1
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Schrader M. Origins, Technological Advancement, and Applications of Peptidomics. Methods Mol Biol 2024; 2758:3-47. [PMID: 38549006 DOI: 10.1007/978-1-0716-3646-6_1] [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 comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.
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Affiliation(s)
- Michael Schrader
- Department of Bioengineering Sciences, Weihenstephan-Tr. University of Applied Sciences, Freising, Germany.
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2
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Hellinger R, Sigurdsson A, Wu W, Romanova EV, Li L, Sweedler JV, Süssmuth RD, Gruber CW. Peptidomics. NATURE REVIEWS. METHODS PRIMERS 2023; 3:25. [PMID: 37250919 PMCID: PMC7614574 DOI: 10.1038/s43586-023-00205-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 05/31/2023]
Abstract
Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Arnar Sigurdsson
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Wenxin Wu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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3
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Piekut T, Wong YY, Walker SE, Smith CL, Gauberg J, Harracksingh AN, Lowden C, Novogradac BB, Cheng HYM, Spencer GE, Senatore A. Early Metazoan Origin and Multiple Losses of a Novel Clade of RIM Presynaptic Calcium Channel Scaffolding Protein Homologs. Genome Biol Evol 2021; 12:1217-1239. [PMID: 32413100 PMCID: PMC7456537 DOI: 10.1093/gbe/evaa097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2020] [Indexed: 12/18/2022] Open
Abstract
The precise localization of CaV2 voltage-gated calcium channels at the synapse active zone requires various interacting proteins, of which, Rab3-interacting molecule or RIM is considered particularly important. In vertebrates, RIM interacts with CaV2 channels in vitro via a PDZ domain that binds to the extreme C-termini of the channels at acidic ligand motifs of D/E-D/E/H-WC-COOH, and knockout of RIM in vertebrates and invertebrates disrupts CaV2 channel synaptic localization and synapse function. Here, we describe a previously uncharacterized clade of RIM proteins bearing domain architectures homologous to those of known RIM homologs, but with some notable differences including key amino acids associated with PDZ domain ligand specificity. This novel RIM emerged near the stem lineage of metazoans and underwent extensive losses, but is retained in select animals including the early-diverging placozoan Trichoplax adhaerens, and molluscs. RNA expression and localization studies in Trichoplax and the mollusc snail Lymnaea stagnalis indicate differential regional/tissue type expression, but overlapping expression in single isolated neurons from Lymnaea. Ctenophores, the most early-diverging animals with synapses, are unique among animals with nervous systems in that they lack the canonical RIM, bearing only the newly identified homolog. Through phylogenetic analysis, we find that CaV2 channel D/E-D/E/H-WC-COOH like PDZ ligand motifs were present in the common ancestor of cnidarians and bilaterians, and delineate some deeply conserved C-terminal structures that distinguish CaV1 from CaV2 channels, and CaV1/CaV2 from CaV3 channels.
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Affiliation(s)
| | | | - Sarah E Walker
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Carolyn L Smith
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | | | | | | | | | | | - Gaynor E Spencer
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
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4
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Wood EA, Stopka SA, Zhang L, Mattson S, Maasz G, Pirger Z, Vertes A. Neuropeptide Localization in Lymnaea stagnalis: From the Central Nervous System to Subcellular Compartments. Front Mol Neurosci 2021; 14:670303. [PMID: 34093125 PMCID: PMC8172996 DOI: 10.3389/fnmol.2021.670303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/09/2021] [Indexed: 12/02/2022] Open
Abstract
Due to the relatively small number of neurons (few tens of thousands), the well-established multipurpose model organism Lymnaea stagnalis, great pond snail, has been extensively used to study the functioning of the nervous system. Unlike the more complex brains of higher organisms, L. stagnalis has a relatively simple central nervous system (CNS) with well-defined circuits (e.g., feeding, locomotion, learning, and memory) and identified individual neurons (e.g., cerebral giant cell, CGC), which generate behavioral patterns. Accumulating information from electrophysiological experiments maps the network of neuronal connections and the neuronal circuits responsible for basic life functions. Chemical signaling between synaptic-coupled neurons is underpinned by neurotransmitters and neuropeptides. This review looks at the rapidly expanding contributions of mass spectrometry (MS) to neuropeptide discovery and identification at different granularity of CNS organization. Abundances and distributions of neuropeptides in the whole CNS, eleven interconnected ganglia, neuronal clusters, single neurons, and subcellular compartments are captured by MS imaging and single cell analysis techniques. Combining neuropeptide expression and electrophysiological data, and aided by genomic and transcriptomic information, the molecular basis of CNS-controlled biological functions is increasingly revealed.
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Affiliation(s)
- Ellen A. Wood
- Department of Chemistry, The George Washington University, Washington, DC, United States
| | - Sylwia A. Stopka
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Linwen Zhang
- Department of Chemistry, The George Washington University, Washington, DC, United States
| | - Sara Mattson
- Department of Chemistry, The George Washington University, Washington, DC, United States
| | - Gabor Maasz
- Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Tihany, Hungary
- Soós Ernő Research and Development Center, University of Pannonia, Nagykanizsa, Hungary
| | - Zsolt Pirger
- Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Tihany, Hungary
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, United States
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5
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Dong N, Bandura J, Zhang Z, Wang Y, Labadie K, Noel B, Davison A, Koene JM, Sun HS, Coutellec MA, Feng ZP. Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis. BMC Genomics 2021; 22:18. [PMID: 33407100 PMCID: PMC7789530 DOI: 10.1186/s12864-020-07287-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/28/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST libraries and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome. RESULTS In this study, taking advantage of the recent availability of a preliminary L. stagnalis genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca2+ channels showed the most sequence similarity to those of Mus musculus, Danio rerio, Xenopus tropicalis, Drosophila melanogaster, and Caenorhabditis elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved. CONCLUSIONS Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study provides a complete characterization of the ion channels of Lymnaea stagnalis, opening new avenues for future research on fundamental neurobiological processes in this model system.
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Affiliation(s)
- Nancy Dong
- Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Julia Bandura
- Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Yan Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Karine Labadie
- Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, BP5706, 91057, Evry, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry, Université Paris-Saclay, 91057, Evry, France
| | - Angus Davison
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK, NG7 2RD, UK
| | - Joris M Koene
- Department of Ecological Science, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
| | - Hong-Shuo Sun
- Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | | | - Zhong-Ping Feng
- Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
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6
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Corbière A, Vaudry H, Chan P, Walet-Balieu ML, Lecroq T, Lefebvre A, Pineau C, Vaudry D. Strategies for the Identification of Bioactive Neuropeptides in Vertebrates. Front Neurosci 2019; 13:948. [PMID: 31619945 PMCID: PMC6759750 DOI: 10.3389/fnins.2019.00948] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/22/2019] [Indexed: 11/13/2022] Open
Abstract
Neuropeptides exert essential functions in animal physiology by controlling e.g., reproduction, development, growth, energy homeostasis, cardiovascular activity and stress response. Thus, identification of neuropeptides has been a very active field of research over the last decades. This review article presents the various methods used to discover novel bioactive peptides in vertebrates. Initially identified on the basis of their biological activity, some neuropeptides have also been discovered for their ability to bind/activate a specific receptor or based on their biochemical characteristics such as C-terminal amidation which concerns half of the known neuropeptides. More recently, sequencing of the genome of many representative species has facilitated peptidomic approaches using mass spectrometry and in silico screening of genomic libraries. Through these different approaches, more than a hundred of bioactive neuropeptides have already been identified in vertebrates. Nevertheless, researchers continue to find new neuropeptides or to identify novel functions of neuropeptides that had not been detected previously, as it was recently the case for nociceptin.
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Affiliation(s)
- Auriane Corbière
- Normandie Univ, UNIROUEN, Inserm, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Neuropeptides, Neuronal Death and Cell Plasticity Team, Rouen, France
| | - Hubert Vaudry
- Normandie Univ, UNIROUEN, Inserm, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Neuropeptides, Neuronal Death and Cell Plasticity Team, Rouen, France.,Normandie Univ, UNIROUEN, Regional Cell Imaging Platform of Normandy (PRIMACEN), Rouen, France
| | - Philippe Chan
- Normandie Univ, UNIROUEN, Rouen Proteomic Platform (PISSARO), Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Marie-Laure Walet-Balieu
- Normandie Univ, UNIROUEN, Rouen Proteomic Platform (PISSARO), Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Thierry Lecroq
- Normandie Univ, UNIROUEN, LITIS EA 4108, Information Processing in Biology & Health, Rouen, France
| | - Arnaud Lefebvre
- Normandie Univ, UNIROUEN, LITIS EA 4108, Information Processing in Biology & Health, Rouen, France
| | | | - David Vaudry
- Normandie Univ, UNIROUEN, Inserm, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Neuropeptides, Neuronal Death and Cell Plasticity Team, Rouen, France.,Normandie Univ, UNIROUEN, Regional Cell Imaging Platform of Normandy (PRIMACEN), Rouen, France.,Normandie Univ, UNIROUEN, Rouen Proteomic Platform (PISSARO), Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
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7
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Lietz CB, Toneff T, Mosier C, Podvin S, O'Donoghue AJ, Hook V. Phosphopeptidomics Reveals Differential Phosphorylation States and Novel SxE Phosphosite Motifs of Neuropeptides in Dense Core Secretory Vesicles. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:935-947. [PMID: 29556927 PMCID: PMC5943185 DOI: 10.1007/s13361-018-1915-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 05/23/2023]
Abstract
Neuropeptides are vital for cell-cell communication and function in the regulation of the nervous and endocrine systems. They are generated by post-translational modification (PTM) steps resulting in small active peptides generated from prohormone precursors. Phosphorylation is a significant PTM for the bioactivity of neuropeptides. From the known diversity of distinct neuropeptide functions, it is hypothesized that the extent of phosphorylation varies among different neuropeptides. To assess this hypothesis, neuropeptide-containing dense core secretory vesicles from bovine adrenal medullary chromaffin cells were subjected to global phosphopeptidomics analyses by liquid chromatography (LC)-mass spectrometry (MS/MS). Phosphopeptides were identified directly by LC-MS/MS and indirectly by phosphatase treatment followed by LC-MS/MS. The data identified numerous phosphorylated peptides derived from neuropeptide precursors such as chromogranins, secretogranins, proenkephalin and pro-NPY. Phosphosite occupancies were observed at high and low levels among identified peptides and many of the high occupancy phosphopeptides represent prohormone-derived peptides with currently unknown bioactivities. Peptide sequence analyses demonstrated SxE as the most prevalent phosphorylation site motif, corresponding to phosphorylation sites of the Fam20C protein kinase known to be present in the secretory pathway. The range of high to low phosphosite occupancies for neuropeptides demonstrates cellular regulation of neuropeptide phosphorylation. Graphical Abstract ᅟ.
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Affiliation(s)
- Christopher B Lietz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Thomas Toneff
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Charles Mosier
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA.
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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8
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Monroe EB, Annangudi SP, Wadhams AA, Richmond TA, Yang N, Southey BR, Romanova EV, Schoofs L, Baggerman G, Sweedler JV. Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:923-934. [PMID: 29667164 PMCID: PMC5943159 DOI: 10.1007/s13361-018-1898-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/04/2017] [Accepted: 12/16/2017] [Indexed: 05/08/2023]
Abstract
Neuropeptides are essential cell-to-cell signaling messengers and serve important regulatory roles in animals. Although remarkable progress has been made in peptide identification across the Metazoa, for some phyla such as Echinodermata, limited neuropeptides are known and even fewer have been verified on the protein level. We employed peptidomic approaches using bioinformatics and mass spectrometry (MS) to experimentally confirm 23 prohormones and to characterize a new prohormone in nervous system tissue from Strongylocentrotus purpuratus, the purple sea urchin. Ninety-three distinct peptides from known and novel prohormones were detected with MS from extracts of the radial nerves, many of which are reported or experimentally confirmed here for the first time, representing a large-scale study of neuropeptides from the phylum Echinodermata. Many of the identified peptides and their precursor proteins have low homology to known prohormones from other species/phyla and are unique to the sea urchin. By pairing bioinformatics with MS, the capacity to characterize novel peptides and annotate prohormone genes is enhanced. Graphical Abstract.
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Affiliation(s)
- Eric B Monroe
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Suresh P Annangudi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andinet A Wadhams
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Timothy A Richmond
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ning Yang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Liliane Schoofs
- Functional Genomics and Proteomics Unit, KU Leuven, 3000, Leuven, Belgium
| | - Geert Baggerman
- ProMeta Interfacultary Center for Proteomics and Metabolomics, KU Leuven, 3000, Leuven, Belgium
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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9
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Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.
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10
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Schoofs L, De Loof A, Van Hiel MB. Neuropeptides as Regulators of Behavior in Insects. ANNUAL REVIEW OF ENTOMOLOGY 2017; 62:35-52. [PMID: 27813667 DOI: 10.1146/annurev-ento-031616-035500] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Neuropeptides are by far the largest and most diverse group of signaling molecules in multicellular organisms. They are ancient molecules important in regulating a multitude of processes. Their small proteinaceous character allowed them to evolve and radiate quickly into numerous different molecules. On average, hundreds of distinct neuropeptides are present in animals, sometimes with unique classes that do not occur in distantly related species. Acting as neurotransmitters, neuromodulators, hormones, or growth factors, they are extremely diverse and are involved in controlling growth, development, ecdysis, digestion, diuresis, and many more physiological processes. Neuropeptides are also crucial in regulating myriad behavioral actions associated with feeding, courtship, sleep, learning and memory, stress, addiction, and social interactions. In general, behavior ensures that an organism can survive in its environment and is defined as any action that can change an organism's relationship to its surroundings. Even though the mode of action of neuropeptides in insects has been vigorously studied, relatively little is known about most neuropeptides and only a few model insects have been investigated. Here, we provide an overview of the roles neuropeptides play in insect behavior. We conclude that multiple neuropeptides need to work in concert to coordinate certain behaviors. Additionally, most neuropeptides studied to date have more than a single function.
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Affiliation(s)
- Liliane Schoofs
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, 3000 Leuven, Belgium; , ,
| | - Arnold De Loof
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, 3000 Leuven, Belgium; , ,
| | - Matthias Boris Van Hiel
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, 3000 Leuven, Belgium; , ,
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11
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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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12
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Twiss JL, Fainzilber M. Neuroproteomics: How Many Angels can be Identified in an Extract from the Head of a Pin? Mol Cell Proteomics 2016; 15:341-3. [PMID: 26729708 DOI: 10.1074/mcp.e116.057828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jeffery L Twiss
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208;
| | - Mike Fainzilber
- §Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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13
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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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Pauls D, Chen J, Reiher W, Vanselow JT, Schlosser A, Kahnt J, Wegener C. Peptidomics and processing of regulatory peptides in the fruit fly Drosophila. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Meng L, Xing G, Cui C, Han J. WITHDRAWN: Enkephalin- and dynorphin-release produced by electrical stimulation of different frequencies in rat brain slices. Brain Res 2014:S0006-8993(14)00071-7. [PMID: 24462938 DOI: 10.1016/j.brainres.2014.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/30/2013] [Accepted: 01/15/2014] [Indexed: 10/25/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Li Meng
- Neuroscience Research Institute, School of Basic Medical Science, Peking University, 38 Xue-Yuan Road, Beijing 100191, China
| | - Guogang Xing
- Neuroscience Research Institute, School of Basic Medical Science, Peking University, 38 Xue-Yuan Road, Beijing 100191, China
| | - Cailian Cui
- Neuroscience Research Institute, School of Basic Medical Science, Peking University, 38 Xue-Yuan Road, Beijing 100191, China
| | - Jisheng Han
- Neuroscience Research Institute, School of Basic Medical Science, Peking University, 38 Xue-Yuan Road, Beijing 100191, China
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16
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Romanova EV, Aerts JT, Croushore CA, Sweedler JV. Small-volume analysis of cell-cell signaling molecules in the brain. Neuropsychopharmacology 2014; 39:50-64. [PMID: 23748227 PMCID: PMC3857641 DOI: 10.1038/npp.2013.145] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/26/2013] [Accepted: 05/06/2013] [Indexed: 12/19/2022]
Abstract
Modern science is characterized by integration and synergy between research fields. Accordingly, as technological advances allow new and more ambitious quests in scientific inquiry, numerous analytical and engineering techniques have become useful tools in biological research. The focus of this review is on cutting edge technologies that aid direct measurement of bioactive compounds in the nervous system to facilitate fundamental research, diagnostics, and drug discovery. We discuss challenges associated with measurement of cell-to-cell signaling molecules in the nervous system, and advocate for a decrease of sample volumes to the nanoliter volume regimen for improved analysis outcomes. We highlight effective approaches for the collection, separation, and detection of such small-volume samples, present strategies for targeted and discovery-oriented research, and describe the required technology advances that will empower future translational science.
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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, IL, USA
| | - Jordan T Aerts
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Callie A Croushore
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Zatylny-Gaudin C, Favrel P. Diversity of the RFamide Peptide Family in Mollusks. Front Endocrinol (Lausanne) 2014; 5:178. [PMID: 25386166 PMCID: PMC4208409 DOI: 10.3389/fendo.2014.00178] [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: 07/15/2014] [Accepted: 10/06/2014] [Indexed: 01/25/2023] Open
Abstract
Since the initial characterization of the cardioexcitatory peptide FMRFamide in the bivalve mollusk Macrocallista nimbosa, a great number of FMRFamide-like peptides (FLPs) have been identified in mollusks. FLPs were initially isolated and molecularly characterized in model mollusks using biochemical methods. The development of recombinant technologies and, more recently, of genomics has boosted knowledge on their diversity in various mollusk classes. Today, mollusk FLPs represent approximately 75 distinct RFamide peptides that appear to result from the expression of only five genes: the FMRFamide-related peptide gene, the LFRFamide gene, the luqin gene, the neuropeptide F gene, and the cholecystokinin/sulfakinin gene. FLPs display a complex spatiotemporal pattern of expression in the central and peripheral nervous system. Working as neurotransmitters, neuromodulators, or neurohormones, FLPs are involved in the control of a great variety of biological and physiological processes including cardiovascular regulation, osmoregulation, reproduction, digestion, and feeding behavior. From an evolutionary viewpoint, the major challenge will then logically concern the elucidation of the FLP repertoire of orphan mollusk classes and the way they are functionally related. In this respect, deciphering FLP signaling pathways by characterizing the specific receptors these peptides bind remains another exciting objective.
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Affiliation(s)
- Celine Zatylny-Gaudin
- Université de Caen Basse-Normandie, Normandie Université, Biology of Aquatic Organisms and Ecosystems (BOREA), Caen, France
- Muséum National d’Histoire Naturelle, Sorbonne Universités, BOREA, Paris, France
- Université Pierre et Marie Curie, BOREA, Paris, France
- UMR 7208 Centre National de la Recherche Scientifique, BOREA, Paris, France
- IRD 207, L’Institut de recherche pour le développement, BOREA, Paris, France
| | - Pascal Favrel
- Université de Caen Basse-Normandie, Normandie Université, Biology of Aquatic Organisms and Ecosystems (BOREA), Caen, France
- Muséum National d’Histoire Naturelle, Sorbonne Universités, BOREA, Paris, France
- Université Pierre et Marie Curie, BOREA, Paris, France
- UMR 7208 Centre National de la Recherche Scientifique, BOREA, Paris, France
- IRD 207, L’Institut de recherche pour le développement, BOREA, Paris, France
- *Correspondence: Pascal Favrel, Université de Caen Basse-Normandie, Esplanade de la Paix, CS 14032, Caen Cedex 5 14032, France e-mail:
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Jia C, Lietz CB, Ye H, Hui L, Yu Q, Yoo S, Li L. A multi-scale strategy for discovery of novel endogenous neuropeptides in the crustacean nervous system. J Proteomics 2013; 91:1-12. [PMID: 23806756 DOI: 10.1016/j.jprot.2013.06.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/26/2013] [Accepted: 06/16/2013] [Indexed: 12/18/2022]
Abstract
UNLABELLED The conventional mass spectrometry (MS)-based strategy is often inadequate for the comprehensive characterization of various size neuropeptides without the assistance of genomic information. This study evaluated sequence coverage of different size neuropeptides in two crustacean species, blue crab Callinectes sapidus and Jonah crab Cancer borealis using conventional MS methodologies and revealed limitations to mid- and large-size peptide analysis. Herein we attempt to establish a multi-scale strategy for simultaneous and confident sequence elucidation of various sizes of peptides in the crustacean nervous system. Nine novel neuropeptides spanning a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ, the sinus gland of the spiny lobster Panulirus interruptus. These novel neuropeptides included seven allatostatin (A- and B-type) peptides, one crustacean hyperglycemic hormone precursor-related peptide, and one crustacean hyperglycemic hormone. Highly accurate multi-scale characterization of a collection of varied size neuropeptides was achieved by integrating traditional data-dependent tandem MS, improved bottom-up sequencing, multiple fragmentation technique-enabled top-down sequencing, chemical derivatization, and in silico homology search. Collectively, the ability to characterize a neuropeptidome with vastly differing molecule sizes from a neural tissue extract could find great utility in unraveling complex signaling peptide mixtures employed by other biological systems. BIOLOGICAL SIGNIFICANCE Mass spectrometry (MS)-based neuropeptidomics aims to completely characterize the neuropeptides in a target organism as an important first step toward a better understanding of the structure and function of these complex signaling molecules. Although liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) with data-dependent acquisition is a powerful tool in peptidomic research, it often lacks the capability for de novo sequencing of mid-size and large peptides due to inefficient fragmentation of peptides larger than 4kDa. This study describes a multi-scale strategy for complete and confident sequence elucidation of various sizes of neuropeptides in the crustacean nervous system. The aim is to fill a technical gap where the conventional strategy is inefficient for comprehensive characterization of a complex neuropeptidome without assistance of genomic information. Nine novel neuropeptides in a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ of the spiny lobster, P. interruptus. The resulting molecular information extracted from such multi-scale peptidomic analysis will greatly accelerate functional studies of these novel neuropeptides.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison, WI, USA; Department of Chemistry, University of Wisconsin-Madison, WI, USA
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Jia C, Hui L, Cao W, Lietz CB, Jiang X, Chen R, Catherman AD, Thomas PM, Ge Y, Kelleher NL, Li L. High-definition de novo sequencing of crustacean hyperglycemic hormone (CHH)-family neuropeptides. Mol Cell Proteomics 2012; 11:1951-64. [PMID: 23028060 DOI: 10.1074/mcp.m112.020537] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A complete understanding of the biological functions of large signaling peptides (>4 kDa) requires comprehensive characterization of their amino acid sequences and post-translational modifications, which presents significant analytical challenges. In the past decade, there has been great success with mass spectrometry-based de novo sequencing of small neuropeptides. However, these approaches are less applicable to larger neuropeptides because of the inefficient fragmentation of peptides larger than 4 kDa and their lower endogenous abundance. The conventional proteomics approach focuses on large-scale determination of protein identities via database searching, lacking the ability for in-depth elucidation of individual amino acid residues. Here, we present a multifaceted MS approach for identification and characterization of large crustacean hyperglycemic hormone (CHH)-family neuropeptides, a class of peptide hormones that play central roles in the regulation of many important physiological processes of crustaceans. Six crustacean CHH-family neuropeptides (8-9.5 kDa), including two novel peptides with extensive disulfide linkages and PTMs, were fully sequenced without reference to genomic databases. High-definition de novo sequencing was achieved by a combination of bottom-up, off-line top-down, and on-line top-down tandem MS methods. Statistical evaluation indicated that these methods provided complementary information for sequence interpretation and increased the local identification confidence of each amino acid. Further investigations by MALDI imaging MS mapped the spatial distribution and colocalization patterns of various CHH-family neuropeptides in the neuroendocrine organs, revealing that two CHH-subfamilies are involved in distinct signaling pathways.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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20
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TARGETED MASS spectrometry Imaging: Specific Targeting Mass Spectrometry imaging technologies from history to perspective. ACTA ACUST UNITED AC 2012; 47:133-74. [DOI: 10.1016/j.proghi.2012.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2012] [Indexed: 12/28/2022]
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21
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Kodirov SA. The neuronal control of cardiac functions in Molluscs. Comp Biochem Physiol A Mol Integr Physiol 2011; 160:102-16. [PMID: 21736949 PMCID: PMC5480900 DOI: 10.1016/j.cbpa.2011.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 05/12/2011] [Accepted: 06/17/2011] [Indexed: 01/19/2023]
Abstract
In this manuscript, I review the current and relevant classical studies on properties of the Mollusca heart and their central nervous system including ganglia, neurons, and nerves involved in cardiomodulation. Similar to mammalian brain hemispheres, these invertebrates possess symmetrical pairs of ganglia albeit visceral (only one) ganglion and the parietal ganglia (the right ganglion is bigger than the left one). Furthermore, there are two major regulatory drives into the compartments (pericard, auricle, and ventricle) and cardiomyocytes of the heart. These are the excitatory and inhibitory signals that originate from a few designated neurons and their putative neurotransmitters. Many of these neurons are well-identified, their specific locations within the corresponding ganglion are mapped, and some are termed as either heart excitatory (HE) or inhibitory (HI) cells. The remaining neurons are classified as cardio-regulatory, and their direct and indirect actions on the heart's function have been documented. The cardiovascular anatomy of frequently used experimental animals, Achatina, Aplysia, Helix, and Lymnaea is relatively simple. However, as in humans, it possesses all major components including even trabeculae and atrio-ventricular valves. Since the myocardial cells are enzymatically dispersible, multiple voltage dependent cationic currents in isolated cardiomyocytes are described. The latter include at least the A-type K(+), delayed rectifier K(+), TTX-sensitive Na(+), and L-type Ca(2+) channels.
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Affiliation(s)
- Sodikdjon A Kodirov
- Department of Biophysics, Saint Petersburg University, Saint Petersburg 199034, Russia.
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22
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Aseyev N, Zakharov IS, Balaban PM. Morphology of neuropeptide CNP2 modulation of heart activity in terrestrial snail. Peptides 2010; 31:1301-8. [PMID: 20399241 DOI: 10.1016/j.peptides.2010.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 04/06/2010] [Accepted: 04/06/2010] [Indexed: 11/29/2022]
Abstract
A family of neuropeptides called Command Neuron Peptides (CNPs) was described ten years ago as the protein products of the gene HCS2, specifically expressed in the identified interneurons of the nervous system of terrestrial snail (Helix lucorum L. and H. pomatia L.). Recently, the CNP-like peptides have been detected by immunochemistry and immunoblotting in nervous systems of representatives of different invertebrate phyla (Mollusca, Annelida, and Insecta). Still, the function of these peptides remains largely unknown. In Helix it is shown that CNPs: modulate the electrical activity of unidentified central neurons, modulate the pneumostome motoneurons, stimulate neural cones growth in neural cultures. Here, we describe for the first time the CNPs-immunoreactive neural fibers in walls of both auricle and ventricle of the snail heart. We show that application of the synthetic neuropeptide CNP2 (DYPRLamide) in perfusion saline affects heart rate and magnitude of beats in isolated snail heart. The results suggest that in Helix the Command Neuron Peptides could participate in neural modulation of cardiovascular system.
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Affiliation(s)
- Nikolay Aseyev
- Laboratory of Cellular Neurobiology of Learning, Institute of Higher Nervous Activity and Neurophysiology, RAS, Butlerova 5A, 117485 Moscow, Russia.
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Abstract
Osteoporosis is prevalent among the elderly and is a major cause of bone fracture in this population. Bone integrity is maintained by the dynamic processes of bone resorption and bone formation (bone remodeling). Osteoporosis results when there is an imbalance of the two counteracting processes. Bone mineral density, measured by dual-energy x-ray absorptiometry has been the primary method to assess fracture risk for decades. Recent studies demonstrated that measurement of bone turnover markers allows for a dynamic assessment of bone remodeling, while imaging techniques, such as dual-energy x-ray absorptiometry, do not. The application of proteomics has permitted discoveries of new, sensitive, bone turnover markers, which provide unique information for clinical diagnosis and treatment of patients with bone diseases. This review summarizes the recent findings of proteomic studies on bone diseases, properties of mesenchymal stem cells with high expansion rates and osteoblast and osteoclast differentiation, with emphasis on the role of quantitative proteomics in the study of signaling dynamics, biomarkers and discovery of therapeutic targets.
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Affiliation(s)
- Hengwei Zhang
- Genomics & Functional Proteomics Laboratories, Osteoporosis Research Center; Creighton University Medical Center, 601 N 30th Street, Suite 6730, Omaha, NE 68131, USA.
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Abstract
The central nervous systems of molluscan species contain high levels of structurally diverse peptides that function as neurotransmitters, neuromodulators or neurohormones. Peptide diversity is believed to be a way to increase the information handling capacity of neurons in the context of a brain with low cell numbers and neuronal connectivity. Accordingly, much effort has been made to identify peptides from single neurons and tissues of interest. In the past decade a mass spectrometry-based approach has been applied to detect and characterize peptides from single neurons, nerves and tissues of the molluscan brain. Peptides from single neurons are often analysed directly by mass spectrometry without prior sample preparation. Single neurons from the molluscan brain may be identified based on their position, cell morphology and colour. Neurons that cannot be readily identified can be tagged functionally or chemically. For the analysis of peptides from tissues, special extraction methods in conjunction with peptide separation by liquid chromatography coupled to mass spectrometry have been developed. Tens to hundreds of peptides from the tissue extract can be detected and characterized in a single analysis.
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Affiliation(s)
- Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Centre for Neurogenomics and Cognitive Research, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Nederlands.
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Abstract
In this study, intact flagellin proteins were purified from strains of Clostridium difficile and analyzed using quadrupole time of flight and linear ion trap mass spectrometers. Top-down studies showed the flagellin proteins to have a mass greater than that predicted from the corresponding gene sequence. These top-down studies revealed marker ions characteristic of glycan modifications. Additionally, diversity in the observed masses of glycan modifications was seen between strains. Electron transfer dissociation mass spectrometry was used to demonstrate that the glycan was attached to the flagellin protein backbone in O linkage via a HexNAc residue in all strains examined. Bioinformatic analysis of C. difficile genomes revealed diversity with respect to glycan biosynthesis gene content within the flagellar biosynthesis locus, likely reflected by the observed flagellar glycan diversity. In C. difficile strain 630, insertional inactivation of a glycosyltransferase gene (CD0240) present in all sequenced genomes resulted in an inability to produce flagellar filaments at the cell surface and only minor amounts of unmodified flagellin protein.
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Rubakhin SS, Sweedler JV. Quantitative measurements of cell-cell signaling peptides with single-cell MALDI MS. Anal Chem 2008; 80:7128-36. [PMID: 18707135 PMCID: PMC2646760 DOI: 10.1021/ac8010389] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 07/14/2008] [Indexed: 11/28/2022]
Abstract
Cell-to-cell signaling peptides play important roles in neurotransmission, neuromodulation, and hormonal signaling. Significant progress has been achieved in qualitative investigations of signaling peptides in the nervous system using single cell matrix-assisted laser desorption/ionization mass spectrometry. However, quantitative information about signaling peptides is difficult to obtain with this approach because only small amounts of analytes are available for analysis. Here we describe several methods for quantitative microanalysis of peptides in individual Aplysia californica neurons and small pieces of tissue. Stable isotope labeling with d0- and d4-succinic anhydride and iTRAQ reagents has been successfully adopted for relative quantitation of nanoliter volume samples containing the Aplysia insulin C beta peptide. Comparative analysis of the C beta peptide release site, the upper labial nerve, and its synthesis location, the F- and C-clusters, shows that the release site possesses almost three times more of this compound. The method of standard addition permits absolute quantitation of the physiologically active neuropeptide cerebrin from small structures, including nerves and neuronal clusters, in the femtomole range with a limit of detection of 19 fmol. The simplicity of these methods and the commercial availability of the reagents allow quantitative measurements from a variety of small-volume biological samples.
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Affiliation(s)
- Stanislav S. Rubakhin
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
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Goldberg JI, Doran SA, Shartau RB, Pon JR, Ali DW, Tam R, Kuang S. Integrative biology of an embryonic respiratory behaviour in pond snails:the `embryo stir-bar hypothesis'. J Exp Biol 2008; 211:1729-36. [DOI: 10.1242/jeb.016014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARYEmbryos of freshwater snails undergo direct development from single cell to juvenile inside egg masses that are deposited on vegetation and other substratum in pond, lake and stream habitats. Helisoma trivolvis, a member of the Planorbidae family of basommatophoran snails, has served as a model for studying the developmental and physiological roles for neurotransmitters during embryogenesis. Early studies revealed that H. trivolvis embryos from stage E15 to E30, the period between gastrulation and the trochophore–juvenile transition, display a cilia-driven behaviour consisting of slow basal rotation and transient periods of rapid rotation. The discovery of a bilateral pair of early serotonergic neurons,named ENC1, which project an apical process to the embryo surface and basal neurites to ciliated cells, prompted the hypothesis that each ENC1 is a dual-function sensory and motor neuron mediating a physiological embryonic response. This article reviews our past and present studies and addresses questions concerning this hypothesis, including the following. (1) What environmental signal regulates ENC1 activity and rotational behaviour? (2)Does ENC1 function as both a primary sensory and motor neuron underlying the rotational behaviour? (3) What are the sensory transduction mechanisms? (4)How does ENC1 regulate ciliary beating? (5) Do other basommatophoran species have similar neural–ciliary pathways and behavioural responses? (6) How is the behaviour manifest in the dynamic natural environment? In this review,we introduce the `embryo stir-bar hypothesis', which proposes that embryonic rotation is a hypoxia-sensitive respiratory behaviour responsible for mixing the egg capsule fluid, thereby enhancing delivery of environmental oxygen to the embryo.
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Affiliation(s)
- Jeffrey I. Goldberg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta,Canada, T2N 1N4
| | - Shandra A. Doran
- Department of Biological Sciences, University of Calgary, Calgary, Alberta,Canada, T2N 1N4
| | - Ryan B. Shartau
- Department of Biological Sciences, University of Calgary, Calgary, Alberta,Canada, T2N 1N4
| | - Julia R. Pon
- Department of Biological Sciences, University of Calgary, Calgary, Alberta,Canada, T2N 1N4
| | - Declan W. Ali
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta,Canada, T6G 2E9
| | - Rose Tam
- Department of Biological Sciences, University of Calgary, Calgary, Alberta,Canada, T2N 1N4
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907-2054, USA
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Boonen K, Landuyt B, Baggerman G, Husson SJ, Huybrechts J, Schoofs L. Peptidomics: The integrated approach of MS, hyphenated techniques and bioinformatics for neuropeptide analysis. J Sep Sci 2008; 31:427-45. [DOI: 10.1002/jssc.200700450] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Abstract
Early diagnosis and prevention is a key factor in reducing the mortality and morbidity of cancer. However, currently available screening tools lack enough sensitivity for early diagnosis. It is important to develop noninvasive techniques and methods that can screen and identify asymptomatic patients who have cancer. Biomarkers of cancer status can also serve as powerful tools in monitoring the course of cancer and in determining the efficacy and safety of novel therapies. Thus, discovery of novel specific biomarkers are needed that may provide informative clues for early diagnosis and treatment of cancer. Recently, remarkable progress has been made in the development of new proteomics technology. The progress that has been made in this field is helpful in identifying biomarkers that can be used for early diagnosis of cancer and improving the understanding of the molecular etiological mechanism of cancer. This article describes the current state of the art in this field.
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Affiliation(s)
- Gary Guishan Xiao
- Osteoporosis Research Center, Departments of Medicine and Biomedical Sciences, Creighton University, 601 N 30 ST, Suite 6730, Omaha, NE 68131
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Schmidt JJ, McIlwain S, Page D, Christie AE, Li L. Combining MALDI-FTMS and bioinformatics for rapid peptidomic comparisons. J Proteome Res 2008; 7:887-96. [PMID: 18205299 DOI: 10.1021/pr070390p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing research efforts in large-scale mass spectral analyses of peptides and proteins have led to many advances in technology and method development for collecting data and improving the quality of data. However, the resultant large data sets often pose significant challenges in extracting useful information in a high-throughput manner. Here, we describe one such method where we analyzed a large mass spectral data set collected using decapod crustacean nervous tissue extracts separated via high-performance liquid chromatography (HPLC) coupled to high-resolution matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS). Following their acquisition, the data collected from discrete LC fractions was compiled and analyzed using an in-house developed software package that deisotoped, compressed, calibrated, and matched peaks to a list of known crustacean neuropeptides. By processing these data via bioinformatics tools such as hierarchical clustering, more than 110 neuropeptides that belong to 14 peptide families were mapped in five crustacean species. Overall, we demonstrate the utility of MALDI-FTMS in combination with a bioinformatics software package for the elucidation and comparison of peptidomes of varying crustacean species. This study established an effective methodology and will provide the basis for future investigations into more comprehensive comparative peptidomics with larger collection of species and phyla in order to gain a deeper understanding of the evolution and diversification of peptide families.
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Affiliation(s)
- Joshua J Schmidt
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, USA
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DeKeyser SS, Kutz-Naber KK, Schmidt JJ, Barrett-Wilt GA, Li L. Imaging mass spectrometry of neuropeptides in decapod crustacean neuronal tissues. J Proteome Res 2007; 6:1782-91. [PMID: 17381149 PMCID: PMC2529365 DOI: 10.1021/pr060603v] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Imaging mass spectrometry (IMS) of neuropeptides in crustacean neuronal tissues was performed on a MALDI-TOF/TOF instrument. Sample preparation protocols were developed for the sensitive detection of these highly complex endogenous signaling molecules. The neuromodulatory complements of the pericardial organ (PO) and brain of the Jonah crab, Cancer borealis, were mapped. Distributions of peptide isoforms belonging to 10 neuropeptide families were investigated using the IMS technique. Often, neuropeptides of high sequence homology were similarly located. However, two RFamide-family peptides and a truncated orcokinin peptide were mapped to locations distinct from other members of their respective families. Over 30 previously sequenced neuropeptides were identified based on mass measurement. For increased confidence of identification, select peptides were fragmented by post-source decay (PSD) and collisional-induced dissociation (CID). Collectively, this organ-level IMS study elucidates the spatial relationships between multiple neuropeptide isoforms of the same family as well as the relative distributions of neuropeptide families.
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Affiliation(s)
- Stephanie S. DeKeyser
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705−2222, USA
| | - Kimberly K. Kutz-Naber
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705−2222, USA
| | - Joshua J. Schmidt
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705−2222, USA
| | | | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705−2222, USA
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Rubakhin SS, Churchill JD, Greenough WT, Sweedler JV. Profiling signaling peptides in single mammalian cells using mass spectrometry. Anal Chem 2007; 78:7267-72. [PMID: 17037931 PMCID: PMC2530951 DOI: 10.1021/ac0607010] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peptide content of individual mammalian cells is profiled using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. Both enzymatic and nonenzymatic procedures, including a glycerol cell stabilization method, are reported for the isolation of individual mammalian cells in a manner compatible with MALDI MS measurements. Guided microdeposition of MALDI matrix allows samples to be created with suitable analyte-to-matrix ratios. More than 15 peptides are observed in individual rat intermediate pituitary cells. The combination of accurate mass data, expected cleavages by proteolytic enzymes, and postsource decay sequencing allows identification of 14 of these peptides as pro-opiomelanocortin prohormone-derived molecules. These protocols permit the classification of individual mammalian cells by peptide profile, the elucidation of cell-specific prohormone processing, and the discovery of new signaling peptides on a cell-to-cell basis in a wide variety of mammalian cell types.
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Affiliation(s)
| | - James D. Churchill
- Department of Psychology, and the Beckman Institute, University of Illinois, Urbana, IL, 61801
| | - William T. Greenough
- Department of Psychology, and the Beckman Institute, University of Illinois, Urbana, IL, 61801
| | - Jonathan V. Sweedler
- Department of Chemistry, University of Illinois, Urbana, IL, 61801
- CORRESPONDING AUTHOR: Jonathan V. Sweedler, Department of Chemistry, 600 S. Mathews, 64-5, Urbana, IL 61801,
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Dowell JA, Heyden WV, Li L. Rat Neuropeptidomics by LC−MS/MS and MALDI−FTMS: Enhanced Dissection and Extraction Techniques Coupled with 2D RP-RP HPLC. J Proteome Res 2006; 5:3368-75. [PMID: 17137338 DOI: 10.1021/pr0603452] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently developed sample preparation techniques employing microwave irradiation have enabled the comprehensive study of endogenous mammalian neuropeptides. These methods reduce interference from post-mortem protein degradation by deactivating proteases via heat denaturation. Alternatively, we have developed a protocol using cryostat dissection and a boiling extraction buffer to achieve a similar effect. This novel methodology greatly reduces post-mortem protein contamination and increases neuropeptide identification without the use of specialized equipment. In addition, a 2D HPLC scheme employing differential pH selectivity in the first and second dimensions has been used to enhance neuropeptidome coverage. By using our novel dissection protocol in tandem with 2D RP-RP HPLC, we were able to identify a total of 56 peptides from known neuropeptide precursors, including 17 previously unidentified peptides. The use of cryostat dissection and two-dimensional RP-RP HPLC enhances the detection of novel neuropeptides by deactivating proteases and reducing sample complexity.
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Affiliation(s)
- James A Dowell
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
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Dickinson PS. Neuromodulation of central pattern generators in invertebrates and vertebrates. Curr Opin Neurobiol 2006; 16:604-14. [PMID: 17085040 DOI: 10.1016/j.conb.2006.10.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Accepted: 10/25/2006] [Indexed: 10/23/2022]
Abstract
Central pattern generators are subject to extensive modulation that generates flexibility in the rhythmic outputs of these neural networks. The effects of neuromodulators interact with one another, and modulatory neurons are themselves often subject to modulation, enabling both higher order control and indirect interactions among central pattern generators. In addition, modulators often directly mediate the interactions between functionally related central pattern generators. In systems such as the vertebrate respiratory central pattern generator, multiple pacemaker types interact to produce rhythmic output. Modulators can then alter the relative contributions of the different pacemakers, leading to substantial changes in motor output and hence to different behaviors. Surprisingly, substantial changes in some aspects of the circuitry of a central pattern generator, such as a several-fold increase in synaptic strength, can sometimes have little effect on the output of the CPG, whereas other changes have profound effects.
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Affiliation(s)
- Patsy S Dickinson
- Department of Biology, 6500 College Station, Bowdoin College, Brunswick, ME 04011, USA.
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