maurizio Camagna
- Laboratory of Plant Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Beixi Jia
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, 468-8502, Japan
| | - Naoto Nemoto
- Laboratory of Evolutionary Molecular Engineering, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Kiyotaka Hitomi
- Laboratory of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Hideo Nakano
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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3
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Du Y, Hultquist JF, Zhou Q, Olson A, Tseng Y, Zhang TH, Hong M, Tang K, Chen L, Meng X, McGregor MJ, Dai L, Gong D, Martin-Sancho L, Chanda S, Li X, Bensenger S, Krogan NJ, Sun R. mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Nat Commun 2020; 11:2449. [PMID: 32415096 PMCID: PMC7229031 DOI: 10.1038/s41467-020-16140-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/13/2020] [Indexed: 12/19/2022] Open
Abstract
A comprehensive examination of protein-protein interactions (PPIs) is fundamental for the understanding of cellular machineries. However, limitations in current methodologies often prevent the detection of PPIs with low abundance proteins. To overcome this challenge, we develop a mRNA display with library of even-distribution (md-LED) method that facilitates the detection of low abundance binders with high specificity and sensitivity. As a proof-of-principle, we apply md-LED to IAV NS1 protein. Complementary to AP-MS, md-LED enables us to validate previously described PPIs as well as to identify novel NS1 interactors. We show that interacting with FASN allows NS1 to directly regulate the synthesis of cellular fatty acids. We also use md-LED to identify a mutant of NS1, D92Y, results in a loss of interaction with CPSF1. The use of high-throughput sequencing as the readout for md-LED enables sensitive quantification of interactions, ultimately enabling massively parallel experimentation for the investigation of PPIs.
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Affiliation(s)
- Yushen Du
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA.
- Cancer Institute, ZJU-UCLA Joint Center for Medical Education and Research, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
- California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Quan Zhou
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Anders Olson
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Yenwen Tseng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Tian-Hao Zhang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Mengying Hong
- Cancer Institute, ZJU-UCLA Joint Center for Medical Education and Research, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Kejun Tang
- Cancer Institute, ZJU-UCLA Joint Center for Medical Education and Research, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Liubo Chen
- Cancer Institute, ZJU-UCLA Joint Center for Medical Education and Research, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xiangzhi Meng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Michael J McGregor
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
- California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Lei Dai
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Laura Martin-Sancho
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sumit Chanda
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Xinming Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, L, Los Angeles, CA, 90095, USA
| | - Steve Bensenger
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
- California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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4
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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5
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Bhagwat SR, Hajela K, Kumar A. Proteolysis to Identify Protease Substrates: Cleave to Decipher. Proteomics 2018; 18:e1800011. [DOI: 10.1002/pmic.201800011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/03/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Sonali R. Bhagwat
- Discipline of Biosciences and Biomedical Engineering; Indian Institute of Technology; Indore 453552 Simrol India
| | - Krishnan Hajela
- School of Life Sciences; Devi Ahilya Vishwavidyalaya; Indore 452001 India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering; Indian Institute of Technology; Indore 453552 Simrol India
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6
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Liu D, Liu M, Wang W, Pang L, Wang Z, Yuan C, Liu K. Overexpression of apoptosis-inducing factor mitochondrion-associated 1 (AIFM1) induces apoptosis by promoting the transcription of caspase3 and DRAM in hepatoma cells. Biochem Biophys Res Commun 2018; 498:453-457. [PMID: 29501488 DOI: 10.1016/j.bbrc.2018.02.203] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Full-length apoptosis-inducing factor mitochondrion-associated 1 (AIFM1) (∼67 kDa) induces apoptosis in a caspase-independent manner when it is cleaved at its N-terminus to produce truncated AIFM1 (∼57 kDa). Here, we produced recombinant adenovirus AIFM1 (rAd-AIFM1) encoding full-length AIFM1 to detect whether full-length AIFM1 suppresses cell growth and induces apoptosis of hepatoma cell lines (HepG2 and Hep3B). Hepatocellular carcinoma (HCC) is one of the most difficult cancers to treat worldwide. The MTT assay demonstrated that full-length AIFM1 inhibited the growth of hepatoma cells because rAd-AIFM1 infection suppressed the proliferation of HepG2 and Hep3B cells. TUNEL assay demonstrated that full-length AIFM1 overexpression induced apoptosis in HepG2 and Hep3B cells infected with rAd-AIFM1, suggesting an apoptosis-inducing ability of full-length AIFM1. Our data further showed that the expression of two pro-apoptotic genes, caspase3 and DRAM, were involved in full-length AIFM1 infection-induced apoptosis, and full-length AIFM1 could also positively regulate the transcription of caspase3 and DRAM. Thus, overexpression of full-length AIFM1 can induce caspase-dependent apoptosis and suppresses cell growth of hepatoma cells. Our data uncover a potential role of rAd-AIFM1 in HCC gene therapy.
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Affiliation(s)
- Dongjie Liu
- Beijing Institute of Hepatology, Beijing, 100069, China; Capital Medical University Affiliated Beijing You an Hospital, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engineering Technology Research Center of Hepatitis and Liver Cancer, 100069, China; Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou 014040, China
| | - Mingyang Liu
- General Hospital of Heilongjiang Province Land Reclamation Bureau, Harbin 150088, China
| | - Wenjing Wang
- Beijing Institute of Hepatology, Beijing, 100069, China; Capital Medical University Affiliated Beijing You an Hospital, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engineering Technology Research Center of Hepatitis and Liver Cancer, 100069, China
| | - Lijun Pang
- Beijing Institute of Hepatology, Beijing, 100069, China; Capital Medical University Affiliated Beijing You an Hospital, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engineering Technology Research Center of Hepatitis and Liver Cancer, 100069, China
| | - Zhenchang Wang
- Beijing Friendship Hospital, Capital Medical University, 100050, China
| | - Chunwang Yuan
- Capital Medical University Affiliated Beijing You an Hospital, Beijing, 100069, China.
| | - Kai Liu
- Beijing Institute of Hepatology, Beijing, 100069, China; Capital Medical University Affiliated Beijing You an Hospital, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engineering Technology Research Center of Hepatitis and Liver Cancer, 100069, China.
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7
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Liu Q, Zhang H, Xu J, Zhao D. Neuritin provides neuroprotection against experimental traumatic brain injury in rats. Int J Neurosci 2018; 128:811-820. [PMID: 29334295 DOI: 10.1080/00207454.2018.1424155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVES Traumatic brain injury (TBI) is a leading cause of death and disability worldwide. Neuritin is a neurotrophic factor that regulates neural growth and development. However, the role of neuritin in alleviating TBI has not been investigated. METHODS In this study, Sprague Dawley rats (n = 144) weighing 300 ± 50 g were categorized into control, sham, TBI and TBI + neuritin groups. The neurological scores and the ultrastructure of cortical neurons, apoptotic cells and caspase-3 were measured by using Garcia scoring system, transmission electron microscopy, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling, Western blot analysis and real-time RT-PCR at various time points post-TBI. CONCLUSIONS Our findings indicated that neuritin plays a protective role in TBI by improving neurological scores, repairing injured neurons and protecting the cortical neurons against apoptosis through inhibition of caspase-3 expression. Further investigation of the molecular mechanisms underlying caspase-3 inhibition by neuritin will provide a research avenue for potential TBI therapeutics.
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Affiliation(s)
- Qi Liu
- a Department of Neurosurgery , First Affiliated Hospital of Medical College, Shihezi University , Shihezi , Xinjiang , China.,b The Key Laboratory of Xinjiang Endemic and Ethnic Diseases , Medical College of Shihezi University , Shihezi , Xinjiang , China
| | - Hang Zhang
- a Department of Neurosurgery , First Affiliated Hospital of Medical College, Shihezi University , Shihezi , Xinjiang , China.,b The Key Laboratory of Xinjiang Endemic and Ethnic Diseases , Medical College of Shihezi University , Shihezi , Xinjiang , China
| | - Jian Xu
- a Department of Neurosurgery , First Affiliated Hospital of Medical College, Shihezi University , Shihezi , Xinjiang , China.,b The Key Laboratory of Xinjiang Endemic and Ethnic Diseases , Medical College of Shihezi University , Shihezi , Xinjiang , China
| | - Dong Zhao
- a Department of Neurosurgery , First Affiliated Hospital of Medical College, Shihezi University , Shihezi , Xinjiang , China.,b The Key Laboratory of Xinjiang Endemic and Ethnic Diseases , Medical College of Shihezi University , Shihezi , Xinjiang , China
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8
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Ankyrin Repeat Domain 1 Protein: A Functionally Pleiotropic Protein with Cardiac Biomarker Potential. Int J Mol Sci 2017; 18:ijms18071362. [PMID: 28672880 PMCID: PMC5535855 DOI: 10.3390/ijms18071362] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 12/20/2022] Open
Abstract
The ankyrin repeat domain 1 (ANKRD1) protein is a cardiac-specific stress-response protein that is part of the muscle ankyrin repeat protein family. ANKRD1 is functionally pleiotropic, playing pivotal roles in transcriptional regulation, sarcomere assembly and mechano-sensing in the heart. Importantly, cardiac ANKRD1 has been shown to be highly induced in various cardiomyopathies and in heart failure, although it is still unclear what impact this may have on the pathophysiology of heart failure. This review aims at highlighting the known properties, functions and regulation of ANKRD1, with focus on the underlying mechanisms that may be involved. The current views on the actions of ANKRD1 in cardiovascular disease and its utility as a candidate cardiac biomarker with diagnostic and/or prognostic potential are also discussed. More studies of ANKRD1 are warranted to obtain deeper functional insights into this molecule to allow assessment of its potential clinical applications as a diagnostic or prognostic marker and/or as a possible therapeutic target.
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9
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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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10
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Riechers SP, Butland S, Deng Y, Skotte N, Ehrnhoefer DE, Russ J, Laine J, Laroche M, Pouladi MA, Wanker EE, Hayden MR, Graham RK. Interactome network analysis identifies multiple caspase-6 interactors involved in the pathogenesis of HD. Hum Mol Genet 2016; 25:1600-18. [DOI: 10.1093/hmg/ddw036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/05/2016] [Indexed: 11/14/2022] Open
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11
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Lun AS, Chen J, Lange S. Probing muscle ankyrin-repeat protein (MARP) structure and function. Anat Rec (Hoboken) 2015; 297:1615-29. [PMID: 25125175 DOI: 10.1002/ar.22968] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/02/2014] [Indexed: 12/20/2022]
Abstract
Muscle ankyrin-repeat proteins (MARPs) have been shown to serve diverse functions within cardiac and skeletal muscle cells. Apart from their interactions with sarcomeric proteins like titin or myopalladin that locate them along myofilaments, MARPs are able to shuttle to the nucleus where they act as modulators for a variety of transcription factors. The deregulation of MARPs in many cardiac and skeletal myopathies contributes to their use as biomarkers for these diseases. Many of their functions are attributed to their domain composition. MARPs consist of an N-terminal coiled-coil domain responsible for their dimerization. The C-terminus contains a series of ankyrin repeats, whose best-characterized function is to bind to the N2A region of the giant sarcomeric protein titin. Here we investigate the nature of their dimerization and their interaction with titin more closely. We demonstrate that the coiled-coil domain in all MARPs enables their homo- and hetero-dimerization in antiparallel fashion. Protein complementation experiments indicate further antiparallel binding of the ankyrin repeats to titin's N2A region. Binding of MARP to titin also affects its PKA mediated phosphorylation. We demonstrate further that MARPs themselves are phosphorylated by PKA and PKC, potentially altering their structure or function. These studies elucidate structural relationships within the stretch-responsive MARP/titin complex in cross-striated muscle cells, and may relate to disease relevant posttranslational modifications of MARPs and titin that alter muscle compliance.
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12
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Wall DM, McCormick BA. Bacterial secreted effectors and caspase-3 interactions. Cell Microbiol 2014; 16:1746-56. [PMID: 25262664 PMCID: PMC4257569 DOI: 10.1111/cmi.12368] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/10/2014] [Accepted: 09/15/2014] [Indexed: 12/29/2022]
Abstract
Apoptosis is a critical process that intrinsically links organism survival to its ability to induce controlled death. Thus, functional apoptosis allows organisms to remove perceived threats to their survival by targeting those cells that it determines pose a direct risk. Central to this process are apoptotic caspases, enzymes that form a signalling cascade, converting danger signals via initiator caspases into activation of the executioner caspase, caspase-3. This enzyme begins disassembly of the cell by activating DNA degrading enzymes and degrading the cellular architecture. Interaction of pathogenic bacteria with caspases, and in particular, caspase-3, can therefore impact both host cell and bacterial survival. With roles outside cell death such as cell differentiation, control of signalling pathways and immunomodulation also being described for caspase-3, bacterial interactions with caspase-3 may be of far more significance in infection than previously recognized. In this review, we highlight the ways in which bacterial pathogens have evolved to subvert caspase-3 both through effector proteins that directly interact with the enzyme or by modulating pathways that influence its activation and activity.
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Affiliation(s)
- Daniel M Wall
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, UK
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13
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Van Damme P, Plasman K, Vandemoortele G, Jonckheere V, Maurer-Stroh S, Gevaert K. Importance of extended protease substrate recognition motifs in steering BNIP-2 cleavage by human and mouse granzymes B. BMC BIOCHEMISTRY 2014; 15:21. [PMID: 25208769 PMCID: PMC4169252 DOI: 10.1186/1471-2091-15-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/13/2014] [Indexed: 01/14/2023]
Abstract
Background Previous screening of the substrate repertoires and substrate specificity profiles of granzymes resulted in long substrate lists highly likely containing bystander substrates. Here, a recently developed degradomics technology that allows distinguishing efficiently from less efficiently cleaved substrates was applied to study the degradome of mouse granzyme B (mGrB). Results In vitro kinetic degradome analysis resulted in the identification of 37 mGrB cleavage events, 9 of which could be assigned as efficiently targeted ones. Previously, cleavage at the IEAD75 tetrapeptide motif of Bid was shown to be efficiently and exclusively targeted by human granzyme B (hGrB) and thus not by mGrB. Strikingly, and despite holding an identical P4-P1 human Bid (hBid) cleavage motif, mGrB was shown to efficiently cleave the BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 or BNIP-2 at IEAD28. Like Bid, BNIP-2 represents a pro-apoptotic Bcl-2 protein family member and a potential regulator of GrB induced cell death. Next, in vitro analyses demonstrated the increased efficiency of human and mouse BNIP-2 cleavage by mGrB as compared to hGrB indicative for differing Bid/BNIP-2 substrate traits beyond the P4-P1 IEAD cleavage motif influencing cleavage efficiency. Murinisation of differential primed site residues in hBNIP-2 revealed that, although all contributing, a single mutation at the P3′ position was found to significantly increase the mGrB/hGrB cleavage ratio, whereas mutating the P1′ position from I29 > T yielded a 4-fold increase in mGrB cleavage efficiency. Finally, mutagenesis analyses revealed the composite BNIP-2 precursor patterns to be the result of alternative translation initiation at near-cognate start sites within the 5′ leader sequence (5′UTR) of BNIP-2. Conclusions Despite their high sequence similarity, and previously explained by their distinct tetrapeptide specificities observed, the substrate repertoires of mouse and human granzymes B only partially overlap. Here, we show that the substrate sequence context beyond the P4-P1 positions can influence orthologous granzyme B cleavage efficiencies to an unmatched extent. More specifically, in BNIP-2, the identical and hGrB optimal IEAD tetrapeptide substrate motif is targeted highly efficiently by mGrB, while this tetrapeptide motif is refractory towards mGrB cleavage in Bid.
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Affiliation(s)
- Petra Van Damme
- Department of Medical Protein Research, VIB, Flanders Interuniversity Institute for Biotechnology, Ghent University, A, Baertsoenkaai 3, B9000 Ghent, Belgium.
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PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites. PLoS One 2012; 7:e50300. [PMID: 23209700 PMCID: PMC3510211 DOI: 10.1371/journal.pone.0050300] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 10/18/2012] [Indexed: 12/04/2022] Open
Abstract
The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s). Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database) with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate sequence using machine learning techniques. It is freely available at http://lightning.med.monash.edu.au/PROSPER/.
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15
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Valencia CA, Zou J, Liu R. In vitro selection of proteins with desired characteristics using mRNA-display. Methods 2012. [PMID: 23201412 DOI: 10.1016/j.ymeth.2012.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
mRNA-display is an amplification-based, iterative rounds of in vitro protein selection technique that circumvents a number of difficulties associated with yeast two-hybrid and phage display. Because of the covalent linkage between the genotype and the phenotype, mRNA-display provides a powerful means for reading and amplifying a peptide or protein sequence after it has been selected from a library with very high diversity. The purpose of this article is to provide a summary of the field and practical framework of mRNA-display-based selections. We summarize the advantages and limitations of selections using mRNA-display as well as the recent applications, namely, the identification of novel affinity reagents, target-binding partners, and enzyme substrates from synthetic peptide or natural proteome libraries. Practically, we provide a detailed procedure for performing mRNA-display-based selections with the aim of identifying protease substrates and binding partners of a target protein. Furthermore, we describe how to confirm the function of the selected protein sequences by biochemical assays and bioinformatic tools.
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Affiliation(s)
- C Alexander Valencia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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16
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Samaras SE, Chen B, Koch SR, Sawyer DB, Lim CC, Davidson JM. 26S proteasome regulation of Ankrd1/CARP in adult rat ventricular myocytes and human microvascular endothelial cells. Biochem Biophys Res Commun 2012; 425:830-5. [PMID: 22892129 DOI: 10.1016/j.bbrc.2012.07.162] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 07/30/2012] [Indexed: 01/04/2023]
Abstract
Ankyrin repeat domain 1 protein (Ankrd1), also known as cardiac ankyrin repeat protein (CARP), increases dramatically after tissue injury, and its overexpression improves aspects of wound healing. Reports that Ankrd1/CARP protein stability may affect cardiovascular organization, together with our findings that the protein is crucial to stability of the cardiomyocyte sarcomere and increased in wound healing, led us to compare the contribution of Ankrd1/CARP stability to its abundance. We found that the 26S proteasome is the dominant regulator of Ankrd1/CARP degradation, and that Ankrd1/CARP half-life is significantly longer in cardiomyocytes (h) than endothelial cells (min). In addition, higher endothelial cell density decreased the abundance of the protein without affecting steady state mRNA levels. Taken together, our data and that of others indicate that Ankrd1/CARP is highly regulated at multiple levels of its expression. The striking difference in protein half-life between a muscle and a non-muscle cell type suggests that post-translational proteolysis is correlated with the predominantly structural versus regulatory role of the protein in the two cell types.
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Affiliation(s)
- Susan E Samaras
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2561, USA
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17
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Lam E, Zhang Y. Regulating the reapers: activating metacaspases for programmed cell death. TRENDS IN PLANT SCIENCE 2012; 17:487-94. [PMID: 22658651 DOI: 10.1016/j.tplants.2012.05.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/01/2012] [Accepted: 05/01/2012] [Indexed: 05/03/2023]
Abstract
Research during the past two decades has revealed that specialized cysteine proteases act as conserved initiators or executioners for programmed cell death (PCD) in eukaryotes. Caspases were first identified as common regulators of PCD in metazoans, whereas the role of metacaspases (MCs) as regulators of cellular suicide in plants has only been shown genetically in the past several years. Together with recent biochemical and molecular characterizations of some of the representative MCs from different model systems, multiple mechanisms that can mediate the post-translational regulation of these proteases are beginning to emerge. Further elucidation of these regulatory pathways and definition of the downstream degradomes targeted by MCs should lead to a better understanding of cell death control in plants, protozoans, and fungi.
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Affiliation(s)
- Eric Lam
- Department of Plant Biology & Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA.
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18
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Wejda M, Impens F, Takahashi N, Van Damme P, Gevaert K, Vandenabeele P. Degradomics reveals that cleavage specificity profiles of caspase-2 and effector caspases are alike. J Biol Chem 2012; 287:33983-95. [PMID: 22825847 DOI: 10.1074/jbc.m112.384552] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Caspase-2 is considered an initiator caspase because its long prodomain contains a CARD domain that allows its recruitment and activation in several complexes by homotypic death domain-fold interactions. Because little is known about the function and specificity of caspase-2 and its physiological substrates, we compared the cleavage specificity profile of recombinant human caspase-2 with those of caspase-3 and -7 by analyzing cell lysates using N-terminal COmbined FRActional DIagonal Chromatography (COFRADIC). Substrate analysis of the 68 cleavage sites identified in 61 proteins revealed that the protease specificities of human caspases-2, -3, and -7 largely overlap, revealing the DEVD↓G consensus cleavage sequence. We confirmed that Asp(563) in eukaryotic translation initiation factor 4B (eIF4B) is a cleavage site preferred by caspase-2 not only in COFRADIC setup but also upon co-expression in HEK 293T cells. These results demonstrate that activated human caspase-2 shares remarkably overlapping protease specificity with the prototype apoptotic executioner caspases-3 and -7, suggesting that caspase-2 could function as a proapoptotic caspase once released from the activating complex.
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Affiliation(s)
- Magdalena Wejda
- Department for Molecular Biomedical Research, Flanders Institute for Biotechnology (VIB), Ghent University, B-9052 Ghent (Zwijnaarde), Belgium
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19
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Neubrand VE, Cesca F, Benfenati F, Schiavo G. Kidins220/ARMS as a functional mediator of multiple receptor signalling pathways. J Cell Sci 2012; 125:1845-54. [PMID: 22562556 DOI: 10.1242/jcs.102764] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
An increasing body of evidence suggests that several membrane receptors--in addition to activating distinct signalling cascades--also engage in substantial crosstalk with each other, thereby adjusting their signalling outcome as a function of specific input information. However, little is known about the molecular mechanisms that control their coordination and integration of downstream signalling. A protein that is likely to have a role in this process is kinase-D-interacting substrate of 220 kDa [Kidins220, also known as ankyrin repeat-rich membrane spanning (ARMS), hereafter referred to as Kidins220/ARMS]. Kidins220/ARMS is a conserved membrane protein that is preferentially expressed in the nervous system and interacts with the microtubule and actin cytoskeleton. It interacts with neurotrophin, ephrin, vascular endothelial growth factor (VEGF) and glutamate receptors, and is a common downstream target of several trophic stimuli. Kidins220/ARMS is required for neuronal differentiation and survival, and its expression levels modulate synaptic plasticity. Kidins220/ARMS knockout mice show developmental defects mainly in the nervous and cardiovascular systems, suggesting a crucial role for this protein in modulating the cross talk between different signalling pathways. In this Commentary, we summarise existing knowledge regarding the physiological functions of Kidins220/ARMS, and highlight some interesting directions for future studies on the role of this protein in health and disease.
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Affiliation(s)
- Veronika E Neubrand
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, Armilla, Granada, Spain
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20
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Abstract
mRNA display is a powerful in vitro selection technique that can be applied toward the identification of peptides or proteins with desired properties. The physical conjugation between a protein and its own RNA presents unique challenges in manipulating the displayed proteins in an RNase-free environment. This protocol outlines the generation of synthetic peptide and natural proteome libraries as well as the steps required for generation of mRNA-protein fusion libraries, in vitro selection, and regeneration of the selected sequences. The selection procedures for the identification of Ca(2+)-dependent, calmodulin-binding proteins from synthetic peptide and natural proteome libraries are presented.
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21
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Wang H, Liu R. Advantages of mRNA display selections over other selection techniques for investigation of protein-protein interactions. Expert Rev Proteomics 2011; 8:335-46. [PMID: 21679115 PMCID: PMC7103729 DOI: 10.1586/epr.11.15] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
mRNA display is a genotype–phenotype conjugation method that allows for amplification-based, iterative rounds of in vitro selection to be applied to peptides and proteins. mRNA display can be used to display both long natural protein and short synthetic peptide libraries with unusually high diversities for the investigation of protein–protein interactions. Here, we summarize the advantages of mRNA display by comparing it with other widely used peptide or protein-selection techniques, and discuss various applications of this technique in studying protein–protein interactions.
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Affiliation(s)
- Hui Wang
- University of North Carolina, Chapel Hill, NC 27599-7568, USA
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22
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Cotten SW, Zou J, Valencia CA, Liu R. Selection of proteins with desired properties from natural proteome libraries using mRNA display. Nat Protoc 2011; 6:1163-82. [DOI: 10.1038/nprot.2011.354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Song J, Tan H, Boyd SE, Shen H, Mahmood K, Webb GI, Akutsu T, Whisstock JC, Pike RN. Bioinformatic approaches for predicting substrates of proteases. J Bioinform Comput Biol 2011; 9:149-78. [PMID: 21328711 DOI: 10.1142/s0219720011005288] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/08/2010] [Accepted: 10/09/2010] [Indexed: 11/18/2022]
Abstract
Proteases have central roles in "life and death" processes due to their important ability to catalytically hydrolyze protein substrates, usually altering the function and/or activity of the target in the process. Knowledge of the substrate specificity of a protease should, in theory, dramatically improve the ability to predict target protein substrates. However, experimental identification and characterization of protease substrates is often difficult and time-consuming. Thus solving the "substrate identification" problem is fundamental to both understanding protease biology and the development of therapeutics that target specific protease-regulated pathways. In this context, bioinformatic prediction of protease substrates may provide useful and experimentally testable information about novel potential cleavage sites in candidate substrates. In this article, we provide an overview of recent advances in developing bioinformatic approaches for predicting protease substrate cleavage sites and identifying novel putative substrates. We discuss the advantages and drawbacks of the current methods and detail how more accurate models can be built by deriving multiple sequence and structural features of substrates. We also provide some suggestions about how future studies might further improve the accuracy of protease substrate specificity prediction.
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Affiliation(s)
- Jiangning Song
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia.
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24
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Identification of the BCL2/adenovirus E1B-19K protein-interacting protein 2 (BNIP-2) as a granzyme B target during human natural killer cell-mediated killing. Biochem J 2010; 431:423-31. [PMID: 20704564 DOI: 10.1042/bj20091073] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cytotoxic lymphocytes eliminate infected cells and tumours via the perforin-mediated delivery of pro-apoptotic serine proteases known as granzymes. Granzyme B triggers apoptosis via the cleavage of a repertoire of cellular proteins, leading to caspase activation and mitochondrial depolarization. A simple bioinformatics strategy identified a candidate granzyme B cleavage site in the widely expressed BNIP-2 (BCL2/adenovirus E1B-19K protein-interacting protein 2). Granzyme B cleaved recombinant BNIP-2 in vitro and endogenous BNIP-2 was cleaved during the NK (natural killer) cell-mediated killing of tumour cells. Cleavage required the site identified in the bioinformatics screen and was caspase-independent. Expression of either full-length BNIP-2 or a truncated molecule mimicking the granzyme B cleaved form was pro-apoptotic and led to the caspase-dependent cleavage of BNIP-2 at a site distinct from granzyme B cleavage. Inhibition of BNIP-2 expression did not affect the susceptibility to NK cell-mediated killing. Furthermore, target cells in which BID (BH3-interacting domain death agonist) expression was inhibited also remained highly susceptible to NK cell-mediated killing, revealing redundancy in the pro-apoptotic response to human cytotoxic lymphocytes. Such redundancy reduces the opportunity for escape from apoptosis induction and maximizes the chances of immune-mediated clearance of infected cells or tumour cells.
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25
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Cauwe B, Opdenakker G. Intracellular substrate cleavage: a novel dimension in the biochemistry, biology and pathology of matrix metalloproteinases. Crit Rev Biochem Mol Biol 2010; 45:351-423. [DOI: 10.3109/10409238.2010.501783] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Song J, Tan H, Shen H, Mahmood K, Boyd SE, Webb GI, Akutsu T, Whisstock JC. Cascleave: towards more accurate prediction of caspase substrate cleavage sites. ACTA ACUST UNITED AC 2010; 26:752-60. [PMID: 20130033 DOI: 10.1093/bioinformatics/btq043] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
MOTIVATION The caspase family of cysteine proteases play essential roles in key biological processes such as programmed cell death, differentiation, proliferation, necrosis and inflammation. The complete repertoire of caspase substrates remains to be fully characterized. Accordingly, systematic computational screening studies of caspase substrate cleavage sites may provide insight into the substrate specificity of caspases and further facilitating the discovery of putative novel substrates. RESULTS In this article we develop an approach (termed Cascleave) to predict both classical (i.e. following a P(1) Asp) and non-typical caspase cleavage sites. When using local sequence-derived profiles, Cascleave successfully predicted 82.2% of the known substrate cleavage sites, with a Matthews correlation coefficient (MCC) of 0.667. We found that prediction performance could be further improved by incorporating information such as predicted solvent accessibility and whether a cleavage sequence lies in a region that is most likely natively unstructured. Novel bi-profile Bayesian signatures were found to significantly improve the prediction performance and yielded the best performance with an overall accuracy of 87.6% and a MCC of 0.747, which is higher accuracy than published methods that essentially rely on amino acid sequence alone. It is anticipated that Cascleave will be a powerful tool for predicting novel substrate cleavage sites of caspases and shedding new insights on the unknown caspase-substrate interactivity relationship. AVAILABILITY http://sunflower.kuicr.kyoto-u.ac.jp/ approximately sjn/Cascleave/ CONTACT jiangning.song@med.monash.edu.au; takutsu@kuicr.kyoto-u.ac.jp; james; whisstock@med.monash.edu.au SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiangning Song
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.
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Demon D, Van Damme P, Vanden Berghe T, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P. Caspase substrates: easily caught in deep waters? Trends Biotechnol 2009; 27:680-8. [PMID: 19879007 DOI: 10.1016/j.tibtech.2009.09.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/18/2009] [Accepted: 09/22/2009] [Indexed: 11/29/2022]
Abstract
Caspases are key players in various cellular processes, such as apoptosis, proliferation and differentiation, and in pathological conditions including cancer and inflammation. Although caspases preferentially cleave C-terminal of aspartic acid residues, their action is restricted generally to one or a few sites per protein substrate. Caspase-specific substrate recognition appears to be determined by the substrate sequences adjacent to the scissile bond. Knowledge of these substrates and the generated fragments is crucial for a thorough understanding of the functional implications of caspase-mediated proteolysis. In addition, insight into the cleavage specificity might assist in designing inhibitors that target disease-related caspase activities. Here, we critically review recently published procedures used to generate a proteome-wide view of caspase substrates.
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Affiliation(s)
- Dieter Demon
- Department for Molecular Biomedical Research, VIB, B-9052 Ghent, Belgium
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28
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Demon D, Van Damme P, Vanden Berghe T, Deceuninck A, Van Durme J, Verspurten J, Helsens K, Impens F, Wejda M, Schymkowitz J, Rousseau F, Madder A, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P. Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity. Mol Cell Proteomics 2009; 8:2700-14. [PMID: 19759058 DOI: 10.1074/mcp.m900310-mcp200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Caspase-3 and -7 are considered functionally redundant proteases with similar proteolytic specificities. We performed a proteome-wide screen on a mouse macrophage lysate using the N-terminal combined fractional diagonal chromatography technology and identified 46 shared, three caspase-3-specific, and six caspase-7-specific cleavage sites. Further analysis of these cleavage sites and substitution mutation experiments revealed that for certain cleavage sites a lysine at the P5 position contributes to the discrimination between caspase-7 and -3 specificity. One of the caspase-7-specific substrates, the 40 S ribosomal protein S18, was studied in detail. The RPS18-derived P6-P5' undecapeptide retained complete specificity for caspase-7. The corresponding P6-P1 hexapeptide still displayed caspase-7 preference but lost strict specificity, suggesting that P' residues are additionally required for caspase-7-specific cleavage. Analysis of truncated peptide mutants revealed that in the case of RPS18 the P4-P1 residues constitute the core cleavage site but that P6, P5, P2', and P3' residues critically contribute to caspase-7 specificity. Interestingly, specific cleavage by caspase-7 relies on excluding recognition by caspase-3 and not on increasing binding for caspase-7.
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Affiliation(s)
- Dieter Demon
- Department for Molecular Biomedical Research, Flanders Institute for Biotechnology (VIB), Ghent 9052, Belgium
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Venkatraman P, Balakrishnan S, Rao S, Hooda Y, Pol S. A sequence and structure based method to predict putative substrates, functions and regulatory networks of endo proteases. PLoS One 2009; 4:e5700. [PMID: 19492082 PMCID: PMC2683571 DOI: 10.1371/journal.pone.0005700] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Accepted: 04/28/2009] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Proteases play a central role in cellular homeostasis and are responsible for the spatio-temporal regulation of function. Many putative proteases have been recently identified through genomic approaches, leading to a surge in global profiling attempts to characterize their function. Through such efforts and others it has become evident that many proteases play non-traditional roles. Accordingly, the number and the variety of the substrate repertoire of proteases are expected to be much larger than previously assumed. In line with such global profiling attempts, we present here a method for the prediction of natural substrates of endo proteases (human proteases used as an example) by employing short peptide sequences as specificity determinants. METHODOLOGY/PRINCIPAL FINDINGS Our method incorporates specificity determinants unique to individual enzymes and physiologically relevant dual filters namely, solvent accessible surface area--a parameter dependent on protein three-dimensional structure and subcellular localization. By incorporating such hitherto unused principles in prediction methods, a novel ligand docking strategy to mimic substrate binding at the active site of the enzyme, and GO functions, we identify and perform subjective validation on putative substrates of matriptase and highlight new functions of the enzyme. Using relative solvent accessibility to rank order we show how new protease regulatory networks and enzyme cascades can be created. CONCLUSION We believe that our physiologically relevant computational approach would be a very useful complementary method in the current day attempts to profile proteases (endo proteases in particular) and their substrates. In addition, by using functional annotations, we have demonstrated how normal and unknown functions of a protease can be envisaged. We have developed a network which can be integrated to create a proteolytic world. This network can in turn be extended to integrate other regulatory networks to build a system wide knowledge of the proteome.
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Affiliation(s)
- Prasanna Venkatraman
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India.
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Alves J, Wurdak H, Garay-Malpartida HM, Harris JL, Occhiucci JM, Belizário JE, Li J. TAF15 and the leukemia-associated fusion protein TAF15-CIZ/NMP4 are cleaved by caspases-3 and -7. Biochem Biophys Res Commun 2009; 384:495-500. [PMID: 19426707 DOI: 10.1016/j.bbrc.2009.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/02/2009] [Indexed: 10/20/2022]
Abstract
Caspases are central players in proteolytic pathways that regulate cellular processes such as apoptosis and differentiation. To accelerate the discovery of novel caspase substrates we developed a method combining in silico screening and in vitro validation. With this approach, we identified TAF15 as a novel caspase substrate in a trial study. We find that TAF15 was specifically cleaved by caspases-3 and -7. Site-directed mutagenesis revealed the consensus sequence 106DQPD/Y110 as the only site recognized by these caspases. Surprisingly, TAF15 was cleaved at more than one site in staurosporine-treated Jurkat cells. In addition, we generated two oncogenic TAF15-CIZ/NMP4-fused proteins which have been found in acute myeloid leukemia and demonstrate that caspases-3 and -7 cleave the fusion proteins at one single site. Broad application of this combination approach should expedite identification of novel caspase-interacting proteins and provide new insights into the regulation of caspase pathways leading to cell death in normal and cancer cells.
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Affiliation(s)
- Juliano Alves
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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31
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Weimer JM, Stanco A, Cheng JG, Vargo AC, Voora S, Anton ES. A BAC transgenic mouse model to analyze the function of astroglial SPARCL1 (SC1) in the central nervous system. Glia 2008; 56:935-41. [PMID: 18381651 DOI: 10.1002/glia.20666] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Extracellular matrix associated Sparc-like 1 (SC1/SPARCL1) can influence the function of astroglial cells in the developing and mature central nervous system (CNS). To examine SC1's significance in the CNS, we generated a BAC transgenic mouse model in which Sc1 is expressed in radial glia and their astrocyte derivatives using the astroglial-specific Blbp (Brain-lipid binding protein; [Feng et al., (1994) Neuron 12:895-908]) regulatory elements. Characterization of these Blbf-Sc1 transgenic mice show elevated Sc1 transcript and protein in an astroglial selective pattern throughout the CNS. This model provides a novel in vivo system for evaluating the role of SC1 in brain development and function, in general, and for understanding SC1's significance in the fate and function of astroglial cells, in particular.
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Affiliation(s)
- Jill M Weimer
- UNC Neuroscience Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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Van Damme P, Vandekerckhove J, Gevaert K. Disentanglement of protease substrate repertoires. Biol Chem 2008; 389:371-81. [PMID: 18208357 DOI: 10.1515/bc.2008.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Identification of protease substrates and detailed characterization of processed sites are essential for understanding the biological function of proteases. Because of inherent complexity reasons, this however remains a formidable analytical challenge, illustrated by the fact that the majority of the more than 500 human proteases are uncharacterized to date. Recently, in addition to conventional genetic and biochemical approaches, diverse quantitative peptide-centric proteomics approaches, some of which selectively recover N-terminal peptides, have emerged. These latter proteomic technologies in particular allow the identification of natural protease substrates and delineation of cleavage sites in a complex, natural background of thousands of different proteins. We here review current biochemical, genetic and proteomic methods for global analysis of substrates of proteases and discuss selected applications.
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Affiliation(s)
- Petra Van Damme
- Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology (VIB), B-9000 Ghent, Belgium
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Dix MM, Simon GM, Cravatt BF. Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell 2008; 134:679-91. [PMID: 18724940 DOI: 10.1016/j.cell.2008.06.038] [Citation(s) in RCA: 282] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/14/2008] [Accepted: 06/19/2008] [Indexed: 11/18/2022]
Abstract
Proteolysis is a key regulatory process that promotes the (in)activation, translocation, and/or degradation of proteins. As such, there is considerable interest in methods to comprehensively characterize proteolytic pathways in biological systems. Here, we describe a robust and versatile proteomic platform that enables direct visualization of the topography and magnitude of proteolytic events on a global scale. We use this method to generate a proteome-wide map of proteolytic events induced by the intrinsic apoptotic pathway. This profile contained 91 characterized caspase substrates as well as 170 additional proteins not previously known to be cleaved during apoptosis. Surprisingly, the vast majority of proteolyzed proteins, regardless of the extent of cleavage, yielded persistent fragments that correspond to discrete protein domains, suggesting that the generation of active effector proteins may be a principal function of apoptotic proteolytic cascades.
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Affiliation(s)
- Melissa M Dix
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Klaiman G, Petzke TL, Hammond J, Leblanc AC. Targets of caspase-6 activity in human neurons and Alzheimer disease. Mol Cell Proteomics 2008; 7:1541-55. [PMID: 18487604 DOI: 10.1074/mcp.m800007-mcp200] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Caspase-6 activation occurs early in Alzheimer disease and sometimes precedes the clinical manifestation of the disease in aged individuals. The active Caspase-6 is localized in neuritic plaques, in neuropil threads, and in neurofibrillary tangles containing neurons that are not morphologically apoptotic in nature. To investigate the potential consequences of the activation of Caspase-6 in neurons, we conducted a proteomics analysis of Caspase-6-mediated cleavage of human neuronal proteins. Proteins from the cytosolic and membrane subcellular compartments were treated with recombinant active Caspase-6 and compared with undigested proteins by two-dimensional gel electrophoresis. LC/MS/MS analyses of the proteins that were cleaved identified 24 different potential protein substrates. Of these, 40% were cytoskeleton or cytoskeleton-associated proteins. We focused on the cytoskeleton proteins because these are critical for neuronal structure and function. Caspase-6 cleavage of alpha-Tubulin, alpha-Actinin-4, Spinophilin, and Drebrin was confirmed. At least one Caspase-6 cleavage site was identified for Drebrin, Spinophilin, and alpha-Tubulin. A neoepitope antiserum to alpha-Tubulin cleaved by Caspase-6 immunostained neurons, neurofibrillary tangles, neuropil threads, and neuritic plaques in Alzheimer disease and co-localized with active Caspase-6. These results imply that the early and neuritic activation of Caspase-6 in Alzheimer disease could disrupt the cytoskeleton network of neurons, resulting in impaired neuronal structure and function in the absence of cell death. This study provides novel insights into the pathophysiology of Alzheimer disease.
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Affiliation(s)
- Guy Klaiman
- The Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, Quebec H3T 1E2, Canada
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Modulation of nucleobindin-1 and nucleobindin-2 by caspases. FEBS Lett 2007; 582:286-90. [PMID: 18154733 DOI: 10.1016/j.febslet.2007.12.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/30/2007] [Accepted: 12/08/2007] [Indexed: 11/22/2022]
Abstract
Nucleobindin-1 (NUCB1) and nucleobindin-2 (NUCB2) are multifunctional proteins that interact with Ca(2+), nucleic acids and various regulatory proteins in different signaling pathways. So far, our understanding of the regulation of the biological functions of nucleobindins remains limited. In our proteome-wide selection for downstream caspase substrates, both NUCB1 and NUCB2 are found to be the downstream substrates of caspases. We report here the detailed analyses of the cleavage of nucleobindins by caspases. Significantly, the caspase cleavage sites are located exactly at one of the Ca(2+)-binding EF-hand motifs. Our results suggest that the functions of nucleobindins could be modulated by caspase-mediated cleavage in apoptosis.
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Valencia CA, Cotten SW, Liu R. Cleavage of BNIP-2 and BNIP-XL by caspases. Biochem Biophys Res Commun 2007; 364:495-501. [PMID: 17961507 DOI: 10.1016/j.bbrc.2007.10.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 10/06/2007] [Indexed: 11/30/2022]
Abstract
BNIP-2 and BNIP-XL are BCH domain-containing proteins that are implicated in programmed cell death. It has been reported that overexpression of BNIP-2 in neuroblastoma cell lines resulted in massive cell death, whereas BNIP-XL was upregulated during NGF-depletion-induced apoptosis in neuroblastoma and was involved in the regulation of differentiation, survival, and aggressiveness of tumor cells. Despite their importance in apoptosis, our understanding of BNIP-2 containing proteins is limited. In this communication, we demonstrate that both BNIP-2 and BNIP-XL are cleaved by caspases during apoptosis. Significantly, the caspase cleavage sites on BNIP-2 are located on its N-terminal EF-hand motif, while that on BNIP-XL is located upstream of the C-terminal BCH domain. Our results suggest that the caspase-mediated cleavage of BNIP-2 and BNIP-XL could result in the release of the BCH domain or smaller fragments that are crucial for their proapoptotic activities.
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Affiliation(s)
- C Alexander Valencia
- School of Pharmacy and Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Valencia CA, Bailey C, Liu R. Novel zebrafish caspase-3 substrates. Biochem Biophys Res Commun 2007; 361:311-6. [PMID: 17643392 DOI: 10.1016/j.bbrc.2007.06.173] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 06/28/2007] [Indexed: 11/28/2022]
Abstract
The zebrafish model has been widely used to investigate numerous signaling pathways in vertebrates, including programmed cell death. Although several zebrafish proteins homologous to mammalian caspases have been identified, our understanding of these zebrafish caspases is still limited. Recently, we identified a large number of natural caspase-3 substrates from the human proteome by using the mRNA-display selection method. Through comparative analysis, we found that the cleavage sites on some of these novel human caspase-3 substrates are highly conserved in their zebrafish orthologs. We report here the identification and characterization of 14 natural zebrafish caspase-3 substrates that have not yet been previously studied. The specific cleavage of these zebrafish proteins was compared with caspases from different species, and the protein fragments that contain the putative cleavage sites were mapped. The work described here could facilitate our understanding of the downstream signaling pathways that are mediated by caspase-3 in zebrafish.
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Affiliation(s)
- C Alexander Valencia
- School of Pharmacy and Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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