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Miyamoto JG, Kitano ES, Zelanis A, Nachtigall PG, Junqueira-de-Azevedo I, Sant'Anna SS, Lauria da Silva R, Bersanetti PA, Carmona AK, Barbosa Pereira PJ, Serrano SMT, Vilela Oliva ML, Tashima AK. A novel metalloproteinase-derived cryptide from Bothrops cotiara venom inhibits angiotensin-converting enzyme activity. Biochimie 2024; 216:90-98. [PMID: 37839625 DOI: 10.1016/j.biochi.2023.10.010] [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: 08/30/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023]
Abstract
Snake venoms are primarily composed of proteins and peptides, which selectively interact with specific molecular targets, disrupting prey homeostasis. Identifying toxins and the mechanisms involved in envenoming can lead to the discovery of new drugs based on natural peptide scaffolds. In this study, we used mass spectrometry-based peptidomics to sequence 197 peptides in the venom of Bothrops cotiara, including a novel 7-residue peptide derived from a snake venom metalloproteinase. This peptide, named Bc-7a, features a pyroglutamic acid at the N-terminal and a PFR motif at the C-terminal, homologous to bradykinin. Using FRET (fluorescence resonance energy transfer) substrate assays, we demonstrated that Bc-7a strongly inhibits the two domains of angiotensin converting enzyme (Ki < 1 μM). Our findings contribute to the repertoire of biologically active peptides from snake venoms capable of inhibiting angiotensin-converting enzyme (ACE), beyond current known structural motifs and precursors. In summary, we report a novel snake venom peptide with ACE inhibitory activity, suggesting its potential contribution to the hypotensive effect observed in envenomation.
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Affiliation(s)
- Jackson Gabriel Miyamoto
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, Brazil
| | - Eduardo Shigueo Kitano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, SP, 05503-900, São Paulo, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo (ICT-UNIFESP), São José dos Campos, Brazil
| | - Pedro Gabriel Nachtigall
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, SP, 05503-900, São Paulo, Brazil
| | - Inácio Junqueira-de-Azevedo
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, SP, 05503-900, São Paulo, Brazil
| | | | - Rogério Lauria da Silva
- Department of Biophysics, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, Brazil
| | | | | | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Solange M T Serrano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, SP, 05503-900, São Paulo, Brazil
| | - Maria Luiza Vilela Oliva
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, Brazil
| | - Alexandre Keiji Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, Brazil.
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2
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Tashima AK, de Castro LM, Fricker LD. Quantitative Peptidomics Using Reductive Methylation of Amines. Methods Mol Biol 2024; 2758:109-124. [PMID: 38549011 DOI: 10.1007/978-1-0716-3646-6_6] [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] [Indexed: 04/02/2024]
Abstract
A number of different approaches have been used for quantitative peptidomics. In this protocol, we describe the method in which peptides are reacted with formaldehyde and sodium cyanoborohydride, which converts primary and secondary amines into tertiary amines. By using different combinations of regular reagents, deuterated reagents (2H), and reagents containing deuterium and 13C, it is possible to produce five isotopically distinct forms of the methylated peptides, which can be quantified by mass spectrometry. Peptides with free N-termini that are primary amines incorporate two methyl groups using this procedure, which differ by 2 Da for each of the five isotopic combinations. Peptides that contain unmodified lysine residues incorporate additional pairs of methyl groups, leading to larger mass differences between isotopic forms. The reagents are commercially available, relatively inexpensive, and chemically stable.
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Affiliation(s)
- Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.
| | - Leandro M de Castro
- Biodiversity of Coastal Environments Postgraduate Program, Bioscience Institute, São Paulo State University, São Vicente, SP, Brazil
| | - Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
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3
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Fricker LD. Quantitative Peptidomics: General Considerations. Methods Mol Biol 2024; 2758:89-108. [PMID: 38549010 DOI: 10.1007/978-1-0716-3646-6_5] [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] [Indexed: 04/02/2024]
Abstract
Peptidomics is the detection and identification of the peptides present in a sample, and quantitative peptidomics provides additional information about the amounts of these peptides. It is possible to perform absolute quantitation of peptide levels in which the biological sample is compared to synthetic standards of each peptide. More commonly, relative quantitation is performed to compare peptide levels between two or more samples. Relative quantitation can measure differences between all peptides that are detectable, which can exceed 1000 peptides in a complex sample. In this chapter, various techniques used for quantitative peptidomics are described along with discussion of the advantages and disadvantages of each approach. A guide to selecting the optimal quantitative approach is provided, based on the goals of the experiment and the resources that are available.
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Affiliation(s)
- Lloyd D Fricker
- Departments of Molecular Pharmacology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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4
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Abid MSR, Qiu H, Checco JW. Label-Free Quantitation of Endogenous Peptides. Methods Mol Biol 2024; 2758:125-150. [PMID: 38549012 PMCID: PMC11027169 DOI: 10.1007/978-1-0716-3646-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex biological mixture in an untargeted manner. Quantitative peptidomics approaches allow for comparisons of peptide abundance between different samples, allowing one to draw conclusions about peptide differences as a function of experimental treatment or physiology. While stable isotope labeling is a powerful approach for quantitative proteomics and peptidomics, advances in mass spectrometry instrumentation and analysis tools have allowed label-free methods to gain popularity in recent years. In a general label-free quantitative peptidomics experiment, peak intensity information for each peptide is compared across multiple LC-MS runs. Here, we outline a general approach for label-free quantitative peptidomics experiments, including steps for sample preparation, LC-MS data acquisition, data processing, and statistical analysis. Special attention is paid to address run-to-run variability, which can lead to several major problems in label-free experiments. Overall, our method provides researchers with a framework for the development of their own quantitative peptidomics workflows applicable to quantitation of peptides from a wide variety of different biological sources.
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Affiliation(s)
| | - Haowen Qiu
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
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5
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Ito LT, Miyamoto JG, Sant'Anna SS, Grego KF, Tanaka-Azevedo AM, Tashima AK. Unveiling the peptidome diversity of Lachesismuta snake venom: Discovery of novel fragments of metalloproteinase, l-amino acid oxidase, and bradykinin potentiating peptides. Biochem Biophys Res Commun 2023; 683:149090. [PMID: 37862779 DOI: 10.1016/j.bbrc.2023.10.022] [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: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023]
Abstract
Snake venoms are known to be major sources of peptides with different pharmacological properties. In this study, we comprehensively explored the venom peptidomes of three specimens of Lachesismuta, the largest venomous snake in South America, using mass spectrometry techniques. The analysis revealed 19 main chromatographic peaks common to all specimens. A total of 151 peptides were identified, including 69 from a metalloproteinase, 58 from the BPP-CNP precursor, and 24 from a l-amino acid oxidase. To our knowledge, 126 of these peptides were reported for the first time in this work, including a new SVMP-derived peptide fragment, Lm-10a. Our findings highlight the dynamic nature of toxin maturation in snake venoms, driven by proteolytic processing, post-translational modifications, and cryptide formation.
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Affiliation(s)
- Lucas T Ito
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, 04023-901, Brazil
| | - Jackson G Miyamoto
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, 04023-901, Brazil
| | | | - Kathleen F Grego
- Laboratory of Herpetology, Instituto Butantan, São Paulo, Brazil
| | | | - Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, 04023-901, Brazil.
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6
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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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7
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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8
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Nishiduka ES, Abreu TF, Abukawa FM, Oliveira UC, Tardivo CEO, Nascimento SM, Meissner GO, Chaim OM, Juliano MA, Kitano ES, Zelanis A, Serrano SMT, da Silva PI, Junqueira-de-Azevedo IL, Nishiyama-Jr MY, Tashima AK. Multiomics Profiling of Toxins in the Venom of the Amazonian Spider Acanthoscurria juruenicola. J Proteome Res 2022; 21:2783-2797. [PMID: 36260604 DOI: 10.1021/acs.jproteome.2c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acanthoscurria juruenicola is an Amazonian spider described for the first time almost a century ago. However, little is known about their venom composition. Here, we present a multiomics characterization of A. juruenicola venom by a combination of transcriptomics, proteomics, and peptidomics approaches. Transcriptomics of female venom glands resulted in 93,979 unique assembled mRNA transcript encoding proteins. A total of 92 proteins were identified in the venom by mass spectrometry, including 14 mature cysteine-rich peptides (CRPs). Quantitative analysis showed that CRPs, cysteine-rich secretory proteins, metalloproteases, carbonic anhydrases, and hyaluronidase comprise >90% of the venom proteome. Relative quantification of venom toxins was performed by DIA and DDA, revealing converging profiles of female and male specimens by both methods. Biochemical assays confirmed the presence of active hyaluronidases, phospholipases, and proteases in the venom. Moreover, the venom promoted in vivo paralytic activities in crickets, consistent with the high concentration of CRPs. Overall, we report a comprehensive analysis of the arsenal of toxins of A. juruenicola and highlight their potential biotechnological and pharmacological applications. Mass spectrometry data were deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD013149 and via the MassIVE repository with the dataset identifier MSV000087777.
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Affiliation(s)
- Erika S Nishiduka
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | - Thiago F Abreu
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | - Fernanda Midori Abukawa
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Ursula C Oliveira
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Caio E O Tardivo
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | - Soraia M Nascimento
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Gabriel O Meissner
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, Puerto Rico, Brazil
| | - Olga M Chaim
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, Puerto Rico, Brazil.,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Maria A Juliano
- Department of Biophysics, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04021-001, Brazil
| | - Eduardo S Kitano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo, (ICT-UNIFESP), São José dos Campos 12231-280, Brazil
| | - Solange M T Serrano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Pedro I da Silva
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Inácio L Junqueira-de-Azevedo
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Milton Y Nishiyama-Jr
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04023-901, Brazil
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Fricker LD, Lemos Duarte M, Jeltyi A, Lueptow L, Fakira AK, Tashima AK, Hochgeschwender U, Wetsel WC, Devi LA. Mice heterozygous for a null mutation of Cpe show reduced expression of carboxypeptidase E mRNA and enzyme activity but normal physiology, behavior, and levels of neuropeptides. Brain Res 2022; 1789:147951. [PMID: 35618016 DOI: 10.1016/j.brainres.2022.147951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/02/2022]
Abstract
Carboxypeptidase E (CPE) is an essential enzyme that contributes to the biosynthesis of the vast majority of neuropeptides and peptide hormones. There are several reports claiming that small decreases in CPE activity cause physiological changes in animals and/or cultured cells, but these studies did not provide evidence that neuropeptide levels were affected by decreased CPE activity. In the present study, we tested if CPE is a rate-limiting enzyme in neuropeptide production using CpeNeo mice, which contain a neomycin cassette within the Cpe gene that eliminates enzyme expression. Homozygous CpeNeo/Neo mice show defects found in Cpefat/fat and/or Cpe global knockout (KO) mice, including greatly decreased levels of most neuropeptides, severely impaired fertility, depressive-like behavior, adult-onset obesity, and anxiety-like behavior. Removal of the neomycin cassette with Flp recombinase under a germline promoter restored expression of CPE activity and resulted in normal behavioral and physiological properties, including levels of neuropeptides. Mice heterozygous for the CpeNeo allele have greatly reduced levels of Cpe mRNA and CPE-like enzymatic activity. Despite the decreased levels of Cpe expression, heterozygous CpeNeo mice are behaviorally and physiologically identical to wild-type mice, with normal levels of most neuropeptides. These results indicate that CPE is not a rate-limiting enzyme in the production of most neuropeptides, casting doubt upon studies claiming small decreases in CPE activity contribute to obesity or other physiological effects.
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Affiliation(s)
- Lloyd D Fricker
- Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461.
| | - Mariana Lemos Duarte
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
| | - Andrei Jeltyi
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
| | - Lindsay Lueptow
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
| | - Amanda K Fakira
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
| | - Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP 04023-901, Brazil.
| | | | - William C Wetsel
- Departments of Psychiatry and Behavioral Sciences, Neurobiology, and Cell Biology, Duke University Medical Center, Durham, NC, 27710.
| | - Lakshmi A Devi
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
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10
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Multiplexed quantitative neuropeptidomics via DiLeu isobaric tagging. Methods Enzymol 2022; 663:235-257. [DOI: 10.1016/bs.mie.2021.10.011] [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]
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11
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Sauer CS, Phetsanthad A, Riusech OL, Li L. Developing mass spectrometry for the quantitative analysis of neuropeptides. Expert Rev Proteomics 2021; 18:607-621. [PMID: 34375152 PMCID: PMC8522511 DOI: 10.1080/14789450.2021.1967146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Neuropeptides are signaling molecules originating in the neuroendocrine system that can act as neurotransmitters and hormones in many biochemical processes. Their exact function is difficult to characterize, however, due to dependence on concentration, post-translational modifications, and the presence of other comodulating neuropeptides. Mass spectrometry enables sensitive, accurate, and global peptidomic analyses that can profile neuropeptide expression changes to understand their roles in many biological problems, such as neurodegenerative disorders and metabolic function. AREAS COVERED We provide a brief overview of the fundamentals of neuropeptidomic research, limitations of existing methods, and recent progress in the field. This review is focused on developments in mass spectrometry and encompasses labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements. EXPERT OPINION Neuropeptidomics is critical for future clinical research with impacts in biomarker discovery, receptor identification, and drug design. While advancements are being made to improve sensitivity and accuracy, there is still room for improvement. Better quantitative strategies are required for clinical analyses, and these methods also need to be amenable to mass spectrometry imaging, post-translational modification analysis, and multi-omics to facilitate understanding and future treatment of many diseases.
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Affiliation(s)
- Christopher S. Sauer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Olga L. Riusech
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075, USA
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12
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Neuropeptidomic Analysis of a Genetically Defined Cell Type in Mouse Brain and Pituitary. Cell Chem Biol 2020; 28:105-112.e4. [PMID: 33217339 DOI: 10.1016/j.chembiol.2020.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/09/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
Neuropeptides and peptide hormones are important cell-cell signaling molecules that mediate many physiological processes. Unlike classic neurotransmitters, peptides undergo cell-type-specific post-translational modifications that affect their biological activity. To enable the identification of the peptide repertoire of a genetically defined cell type, we generated mice with a conditional disruption of the gene for carboxypeptidase E (Cpe), an essential neuropeptide-processing enzyme. The loss of Cpe leads to accumulation of neuropeptide precursors containing C-terminal basic residues, which serve as tags for affinity purification. The purified peptides are subsequently identified using quantitative peptidomics, thereby revealing the specific forms of neuropeptides in cells with the disrupted Cpe gene. To validate the method, we used mice expressing Cre recombinase under the proopiomelanocortin (Pomc) promoter and analyzed hypothalamic and pituitary extracts, detecting peptides derived from proopiomelanocortin (as expected) and also proSAAS in POMC neurons. This technique enables the analyses of specific forms of peptides in any Cre-expressing cell type.
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13
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Simizo A, Kitano ES, Sant'Anna SS, Grego KF, Tanaka-Azevedo AM, Tashima AK. Comparative gender peptidomics of Bothrops atrox venoms: are there differences between them? J Venom Anim Toxins Incl Trop Dis 2020; 26:e20200055. [PMID: 33088286 PMCID: PMC7546584 DOI: 10.1590/1678-9199-jvatitd-2020-0055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Bothrops atrox is known to be the pit viper responsible for
most snakebites and human fatalities in the Amazon region. It can be found
in a wide geographical area including northern South America, the east of
Andes and the Amazon basin. Possibly, due to its wide distribution and
generalist feeding, intraspecific venom variation was reported by previous
proteomics studies. Sex-based and ontogenetic variations on venom
compositions of Bothrops snakes were also subject of
proteomic and peptidomic analysis. However, the venom peptidome of
B. atrox remains unknown. Methods: We conducted a mass spectrometry-based analysis of the venom peptides of
individual male and female specimens combining bottom-up and top-down
approaches. Results: We identified in B. atrox a total of 105 native peptides in
the mass range of 0.4 to 13.9 kDa. Quantitative analysis showed that
phospholipase A2 and bradykinin potentiating peptides were the
most abundant peptide families in both genders, whereas disintegrin levels
were significantly increased in the venoms of females. Known peptides
processed at non-canonical sites and new peptides as the Ba1a, which
contains the SVMP BATXSVMPII1 catalytic site, were also revealed in this
work. Conclusion: The venom peptidomes of male and female specimens of B.
atrox were analyzed by mass spectrometry-based approaches in
this work. The study points to differences in disintegrin levels in the
venoms of females that may result in distinct pathophysiology of
envenomation. Further research is required to explore the potential
biological implications of this finding.
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Affiliation(s)
- Adriana Simizo
- Department of Biochemistry, Federal University of São Paulo (Unifesp), São Paulo, SP, Brazil
| | - Eduardo S Kitano
- Laboratory of Immunology, Heart Institute, Medical School, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Sávio S Sant'Anna
- Laboratory of Herpetology, Butantan Institute, São Paulo, SP, Brazil
| | | | | | - Alexandre K Tashima
- Department of Biochemistry, Federal University of São Paulo (Unifesp), São Paulo, SP, Brazil.,Special Laboratory for Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, SP, Brazil
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14
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Buchberger AR, Sauer CS, Vu NQ, DeLaney K, Li L. Temporal Study of the Perturbation of Crustacean Neuropeptides Due to Severe Hypoxia Using 4-Plex Reductive Dimethylation. J Proteome Res 2020; 19:1548-1555. [PMID: 32062973 DOI: 10.1021/acs.jproteome.9b00787] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hypoxia (i.e., low oxygen (O2) levels) is a common environmental challenge for several aquatic species, including fish and invertebrates. To survive or escape these conditions, these animals have developed novel biological mechanisms, some regulated by neuropeptides. By utilizing mass spectrometry (MS), this study aims to provide a global perspective of neuropeptides in the blue crab, Callinectes sapidus, and their changes over time (0, 1, 4, and 8 h) due to acute, severe hypoxia (∼10% O2 water saturation) stress using a 4-plex reductive dimethylation strategy to increase throughput. Using both electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) MS, this study provides complementary coverage, allowing 88 neuropeptides to be identified. Interesting trends include (1) an overall decrease in neuropeptide expression due to hypoxia exposure, (2) a return to basal levels after 4 or 8 h of exposure following an initial response, (3) changes only after 4+ h exposure, and (4) an oscillating pattern. Overall, this study boosts the power of multiplexed quantitation to understand the large-scale changes due to severe hypoxia stress over time.
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Affiliation(s)
- Amanda R Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Christopher S Sauer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nhu Q Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
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15
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The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity. Biomolecules 2020; 10:biom10020321. [PMID: 32079362 PMCID: PMC7072564 DOI: 10.3390/biom10020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15; EP24.15; THOP1) is a potential therapeutic target, as it plays key biological functions in processing biologically functional peptides. The structural conformation of THOP1 provides a unique restriction regarding substrate size, in that it only hydrolyzes peptides (optimally, those ranging from eight to 12 amino acids) and not proteins. The proteasome activity of hydrolyzing proteins releases a large number of intracellular peptides, providing THOP1 substrates within cells. The present study aimed to investigate the possible function of THOP1 in the development of diet-induced obesity (DIO) and insulin resistance by utilizing a murine model of hyperlipidic DIO with both C57BL6 wild-type (WT) and THOP1 null (THOP1−/−) mice. After 24 weeks of being fed a hyperlipidic diet (HD), THOP1−/− and WT mice ingested similar chow and calories; however, the THOP1−/− mice gained 75% less body weight and showed neither insulin resistance nor non-alcoholic fatty liver steatosis when compared to WT mice. THOP1−/− mice had increased adrenergic-stimulated adipose tissue lipolysis as well as a balanced level of expression of genes and microRNAs associated with energy metabolism, adipogenesis, or inflammation. Altogether, these differences converge to a healthy phenotype of THOP1−/− fed a HD. The molecular mechanism that links THOP1 to energy metabolism is suggested herein to involve intracellular peptides, of which the relative levels were identified to change in the adipose tissue of WT and THOP1−/− mice. Intracellular peptides were observed by molecular modeling to interact with both pre-miR-143 and pre-miR-222, suggesting a possible novel regulatory mechanism for gene expression. Therefore, we successfully demonstrated the previously anticipated relevance of THOP1 in energy metabolism regulation. It was suggested that intracellular peptides were responsible for mediating the phenotypic differences that are described herein by a yet unknown mechanism of action.
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