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Irvine A, McKenzie D, McCoy CJ, Graham RLJ, Graham C, Huws SA, Atkinson LE, Mousley A. Novel integrated computational AMP discovery approaches highlight diversity in the helminth AMP repertoire. PLoS Pathog 2023; 19:e1011508. [PMID: 37523405 PMCID: PMC10414684 DOI: 10.1371/journal.ppat.1011508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/10/2023] [Accepted: 06/23/2023] [Indexed: 08/02/2023] Open
Abstract
Antimicrobial Peptides (AMPs) are immune effectors that are key components of the invertebrate innate immune system providing protection against pathogenic microbes. Parasitic helminths (phylum Nematoda and phylum Platyhelminthes) share complex interactions with their hosts and closely associated microbiota that are likely regulated by a diverse portfolio of antimicrobial immune effectors including AMPs. Knowledge of helminth AMPs has largely been derived from nematodes, whereas the flatworm AMP repertoire has not been described. This study highlights limitations in the homology-based approaches, used to identify putative nematode AMPs, for the characterisation of flatworm AMPs, and reveals that innovative algorithmic AMP prediction approaches provide an alternative strategy for novel helminth AMP discovery. The data presented here: (i) reveal that flatworms do not encode traditional lophotrochozoan AMP groups (Big Defensin, CSαβ peptides and Myticalin); (ii) describe a unique integrated computational pipeline for the discovery of novel helminth AMPs; (iii) reveal >16,000 putative AMP-like peptides across 127 helminth species; (iv) highlight that cysteine-rich peptides dominate helminth AMP-like peptide profiles; (v) uncover eight novel helminth AMP-like peptides with diverse antibacterial activities, and (vi) demonstrate the detection of AMP-like peptides from Ascaris suum biofluid. These data represent a significant advance in our understanding of the putative helminth AMP repertoire and underscore a potential untapped source of antimicrobial diversity which may provide opportunities for the discovery of novel antimicrobials. Further, unravelling the role of endogenous worm-derived antimicrobials and their potential to influence host-worm-microbiome interactions may be exploited for the development of unique helminth control approaches.
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Affiliation(s)
- Allister Irvine
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Darrin McKenzie
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Ciaran J. McCoy
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Robert L. J. Graham
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Ciaren Graham
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Sharon A. Huws
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Louise E. Atkinson
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Angela Mousley
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
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Pérez-Polo S, Imran MAS, Dios S, Pérez J, Barros L, Carrera M, Gestal C. Identifying Natural Bioactive Peptides from the Common Octopus ( Octopus vulgaris Cuvier, 1797) Skin Mucus By-Products Using Proteogenomic Analysis. Int J Mol Sci 2023; 24:ijms24087145. [PMID: 37108304 PMCID: PMC10138644 DOI: 10.3390/ijms24087145] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The common octopus is a cephalopod species subject to active fisheries, with great potential in the aquaculture and food industry, and which serves as a model species for biomedical and behavioral studies. The analysis of the skin mucus allows us to study their health in a non-invasive way, by using a hardly exploited discard of octopus in the fishing sector. A shotgun proteomics approach combined with liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) using an Orbitrap-Elite instrument was used to create a reference dataset from octopus skin mucus. The final proteome compilation was investigated by integrated in-silico studies, including Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, network studies, and prediction and characterization analysis of potential bioactive peptides. This work presents the first proteomic analysis of the common octopus skin mucus proteome. This library was created by merging 5937 identified spectra of 2038 different peptides. A total of 510 non-redundant proteins were identified. Obtained results show proteins closely related to the defense, which highlight the role of skin mucus as the first barrier of defense and the interaction with the environment. Finally, the potential of the bioactive peptides with antimicrobial properties, and their possible application in biomedicine, pharmaceutical, and nutraceutical industry was addressed.
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Affiliation(s)
- Sara Pérez-Polo
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Md Abdus Shukur Imran
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Sonia Dios
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Jaime Pérez
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Lorena Barros
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Mónica Carrera
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Camino Gestal
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
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PepTraq: a toolbox for in silico data mining and fast sequence filtering. Amino Acids 2023:10.1007/s00726-023-03251-y. [PMID: 36884076 DOI: 10.1007/s00726-023-03251-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023]
Abstract
The development of de novo sequencing tools has led to the massive production of genomes and transcriptomes from many unconventional animal models. To tackle this huge flow of data, PepTraq brings together many functionalities generally scattered in multiple tools, so that sequences can be filtered on the basis of multiple criteria. It is particularly suitable for the identification of non-annotated transcripts, re-annotation, extraction of secretomes, neuropeptidomes, targeted search for peptides and proteins, preparing specific proteomics/peptidomics fasta files for mass spectrometry (MS) applications, MS data processing, etc. PepTraq is developed in Java, and is available as a desktop application that can be downloaded from https://peptraq.greyc.fr . It is also available as a web application at the same URL for processing small files (10-20 MB). The source code is open under a CeCILL-B licence.
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Mladineo I, Rončević T, Gerdol M, Tossi A. Helminthic host defense peptides: using the parasite to defend the host. Trends Parasitol 2023; 39:345-357. [PMID: 36890022 DOI: 10.1016/j.pt.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 03/08/2023]
Abstract
Parasitic helminths are destined to share niches with a variety of microbiota that inevitably influence their interaction with the host. To modulate the microbiome for their benefit and defend against pathogenic isolates, helminths have developed host defense peptides (HDPs) and proteins as integral elements of their immunity. These often exert a relatively nonspecific membranolytic activity toward bacteria, sometimes with limited or no toxicity toward host cells. With a few exceptions, such as nematode cecropin-like peptides and antibacterial factors (ABFs), helminthic HDPs are largely underexplored. This review scrutinizes current knowledge on the repertoire of such peptides in helminths and promotes their research as potential leads for an anti-infective solution to the burgeoning problem of antibiotic resistance.
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Affiliation(s)
- Ivona Mladineo
- Laboratory of Functional Helminthology, Biology Centre, Czech Academy of Sciences, Institute of Parasitology BC CAS, Branišovska 31, Česke Budejovice 37005, Czech Republic.
| | - Tomislav Rončević
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, Split 21000, Croatia
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
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Marine Transcriptomics Analysis for the Identification of New Antimicrobial Peptides. Mar Drugs 2021; 19:md19090490. [PMID: 34564152 PMCID: PMC8468504 DOI: 10.3390/md19090490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) participate in the immune system to avoid infection, are present in all living organisms and can be used as drugs. Fish express numerous AMP families including defensins, cathelicidins, liver-expressed antimicrobial peptides (LEAPs), histone-derived peptides, and piscidins (a fish-specific AMP family). The present study demonstrates for the first time the occurrence of several AMPs in lionfish (Pterois volitans). Using the lionfish transcriptome, we identified four transcript sequences encoding cysteine-rich AMPs and two new transcripts encoding piscidin-like peptides. These AMPs are described for the first time in a species of the Scorpaenidae family. A functional approach on new pteroicidins was carried out to determine antimicrobial sequences and potential uses, with a view to using some of these AMPs for human health or in aquaculture.
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Fleury Y. Marine Antibiotics 2020. Mar Drugs 2021; 19:md19060351. [PMID: 34205614 PMCID: PMC8234219 DOI: 10.3390/md19060351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yannick Fleury
- Laboratoire de Biotechnologie et Chimie Marine, EA3884, Université de Bretagne Occidentale, Université Bretagne Sud, 29334 Quimper, France
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Ebou A, Koua D, Addablah A, Kakou-Ngazoa S, Dutertre S. Combined Proteotranscriptomic-Based Strategy to Discover Novel Antimicrobial Peptides from Cone Snails. Biomedicines 2021; 9:344. [PMID: 33805497 PMCID: PMC8066717 DOI: 10.3390/biomedicines9040344] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/21/2022] Open
Abstract
Despite their impressive diversity and already broad therapeutic applications, cone snail venoms have received less attention as a natural source in the investigation of antimicrobial peptides than other venomous animals such as scorpions, spiders, or snakes. Cone snails are among the largest genera (Conus sp.) of marine invertebrates, with more than seven hundred species described to date. These predatory mollusks use their sophisticated venom apparatus to capture prey or defend themselves. In-depth studies of these venoms have unraveled many biologically active peptides with pharmacological properties of interest in the field of pain management, the treatment of epilepsy, neurodegenerative diseases, and cardiac ischemia. Considering sequencing efficiency and affordability, cone snail venom gland transcriptome analyses could allow the discovery of new, promising antimicrobial peptides. We first present here the need for novel compounds like antimicrobial peptides as a viable alternative to conventional antibiotics. Secondly, we review the current knowledge on cone snails as a source of antimicrobial peptides. Then, we present the current state of the art in analytical methods applied to crude or milked venom followed by how antibacterial activity assay can be implemented for fostering cone snail antimicrobial peptides studies. We also propose a new innovative profile Hidden Markov model-based approach to annotate full venom gland transcriptomes and speed up the discovery of potentially active peptides from cone snails.
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Affiliation(s)
- Anicet Ebou
- Bioinformatic Team, Département Agriculture et Ressource Animales, UMRI 28, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro BP 1093, Ivory Coast;
| | - Dominique Koua
- Bioinformatic Team, Département Agriculture et Ressource Animales, UMRI 28, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro BP 1093, Ivory Coast;
| | - Audrey Addablah
- Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d’Ivoire, Abidjan BP 490, Ivory Coast; (A.A.); (S.K.-N.)
| | - Solange Kakou-Ngazoa
- Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d’Ivoire, Abidjan BP 490, Ivory Coast; (A.A.); (S.K.-N.)
| | - Sébastien Dutertre
- Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
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