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Lyapina I, Ivanov V, Fesenko I. Peptidome: Chaos or Inevitability. Int J Mol Sci 2021; 22:13128. [PMID: 34884929 PMCID: PMC8658490 DOI: 10.3390/ijms222313128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups-functional protein "degradome", small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the "degradome" in promoting defense signaling, are also considered.
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Affiliation(s)
| | | | - Igor Fesenko
- Department of Functional Genomics and Proteomics of Plants, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (I.L.); (V.I.)
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2
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Schistocins: Novel antimicrobial peptides encrypted in the Schistosoma mansoni Kunitz Inhibitor SmKI-1. Biochim Biophys Acta Gen Subj 2021; 1865:129989. [PMID: 34389467 DOI: 10.1016/j.bbagen.2021.129989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Here we describe a new class of cryptides (peptides encrypted within a larger protein) with antimicrobial properties, named schistocins, derived from SmKI-1, a key protein in Shistosoma mansoni survival. This is a multi-functional protein with biotechnological potential usage as a therapeutic molecule in inflammatory diseases and to control schistosomiasis. METHODS We used our algorithm enCrypted, to perform an in silico proteolysis of SmKI-1 and a screening for potential antimicrobial activity. The selected peptides were chemically synthesized, tested in vitro and evaluated by both structural (CD, NMR) and biophysical (ITC) studies to access their structure-function relationship. RESULTS EnCrypted was capable of predicting AMPs in SmKI-1. Our biophysical analyses described a membrane-induced conformational change from random coil-to-α-helix and a peptide-membrane equilibrium for all schistocins. Our structural data allowed us to suggest a well-known mode of peptide-membrane interaction in which electrostatic attraction between the cationic peptides and anionic membranes results in the bilayer disordering. Moreover, the NMR exchange H/D data with the higher entropic contribution observed for the peptide-membrane interaction showed that shistocins have different orientations upon the membrane. CONCLUSIONS This work demonstrate the robustness for using the physicochemical features of predicted peptides in the identification of new bioactive cryptides besides the relevance of combining these analyses with biophysical methods to understand the peptide-membrane affinity and improve further algorithms. GENERAL SIGNIFICANCE Bioprospecting cryptides can be conducted through data mining of protein databases demonstrating the success of our strategy. The peptides-based agents derived from SmKI-1 might have high impact for system-biology and biotechnology.
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3
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Mitocryptide-2: Identification of Its Minimum Structure for Specific Activation of FPR2-Possible Receptor Switching from FPR2 to FPR1 by Its Physiological C-terminal Cleavages. Int J Mol Sci 2021; 22:ijms22084084. [PMID: 33920954 PMCID: PMC8071274 DOI: 10.3390/ijms22084084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Mitocryptides are a novel family of endogenous neutrophil-activating peptides originating from various mitochondrial proteins. Mitocryptide-2 (MCT-2) is one of such neutrophil-activating peptides, and is produced as an N-formylated pentadecapeptide from mitochondrial cytochrome b. Although MCT-2 is a specific endogenous ligand for formyl peptide receptor 2 (FPR2), the chemical structure within MCT-2 that is responsible for FPR2 activation is still obscure. Here, we demonstrate that the N-terminal heptapeptide structure of MCT-2 with an N-formyl group is the minimum structure that specifically activates FPR2. Moreover, the receptor molecule for MCT-2 is suggested to be shifted from FPR2 to its homolog formyl peptide receptor 1 (FPR1) by the physiological cleavages of its C-terminus. Indeed, N-terminal derivatives of MCT-2 with seven amino acid residues or longer caused an increase of intracellular free Ca2+ concentration in HEK-293 cells expressing FPR2, but not in those expressing FPR1. Those MCT-2 derivatives also induced β-hexosaminidase secretion in neutrophilic/granulocytic differentiated HL-60 cells via FPR2 activation. In contrast, MCT-2(1–4), an N-terminal tetrapeptide of MCT-2, specifically activated FPR1 to promote those functions. Moreover, MCT-2 was degraded in serum to produce MCT-2(1–4) over time. These findings suggest that MCT-2 is a novel critical factor that not only initiates innate immunity via the specific activation of FPR2, but also promotes delayed responses by the activation of FPR1, which may include resolution and tissue regeneration. The present results also strongly support the necessity of considering the exact chemical structures of activating factors for the investigation of innate immune responses.
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4
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de Oliveira Costa B, Franco OL. Cryptic Host Defense Peptides: Multifaceted Activity and Prospects for Medicinal Chemistry. Curr Top Med Chem 2021; 20:1274-1290. [PMID: 32209042 DOI: 10.2174/1568026620666200325112425] [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: 11/11/2019] [Revised: 02/03/2020] [Accepted: 02/24/2020] [Indexed: 01/22/2023]
Abstract
Host defense peptides (HDPs) comprise a heterogeneous group of evolutionarily conserved and biologically active small molecules that are produced by different organisms. HDPs are widely researched because they often have multiple biological activities, for example antimicrobial, immunomodulatory and anticancer activity. In this context, in this review we focus on cryptic HDPs, molecules derived specifically from proteolytic processing of endogenous precursor proteins. Here, we explore the biological activity of such molecules and we further discuss the development of optimized sequences based on these natural cryptic HDPs. In addition, we present clinical-phase studies of cryptic HDPs (natural or optimized), and point out the possible applicability of these molecules in medicinal chemistry.
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Affiliation(s)
- Bruna de Oliveira Costa
- S-inova Biotech, Graduate Program in Biotechnology, Universidade Catolica Dom Bosco, Campo Grande, MS, Brazil
| | - Octávio Luiz Franco
- S-inova Biotech, Graduate Program in Biotechnology, Universidade Catolica Dom Bosco, Campo Grande, MS, Brazil.,Department of Genomic Sciences and Biotechnology, Center for Analysis of Proteomics and Biochemistry, Catholic University of Brasília, Brasília, DF, Brazil.,Department of Molecular Pathology, Faculty of Medicine, University of Brasília, Brasília-DF, Brazil
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5
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Gaglione R, Pizzo E, Notomista E, de la Fuente-Nunez C, Arciello A. Host Defence Cryptides from Human Apolipoproteins: Applications in Medicinal Chemistry. Curr Top Med Chem 2021; 20:1324-1337. [PMID: 32338222 DOI: 10.2174/1568026620666200427091454] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Several eukaryotic proteins with defined physiological roles may act as precursors of cryptic bioactive peptides released upon protein cleavage by the host and/or bacterial proteases. Based on this, the term "cryptome" has been used to define the unique portion of the proteome encompassing proteins with the ability to generate bioactive peptides (cryptides) and proteins (crypteins) upon proteolytic cleavage. Hence, the cryptome represents a source of peptides with potential pharmacological interest. Among eukaryotic precursor proteins, human apolipoproteins play an important role, since promising bioactive peptides have been identified and characterized from apolipoproteins E, B, and A-I sequences. Human apolipoproteins derived peptides have been shown to exhibit antibacterial, anti-biofilm, antiviral, anti-inflammatory, anti-atherogenic, antioxidant, or anticancer activities in in vitro assays and, in some cases, also in in vivo experiments on animal models. The most interesting Host Defence Peptides (HDPs) identified thus far in human apolipoproteins are described here with a focus on their biological activities applicable to biomedicine. Altogether, reported evidence clearly indicates that cryptic peptides represent promising templates for the generation of new drugs and therapeutics against infectious diseases.
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Affiliation(s)
- Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.,Istituto Nazionale di Biostrutture e Biosistemi (INBB), 00136 Rome, Italy
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6
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Arciello A. Host Defence Peptides in Medicinal Chemistry: Identification, Engineering, Characterization and Beyond. Curr Top Med Chem 2020; 20:1235-1237. [PMID: 32538715 DOI: 10.2174/156802662014200519082814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Angela Arciello
- Department of Chemical Sciences University of Naples Federico II Room 2Mb-16 80126, Naples, Italy
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7
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Gabl M, Sundqvist M, Holdfeldt A, Lind S, Mårtensson J, Christenson K, Marutani T, Dahlgren C, Mukai H, Forsman H. Mitocryptides from Human Mitochondrial DNA-Encoded Proteins Activate Neutrophil Formyl Peptide Receptors: Receptor Preference and Signaling Properties. THE JOURNAL OF IMMUNOLOGY 2018; 200:3269-3282. [PMID: 29602776 DOI: 10.4049/jimmunol.1701719] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/07/2018] [Indexed: 12/21/2022]
Abstract
Phagocytic neutrophils express formyl peptide receptors (FPRs; FPR1 and FPR2) that distinctly recognize peptides starting with an N-formylated methionine (fMet). This is a hallmark of bacterial metabolism; similar to prokaryotes, the starting amino acid in synthesis of mitochondrial DNA-encoded proteins is an fMet. Mitochondrial cryptic peptides (mitocryptides; MCTs) with an N-terminal fMet could be identified by our innate immune system; however, in contrast to our knowledge about bacterial metabolites, very little is known about the recognition profiles of MCTs. In this study, we determined the neutrophil-recognition profiles and functional output of putative MCTs originating from the N termini of the 13 human mitochondrial DNA-encoded proteins. Six of the thirteen MCTs potently activated neutrophils with distinct FPR-recognition profiles: MCTs from ND3 and ND6 have a receptor preference for FPR1; MCTs from the proteins ND4, ND5, and cytochrome b prefer FPR2; and MCT-COX1 is a dual FPR1/FPR2 agonist. MCTs derived from ND2 and ND4L are very weak neutrophil activators, whereas MCTs from ND1, ATP6, ATP8, COX2, and COX3, do not exert agonistic or antagonistic FPR effects. In addition, the activating MCTs heterologously desensitized IL-8R but primed the response to the platelet-activating factor receptor agonist. More importantly, our data suggest that MCTs have biased signaling properties in favor of activation of the superoxide-generating NADPH oxidase or recruitment of β-arrestin. In summary, we identify several novel FPR-activating peptides with sequences present in the N termini of mitochondrial DNA-encoded proteins, and our data elucidate the molecular basis of neutrophil activation by MCTs.
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Affiliation(s)
- Michael Gabl
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Martina Sundqvist
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Andre Holdfeldt
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Simon Lind
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Jonas Mårtensson
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Karin Christenson
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden; and
| | - Takayuki Marutani
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, 526-0829 Nagahama, Japan
| | - Claes Dahlgren
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Hidehito Mukai
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, 526-0829 Nagahama, Japan
| | - Huamei Forsman
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 41390 Gothenburg, Sweden;
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8
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Iavarone F, Desiderio C, Vitali A, Messana I, Martelli C, Castagnola M, Cabras T. Cryptides: latent peptides everywhere. Crit Rev Biochem Mol Biol 2018; 53:246-263. [PMID: 29564928 DOI: 10.1080/10409238.2018.1447543] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Proteomic surveys with top-down platforms are today revealing thousands of naturally occurring fragments of bigger proteins. Some of them have not functional meaning because they derive from pathways responsible for protein degradation, but many have specific functions, often completely different from that one of the parent proteins. These peptides encrypted in the protein sequence are nowadays called cryptides. They are frequent in the animal and plant kingdoms and represent a new interesting -omic field of investigation. To point out how much widespread is their presence, we describe here the most studied cryptides from very common sources such as serum albumin, immunoglobulins, hemoglobin, and from saliva and milk proteins. Given its vastness, it is unfeasible to cover the topic exhaustively, therefore only several selected examples of cryptides from other sources are thereafter reported. Demanding is the development of new -omic platforms for the functional screening of new cryptides, which could provide suggestion for peptides and peptido-mimetics with variegate fields of application.
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Affiliation(s)
- Federica Iavarone
- a Istituto di Biochimica e Biochimica Clinica, Università Cattolica , Roma , Italy
| | - Claudia Desiderio
- b Istituto di Chimica del Riconoscimento Molecolare, CNR , Roma , Italy
| | - Alberto Vitali
- b Istituto di Chimica del Riconoscimento Molecolare, CNR , Roma , Italy
| | - Irene Messana
- b Istituto di Chimica del Riconoscimento Molecolare, CNR , Roma , Italy
| | - Claudia Martelli
- a Istituto di Biochimica e Biochimica Clinica, Università Cattolica , Roma , Italy
| | - Massimo Castagnola
- a Istituto di Biochimica e Biochimica Clinica, Università Cattolica , Roma , Italy.,b Istituto di Chimica del Riconoscimento Molecolare, CNR , Roma , Italy
| | - Tiziana Cabras
- c Dipartimento di Scienze della Vita e dell'Ambiente , Università di Cagliari , Cagliari , Italy
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9
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Yamamoto H, Saito S, Sawaguchi Y, Kimura M. Identification of Protease Specificity Using Biotin-Labeled Substrates. Open Biochem J 2017; 11:27-35. [PMID: 28567123 PMCID: PMC5418938 DOI: 10.2174/1874091x01711010027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 02/14/2017] [Accepted: 03/17/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Proteolysis constitutes a major post-translational modification. For example, proteases regulate the activation or inactivation of various proteins, such as enzymes, growth factors, and peptide hormones. Proteases have substrate specificity, and protease expression regulates the specific and regional activation or inactivation of several functional proteins. METHODS We demonstrate a novel method for determining protease specificity through the use of MALDI-TOF mass spectrometry with biotin-labeled substrates. RESULTS This method was able to determine the specificity of TPCK-trypsin, V8 protease, elastase and cyanogen bromide cleavage, and the results were similar to previous reports. In addition, the method can be used to measure crude samples, such as tumor extracts. CONCLUSION We demonstrated that this method could identify protease specificity after simple processing, even for crude samples.
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Affiliation(s)
- Hiroyuki Yamamoto
- Department of Microbiology and Molecular Cell Biology, Nihon Pharmaceutical University, 10281 Komuro, Inamachi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Syota Saito
- Department of Microbiology and Molecular Cell Biology, Nihon Pharmaceutical University, 10281 Komuro, Inamachi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Yoshikazu Sawaguchi
- Department of Clinical Pharmaceutics, Nihon Pharmaceutical University, 10281 Komuro, Inamachi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Michio Kimura
- Department of Microbiology and Molecular Cell Biology, Nihon Pharmaceutical University, 10281 Komuro, Inamachi, Kitaadachi-gun, Saitama, 362-0806, Japan
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10
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Hattori T, Yamada T, Morikawa H, Marutani T, Tsutsumi K, Nishino K, Shimizu T, Nishi Y, Kiso Y, Mukai H. Generation of monoclonal antibodies against mitocryptide-2: toward a new strategy to investigate the biological roles of cryptides. J Pept Sci 2017; 23:610-617. [DOI: 10.1002/psc.3000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/06/2017] [Accepted: 03/08/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Tatsuya Hattori
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Takenori Yamada
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Hiroki Morikawa
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Takayuki Marutani
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Koki Tsutsumi
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Kodai Nishino
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Toshihiro Shimizu
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Yoshisuke Nishi
- Laboratory of Protein Engineering, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Yoshiaki Kiso
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
| | - Hidehito Mukai
- Laboratory of Peptide Science, Graduate School of Bio-Science; Nagahama Institute of Bio-Science and Technology; Nagahama Shiga 526-0829 Japan
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11
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Marutani T, Hattori T, Tsutsumi K, Koike Y, Harada A, Noguchi K, Kiso Y, Mukai H. Mitochondrial protein-derived cryptides: Are endogenous N-formylated peptides including mitocryptide-2 components of mitochondrial damage-associated molecular patterns? Biopolymers 2017; 106:580-7. [PMID: 26600263 DOI: 10.1002/bip.22788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 11/08/2022]
Abstract
Recently, much attention has been paid to "nonclassical" bioactive peptides, which are fragmented peptides simultaneously produced during maturation and degradation of various functional proteins. We identified many fragmented peptides derived from various mitochondrial proteins including mitocryptide-1 and mitocryptide-2 that efficiently activate neutrophils. These endogenous, functionally active, fragmented peptides are referred to as "cryptides." Among them, mitocryptide-2 is an N-formylated cryptide cleaved from mitochondrial cytochrome b that is encoded in mitochondrial DNA (mtDNA). It is known that 13 proteins encoded in mtDNA are translated in mitochondria as N-formylated forms, suggesting the existence of endogenous N-formylated peptides other than mitocryptide-2. Here, we investigated the effects of N-formylated peptides presumably cleaved from mtDNA-encoded proteins other than cytochrome b on the functions of neutrophilic cells to elucidate possible regulation by endogenous N-formylated cryptides. Four N-formylated cryptides derived from cytochrome c oxidase subunit I and NADH dehydrogenase subunits 4, 5, and 6 among 12 peptides from mtDNA-encoded proteins efficiently induced not only migration but also β-hexosaminidase release, which is an indicator of neutrophilic phagocytosis, in HL-60 cells differentiated into neutrophilic cells. These activities were comparable to or higher than those induced by mitocryptide-2. Although endogenous N-formylated peptides that are contained in mitochondrial damage-associated molecular patterns (DAMPs) have yet to be molecularly identified, they have been implicated in innate immunity. Thus, N-formylated cryptides including mitocryptide-2 are first-line candidates for the contents of mitochondrial DAMPs to promote innate immune responses. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 580-587, 2016.
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Affiliation(s)
- Takayuki Marutani
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Tatsuya Hattori
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Koki Tsutsumi
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Yusuke Koike
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Akihiko Harada
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Kosuke Noguchi
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Yoshiaki Kiso
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Hidehito Mukai
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
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12
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Pierzchalska M, Grabacka M. The potential role of some phytochemicals in recognition of mitochondrial damage-associated molecular patterns. Mitochondrion 2016; 30:24-34. [PMID: 27288721 DOI: 10.1016/j.mito.2016.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 02/07/2023]
Abstract
Mitochondria are the source of damage-associated molecular patterns (DAMPs). DAMPs modulate responses to stress and trauma in animals, influencing the onset of many diseases. Dietary phytochemicals, which target various cellular molecules, are potential modulators of immunological status. In this review the existence of the possible impact of some plant-derived compounds with proven anti-cancer and anti-inflammatory properties (isothiocyanates and curcumin) on DAMPs recognition is highlighted. Special consideration is given to the mtDNA recognizing Toll-like receptor 9 and formyl peptide receptors. In the context of the phytochemicals action, the role of these receptors in epithelial homeostasis is also discussed.
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Affiliation(s)
- Malgorzata Pierzchalska
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Poland.
| | - Maja Grabacka
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Poland
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13
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Hattori T, Nakashima K, Marutani T, Kiso Y, Nishi Y, Mukai H. Successful acquisition of a neutralizing monoclonal antibody against a novel neutrophil-activating peptide, mitocryptide-1. Biochem Biophys Res Commun 2015; 463:54-9. [PMID: 25986736 DOI: 10.1016/j.bbrc.2015.05.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/07/2015] [Indexed: 10/23/2022]
Abstract
Mitocryptide-1 (MCT-1) is a novel neutrophil-activating peptide derived from mitochondrial cytochrome c oxidase subunit VIII, and its physiological role and involvement in various diseases have not yet been elucidated. Generating neutralizing antibodies against the function of MCT-1 is of particular importance for investigating its physiological and pathophysiological roles, because MCT-1 is a fragmented peptide of its mother protein and hence it is very difficult to manipulate its expression level genetically without affecting expression of the mother protein. Here, we report the successful generation of a neutralizing monoclonal antibody (MAb) against MCT-1. This MAb, designated NM1B1, which specifically bound to the region of positions 9-22 of MCT-1, showed concentration-dependent inhibition of MCT-1-induced migration and β-hexosaminidase release in neutrophilic/granulocytic differentiated HL-60 cells. Thus, NM1B1, as a neutralizing MAb against MCT-1, could elucidate not just the physiological regulatory mechanisms of MCT-1 but also its pathophysiological involvement in various inflammatory diseases in vivo.
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Affiliation(s)
- Tatsuya Hattori
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan; Laboratory of Protein Engineering, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Kenta Nakashima
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Takayuki Marutani
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Yoshiaki Kiso
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Yoshisuke Nishi
- Laboratory of Protein Engineering, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan.
| | - Hidehito Mukai
- Laboratory of Peptide Science, Graduate School of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan.
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Hattori T, Mukai H. [Cryptides: biologically active peptides hidden in protein structures]. Nihon Yakurigaku Zasshi 2014; 144:234-238. [PMID: 25381893 DOI: 10.1254/fpj.144.234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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15
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Maximov VV, Martynenko AV, Arman IP, Tarantul VZ. Humanin binds MPP8: mapping interaction sites of the peptide and protein. J Pept Sci 2013; 19:301-7. [PMID: 23532874 DOI: 10.1002/psc.2500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 11/11/2022]
Abstract
Humanin (HN), a 24-amino acid peptide encoded by the mitochondrial 16S rRNA gene, was discovered by screening a cDNA library from the occipital cortex of a patient with Alzheimer's disease (AD) for a protection factor against AD-relevant insults. Earlier, using the yeast two-hybrid system, we have identified the M-phase phosphoprotein 8 (MPP8) as a binding partner for HN. In the present work, we further confirmed interaction of HN with MPP8 in co-immunoprecipitation experiments and localized an MPP8-binding site in the region between 5 and 12 aa. of HN. We have also shown that an MPP8 fragment (residues 431-560) is sufficient to bind HN. Further studies on functional consequences of the interaction between the potential oncopetide and the oncoprotein may elucidate some aspects of the molecular mechanisms of carcinogenesis.
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Affiliation(s)
- Vadim V Maximov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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16
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Tamamura H. Development of Anti-HIV Agents Based on Chemical Biology. YAKUGAKU ZASSHI 2012; 132:69-78. [DOI: 10.1248/yakushi.132.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University
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17
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Agrawal V, Kelly J, Tottey S, Daly KA, Johnson SA, Siu BF, Reing J, Badylak SF. An isolated cryptic peptide influences osteogenesis and bone remodeling in an adult mammalian model of digit amputation. Tissue Eng Part A 2011; 17:3033-44. [PMID: 21740273 DOI: 10.1089/ten.tea.2011.0257] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Biologic scaffolds composed of extracellular matrix (ECM) have been used successfully in preclinical models and humans for constructive remodeling of functional, site-appropriate tissue after injury. The mechanisms underlying ECM-mediated constructive remodeling are not completely understood, but scaffold degradation and site-directed recruitment of progenitor cells are thought to play critical roles. Previous studies have identified a cryptic peptide derived from the C-terminal telopeptide of collagen IIIα that has chemotactic activity for progenitor cells. The present study characterized the osteogenic activity of the same peptide in vitro and in vivo in an adult murine model of digit amputation. The present study showed that the cryptic peptide increased calcium deposition, alkaline phosphatase activity, and osteogenic gene expression in human perivascular stem cells in vitro. Treatment with the cryptic peptide in a murine model of mid-second phalanx digit amputation led to the formation of a bone nodule at the site of amputation. In addition to potential therapeutic implications for the treatment of bone injuries and facilitation of reconstructive surgical procedures, cryptic peptides with the ability to alter stem cell recruitment and differentiation at a site of injury may serve as powerful new tools for influencing stem cell fate in the local injury microenvironment.
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Affiliation(s)
- Vineet Agrawal
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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18
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Samir P, Link AJ. Analyzing the cryptome: uncovering secret sequences. AAPS JOURNAL 2011; 13:152-8. [PMID: 21327597 DOI: 10.1208/s12248-011-9252-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Accepted: 12/23/2010] [Indexed: 12/21/2022]
Abstract
The mammalian cryptome consists of bioactive peptides generated by the proteolysis of precursor proteins. It is speculated that the cryptide repertoire increases the complexity of the proteome by an order of magnitude. Cryptides have been found to function in a wide range of processes including neuronal signaling, antigen presentation, and the inflammatory response. Due to their potential as therapeutic agents, there has been an increasing interest in studying cryptides. In this review, we discuss different approaches for discovering these hidden peptides and how proteomic tools can be utilized to aid in their identification and characterization.
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Affiliation(s)
- Parimal Samir
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2363, USA
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19
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Seki T, Fukamizu A, Kiso Y, Mukai H. Mitocryptide-2, a neutrophil-activating cryptide, is a specific endogenous agonist for formyl-peptide receptor-like 1. Biochem Biophys Res Commun 2011; 404:482-7. [DOI: 10.1016/j.bbrc.2010.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 12/02/2010] [Indexed: 10/18/2022]
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20
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Gelman JS, Fricker LD. Hemopressin and other bioactive peptides from cytosolic proteins: are these non-classical neuropeptides? AAPS JOURNAL 2010; 12:279-89. [PMID: 20383670 DOI: 10.1208/s12248-010-9186-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 03/22/2010] [Indexed: 12/31/2022]
Abstract
Peptides perform many roles in cell-cell signaling; examples include neuropeptides, hormones, and growth factors. Although the vast majority of known neuropeptides are produced in the secretory pathway, a number of bioactive peptides are derived from cytosolic proteins. For example, the hemopressins are a family of peptides derived from alpha and beta hemoglobin which bind to the CB1 cannabinoid receptor, functioning as agonists or antagonists/inverse agonists depending on the size of the peptide. However, the finding that peptides derived from cytosolic proteins can affect receptors does not prove that these peptides are true endogenous signaling molecules. In order for the hemopressins and other peptides derived from cytosolic proteins to be considered neuropeptide-like signaling molecules, they must be synthesized in brain, they must be secreted in levels sufficient to produce effects, and either their synthesis or secretion should be regulated. If these criteria are met, we propose the name "non-classical neuropeptide" for this category of cytosolic bioactive peptide. This would be analogous to the non-classical neurotransmitters, such as nitric oxide and anandamide, which are not stored in secretory vesicles and released upon stimulation but are synthesized upon stimulation and constitutively released. We review some examples of cytosolic peptides from various protein precursors, describe potential mechanisms of their biosynthesis and secretion, and discuss the possibility that these peptides are signaling molecules in the brain, focusing on the criteria that these peptides would have to fill in order to be considered non-classical neuropeptides.
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Affiliation(s)
- Julia S Gelman
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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21
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Mukai H, Seki T, Nakano H, Hokari Y, Takao T, Kawanami M, Tsukagoshi H, Kimura H, Kiso Y, Shimonishi Y, Nishi Y, Munekata E. Mitocryptide-2: purification, identification, and characterization of a novel cryptide that activates neutrophils. THE JOURNAL OF IMMUNOLOGY 2009; 182:5072-80. [PMID: 19342687 DOI: 10.4049/jimmunol.0802965] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Neutrophils are a class of leukocytes involved in innate immunity by monitoring and scavenging invading microorganisms and toxic substances. The actions of neutrophils in damaged tissues are still not well understood, particularly in the early stage of inflammation, and as-yet-unknown neutrophil-activating substances are proposed to induce their acute transmigration and activation. Here, we isolated and identified from porcine hearts a neutrophil-activating peptide. Structural analyses indicated that the primary structure of this peptide is formyl-Met-Thr-Asn-Ile-Arg-Lys-Ser-His-Pro-Leu-Met-Lys-Ile-Ile-Asn, which is identical to that of the N-terminal pentadecapeptide of porcine mitochondrial cytochrome b; we therefore named the newly isolated peptide "mitocryptide-2" (MCT-2), since we have recently purified and identified mitocryptide-1, a different class of a neutrophil-activating peptide. Synthetic MCT-2 and its human homolog hMCT-2 induced beta-hexosaminidase release in and chemotaxis of HL-60 cells differentiated into neutrophilic/granulocytic cells. The induction of beta-hexosaminidase release, chemotaxis, and the increase in the intracellular free Ca(2+) concentration by hMCT-2 were completely suppressed by pertussis toxin, indicating the involvement of G(i)- or G(o)-type G proteins in the signaling pathways. Moreover, MCT-2 and hMCT-2 also stimulated beta-hexosaminidase secretion in human neutrophils isolated from peripheral blood in a concentration-dependent manner. Additionally, these peptides partially competed with [(3)H]formyl-Met-Leu-Phe binding to HL-60 cells differentiated into neutrophilic/granulocytic cells, presenting the possibility that the receptor for MCT-2 and hMCT-2 is one of the formyl peptide receptors. These results demonstrate that MCT-2 and its human homolog hMCT-2 are cryptides that activate neutrophils, thus suggesting the presence of regulatory mechanisms involving such mitocryptides in innate immunity.
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Affiliation(s)
- Hidehito Mukai
- Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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Gomes I, Grushko JS, Golebiewska U, Hoogendoorn S, Gupta A, Heimann AS, Ferro ES, Scarlata S, Fricker LD, Devi LA. Novel endogenous peptide agonists of cannabinoid receptors. FASEB J 2009; 23:3020-9. [PMID: 19380512 DOI: 10.1096/fj.09-132142] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hemopressin (Hp), a 9-residue alpha-hemoglobin-derived peptide, was previously reported to function as a CB(1) cannabinoid receptor antagonist (1) . In this study, we report that mass spectrometry (MS) data from peptidomics analyses of mouse brain extracts identified N-terminally extended forms of Hp containing either three (RVD-Hpalpha) or two (VD-Hpalpha) additional amino acids, as well as a beta-hemoglobin-derived peptide with sequence similarity to that of hemopressin (VD-Hpbeta). Characterization of the alpha-hemoglobin-derived peptides using binding and functional assays shows that in contrast to Hp, which functions as a CB(1) cannabinoid receptor antagonist, both RVD-Hpalpha and VD-Hpalpha function as agonists. Studies examining the increase in the phosphorylation of ERK1/2 levels or release of intracellular Ca(2+) indicate that these peptides activate a signal transduction pathway distinct from that activated by the endocannabinoid, 2-arachidonoylglycerol, or the classic CB(1) agonist, Hu-210. This finding suggests an additional mode of regulation of endogenous cannabinoid receptor activity. Taken together, these results suggest that the CB(1) receptor is involved in the integration of signals from both lipid- and peptide-derived signaling molecules.
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Affiliation(s)
- Ivone Gomes
- Department of Pharmacology and Systems Therapeutics, Mt. Sinai School of Medicine, New York, NY 10029, USA
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