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Klimovich A, Bosch TCG. Novel technologies uncover novel 'anti'-microbial peptides in Hydra shaping the species-specific microbiome. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230058. [PMID: 38497265 PMCID: PMC10945409 DOI: 10.1098/rstb.2023.0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/16/2023] [Indexed: 03/19/2024] Open
Abstract
The freshwater polyp Hydra uses an elaborate innate immune machinery to maintain its specific microbiome. Major components of this toolkit are conserved Toll-like receptor (TLR)-mediated immune pathways and species-specific antimicrobial peptides (AMPs). Our study harnesses advanced technologies, such as high-throughput sequencing and machine learning, to uncover a high complexity of the Hydra's AMPs repertoire. Functional analysis reveals that these AMPs are specific against diverse members of the Hydra microbiome and expressed in a spatially controlled pattern. Notably, in the outer epithelial layer, AMPs are produced mainly in the neurons. The neuron-derived AMPs are secreted directly into the glycocalyx, the habitat for symbiotic bacteria, and display high selectivity and spatial restriction of expression. In the endodermal layer, in contrast, endodermal epithelial cells produce an abundance of different AMPs including members of the arminin and hydramacin families, while gland cells secrete kazal-type protease inhibitors. Since the endodermal layer lines the gastric cavity devoid of symbiotic bacteria, we assume that endodermally secreted AMPs protect the gastric cavity from intruding pathogens. In conclusion, Hydra employs a complex set of AMPs expressed in distinct tissue layers and cell types to combat pathogens and to maintain a stable spatially organized microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Alexander Klimovich
- Zoological Institute, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, Kiel 24118, Germany
| | - Thomas C. G. Bosch
- Zoological Institute, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, Kiel 24118, Germany
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2
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Tanga CM, Ekesi S. Dietary and Therapeutic Benefits of Edible Insects: A Global Perspective. ANNUAL REVIEW OF ENTOMOLOGY 2024; 69:303-331. [PMID: 37758222 DOI: 10.1146/annurev-ento-020123-013621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Edible insects are gaining traction worldwide for research and development. This review synthesizes a large and well-established body of research literature on the high nutritional value and variety of pharmacological properties of edible insects. Positive benefits of insect-derived products include immune enhancement; gastrointestinal protection; antitumor, antioxidant, and anti-inflammatory capacities; antibacterial activities; blood lipid and glucose regulation; lowering of blood pressure; and decreased risk of cardiovascular diseases. However, the pharmacological mechanisms of these active components of edible insects in humans have received limited research attention. In addition, we discuss health risks (safety); application prospects; regulations and policies governing their production and consumption with a view to promote innovations, intraglobal trade, and economic development; and suggestions for future directions for further pharmacological functional studies. The aim is to review the current state of knowledge and research trends on edible insects as functional ingredients beneficial to the nutrition and health of humans and animals (livestock, aquatic species, and pets).
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Affiliation(s)
- Chrysantus Mbi Tanga
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya; ,
| | - Sunday Ekesi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya; ,
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3
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Strauß J. The neuronal innervation pattern of the subgenual organ complex in Peruphasma schultei (Insecta: Phasmatodea). ARTHROPOD STRUCTURE & DEVELOPMENT 2023; 74:101277. [PMID: 37209489 DOI: 10.1016/j.asd.2023.101277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/22/2023]
Abstract
The proximal tibia of orthopteroid insects contains sensory organs, the subgenual organ complex, detecting mechanical stimuli including substrate vibration. In stick insects, two chordotonal organs occur in close proximity, the subgenual organ and the distal organ, which likely detect substrate vibrations. In most stick insects, both organs are innervated by separate nerve branches. To obtain more data on the neuroanatomy of the subgenual organ complex from the New World phasmids (Occidophasmata), the present study documents the neuronal innervation of sensory organs in the subgenual organ complex of Peruphasma schultei, the first species from Pseudophasmatinae investigated for this sensory complex. The innervation pattern shows a distinct nerve branch for the subgenual organ and for the distal organ in most cases. Some variability in the innervation, which generally occurs for these chordotonal organs, was noted for both organs in P. schultei. The most common innervation for both organs was by a single nerve branch for each organ. The innervation of the subgenual organ resembled the nerve pattern of another New World phasmid, but was simpler than in the Old World phasmids (Oriophasmata) studied so far. Therefore, the peripheral neuronal innervation of sensory organs could reflect phylogenetic relationships and provide phylogenetic information, while the overall neuroanatomy of the subgenual organ complex is similar in stick insects.
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Affiliation(s)
- Johannes Strauß
- AG Integrative Sensory Physiology, Institute for Animal Physiology, Justus Liebig University Gießen, Germany; Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus Liebig, University Gießen, Germany.
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4
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Li W, Lan Y, Wang L, He L, Tang R, Price M, Yue B, Fan Z. Comparative transcriptomes of nine tissues for the Heilongjiang brown frog (Rana amurensis). Sci Rep 2022; 12:20759. [PMID: 36456629 PMCID: PMC9715712 DOI: 10.1038/s41598-022-24631-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
The Heilongjiang brown frog (Rana amurensis) is widely used in traditional Chinese medicine. In particular, the oviduct and skin have been developed into various health products. However, limited numbers of complete genomes of amphibian species have been reported, excluding the Heilongjiang brown frog. Here, the transcriptomes of 45 samples from the liver, spleen, heart, ovaries, thigh muscles, skin, oviduct, stomach and intestine of five Heilongjiang brown frog were reassembled and analyzed. A total of 1,085,532 unigenes with an average length of 676.6 bp and N50 of 722 bp were obtained. Comparative transcriptomics of different tissues detected tissue-specific expression. There were 3248 differentially expressed genes (DEGs) in the ovary, and the number of unique DEGs between the ovary and spleen was the largest. The results of DEGs enrichment showed there were many pathways and items related to protein synthesis and metabolism in the oviduct. The DEGs of the skin were enriched with many bacterial defense items, indicating that there were a large number of antimicrobial peptides in the skin. Thus, these were suitable as biological sources for the development and extraction of antimicrobial peptides. Through the assembly of transcriptome sequencing data and functional annotation of the Heilongjiang brown frog genome, this study provides reference materials for further exploring and utilizing functional gene resources of frogs and lays a foundation for medical research and the development of new products.
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Affiliation(s)
- Wanyu Li
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Yue Lan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Lei Wang
- grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,Sichuan Engineering Research Center for Medicinal Animals, Xichang, 615000 Sichuan China
| | - Lewei He
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Ruixiang Tang
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Megan Price
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Bisong Yue
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,Sichuan Engineering Research Center for Medicinal Animals, Xichang, 615000 Sichuan China
| | - Zhenxin Fan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
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Bidoli C, Miccoli A, Buonocore F, Fausto AM, Gerdol M, Picchietti S, Scapigliati G. Transcriptome Analysis Reveals Early Hemocyte Responses upon In Vivo Stimulation with LPS in the Stick Insect Bacillus rossius (Rossi, 1788). INSECTS 2022; 13:insects13070645. [PMID: 35886821 PMCID: PMC9316843 DOI: 10.3390/insects13070645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary Non-model insect species such as B. rossius suffer from a profound gap of knowledge regarding the temporal progression of physiological responses following the challenge with bacterial pathogens or cell wall components thereof. The reason for this mostly lies in the lack of genomic/transcriptomic resources, which would provide an unparalleled in-depth capacity in the analysis of molecular, biochemical, and metabolic mechanisms. We present a high-quality transcriptome obtained from high-coverage sequencing of hemocytes harvested from adult stick insect specimens both pre- and post-LPS stimulation. Such a resource served as the basis for a stringent differential gene expression and functional enrichment analyses, the results of which were characterized and discussed in depth. Selected transcripts encoding for C-type lectins and ML-domain containing proteins were further investigated from a phylogenetic perspective. Overall, these findings shed light on the physiological responses driven by a short-term LPS stimulation in the European stick insect. Abstract Despite a growing number of non-model insect species is being investigated in recent years, a greater understanding of their physiology is prevented by the lack of genomic resources. This is the case of the common European stick insect Bacillus rossius (Rossi, 1788): in this species, some knowledge is available on hemocyte-related defenses, but little is known about the physiological changes occurring in response to natural or experimental challenges. Here, the transcriptional signatures of adult B. rossius hemocytes were investigated after a short-term (2 h) LPS stimulation in vivo: a total of 2191 differentially expressed genes, mostly involved in proteolysis and carbohydrate and lipid metabolic processes, were identified in the de novo assembled transcriptome and in-depth discussed. Overall, the significant modulation of immune signals—such as C-type lectins, ML domain-containing proteins, serpins, as well as Toll signaling-related molecules—provide novel information on the early progression of LPS-induced responses in B. rossius.
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Affiliation(s)
- Carlotta Bidoli
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (C.B.); (M.G.)
| | - Andrea Miccoli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
- Correspondence:
| | - Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
| | - Anna Maria Fausto
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (C.B.); (M.G.)
| | - Simona Picchietti
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
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Potential of Antimicrobial Peptide-Overexpressed Tenebrio molitor Larvae Extract as a Natural Preservative for Korean Traditional Sauces. INSECTS 2022; 13:insects13040381. [PMID: 35447823 PMCID: PMC9027733 DOI: 10.3390/insects13040381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022]
Abstract
Here, we aimed to produce a natural food preservative using a crude extract from edible, immunized Tenebrio molitor larvae (iTME), injected with edible bacteria using an edible solvent. Results showed that iTME had concentration-dependent inhibitory activity against food-poisoning bacteria Escherichia coli, Bacillus cereus, and Staphylococcus aureus, as well as against harmful fungi Aspergillus flavus, Aspergillus parasiticus, and Pichia anomala. Moreover, iTME showed antimicrobial activity against beneficial microorganisms Bacillus subtilis and Aspergillus oryzae, but not Lactobacillus acidophilus. Furthermore, the minimum inhibitory concentration of iTME against E. coli, B. cereus, and S. aureus was 1 mg/mL, and iTME did not lose its inhibitory activity when treated at varying temperature, pH, and salinity. In addition, the antibacterial activity was lost after reacting the iTME with trypsin and chymotrypsin. The addition of iTME to Ganjang inoculated with harmful bacteria inhibited bacterial growth. Therefore, we propose that iTME can be used as a safe natural preservative to prolong food shelf life by inhibiting the growth of food-poisoning bacteria in a variety of foods, including traditional sauces.
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Etebari K, Gharuka M, Asgari S, Furlong MJ. Diverse Host Immune Responses of Different Geographical Populations of the Coconut Rhinoceros Beetle to Oryctes Rhinoceros Nudivirus (OrNV) Infection. Microbiol Spectr 2021; 9:e0068621. [PMID: 34523987 PMCID: PMC8557903 DOI: 10.1128/spectrum.00686-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
Incursions of the coconut rhinoceros beetle (CRB), Oryctes rhinoceros, into different islands in the South Pacific have been detected in recent years. It has been suggested that this range expansion is related to an O. rhinoceros haplotype reported to show reduced susceptibility to the well-established classical biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). Our understanding of the genetic characteristics which distinguish the population of O. rhinoceros that has recently established in Solomon Islands from other well-established populations across the region is very limited. Here, we hypothesized that the recently established O. rhinoceros population should have greater innate immune responses when challenged by OrNV than those of well-established and native O. rhinoceros populations. We used the RNA sequencing (RNA-Seq) approach to generate gene expression profiles of midgut tissue from OrNV-infected and noninfected individuals collected in the Solomon Islands (recent incursion), Papua New Guinea and Fiji (previously established), and the Philippines (within the native range). The collections included individuals from each of the three major mitochondrial lineages (CRB-G, CRB-PNG, and CRB-S) known to the region, allowing us to explore the specific responses of each haplotype to infection. Although insects from the Philippines and Solomon Islands that were tested belong to the same mitochondrial lineage (CRB-G), their overall responses to infection were different. The number of differentially expressed genes between OrNV-infected and noninfected wild-caught individuals from the four different locations varied from 148 to 252. Persistent OrNV infection caused a high level of induced antimicrobial activity and immune responses in O. rhinoceros, but the direction and magnitude of the responses were population specific. The insects tested from the Solomon Islands displayed extremely high expression of genes which are known to be involved in immune responses (e.g. coleoptericin, cecropin, and serpin). These variations in the host immune system among insects from different geographical regions might be driven by variations in the virulence of OrNV isolates, and this requires further investigation. Overall, our current findings support the importance of immunity in insect pest incursion and an expansion of the pest's geographic range. IMPORTANCE Oryctes rhinoceros nudivirus (OrNV) is a double-stranded DNA (dsDNA) virus which has been used as a biocontrol agent to suppress coconut rhinoceros beetle (CRB) in the Pacific Islands. Recently a new wave of CRB incursions in Oceania is thought to be related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles (CRB-G). Our comparative analysis of OrNV-infected and noninfected CRBs revealed that specific sets of genes were induced by viral infection in the beetles. This induction was much stronger in beetles collected from the Solomon Islands, a newly invaded country, than in individuals collected from within the beetle's native range (the Philippines) or from longer-established populations in its exotic range (Fiji and Papua New Guinea [PNG]). Beetles from the Philippines and the Solomon Islands that were tested in this study all belonged to the CRB-G haplotype, but the country-specific responses of the beetles to OrNV infection were different.
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Affiliation(s)
- Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Maria Gharuka
- Research Division, Ministry of Agriculture and Livestock, Honiara, Solomon Islands
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael J. Furlong
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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Rádai Z, Kiss J, Nagy NA. Taxonomic bias in AMP prediction of invertebrate peptides. Sci Rep 2021; 11:17924. [PMID: 34504226 PMCID: PMC8429723 DOI: 10.1038/s41598-021-97415-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Invertebrate antimicrobial peptides (AMPs) are at the forefront in the search for agents of therapeutic utility against multi-resistant microbial pathogens, and in recent years substantial advances took place in the in silico prediction of antimicrobial function of amino acid sequences. A yet neglected aspect is taxonomic bias in the performance of these tools. Owing to differences in the prediction algorithms and used training data sets between tools, and phylogenetic differences in sequence diversity, physicochemical properties and evolved biological functions of AMPs between taxa, notable discrepancies may exist in performance between the currently available prediction tools. Here we tested if there is taxonomic bias in the prediction power in 10 tools with a total of 20 prediction algorithms in 19 invertebrate taxa, using a data set containing 1525 AMP and 3050 non-AMP sequences. We found that most of the tools exhibited considerable variation in performance between tested invertebrate groups. Based on the per-taxa performances and on the variation in performances across taxa we provide guidance in choosing the best-performing prediction tool for all assessed taxa, by listing the highest scoring tool for each of them.
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Affiliation(s)
- Zoltán Rádai
- Lendület Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary.
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary.
| | - Johanna Kiss
- MTA-DE Behavioural Ecology Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
| | - Nikoletta A Nagy
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- MTA-DE Behavioural Ecology Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
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Hwang D, Lim CH, Lee SH, Goo TW, Yun EY. Effect of Feed Containing Hermetia illucens Larvae Immunized by Lactobacillus plantarum Injection on the Growth and Immunity of Rainbow Trout ( Oncorhynchus mykiss). INSECTS 2021; 12:insects12090801. [PMID: 34564241 PMCID: PMC8467036 DOI: 10.3390/insects12090801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 01/18/2023]
Abstract
Simple Summary In this study, we evaluated the effect on the growth and immunity of rainbow trout of a feed formulated using Hermetia illucens with increased antimicrobial peptides expression by Lactobacillus plantarum infection (ImHIL). As a result, growth and immunological indicators improved, and therefore, ImHIL is expected to become a good feed source for rainbow trout aquaculture. Abstract We investigated the effects of a feed containing Hermetia illucens larvae injected with bacteria on the growth and immunity of Oncorhynchus mykiss. The feed was prepared by replacing fishmeal in feed with 25 and 50% nonimmunized (HIL25, HIL50) or immunized HIL (ImHIL25, ImHIL50), and its protein:fat:carbohydrate ratio was 45:15:18. ImHIL extracts showed inhibitory activity against fish pathogenic bacteria. Both red blood cell count and insulin-like growth factor-1 as the growth indicator were the highest among the groups at week 6 after feeding in the ImHIL50 group. As immune indicators, blood aspartate aminotransferase levels were lower in the ImHIL25 and ImHIL50 groups than in that of other groups at week 6 after feeding, and lysozyme content was significantly higher in ImHIL25 and ImHIL50. The above results demonstrate that ImHIL has a beneficial effect on the improvement of growth and immunity. Accordingly, we suggest that ImHIL has the potential to be a good feed source in aquaculture.
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Affiliation(s)
- Dooseon Hwang
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul 05006, Korea; (D.H.); (C.-H.L.); (S.H.L.)
| | - Chae-Hwan Lim
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul 05006, Korea; (D.H.); (C.-H.L.); (S.H.L.)
| | - Seung Hun Lee
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul 05006, Korea; (D.H.); (C.-H.L.); (S.H.L.)
| | - Tae-Won Goo
- Department of Biochemistry, School of Medicine, Dongguk University, Gyeongju 38066, Korea;
| | - Eun-Young Yun
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul 05006, Korea; (D.H.); (C.-H.L.); (S.H.L.)
- Correspondence: ; Tel.: +82-2-6935-2523
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10
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Boone K, Wisdom C, Camarda K, Spencer P, Tamerler C. Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides. BMC Bioinformatics 2021; 22:239. [PMID: 33975547 PMCID: PMC8111958 DOI: 10.1186/s12859-021-04156-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/27/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Current methods in machine learning provide approaches for solving challenging, multiple constraint design problems. While deep learning and related neural networking methods have state-of-the-art performance, their vulnerability in decision making processes leading to irrational outcomes is a major concern for their implementation. With the rising antibiotic resistance, antimicrobial peptides (AMPs) have increasingly gained attention as novel therapeutic agents. This challenging design problem requires peptides which meet the multiple constraints of limiting drug-resistance in bacteria, preventing secondary infections from imbalanced microbial flora, and avoiding immune system suppression. AMPs offer a promising, bioinspired design space to targeting antimicrobial activity, but their versatility also requires the curated selection from a combinatorial sequence space. This space is too large for brute-force methods or currently known rational design approaches outside of machine learning. While there has been progress in using the design space to more effectively target AMP activity, a widely applicable approach has been elusive. The lack of transparency in machine learning has limited the advancement of scientific knowledge of how AMPs are related among each other, and the lack of general applicability for fully rational approaches has limited a broader understanding of the design space. METHODS Here we combined an evolutionary method with rough set theory, a transparent machine learning approach, for designing antimicrobial peptides (AMPs). Our method achieves the customization of AMPs using supervised learning boundaries. Our system employs in vitro bacterial assays to measure fitness, codon-representation of peptides to gain flexibility of sequence selection in DNA-space with a genetic algorithm and machine learning to further accelerate the process. RESULTS We use supervised machine learning and a genetic algorithm to find a peptide active against S. epidermidis, a common bacterial strain for implant infections, with an improved aggregation propensity average for an improved ease of synthesis. CONCLUSIONS Our results demonstrate that AMP design can be customized to maintain activity and simplify production. To our knowledge, this is the first time when codon-based genetic algorithms combined with rough set theory methods is used for computational search on peptide sequences.
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Affiliation(s)
- Kyle Boone
- Bioengineering Program, University of Kansas, Institute of Bioengineering Research, University of Kansas, 1530 W 15th Street, Learned Hall, Room 5109, Lawrence, KS 66045 USA
| | - Cate Wisdom
- Bioengineering Program, University of Kansas, Institute of Bioengineering Research, University of Kansas, 1530 W 15th Street, Learned Hall, Room 5109, Lawrence, KS 66045 USA
| | - Kyle Camarda
- Chemical and Petroleum Engineering Department, University of Kansas, 1530 West 15th Street, Learned Hall, Room 4154, Lawrence, KS 66045 USA
| | - Paulette Spencer
- Mechanical Engineering Department, University of Kansas, 1530 West 15th Street, Learned Hall, Room 3111, Lawrence, KS 66045 USA
- Institute of Bioengineering Research, University of Kansas, 1530 West 15th Street, Learned Hall, Room 3111, Lawrence, KS 66045 USA
| | - Candan Tamerler
- Mechanical Engineering Department, University of Kansas, 1530 W 15th St, Learned Hall, Room 3135A, Lawrence, KS 66045 USA
- Institute of Bioengineering Research, University of Kansas, 1530 W 15th St, Learned Hall, Room 3135A, Lawrence, KS 66045 USA
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11
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Buonocore F, Fausto AM, Della Pelle G, Roncevic T, Gerdol M, Picchietti S. Attacins: A Promising Class of Insect Antimicrobial Peptides. Antibiotics (Basel) 2021; 10:212. [PMID: 33672685 PMCID: PMC7924397 DOI: 10.3390/antibiotics10020212] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Insects produce a large repertoire of antimicrobial peptides (AMPs) as the first line of defense against bacteria, viruses, fungi or parasites. These peptides are produced from a large precursor that contains a signal domain, which is cleaved in vivo to produce the mature protein with antimicrobial activity. At present, AMPs from insects include several families which can be classified as cecropins, ponericins, defensins, lebocins, drosocin, Metchnikowin, gloverins, diptericins and attacins according to their structure and/or function. This short review is focused on attacins, a class of glycine-rich peptides/proteins that have been first discovered in the cecropia moth (Hyalophora cecropia). They are a rather heterogeneous group of immunity-related proteins that exhibit an antimicrobial effect mainly against Gram-negative bacteria. Here, we discuss different attacin and attacin-like AMPs that have been discovered so far and analyze their structure and phylogeny. Special focus is given to the physiological importance and mechanism of action of attacins against microbial pathogens together with their potential pharmacological applications, emphasizing their roles as antimicrobials.
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Affiliation(s)
- Francesco Buonocore
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Largo dell’Università snc, 05100 Viterbo, VT, Italy; (A.M.F.); (G.D.P.); (S.P.)
| | - Anna Maria Fausto
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Largo dell’Università snc, 05100 Viterbo, VT, Italy; (A.M.F.); (G.D.P.); (S.P.)
| | - Giulia Della Pelle
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Largo dell’Università snc, 05100 Viterbo, VT, Italy; (A.M.F.); (G.D.P.); (S.P.)
| | - Tomislav Roncevic
- Department of Biology, Faculty of Science, University of Split, Rudera Boskovica 33, 21000 Split, Croatia;
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, TS, Italy;
| | - Simona Picchietti
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Largo dell’Università snc, 05100 Viterbo, VT, Italy; (A.M.F.); (G.D.P.); (S.P.)
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Hou H, Wang J, Wang J, Tang W, Shaikh AS, Li Y, Fu J, Lu L, Wang F, Sun F, Tan H. A Review of Bioactive Peptides: Chemical Modification, Structural Characterization and Therapeutic Applications. J Biomed Nanotechnol 2021; 16:1687-1718. [PMID: 33485398 DOI: 10.1166/jbn.2020.3001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In recent years, the development and applications of protein drugs have attracted extensive attention from researchers. However, the shortcomings of protein drugs also limit their further development. Therefore, bioactive peptides isolated or simulated from protein polymers have broad application prospects in food, medicine, biotechnology, and other industries. Such peptides have a molecular weight distribution between 180 and 1000 Da. As a small molecule substance, bioactive peptide is usually degraded by various enzymes in the organism and have a short half-life. At the same time, such substances have poor stability and are difficult to produce and store. Therefore, these active peptides may be modified through phosphorylation, glycosylation, and acylation. Compared with other protein drugs, the modified active peptides are more easily absorbed by the body, have longer half-life, stronger targeting, and fewer side effects in addition to higher bioavailability. In the light of their functions, bioactive peptide can be divided into antimicrobial, anti-tumour, anti-angiogenic, antioxidant, anti-fatigue, and anti-hypertensive peptides. This article mainly focuses on the introduction of several promising biologically active peptides functioning as antimicrobial, anti-tumour, antiangiogenic, and antioxidant peptides from the three aspects modification, structural characteristics and mechanism of action.
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Huan Y, Kong Q, Mou H, Yi H. Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields. Front Microbiol 2020; 11:582779. [PMID: 33178164 PMCID: PMC7596191 DOI: 10.3389/fmicb.2020.582779] [Citation(s) in RCA: 552] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a class of small peptides that widely exist in nature and they are an important part of the innate immune system of different organisms. AMPs have a wide range of inhibitory effects against bacteria, fungi, parasites and viruses. The emergence of antibiotic-resistant microorganisms and the increasing of concerns about the use of antibiotics resulted in the development of AMPs, which have a good application prospect in medicine, food, animal husbandry, agriculture and aquaculture. This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. The research progress on antivirus peptides, especially anti-coronavirus (COVID-19) peptides, has been introduced given the COVID-19 pandemic worldwide in 2020.
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Affiliation(s)
| | - Qing Kong
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
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Antimicrobial Peptides from Rat-Tailed Maggots of the Drone Fly Eristalis tenax Show Potent Activity against Multidrug-Resistant Gram-Negative Bacteria. Microorganisms 2020; 8:microorganisms8050626. [PMID: 32344933 PMCID: PMC7284870 DOI: 10.3390/microorganisms8050626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/18/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
The spread of multidrug-resistant Gram-negative bacteria is an increasing threat to human health, because novel compound classes for the development of antibiotics have not been discovered for decades. Antimicrobial peptides (AMPs) may provide a much-needed breakthrough because these immunity-related defense molecules protect many eukaryotes against Gram-negative pathogens. Recent concepts in evolutionary immunology predict the presence of potent AMPs in insects that have adapted to survive in habitats with extreme microbial contamination. For example, the saprophagous and coprophagous maggots of the drone fly Eristalis tenax (Diptera) can flourish in polluted aquatic habitats, such as sewage tanks and farmyard liquid manure storage pits. We used next-generation sequencing to screen the E. tenax immunity-related transcriptome for AMPs that are synthesized in response to the injection of bacterial lipopolysaccharide. We identified 22 AMPs and selected nine for larger-scale synthesis to test their activity against a broad spectrum of pathogens, including multidrug-resistant Gram-negative bacteria. Two cecropin-like peptides (EtCec1-a and EtCec2-a) and a diptericin-like peptide (EtDip) displayed strong activity against the pathogens, even under simulated physiological conditions, and also achieved a good therapeutic window. Therefore, these AMPs could be used as leads for the development of novel antibiotics.
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