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Al-Jawabreh R, Lastik D, McKenzie D, Reynolds K, Suleiman M, Mousley A, Atkinson L, Hunt V. Advancing Strongyloides omics data: bridging the gap with Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220437. [PMID: 38008117 PMCID: PMC10676819 DOI: 10.1098/rstb.2022.0437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/31/2023] [Indexed: 11/28/2023] Open
Abstract
Among nematodes, the free-living model organism Caenorhabditis elegans boasts the most advanced portfolio of high-quality omics data. The resources available for parasitic nematodes, including Strongyloides spp., however, are lagging behind. While C. elegans remains the most tractable nematode and has significantly advanced our understanding of many facets of nematode biology, C. elegans is not suitable as a surrogate system for the study of parasitism and it is important that we improve the omics resources available for parasitic nematode species. Here, we review the omics data available for Strongyloides spp. and compare the available resources to those for C. elegans and other parasitic nematodes. The advancements in C. elegans omics offer a blueprint for improving omics-led research in Strongyloides. We suggest areas of priority for future research that will pave the way for expansions in omics resources and technologies. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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Affiliation(s)
- Reem Al-Jawabreh
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Dominika Lastik
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | - Kieran Reynolds
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Mona Suleiman
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | | | - Vicky Hunt
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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2
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Van Bael S, Ludwig C, Baggerman G, Temmerman L. Identification and Targeted Quantification of Endogenous Neuropeptides in the Nematode Caenorhabditis elegans Using Mass Spectrometry. Methods Mol Biol 2024; 2758:341-373. [PMID: 38549024 DOI: 10.1007/978-1-0716-3646-6_19] [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
The nematode Caenorhabditis elegans lends itself as an excellent model organism for peptidomics studies. Its ease of cultivation and quick generation time make it suitable for high-throughput studies. The nervous system, with its 302 neurons, is probably the best-known and studied endocrine tissue. Moreover, its neuropeptidergic signaling pathways display numerous similarities with those observed in other metazoans. Here, we describe two label-free approaches for neuropeptidomics in C. elegans: one for discovery purposes, and another for targeted quantification and comparisons of neuropeptide levels between different samples. Starting from a detailed peptide extraction procedure, we here outline the liquid chromatography tandem mass spectrometry (LC-MS/MS) setup and describe subsequent data analysis approaches.
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Affiliation(s)
- Sven Van Bael
- Department of Biology, Animal Physiology & Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Geert Baggerman
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Liesbet Temmerman
- Department of Biology, Animal Physiology & Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium.
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3
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Beets I, Zels S, Vandewyer E, Demeulemeester J, Caers J, Baytemur E, Courtney A, Golinelli L, Hasakioğulları İ, Schafer WR, Vértes PE, Mirabeau O, Schoofs L. System-wide mapping of peptide-GPCR interactions in C. elegans. Cell Rep 2023; 42:113058. [PMID: 37656621 PMCID: PMC7615250 DOI: 10.1016/j.celrep.2023.113058] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 07/19/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
Neuropeptides and peptide hormones are ancient, widespread signaling molecules that underpin almost all brain functions. They constitute a broad ligand-receptor network, mainly by binding to G protein-coupled receptors (GPCRs). However, the organization of the peptidergic network and roles of many peptides remain elusive, as our insight into peptide-receptor interactions is limited and many peptide GPCRs are still orphan receptors. Here we report a genome-wide peptide-GPCR interaction map in Caenorhabditis elegans. By reverse pharmacology screening of over 55,384 possible interactions, we identify 461 cognate peptide-GPCR couples that uncover a broad signaling network with specific and complex combinatorial interactions encoded across and within single peptidergic genes. These interactions provide insights into peptide functions and evolution. Combining our dataset with phylogenetic analysis supports peptide-receptor co-evolution and conservation of at least 14 bilaterian peptidergic systems in C. elegans. This resource lays a foundation for system-wide analysis of the peptidergic network.
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Affiliation(s)
- Isabel Beets
- Department of Biology, KU Leuven, 3000 Leuven, Belgium.
| | - Sven Zels
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | | | - Jonas Demeulemeester
- The Francis Crick Institute, London NW1 1AT, UK; VIB - KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Jelle Caers
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Esra Baytemur
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Amy Courtney
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Petra E Vértes
- Department of Psychiatry, Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge CB2 3EB, UK
| | - Olivier Mirabeau
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Inserm U1224, Brain-Immune Communication Lab, 75015 Paris, France
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Cockx B, Van Bael S, Boelen R, Vandewyer E, Yang H, Le TA, Dalzell JJ, Beets I, Ludwig C, Lee J, Temmerman L. Mass Spectrometry-Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes. Mol Cell Proteomics 2023; 22:100479. [PMID: 36481452 PMCID: PMC9881375 DOI: 10.1016/j.mcpro.2022.100479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
Neuropeptides regulate animal physiology and behavior, making them widely studied targets of functional genetics research. While the field often relies on differential -omics approaches to build hypotheses, no such method exists for neuropeptidomics. It would nonetheless be valuable for studying behaviors suspected to be regulated by neuropeptides, especially when little information is otherwise available. This includes nictation, a phoretic strategy of Caenorhabditis elegans dauers that parallels host-finding strategies of infective juveniles of many pathogenic nematodes. We here developed a targeted peptidomics method for the model organism C. elegans and show that 161 quantified neuropeptides are more abundant in its dauer stage compared with L3 juveniles. Many of these have orthologs in the commercially relevant pathogenic nematode Steinernema carpocapsae, in whose infective juveniles, we identified 126 neuropeptides in total. Through further behavioral genetics experiments, we identify flp-7 and flp-11 as novel regulators of nictation. Our work advances knowledge on the genetics of nictation behavior and adds comparative neuropeptidomics as a tool to functional genetics workflows.
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Affiliation(s)
- Bram Cockx
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Sven Van Bael
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Rose Boelen
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Elke Vandewyer
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Tuan Anh Le
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Johnathan J Dalzell
- School of Biological Sciences, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Isabel Beets
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Liesbet Temmerman
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium.
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Buzy A, Allain C, Harrington J, Lesuisse D, Mikol V, Bruhn DF, Maule AG, Guillemot JC. Peptidomics of Haemonchus contortus. ACS OMEGA 2021; 6:10288-10305. [PMID: 34056183 PMCID: PMC8153747 DOI: 10.1021/acsomega.1c00650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
The nematode Haemonchus contortus (the barber's pole worm) is an endoparasite infecting wild and domesticated ruminants worldwide. Widespread anthelmintic resistance of H. contortus requires alternative strategies to control this parasite. Neuropeptide signaling represents a promising target for anthelmintic drugs. Identification and relative quantification of nematode neuropeptides are, therefore, required for the development of such therapeutic targets. In this work, we undertook the profiling of the whole H. contortus larvae at different stages for the direct sequencing of the neuropeptides expressed at low levels in these tissues. We set out a peptide extraction protocol and a peptidomic workflow to biochemically characterize bioactive peptides from both first-stage (L1) and third-stage larvae (L3) of H. contortus. This work led to the identification and quantification at the peptidomic level of more than 180 mature neuropeptides, including amidated and nonamidated peptides, arising from 55 precursors of H. contortus. The differential peptidomic approach provided evidence that both life stages express most FMRFamide-like peptides (FLPs) and neuropeptide-like proteins (NLPs). The H. contortus peptidome resource, established in this work, could add the discovery of neuropeptide system-targeting drugs for ruminants.
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Affiliation(s)
- Armelle Buzy
- Sanofi
R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - Camille Allain
- Sanofi
R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - John Harrington
- Boehringer
Ingelheim Animal Health, Duluth, Georgia 30096, United States
| | | | - Vincent Mikol
- Sanofi
R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - David F. Bruhn
- Boehringer
Ingelheim Animal Health, Duluth, Georgia 30096, United States
| | - Aaron G. Maule
- School
of Biological Sciences, Queens’s
University Belfast, Belfast BT9 7BL, U.K.
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DeLaney K, Hu M, Hellenbrand T, Dickinson PS, Nusbaum MP, Li L. Mass Spectrometry Quantification, Localization, and Discovery of Feeding-Related Neuropeptides in Cancer borealis. ACS Chem Neurosci 2021; 12:782-798. [PMID: 33522802 DOI: 10.1021/acschemneuro.1c00007] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The crab Cancer borealis nervous system is an important model for understanding neural circuit dynamics and modulation, but the identity of neuromodulatory substances and their influence on circuit dynamics in this system remains incomplete, particularly with respect to behavioral state-dependent modulation. Therefore, we used a multifaceted mass spectrometry (MS) method to identify neuropeptides that differentiate the unfed and fed states. Duplex stable isotope labeling revealed that the abundance of 80 of 278 identified neuropeptides was distinct in ganglia and/or neurohemal tissue from fed vs unfed animals. MS imaging revealed that an additional 7 and 11 neuropeptides exhibited altered spatial distributions in the brain and the neuroendocrine pericardial organs (POs), respectively, during these two feeding states. Furthermore, de novo sequencing yielded 69 newly identified putative neuropeptides that may influence feeding state-related neuromodulation. Two of these latter neuropeptides were determined to be upregulated in PO tissue from fed crabs, and one of these two peptides influenced heartbeat in ex vivo preparations. Overall, the results presented here identify a cohort of neuropeptides that are poised to influence feeding-related behaviors, providing valuable opportunities for future functional studies.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Mengzhou Hu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, United States
| | - Tessa Hellenbrand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Patsy S. Dickinson
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, Maine 04011, United States
| | - Michael P. Nusbaum
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 211 Clinical Research Building, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, United States
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Feucherolles M, Poppert S, Utzinger J, Becker SL. MALDI-TOF mass spectrometry as a diagnostic tool in human and veterinary helminthology: a systematic review. Parasit Vectors 2019; 12:245. [PMID: 31101120 PMCID: PMC6525464 DOI: 10.1186/s13071-019-3493-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/06/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a widely used technique for the rapid and accurate identification of bacteria, mycobacteria and certain fungal pathogens in the clinical microbiology laboratory. Thus far, only few attempts have been made to apply the technique in clinical parasitology, particularly regarding helminth identification. METHODS We systematically reviewed the scientific literature on studies pertaining to MALDI-TOF MS as a diagnostic technique for helminths (cestodes, nematodes and trematodes) of medical and veterinary importance. Readily available electronic databases (i.e. PubMed/MEDLINE, ScienceDirect, Cochrane Library, Web of Science and Google Scholar) were searched from inception to 10 October 2018, without restriction on year of publication or language. The titles and abstracts of studies were screened for eligibility by two independent reviewers. Relevant articles were read in full and included in the systematic review. RESULTS A total of 84 peer-reviewed articles were considered for the final analysis. Most papers reported on the application of MALDI-TOF for the study of Caenorhabditis elegans, and the technique was primarily used for identification of specific proteins rather than entire pathogens. Since 2015, a small number of studies documented the successful use of MALDI-TOF MS for species-specific identification of nematodes of human and veterinary importance, such as Trichinella spp. and Dirofilaria spp. However, the quality of available data and the number of examined helminth samples was low. CONCLUSIONS Data on the use of MALDI-TOF MS for the diagnosis of helminths are scarce, but recent evidence suggests a potential role for a reliable identification of nematodes. Future research should explore the diagnostic accuracy of MALDI-TOF MS for identification of (i) adult helminths, larvae and eggs shed in faecal samples; and (ii) helminth-related proteins that are detectable in serum or body fluids of infected individuals.
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Affiliation(s)
- Maureen Feucherolles
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, Belvaux, Luxembourg
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany.
- Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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Fadda M, Hasakiogullari I, Temmerman L, Beets I, Zels S, Schoofs L. Regulation of Feeding and Metabolism by Neuropeptide F and Short Neuropeptide F in Invertebrates. Front Endocrinol (Lausanne) 2019; 10:64. [PMID: 30837946 PMCID: PMC6389622 DOI: 10.3389/fendo.2019.00064] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/23/2019] [Indexed: 12/19/2022] Open
Abstract
Numerous neuropeptide systems have been implicated to coordinately control energy homeostasis, both centrally and peripherally. However, the vertebrate neuropeptide Y (NPY) system has emerged as the best described one regarding this biological process. The protostomian ortholog of NPY is neuropeptide F, characterized by an RXRF(Y)amide carboxyterminal motif. A second neuropeptide system is short NPF, characterized by an M/T/L/FRF(W)amide carboxyterminal motif. Although both short and long NPF neuropeptide systems display carboxyterminal sequence similarities, they are evolutionary distant and likely already arose as separate signaling systems in the common ancestor of deuterostomes and protostomes, indicating the functional importance of both. Both NPF and short-NPF systems seem to have roles in the coordination of feeding across bilaterian species, but during chordate evolution, the short NPF system appears to have been lost or evolved into the prolactin releasing peptide signaling system, which regulates feeding and has been suggested to be orthologous to sNPF. Here we review the roles of both NPF and sNPF systems in the regulation of feeding and metabolism in invertebrates.
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Affiliation(s)
| | | | | | | | | | - Liliane Schoofs
- Department of Biology, Functional Genomics and Proteomics, KU Leuven, Leuven, Belgium
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Schiemann R, Lammers K, Janz M, Lohmann J, Paululat A, Meyer H. Identification and In Vivo Characterisation of Cardioactive Peptides in Drosophila melanogaster. Int J Mol Sci 2018; 20:ijms20010002. [PMID: 30577424 PMCID: PMC6337577 DOI: 10.3390/ijms20010002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/22/2018] [Indexed: 12/23/2022] Open
Abstract
Neuropeptides and peptide hormones serve as critical regulators of numerous biological processes, including development, growth, reproduction, physiology, and behaviour. In mammals, peptidergic regulatory systems are complex and often involve multiple peptides that act at different levels and relay to different receptors. To improve the mechanistic understanding of such complex systems, invertebrate models in which evolutionarily conserved peptides and receptors regulate similar biological processes but in a less complex manner have emerged as highly valuable. Drosophila melanogaster represents a favoured model for the characterisation of novel peptidergic signalling events and for evaluating the relevance of those events in vivo. In the present study, we analysed a set of neuropeptides and peptide hormones for their ability to modulate cardiac function in semi-intact larval Drosophila melanogaster. We identified numerous peptides that significantly affected heart parameters such as heart rate, systolic and diastolic interval, rhythmicity, and contractility. Thus, peptidergic regulation of the Drosophila heart is not restricted to chronotropic adaptation but also includes inotropic modulation. By specifically interfering with the expression of corresponding peptides in transgenic animals, we assessed the in vivo relevance of the respective peptidergic regulation. Based on the functional conservation of certain peptides throughout the animal kingdom, the identified cardiomodulatory activities may be relevant not only to proper heart function in Drosophila, but also to corresponding processes in vertebrates, including humans.
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Affiliation(s)
- Ronja Schiemann
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Kay Lammers
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Maren Janz
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Jana Lohmann
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Achim Paululat
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Heiko Meyer
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
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10
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Van Bael S, Zels S, Boonen K, Beets I, Schoofs L, Temmerman L. A Caenorhabditis elegans Mass Spectrometric Resource for Neuropeptidomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:879-889. [PMID: 29299835 DOI: 10.1007/s13361-017-1856-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/13/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Sven Van Bael
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Sven Zels
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Kurt Boonen
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Isabel Beets
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Liliane Schoofs
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium.
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Abstract
A wide variety of bioactive peptides are present in all metazoan species where they govern diverse functions as small messenger molecules. In the last 15 years, mass spectrometry-based methods have identified endogenous peptides in diverse species. Mass spectrometry enables the precise peptide sequences to be determined, including the potential existence of truncated versions or the presence of post-translational modifications. Because small modifications can have a large effect on biological activity, knowledge of the actual peptide sequences paves the way for further functional studies such as analysis of neuropeptidergic signaling cascades. Zebrafish (Danio rerio) is an important animal model that is commonly used in a wide range of studies. Here we provide a detailed description of the peptide extraction procedure and peptidomics workflow for zebrafish.
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12
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Van Bael S, Edwards SL, Husson SJ, Temmerman L. Identification of Endogenous Neuropeptides in the Nematode C. elegans Using Mass Spectrometry. Methods Mol Biol 2018; 1719:271-291. [PMID: 29476518 DOI: 10.1007/978-1-4939-7537-2_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The nematode Caenorhabditis elegans lends itself as an excellent model organism for peptidomics studies. Its ease of cultivation and quick generation time make it suitable for high-throughput studies. Adult hermaphrodites contain 959 somatic nuclei that are ordered in defined, differentiated tissues. The nervous system, with its 302 neurons, is probably the most known and studied endocrine tissue. Moreover, its neuropeptidergic signaling pathways display a large number of similarities with those observed in other metazoans. However, various other tissues have also been shown to express several neuropeptides. This includes the hypodermis, gonad, gut, and even muscle. Hence, whole mount peptidomics of C. elegans cultures provides an integral overview of peptidergic signaling between the different tissues of the entire organism. Here, we describe a peptidomics approach used for the identification of endogenous (neuro)peptides in C. elegans. Starting from a detailed peptide extraction procedure, we will outline the setup for an online liquid chromatography-mass spectrometry (LC-MS) analysis and describe subsequent data analysis approaches.
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Affiliation(s)
- Sven Van Bael
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Naamsestraat 59 box 2456, 3000, Leuven, Belgium
| | - Samantha L Edwards
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Naamsestraat 59 box 2456, 3000, Leuven, Belgium
| | - Steven J Husson
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, G.U.758, 2020, Antwerp, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Naamsestraat 59 box 2456, 3000, Leuven, Belgium.
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13
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WANG Y, WU L, XU JL, LI SM, LIU N, JIANG L. Effect of Reproducibility of Nano-liquid Chromatography- Mass Spectrometry on Analysis of Urinary Peptidomics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61044-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Van Camp KA, Baggerman G, Blust R, Husson SJ. Peptidomics of the zebrafish Danio rerio : In search for neuropeptides. J Proteomics 2017; 150:290-296. [DOI: 10.1016/j.jprot.2016.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/07/2016] [Accepted: 09/27/2016] [Indexed: 12/27/2022]
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15
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Husson SJ, Moyson S, Valkenborg D, Baggerman G, Mertens I. Proteomics applications in Caenorhabditis elegans research. Biochem Biophys Res Commun 2015; 468:519-24. [DOI: 10.1016/j.bbrc.2015.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 01/04/2023]
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Chang YJ, Burton T, Ha L, Huang Z, Olajubelo A, Li C. Modulation of Locomotion and Reproduction by FLP Neuropeptides in the Nematode Caenorhabditis elegans. PLoS One 2015; 10:e0135164. [PMID: 26406995 PMCID: PMC4583311 DOI: 10.1371/journal.pone.0135164] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/18/2015] [Indexed: 11/18/2022] Open
Abstract
Neuropeptides function in animals to modulate most, if not all, complex behaviors. In invertebrates, neuropeptides can function as the primary neurotransmitter of a neuron, but more generally they co-localize with a small molecule neurotransmitter, as is commonly seen in vertebrates. Because a single neuron can express multiple neuropeptides and because neuropeptides can bind to multiple G protein-coupled receptors, neuropeptide actions increase the complexity by which the neural connectome can be activated or inhibited. Humans are estimated to have 90 plus neuropeptide genes; by contrast, nematodes, a relatively simple organism, have a slightly larger complement of neuropeptide genes. For instance, the nematode Caenorhabditis elegans has over 100 neuropeptide-encoding genes, of which at least 31 genes encode peptides of the FMRFamide family. To understand the function of this large FMRFamide peptide family, we isolated knockouts of different FMRFamide-encoding genes and generated transgenic animals in which the peptides are overexpressed. We assayed these animals on two basic behaviors: locomotion and reproduction. Modulating levels of different neuropeptides have strong as well as subtle effects on these behaviors. These data suggest that neuropeptides play critical roles in C. elegans to fine tune neural circuits controlling locomotion and reproduction.
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Affiliation(s)
- Yan-Jung Chang
- Department of Biology, City College of New York, City University of New York, New York, New York 10031, United States of America
| | - Tina Burton
- Department of Biology, City College of New York, City University of New York, New York, New York 10031, United States of America
| | - Lawrence Ha
- Department of Biology, City College of New York, City University of New York, New York, New York 10031, United States of America
| | - Zi Huang
- Department of Biology, City College of New York, City University of New York, New York, New York 10031, United States of America
| | - Adewale Olajubelo
- Department of Biology, City College of New York, City University of New York, New York, New York 10031, United States of America
| | - Chris Li
- Department of Biology, City College of New York, City University of New York, New York, New York 10031, United States of America
- The Graduate Center, City University of New York, New York, New York 10031, United States of America
- * E-mail:
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De Haes W, Van Sinay E, Detienne G, Temmerman L, Schoofs L, Boonen K. Functional neuropeptidomics in invertebrates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:812-26. [PMID: 25528324 DOI: 10.1016/j.bbapap.2014.12.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/27/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022]
Abstract
Neuropeptides are key messengers in almost all physiological processes. They originate from larger precursors and are extensively processed to become bioactive. Neuropeptidomics aims to comprehensively identify the collection of neuropeptides in an organism, organ, tissue or cell. The neuropeptidome of several invertebrates is thoroughly explored since they are important model organisms (and models for human diseases), disease vectors and pest species. The charting of the neuropeptidome is the first step towards understanding peptidergic signaling. This review will first discuss the latest developments in exploring the neuropeptidome. The physiological roles and modes of action of neuropeptides can be explored in two ways, which are largely orthogonal and therefore complementary. The first way consists of inferring the functions of neuropeptides by a forward approach where neuropeptide profiles are compared under different physiological conditions. Second is the reverse approach were neuropeptide collections are used to screen for receptor-binding. This is followed by localization studies and functional tests. This review will focus on how these different functional screening methods contributed to the field of invertebrate neuropeptidomics and expanded our knowledge of peptidergic signaling. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Wouter De Haes
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Elien Van Sinay
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Giel Detienne
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Liesbet Temmerman
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Kurt Boonen
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium.
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Husson SJ, Reumer A, Temmerman L, De Haes W, Schoofs L, Mertens I, Baggerman G. Worm peptidomics. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Peymen K, Watteyne J, Frooninckx L, Schoofs L, Beets I. The FMRFamide-Like Peptide Family in Nematodes. Front Endocrinol (Lausanne) 2014; 5:90. [PMID: 24982652 PMCID: PMC4058706 DOI: 10.3389/fendo.2014.00090] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/31/2014] [Indexed: 12/31/2022] Open
Abstract
In the three decades since the FMRFamide peptide was isolated from the mollusk Macrocallista nimbosa, structurally similar peptides sharing a C-terminal RFamide motif have been identified across the animal kingdom. FMRFamide-like peptides (FLPs) represent the largest known family of neuropeptides in invertebrates. In the phylum Nematoda, at least 32 flp-genes are classified, making the FLP system of nematodes unusually complex. The diversity of the nematode FLP complement is most extensively mapped in Caenorhabditis elegans, where over 70 FLPs have been predicted. FLPs have shown to be expressed in the majority of the 302 C. elegans neurons including interneurons, sensory neurons, and motor neurons. The vast expression of FLPs is reflected in the broad functional repertoire of nematode FLP signaling, including neuroendocrine and neuromodulatory effects on locomotory activity, reproduction, feeding, and behavior. In contrast to the many identified nematode FLPs, only few peptides have been assigned a receptor and there is the need to clarify the pathway components and working mechanisms of the FLP signaling network. Here, we review the diversity, distribution, and functions of FLPs in nematodes.
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Affiliation(s)
- Katleen Peymen
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jan Watteyne
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Lotte Frooninckx
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Isabel Beets
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
- *Correspondence: Isabel Beets, Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Naamsestraat 59, Leuven 3000, Belgium e-mail:
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Li C, Kim K. Family of FLP Peptides in Caenorhabditis elegans and Related Nematodes. Front Endocrinol (Lausanne) 2014; 5:150. [PMID: 25352828 PMCID: PMC4196577 DOI: 10.3389/fendo.2014.00150] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/09/2014] [Indexed: 11/16/2022] Open
Abstract
Neuropeptides regulate all aspects of behavior in multicellular organisms. Because of their ability to act at long distances, neuropeptides can exert their effects beyond the conventional synaptic connections, thereby adding an intricate layer of complexity to the activity of neural networks. In the nematode Caenorhabditis elegans, a large number of neuropeptide genes that are expressed throughout the nervous system have been identified. The actions of these peptides supplement the synaptic connections of the 302 neurons, allowing for fine tuning of neural networks and increasing the ways in which behaviors can be regulated. In this review, we focus on a large family of genes encoding FMRFamide-related peptides (FaRPs). These genes, the flp genes, have been used as a starting point to identifying flp genes throughout Nematoda. Nematodes have the largest family of FaRPs described thus far. The challenges in the future are the elucidation of their functions and the identification of the receptors and signaling pathways through which they function.
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Affiliation(s)
- Chris Li
- Department of Biology, City College of New York and The Graduate Center, City University of New York, New York, NY, USA
- *Correspondence: Chris Li, 160 Convent Avenue, MR526, New York, NY 10031, USA e-mail: ; Kyuhyung Kim, 333 Techno Jungang-Daero, Hyeonpung-Myeon, Dalseong-Gun, Daegu 711-873, South Korea e-mail:
| | - Kyuhyung Kim
- Department of Brain Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
- *Correspondence: Chris Li, 160 Convent Avenue, MR526, New York, NY 10031, USA e-mail: ; Kyuhyung Kim, 333 Techno Jungang-Daero, Hyeonpung-Myeon, Dalseong-Gun, Daegu 711-873, South Korea e-mail:
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Ofer D, Linial M. NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes. ACTA ACUST UNITED AC 2013; 30:931-40. [PMID: 24336809 DOI: 10.1093/bioinformatics/btt725] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
MOTIVATION The evolution of multicellular organisms is associated with increasing variability of molecules governing behavioral and physiological states. This is often achieved by neuropeptides (NPs) that are produced in neurons from a longer protein, named neuropeptide precursor (NPP). The maturation of NPs occurs through a sequence of proteolytic cleavages. The difficulty in identifying NPPs is a consequence of their diversity and the lack of applicable sequence similarity among the short functionally related NPs. RESULTS Herein, we describe Neuropeptide Precursor Identifier (NeuroPID), a machine learning scheme that predicts metazoan NPPs. NeuroPID was trained on hundreds of identified NPPs from the UniProtKB database. Some 600 features were extracted from the primary sequences and processed using support vector machines (SVM) and ensemble decision tree classifiers. These features combined biophysical, chemical and informational-statistical properties of NPs and NPPs. Other features were guided by the defining characteristics of the dibasic cleavage sites motif. NeuroPID reached 89-94% accuracy and 90-93% precision in cross-validation blind tests against known NPPs (with an emphasis on Chordata and Arthropoda). NeuroPID also identified NPP-like proteins from extensively studied model organisms as well as from poorly annotated proteomes. We then focused on the most significant sets of features that contribute to the success of the classifiers. We propose that NPPs are attractive targets for investigating and modulating behavior, metabolism and homeostasis and that a rich repertoire of NPs remains to be identified. AVAILABILITY NeuroPID source code is freely available at http://www.protonet.cs.huji.ac.il/neuropid
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Affiliation(s)
- Dan Ofer
- Department of Biological Chemistry, Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Givat Ram 91904, Israel
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22
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Jarecki JL, Viola IR, Andersen KM, Miller AH, Ramaker MA, Vestling MM, Stretton AO. Three independent techniques localize expression of transcript afp-11 and its bioactive peptide products to the paired AVK neurons in Ascaris suum: in situ hybridization, immunocytochemistry, and single cell mass spectrometry. ACS Chem Neurosci 2013; 4:418-34. [PMID: 23509978 DOI: 10.1021/cn3001334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We utilized three independent techniques, immunocytochemistry (ICC), single cell mass spectrometry (MS), and in situ hybridization (ISH), to localize neuropeptides and their transcripts in the nervous system of the nematode Ascaris suum . AF11 (SDIGISEPNFLRFa) is an endogenous peptide with potent paralytic effects on A. suum locomotory behavior. A highly specific antibody to AF11 showed robust immunostaining for AF11 in the paired AVK neurons in the ventral ganglion. We traced the processes from the AVK neurons into the ventral nerve cord and identified them as ventral cord interneurons. MS and MS/MS of single dissected AVKs detected AF11, two previously characterized peptides (AF25 and AF26), seven novel sequence-related peptides, including several sharing a PNFLRFamide C-terminus, and peptide NY, a peptide with an unrelated sequence. Also present in a subset of AVKs was AF2, a peptide encoded by the afp-4 transcript. By sequencing the afp-11 transcript, we discovered that it encodes AF11, all the AF11-related peptides detected by MS in AVK, and peptide NY. ISH detected the afp-11 transcript in AVK neurons, consistent with other techniques. ISH did not detect afp-11 in the ALA neuron, although both ICC and MS found AF11 in ca. 30% of ALAs. All 10 AF11-related peptides reduced acetylcholine-induced muscle contraction, but they differed in their rate of reversal of inhibition after removal of the peptide.
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Affiliation(s)
- Jessica L. Jarecki
- Neuroscience Training
Program, ‡Department of Zoology, and §Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - India R. Viola
- Neuroscience Training
Program, ‡Department of Zoology, and §Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Kari M. Andersen
- Neuroscience Training
Program, ‡Department of Zoology, and §Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Andrew H. Miller
- Neuroscience Training
Program, ‡Department of Zoology, and §Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Megan A. Ramaker
- Neuroscience Training
Program, ‡Department of Zoology, and §Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Martha M. Vestling
- Neuroscience Training
Program, ‡Department of Zoology, and §Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Antony O. Stretton
- Neuroscience Training
Program, ‡Department of Zoology, and §Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
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23
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Romanova EV, Sasaki K, Alexeeva V, Vilim FS, Jing J, Richmond TA, Weiss KR, Sweedler JV. Urotensin II in invertebrates: from structure to function in Aplysia californica. PLoS One 2012; 7:e48764. [PMID: 23144960 PMCID: PMC3493602 DOI: 10.1371/journal.pone.0048764] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 10/05/2012] [Indexed: 02/07/2023] Open
Abstract
Neuropeptides are ancient signaling molecules that are involved in many aspects of organism homeostasis and function. Urotensin II (UII), a peptide with a range of hormonal functions, previously has been reported exclusively in vertebrates. Here, we provide the first direct evidence that UII-like peptides are also present in an invertebrate, specifically, the marine mollusk Aplysia californica. The presence of UII in the central nervous system (CNS) of Aplysia implies a more ancient gene lineage than vertebrates. Using representational difference analysis, we identified an mRNA of a protein precursor that encodes a predicted neuropeptide, we named Aplysia urotensin II (apUII), with a sequence and structural similarity to vertebrate UII. With in-situ hybridization and immunohistochemistry, we mapped the expression of apUII mRNA and its prohormone in the CNS and localized apUII-like immunoreactivity to buccal sensory neurons and cerebral A-cluster neurons. Mass spectrometry performed on individual isolated neurons, and tandem mass spectrometry on fractionated peptide extracts, allowed us to define the posttranslational processing of the apUII neuropeptide precursor and confirm the highly conserved cyclic nature of the mature neuropeptide apUII. Electrophysiological analysis of the central effects of a synthetic apUII suggests it plays a role in satiety and/or aversive signaling in feeding behaviors. Finding the homologue of vertebrate UII in the numerically small CNS of an invertebrate animal model is important for gaining insights into the molecular mechanisms and pathways mediating the bioactivity of UII in the higher metazoan.
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Affiliation(s)
- Elena V. Romanova
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Kosei Sasaki
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Vera Alexeeva
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Ferdinand S. Vilim
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Jian Jing
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Timothy A. Richmond
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Klaudiusz R. Weiss
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Jonathan V. Sweedler
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Estes S, Coleman-Hulbert AL, Hicks KA, de Haan G, Martha SR, Knapp JB, Smith SW, Stein KC, Denver DR. Natural variation in life history and aging phenotypes is associated with mitochondrial DNA deletion frequency in Caenorhabditis briggsae. BMC Evol Biol 2011; 11:11. [PMID: 21226948 PMCID: PMC3032685 DOI: 10.1186/1471-2148-11-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 01/12/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. A barrier to rigorous tests of the role of mitochondrial dysfunction in aging processes has been the lack of model systems with relevant, naturally occurring mitochondrial genetic variation. Toward the goal of developing such a model system, we studied natural variation in life history, metabolic, and aging phenotypes as it relates to levels of a naturally-occurring heteroplasmic mitochondrial ND5 deletion recently discovered to segregate among wild populations of the soil nematode, Caenorhabditis briggsae. The normal product of ND5 is a central component of the mitochondrial electron transport chain and integral to cellular energy metabolism. RESULTS We quantified significant variation among C. briggsae isolates for all phenotypes measured, only some of which was statistically associated with isolate-specific ND5 deletion frequency. We found that fecundity-related traits and pharyngeal pumping rate were strongly inversely related to ND5 deletion level and that C. briggsae isolates with high ND5 deletion levels experienced a tradeoff between early fecundity and lifespan. Conversely, oxidative stress resistance was only weakly associated with ND5 deletion level while ATP content was unrelated to deletion level. Finally, mean levels of reactive oxygen species measured in vivo showed a significant non-linear relationship with ND5 deletion level, a pattern that may be driven by among-isolate variation in antioxidant or other compensatory mechanisms. CONCLUSIONS Our findings suggest that the ND5 deletion may adversely affect fitness and mitochondrial functioning while promoting aging in natural populations, and help to further establish this species as a useful model for explicit tests of hypotheses in aging biology and mitochondrial genetics.
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Affiliation(s)
- Suzanne Estes
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | | | - Kiley A Hicks
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Gene de Haan
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Sarah R Martha
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Jeremiah B Knapp
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Samson W Smith
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Kevin C Stein
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Dee R Denver
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
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Meelkop E, Temmerman L, Schoofs L, Janssen T. Signalling through pigment dispersing hormone-like peptides in invertebrates. Prog Neurobiol 2010; 93:125-47. [PMID: 21040756 DOI: 10.1016/j.pneurobio.2010.10.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 10/19/2010] [Accepted: 10/21/2010] [Indexed: 12/19/2022]
Abstract
During recent decades, several research teams engaged in unraveling the molecular structure and the physiological significance of pigment dispersing hormone-like peptides, particularly with respect to colour change and biological rhythms. In this review, we first summarise the entire history of pigment dispersing hormone-like peptide research, thus providing a stepping stone for those who are curious about this growing area of interest. Next, we try to bring order in the plethora of experimental data on the molecular structure of the various peptides and receptors and also discuss immunolocalization, time-related expression and suggested functions in crustaceans, insects and nematodes. In addition, a brief comparison with the vertebrate system is made.
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Affiliation(s)
- E Meelkop
- Laboratory of Functional Genomics and Proteomics, Zoological Institute, K.U. Leuven, Naamsestraat 59, B-3000 Leuven, Belgium
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26
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Collins JJ, Hou X, Romanova EV, Lambrus BG, Miller CM, Saberi A, Sweedler JV, Newmark PA. Genome-wide analyses reveal a role for peptide hormones in planarian germline development. PLoS Biol 2010; 8:e1000509. [PMID: 20967238 PMCID: PMC2953531 DOI: 10.1371/journal.pbio.1000509] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 08/25/2010] [Indexed: 12/02/2022] Open
Abstract
Genomic/peptidomic analyses of the planarian Schmidtea mediterranea identifies >200 neuropeptides and uncovers a conserved neuropeptide required for proper maturation and maintenance of the reproductive system. Bioactive peptides (i.e., neuropeptides or peptide hormones) represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites. Flatworms cause diseases affecting hundreds of millions of people, so understanding what influences their reproductive activity is of fundamental importance. Neurally derived signals have been suggested to coordinate sexual reproduction in free-living flatworms, yet the neuroendocrine signaling repertoire has not been characterized comprehensively for any flatworm. Neuropeptides are a large diverse group of cell-cell signaling molecules and play many roles in vertebrate reproductive development; however, little is known about their function in reproductive development among invertebrates. Here we use biochemical and bioinformatic techniques to identify bioactive peptides in the genome of the planarian flatworm Schmidtea mediterranea and identify 51 genes encoding >200 peptides. Analysis of these genes in both sexual and asexual strains of S. mediterranea identified a neuropeptide Y superfamily member as important for the normal development and maintenance of the planarian reproductive system. We suggest that understanding peptide hormone function in planarian reproduction could have practical implications in the treatment of parasitic flatworms.
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Affiliation(s)
- James J. Collins
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xiaowen Hou
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Elena V. Romanova
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Bramwell G. Lambrus
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Claire M. Miller
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Amir Saberi
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jonathan V. Sweedler
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Phillip A. Newmark
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Lemos MFL, Soares AMVM, Correia AC, Esteves AC. Proteins in ecotoxicology - how, why and why not? Proteomics 2010; 10:873-87. [PMID: 19953548 DOI: 10.1002/pmic.200900470] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The growing interest in the application of proteomic technologies to solve toxicology issues and its relevance in ecotoxicology research has resulted in the emergence of "ecotoxicoproteomics". There is a general consensus that ecotoxicoproteomics is a powerful tool to spot early molecular events involved in toxicant responses, which are responsible for the adverse effects observed at higher levels of biological organization, thus contributing to elucidate the mode of action of stressors and to identify specific biomarkers. Ultimately, early-warning indicators can then be developed and deployed in "in situ" bioassays and in environmental risk assessment. The number of field experiments or laboratory trials using ecologically relevant test-species and involving proteomics has been, until recently, insufficient to allow a critical analysis of the real benefits of the application of this approach to ecotoxicology. This article intends to present an overview on the applications of proteomics in the context of ecotoxicology, focusing mainly on the prospective research to be done in invertebrates. Although these represent around 95% of all animal species and in spite of the key structural and functional roles they play in ecosystems, proteomic research in invertebrates is still in an incipient stage. We will review applications of ecotoxicoproteomics by evaluating the technical methods employed, the organisms and the contexts studied, the advances achieved until now and lastly the limitations yet to overcome will be discussed.
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Affiliation(s)
- Marco F L Lemos
- CESAM and Department of Biology, University of Aveiro, Aveiro, Portugal
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Abstract
Caenorhabditis elegans, a free-living soil nematode, is an ideal model system for studying various physiological problems relevant to human diseases. Despite its short history, C. elegans proteomics is receiving great attention in multiple research areas, including the genome annotation, major signaling pathways (e.g. TGF-beta and insulin/IGF-1 signaling), verification of RNA interference-mediated gene targeting, aging, disease models, as well as peptidomic analysis of neuropeptides involved in behavior and locomotion. For example, a proteome-wide profiling of developmental and aging processes not only provides basic information necessary for constructing a molecular network, but also identifies important target proteins for chemical modulation. Although C. elegans has a simple body system and neural circuitry, it exhibits very complicated functions ranging from feeding to locomotion. Investigation of these functions through proteomic analysis of various C. elegans neuropeptides, some of which are not found in the predicted genome sequence, would open a new field of peptidomics. Given the importance of nematode infection in plants and mammalian pathogenesis pathways, proteomics could be applied to investigate the molecular mechanisms underlying plant- or animal-nematode pathogenesis and to identify novel antinematodal drugs. Thus, C. elegans proteomics, in combination of other molecular, biological and genetic techniques, would provide a versatile new tool box for the systematic analysis of gene functions throughout the entire life cycle of this nematode.
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Affiliation(s)
- Yhong-Hee Shim
- Department of Bioscience and Biotechnology, BMIC, Konkuk University, Gwangjin-Ku, Seoul, Korea
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Jarecki JL, Andersen K, Konop CJ, Knickelbine JJ, Vestling MM, Stretton AO. Mapping neuropeptide expression by mass spectrometry in single dissected identified neurons from the dorsal ganglion of the nematode Ascaris suum. ACS Chem Neurosci 2010; 1:505-519. [PMID: 20806053 PMCID: PMC2929024 DOI: 10.1021/cn1000217] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Accepted: 04/18/2010] [Indexed: 11/30/2022] Open
Abstract
We have developed a method for dissecting single neurons from the nematode Ascaris suum, in order to determine their peptide content by mass spectrometry (MS). In this paper, we use MALDI-TOF MS and tandem MS to enumerate and sequence the peptides present in the two neurons, ALA and RID, that comprise the dorsal ganglion. We compare the peptide content determined by MS with the results of immunocytochemistry and in situ hybridization of previously isolated peptides AF2, AF8 and 6 peptides encoded by the afp-1 transcript. We find complete agreement between the three techniques, which validates single neuron MS as a method for peptide localization. We also discovered and sequenced 6 novel peptides in the ALA neuron. Cloning of cDNAs and database searching of Genomic Survey Sequences showed that transcript afp-12 encodes peptide AF36 (VPSAADMMIRFamide), and afp-13 encodes AF19 (AEGLSSPLIRFamide), AF34 (DSKLMDPLIRFamide), AF35 (DPQQRIVTDETVLRFamide), and 3 non-amidated peptides (PepTT, PepTL, and PepGE). We have found no similarities with reported peptide expression in the nematode Caenorhabditis elegans. This method promises to be ideally suited for determining the peptide content of each of the 298 neurons in the nervous system of this nematode.
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Affiliation(s)
| | - Kari Andersen
- Department of Zoology, University of Wisconsin-Madison
| | | | | | | | - Antony O. Stretton
- Neuroscience Training Program, University of Wisconsin-Madison
- Department of Zoology, University of Wisconsin-Madison
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Walker RJ, Papaioannou S, Holden-Dye L. A review of FMRFamide- and RFamide-like peptides in metazoa. INVERTEBRATE NEUROSCIENCE 2010; 9:111-53. [PMID: 20191373 DOI: 10.1007/s10158-010-0097-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 02/01/2010] [Indexed: 12/13/2022]
Abstract
Neuropeptides are a diverse class of signalling molecules that are widely employed as neurotransmitters and neuromodulators in animals, both invertebrate and vertebrate. However, despite their fundamental importance to animal physiology and behaviour, they are much less well understood than the small molecule neurotransmitters. The neuropeptides are classified into families according to similarities in their peptide sequence; and on this basis, the FMRFamide and RFamide-like peptides, first discovered in molluscs, are an example of a family that is conserved throughout the animal phyla. In this review, the literature on these neuropeptides has been consolidated with a particular emphasis on allowing a comparison between data sets in phyla as diverse as coelenterates and mammals. The intention is that this focus on the structure and functional aspects of FMRFamide and RFamide-like neuropeptides will inform understanding of conserved principles and distinct properties of signalling across the animal phyla.
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Affiliation(s)
- Robert J Walker
- School of Biological Sciences, University of Southampton, Southampton, UK
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