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Lu G, Tran VNH, Wu W, Ma M, Li L. Neuropeptidomics of the American Lobster Homarus americanus. J Proteome Res 2024; 23:1757-1767. [PMID: 38644788 PMCID: PMC11118981 DOI: 10.1021/acs.jproteome.3c00925] [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: 04/23/2024]
Abstract
The American lobster, Homarus americanus, is not only of considerable economic importance but has also emerged as a premier model organism in neuroscience research. Neuropeptides, an important class of cell-to-cell signaling molecules, play crucial roles in a wide array of physiological and psychological processes. Leveraging the recently sequenced high-quality draft genome of the American lobster, our study sought to profile the neuropeptidome of this model organism. Employing advanced mass spectrometry techniques, we identified 24 neuropeptide precursors and 101 unique mature neuropeptides in Homarus americanus. Intriguingly, 67 of these neuropeptides were discovered for the first time. Our findings provide a comprehensive overview of the peptidomic attributes of the lobster's nervous system and highlight the tissue-specific distribution of these neuropeptides. Collectively, this research not only enriches our understanding of the neuronal complexities of the American lobster but also lays a foundation for future investigations into the functional roles that these peptides play in crustacean species. The mass spectrometry data have been deposited in the PRIDE repository with the identifier PXD047230.
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Affiliation(s)
- Gaoyuan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Vu Ngoc Huong Tran
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
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Zhou B, Ran H, Zhang Q, Chen H, Han F, Xu C, Zhao Q. Unveiling the Impact of Rapeseed Meal on Feeding Behavior and Anorexigenic Endocrine in Litopenaeus vannamei. Animals (Basel) 2024; 14:540. [PMID: 38396508 PMCID: PMC10886117 DOI: 10.3390/ani14040540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Litopenaeus vannamei, with high plant protein acceptance and high global aquaculture production, is a potential species for rapeseed meal application. However, rapeseed meal has been associated with anorexia in fish, and whether the same occurs in L. vannamei remains unknown. This study demonstrated the effects of rapeseed meal on the feeding and anorexigenic endocrine of L. vannamei based on feeding behavior and transcriptomics. Soybean meal was replaced with fermented rapeseed meal (50%), and a significant increase in remaining diet and dietary discard was observed with a significant reduction in dietary visits. Transcriptome analysis revealed that the pathways involved in rapeseed meal-induced anorexia mainly included signal transduction, the digestive system, the sensory system, the endocrine system, phototransduction-fly, the thyroid hormone signaling pathway and pancreatic secretion. Moreover, this study further analyzed and identified seven neuropeptides involved in rapeseed meal-induced anorexia, and it explored the complex expression regulation strategies of these neuropeptides. In summary, this study confirmed through feeding behavior that rapeseed meal causes anorexia in L. vannamei, and it identified seven neuropeptides that were closely related to the anorexia process.
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Affiliation(s)
- Bo Zhou
- Fisheries Research Institute of Sichuan Academy of Agricultural Sciences, Yibin 644000, China;
| | - Hongmei Ran
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Qijun Zhang
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Hu Chen
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Fenglu Han
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Chang Xu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Qun Zhao
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
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Wu W, Fields L, DeLaney K, Buchberger AR, Li L. An Updated Guide to the Identification, Quantitation, and Imaging of the Crustacean Neuropeptidome. Methods Mol Biol 2024; 2758:255-289. [PMID: 38549019 PMCID: PMC11071638 DOI: 10.1007/978-1-0716-3646-6_14] [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
Crustaceans serve as a useful, simplified model for studying peptides and neuromodulation, as they contain numerous neuropeptide homologs to mammals and enable electrophysiological studies at the single-cell and neural circuit levels. Crustaceans contain well-defined neural networks, including the stomatogastric ganglion, oesophageal ganglion, commissural ganglia, and several neuropeptide-rich organs such as the brain, pericardial organs, and sinus glands. As existing mass spectrometry (MS) methods are not readily amenable to neuropeptide studies, there is a great need for optimized sample preparation, data acquisition, and data analysis methods. Herein, we present a general workflow and detailed methods for MS-based neuropeptidomic analysis of crustacean tissue samples and circulating fluids. In conjunction with profiling, quantitation can also be performed with isotopic or isobaric labeling. Information regarding the localization patterns and changes of peptides can be studied via mass spectrometry imaging. Combining these sample preparation strategies and MS analytical techniques allows for a multi-faceted approach to obtaining deep knowledge of crustacean peptidergic signaling pathways.
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Affiliation(s)
- Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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Vu NQ, Yen HC, Fields L, Cao W, Li L. HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search. J Proteome Res 2023; 22:420-431. [PMID: 36696582 PMCID: PMC10160011 DOI: 10.1021/acs.jproteome.2c00597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Neuropeptides are a class of endogenous peptides that have key regulatory roles in biochemical, physiological, and behavioral processes. Mass spectrometry analyses of neuropeptides often rely on protein informatics tools for database searching and peptide identification. As neuropeptide databases are typically experimentally built and comprised of short sequences with high sequence similarity to each other, we developed a novel database searching tool, HyPep, which utilizes sequence homology searching for peptide identification. HyPep aligns de novo sequenced peptides, generated through PEAKS software, with neuropeptide database sequences and identifies neuropeptides based on the alignment score. HyPep performance was optimized using LC-MS/MS measurements of peptide extracts from various Callinectes sapidus neuronal tissue types and compared with a commercial database searching software, PEAKS DB. HyPep identified more neuropeptides from each tissue type than PEAKS DB at 1% false discovery rate, and the false match rate from both programs was 2%. In addition to identification, this report describes how HyPep can aid in the discovery of novel neuropeptides.
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Affiliation(s)
- Nhu Q Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Hsu-Ching Yen
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Weifeng Cao
- 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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Salovska B, Liu Y. Post-translational modification and phenotype. Proteomics 2023; 23:e2200535. [PMID: 36799530 DOI: 10.1002/pmic.202200535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/02/2023] [Indexed: 02/18/2023]
Affiliation(s)
- Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, Connecticut, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
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