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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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Thomas AM, Antony SP. Marine Antimicrobial Peptides: An Emerging Nightmare to the Life-Threatening Pathogens. Probiotics Antimicrob Proteins 2024; 16:552-578. [PMID: 37022565 DOI: 10.1007/s12602-023-10061-x] [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] [Accepted: 03/08/2023] [Indexed: 04/07/2023]
Abstract
The emergence of multidrug-resistant pathogens due to improper usage of conventional antibiotics has created a global health crisis. Alternatives to antibiotics being an urgent need, the scientific community is forced to search for new antimicrobials. This exploration has led to the discovery of antimicrobial peptides, a group of small peptides occurring in different phyla such as Porifera, Cnidaria, Annelida, Arthropoda, Mollusca, Echinodermata, and Chordata, as a component of their innate immune system. The marine environment, possessing immense diversity of organisms, is undoubtedly one of the richest sources of unique potential antimicrobial peptides. The distinctiveness of marine antimicrobial peptides lies in their broad-spectrum activity, mechanism of action, less cytotoxicity, and high stability, which form the benchmark for developing a potential therapeutic. This review aims to (1) synthesise the available information on the distinctive antimicrobial peptides discovered from marine organisms, particularly over the last decade, and (2) discuss the distinctiveness of marine antimicrobial peptides and their prospects.
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Affiliation(s)
- Anne Maria Thomas
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India
| | - Swapna P Antony
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India.
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3
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Chen P, Ye T, Li C, Praveen P, Hu Z, Li W, Shang C. Embracing the era of antimicrobial peptides with marine organisms. Nat Prod Rep 2024; 41:331-346. [PMID: 37743806 DOI: 10.1039/d3np00031a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Covering: 2018 to Jun of 2023The efficiency of traditional antibiotics has been undermined by the proliferation of antibiotic-resistant pathogenic microorganisms, necessitating the pursuit of innovative therapeutic agents. Antimicrobial peptides (AMPs), which are part of host defence peptides found ubiquitously in nature, exhibiting a wide range of activity towards bacteria, fungi, and viruses, offer a highly promising candidate solution. The efficacy of AMPs can frequently be augmented via alterations to their amino acid sequences or structural adjustments. Given the vast reservoir of marine life forms and their distinctive ecosystems, marine AMPs stand as a burgeoning focal point in the quest for alternative peptide templates extracted from natural sources. Advances in identification and characterization techniques have accelerated the discoveries of marine AMPs, thereby stimulating AMP customization, optimization, and synthesis research endeavours. This review presents an overview of recent discoveries related to the intriguing qualities of marine AMPs. Emphasis will be placed upon post-translational modifications (PTMs) of marine AMPs and how they may impact functionality and potency. Additionally, this review considers ways in which marine PTM might support larger-scale, heterologous AMP manufacturing initiatives, providing insights into translational applications of these important biomolecules.
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Affiliation(s)
- Pengyu Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ting Ye
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Chunyuan Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Praveen Praveen
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science La Trobe University, Victoria, 3086, Australia.
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science La Trobe University, Victoria, 3086, Australia.
| | - Chenjing Shang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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4
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Villafranca N, Changsut I, Diaz de Villegas S, Womack H, Fuess LE. Characterization of trade-offs between immunity and reproduction in the coral species Astrangia poculata. PeerJ 2023; 11:e16586. [PMID: 38077420 PMCID: PMC10702360 DOI: 10.7717/peerj.16586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Background Living organisms face ubiquitous pathogenic threats and have consequently evolved immune systems to protect against potential invaders. However, many components of the immune system are physiologically costly to maintain and engage, often drawing resources away from other organismal processes such as growth and reproduction. Evidence from a diversity of systems has demonstrated that organisms use complex resource allocation mechanisms to manage competing needs and optimize fitness. However, understanding of resource allocation patterns is limited across taxa. Cnidarians, which include ecologically important organisms like hard corals, have been historically understudied in the context of resource allocations. Improving understanding of resource allocation-associated trade-offs in cnidarians is critical for understanding future ecological dynamics in the face of rapid environmental change. Methods Here, we characterize trade-offs between constitutive immunity and reproduction in the facultatively symbiotic coral Astrangia poculata. Male colonies underwent ex situ spawning and sperm density was quantified. We then examined the effects of variable symbiont density and energetic budget on physiological traits, including immune activity and reproductive investment. Furthermore, we tested for potential trade-offs between immune activity and reproductive investment. Results We found limited associations between energetic budget and immune metrics; melanin production was significantly positively associated with carbohydrate concentration. However, we failed to document any associations between immunity and reproductive output which would be indicative of trade-offs, possibly due to experimental limitations. Our results provide a preliminary framework for future studies investigating immune trade-offs in cnidarians.
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Affiliation(s)
- Natalie Villafranca
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Isabella Changsut
- Department of Biology, Texas State University, San Marcos, TX, United States
| | | | - Haley Womack
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
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5
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Sintsova O, Popkova D, Kalinovskii A, Rasin A, Borozdina N, Shaykhutdinova E, Klimovich A, Menshov A, Kim N, Anastyuk S, Kusaykin M, Dyachenko I, Gladkikh I, Leychenko E. Control of postprandial hyperglycemia by oral administration of the sea anemone mucus-derived α-amylase inhibitor (magnificamide). Biomed Pharmacother 2023; 168:115743. [PMID: 37862974 DOI: 10.1016/j.biopha.2023.115743] [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] [Received: 08/17/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
Diabetes mellitus is a serious threat to human health in both developed and developing countries. Optimal disease control requires the use of a diet and a combination of several medications, including oral hypoglycemic agents such as α-glucosidase inhibitors. Currently, the arsenal of available drugs is insufficient, which determines the relevance of studying new potent α-amylase inhibitors. We implemented the recombinant production of sea anemone derived α-amylase inhibitor magnificamide in Escherichia coli. Peptide was isolated by a combination of liquid chromatography techniques. Its folding and molecular weight was proved by 1H NMR and mass spectrometry. The Ki value of magnificamide against human pancreatic α-amylase is 3.1 nM according to Morrison equation for tight binding inhibitors. Our study of the thermodynamic characteristics of binding of magnificamide to human salivary and pancreatic α-amylases by isothermal titration calorimetry showed the presence of different binding mechanisms with Kd equal to 0.11 µM and 0.1 nM, respectively. Experiments in mice with streptozotocin-induced diabetes mimicking diabetes mellitus type 1 were used to study the efficiency of magnificamide against postprandial hyperglycemia. It was found that at a dose of 0.005 mg kg-1, magnificamide effectively blocks starch breakdown and prevents the development of postprandial hyperglycemia in T1D mice. Our results demonstrated the therapeutic potential of magnificamide for the control of postprandial hyperglycemia.
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Affiliation(s)
- Oksana Sintsova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Darya Popkova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
| | - Aleksandr Kalinovskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anton Rasin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
| | - Natalya Borozdina
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki, 6, 142290 Pushchino, Russia
| | - Elvira Shaykhutdinova
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki, 6, 142290 Pushchino, Russia
| | - Anna Klimovich
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
| | - Alexander Menshov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
| | - Natalia Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
| | - Stanislav Anastyuk
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
| | - Mikhail Kusaykin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
| | - Igor Dyachenko
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki, 6, 142290 Pushchino, Russia
| | - Irina Gladkikh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
| | - Elena Leychenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
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6
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Popkova D, Otstavnykh N, Sintsova O, Baldaev S, Kalina R, Gladkikh I, Isaeva M, Leychenko E. Bioprospecting of Sea Anemones (Cnidaria, Anthozoa, Actiniaria) for β-Defensin-like α-Amylase Inhibitors. Biomedicines 2023; 11:2682. [PMID: 37893056 PMCID: PMC10604346 DOI: 10.3390/biomedicines11102682] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Diabetes mellitus is one of the most serious diseases of our century. The drugs used are limited or have serious side effects. The search for new sources of compounds for effective treatment is relevant. Magnificamide, a peptide inhibitor of mammalian α-amylases, isolated from the venom of sea anemone Heteractis magnifica, can be used for the control of postprandial hyperglycemia in diabetes mellitus. Using the RACE approach, seven isoforms of magnificamide were detected in H. magnifica tentacles. The exon-intron structure of magnificamide genes was first established, and intron retention in the mature peptide-encoding region was revealed. Additionally, an α-amylase inhibitory domain was discovered in the mucins of some sea anemones. According to phylogenetics, sea anemones diverge into two groups depending on the presence of β-defensin-like α-amylase inhibitors and/or mucin-inhibitory domains. It is assumed that the intron retention phenomenon leads to additional diversity in the isoforms of inhibitors and allows for its neofunctionalization in sea anemone tentacles. Bioprospecting of sea anemones of the order Actiniaria for β-defensin-like α-amylase inhibitors revealed a diversity of inhibitory sequences that represents a starting point for the design of effective glucose-lowering drugs.
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Affiliation(s)
| | | | | | | | | | | | | | - Elena Leychenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia; (D.P.); (N.O.); (O.S.); (S.B.); (R.K.); (I.G.); (M.I.)
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7
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Ashwood LM, Elnahriry KA, Stewart ZK, Shafee T, Naseem MU, Szanto TG, van der Burg CA, Smith HL, Surm JM, Undheim EAB, Madio B, Hamilton BR, Guo S, Wai DCC, Coyne VL, Phillips MJ, Dudley KJ, Hurwood DA, Panyi G, King GF, Pavasovic A, Norton RS, Prentis PJ. Genomic, functional and structural analyses elucidate evolutionary innovation within the sea anemone 8 toxin family. BMC Biol 2023; 21:121. [PMID: 37226201 DOI: 10.1186/s12915-023-01617-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The ShK toxin from Stichodactyla helianthus has established the therapeutic potential of sea anemone venom peptides, but many lineage-specific toxin families in Actiniarians remain uncharacterised. One such peptide family, sea anemone 8 (SA8), is present in all five sea anemone superfamilies. We explored the genomic arrangement and evolution of the SA8 gene family in Actinia tenebrosa and Telmatactis stephensoni, characterised the expression patterns of SA8 sequences, and examined the structure and function of SA8 from the venom of T. stephensoni. RESULTS We identified ten SA8-family genes in two clusters and six SA8-family genes in five clusters for T. stephensoni and A. tenebrosa, respectively. Nine SA8 T. stephensoni genes were found in a single cluster, and an SA8 peptide encoded by an inverted SA8 gene from this cluster was recruited to venom. We show that SA8 genes in both species are expressed in a tissue-specific manner and the inverted SA8 gene has a unique tissue distribution. While the functional activity of the SA8 putative toxin encoded by the inverted gene was inconclusive, its tissue localisation is similar to toxins used for predator deterrence. We demonstrate that, although mature SA8 putative toxins have similar cysteine spacing to ShK, SA8 peptides are distinct from ShK peptides based on structure and disulfide connectivity. CONCLUSIONS Our results provide the first demonstration that SA8 is a unique gene family in Actiniarians, evolving through a variety of structural changes including tandem and proximal gene duplication and an inversion event that together allowed SA8 to be recruited into the venom of T. stephensoni.
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Affiliation(s)
- Lauren M Ashwood
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
| | - Khaled A Elnahriry
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Zachary K Stewart
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Thomas Shafee
- Department of Animal Plant & Soil Sciences, La Trobe University, Melbourne, Australia
- Swinburne University of Technology, Melbourne, VIC, Australia
| | - Muhammad Umair Naseem
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Tibor G Szanto
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Chloé A van der Burg
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, 9016, New Zealand
| | - Hayden L Smith
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Eivind A B Undheim
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindern, PO Box 1066, 0316, Oslo, Norway
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Bruno Madio
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Brett R Hamilton
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, 4072, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Shaodong Guo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Victoria L Coyne
- Research Infrastructure, Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Matthew J Phillips
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Kevin J Dudley
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Research Infrastructure, Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - David A Hurwood
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre for Innovations in Peptide and Protein Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ana Pavasovic
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC, 3052, Australia
| | - Peter J Prentis
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
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Islam S, Akhand MRN, Hasan M. Evolutionary trend of bovine β-defensin proteins toward functionality prediction: A domain-based bioinformatics study. Heliyon 2023; 9:e14158. [PMID: 36938430 PMCID: PMC10015202 DOI: 10.1016/j.heliyon.2023.e14158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Defensins are small cationic cysteine-rich and amphipathic peptides that form of three-dimensional β-strand structure connected by disulfide bonds. Defensins form key elements of the innate immune system of multicellular organisms. They not only possess broad-spectrum antimicrobial activity but also have diverse roles, including cell signaling, ion channel agitation, toxic functions, and enzyme inhibitor activities in various animals. Although the role of β-defensins in immune responses against infectious agents and reproduction could be significant, inadequate genomic information is available to explain the whole β-defensin repertoire in cattle. No domain or motif-based functional analyses have been previously reported. In addition, how do defensins possess this magnitude of functions in the immune system is still not clear. Our present study, therefore, investigated the sequence divergence and evolutionary relations of bovine defensin proteins with those of humans. Our domain-based evolutionary analysis revealed four major clusters with significant domain variation while reserving a main antimicrobial activity. Our study revealed the β-defensin domain as the ancestor domain, and it is preserved in the first group of defensin protein with no α-helix in its structure. Due to natural selection, some domains have evolved independently within clusters II and III, while some proteins have lost their domain characteristics. Cluster IV contains the most recently evolved domains. Some proteins of all but cluster I might have adopted the functional characteristics of α-defensins which is largely absent in cattle. The proteins show different patterns of disulfide bridges and multiple signature patterns which might render them specialized functions in different tissue to combat against various pathogens.
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Affiliation(s)
- Saiful Islam
- Department of Physiology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Mst Rubaiat Nazneen Akhand
- Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet-3100, Bangladesh
- Corresponding author.
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
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Analysis of Structural Determinants of Peptide MS 9a-1 Essential for Potentiating of TRPA1 Channel. Mar Drugs 2022; 20:md20070465. [PMID: 35877758 PMCID: PMC9320628 DOI: 10.3390/md20070465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
The TRPA1 channel is involved in a variety of physiological processes and its activation leads to pain perception and the development of inflammation. Peptide Ms 9a-1 from sea anemone Metridium senile is a positive modulator of TRPA1 and causes significant analgesic and anti-inflammatory effects by desensitization of TRPA1-expressing sensory neurons. For structural and functional analysis of Ms 9a-1, we produced four peptides—Ms 9a-1 without C-terminal domain (abbreviated as N-Ms), short C-terminal domain Ms 9a-1 alone (C-Ms), and two homologous peptides (Ms 9a-2 and Ms 9a-3). All tested peptides possessed a reduced potentiating effect on TRPA1 compared to Ms 9a-1 in vitro. None of the peptides reproduced analgesic and anti-inflammatory properties of Ms 9a-1 in vivo. Peptides N-Ms and C-Ms were able to reduce pain induced by AITC (selective TRPA1 agonist) but did not decrease AITC-induced paw edema development. Fragments of Ms 9a-1 did not effectively reverse CFA-induced thermal hyperalgesia and paw edema. Ms 9a-2 and Ms 9a-3 possessed significant effects and anti-inflammatory properties in some doses, but their unexpected efficacy and bell-shape dose–responses support the hypothesis of other targets involved in their effects in vivo. Therefore, activity comparison of Ms 9a-1 fragments and homologues peptides revealed structural determinants important for TRPA1 modulation, as well as analgesic and anti-inflammatory properties of Ms9a-1.
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Tentacle Morphological Variation Coincides with Differential Expression of Toxins in Sea Anemones. Toxins (Basel) 2021; 13:toxins13070452. [PMID: 34209745 PMCID: PMC8310139 DOI: 10.3390/toxins13070452] [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] [Received: 05/26/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 02/08/2023] Open
Abstract
Phylum Cnidaria is an ancient venomous group defined by the presence of cnidae, specialised organelles that serve as venom delivery systems. The distribution of cnidae across the body plan is linked to regionalisation of venom production, with tissue-specific venom composition observed in multiple actiniarian species. In this study, we assess whether morphological variants of tentacles are associated with distinct toxin expression profiles and investigate the functional significance of specialised tentacular structures. Using five sea anemone species, we analysed differential expression of toxin-like transcripts and found that expression levels differ significantly across tentacular structures when substantial morphological variation is present. Therefore, the differential expression of toxin genes is associated with morphological variation of tentacular structures in a tissue-specific manner. Furthermore, the unique toxin profile of spherical tentacular structures in families Aliciidae and Thalassianthidae indicate that vesicles and nematospheres may function to protect branched structures that host a large number of photosynthetic symbionts. Thus, hosting zooxanthellae may account for the tentacle-specific toxin expression profiles observed in the current study. Overall, specialised tentacular structures serve unique ecological roles and, in order to fulfil their functions, they possess distinct venom cocktails.
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11
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Santana FL, Estrada K, Ortiz E, Corzo G. Reptilian β-defensins: Expanding the repertoire of known crocodylian peptides. Peptides 2021; 136:170473. [PMID: 33309943 DOI: 10.1016/j.peptides.2020.170473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 01/31/2023]
Abstract
One of the major families of host defense peptides (HDPs) in vertebrates are β-defensins. They constitute important components of innate immunity and have remained an interesting topic of research for more than two decades. While many β-defensin sequences in mammals and birds have been identified and their properties and functions characterized, β-defensin peptides from other groups of vertebrates, particularly reptiles, are still largely unexplored. In this review, we focus on reptilian β-defensins and summarize different aspects of their biology, such as their genomic organization, evolution, structure, and biological activities. Reptilian β-defensin genes exhibit similar genomic organization to birds and their number and gene structure are variable among different species. During the evolution of reptiles, several gene duplication and deletion events have occurred and the functional diversification of β-defensins has been mainly driven by positive selection. These peptides display broad antimicrobial activity in vitro, but a deeper understanding of their mechanisms of action in vivo, including their role as immunomodulators, is still lacking. Reptilian β-defensins constitute unique polypeptide sequences to expand our current understanding of innate immunity in these animals and elucidate core biological functions of this family of HDPs across amniotes.
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Affiliation(s)
- Felix L Santana
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca Mor., 62250, Mexico.
| | - Karel Estrada
- Unidad de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ernesto Ortiz
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca Mor., 62250, Mexico
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca Mor., 62250, Mexico.
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12
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Histidine-Rich Defensins from the Solanaceae and Brasicaceae Are Antifungal and Metal Binding Proteins. J Fungi (Basel) 2020; 6:jof6030145. [PMID: 32847065 PMCID: PMC7557933 DOI: 10.3390/jof6030145] [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: 07/15/2020] [Revised: 08/08/2020] [Accepted: 08/19/2020] [Indexed: 01/01/2023] Open
Abstract
Plant defensins are best known for their antifungal activity and contribution to the plant immune system. The defining feature of plant defensins is their three-dimensional structure known as the cysteine stabilized alpha-beta motif. This protein fold is remarkably tolerant to sequence variation with only the eight cysteines that contribute to the stabilizing disulfide bonds absolutely conserved across the family. Mature defensins are typically 46–50 amino acids in length and are enriched in lysine and/or arginine residues. Examination of a database of approximately 1200 defensin sequences revealed a subset of defensin sequences that were extended in length and were enriched in histidine residues leading to their classification as histidine-rich defensins (HRDs). Using these initial HRD sequences as a query, a search of the available sequence databases identified over 750 HRDs in solanaceous plants and 20 in brassicas. Histidine residues are known to contribute to metal binding functions in proteins leading to the hypothesis that HRDs would have metal binding properties. A selection of the HRD sequences were recombinantly expressed and purified and their antifungal and metal binding activity was characterized. Of the four HRDs that were successfully expressed all displayed some level of metal binding and two of four had antifungal activity. Structural characterization of the other HRDs identified a novel pattern of disulfide linkages in one of the HRDs that is predicted to also occur in HRDs with similar cysteine spacing. Metal binding by HRDs represents a specialization of the plant defensin fold outside of antifungal activity.
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13
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Tajti G, Wai DCC, Panyi G, Norton RS. The voltage-gated potassium channel K V1.3 as a therapeutic target for venom-derived peptides. Biochem Pharmacol 2020; 181:114146. [PMID: 32653588 DOI: 10.1016/j.bcp.2020.114146] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023]
Abstract
The voltage-gated potassium channel KV1.3 is a well-established therapeutic target for a range of autoimmune diseases, in addition to being the site of action of many venom-derived peptides. Numerous studies have documented the efficacy of venom peptides that target KV1.3, in particular from sea anemones and scorpions, in animal models of autoimmune diseases such as rheumatoid arthritis, psoriasis and multiple sclerosis. Moreover, an analogue of the sea anemone peptide ShK (known as dalazatide) has successfully completed Phase 1 clinical trials in mild-to-moderate plaque psoriasis. In this article we consider other potential therapeutic applications of inhibitors of KV1.3, including in inflammatory bowel disease and neuroinflammatory conditions such as Alzheimer's and Parkinson's diseases, as well as fibrotic diseases. We also summarise strategies for facilitating the entry of peptides to the central nervous system, given that this will be a pre-requisite for the treatment of most neuroinflammatory diseases. Venom-derived peptides that have been reported recently to target KV1.3 are also described. The increasing number of autoimmune and other conditions in which KV1.3 is upregulated and is therefore a potential therapeutic target, combined with the fact that many venom-derived peptides are potent inhibitors of KV1.3, suggests that venoms are likely to continue to serve as a rich source of new pharmacological tools and therapeutic leads targeting this channel.
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Affiliation(s)
- Gabor Tajti
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary.
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC 3052, Australia.
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14
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Shelley JR, Davidson DJ, Dorin JR. The Dichotomous Responses Driven by β-Defensins. Front Immunol 2020; 11:1176. [PMID: 32595643 PMCID: PMC7304343 DOI: 10.3389/fimmu.2020.01176] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022] Open
Abstract
Defensins are short, rapidly evolving, cationic antimicrobial host defence peptides with a repertoire of functions, still incompletely realised, that extends beyond direct microbial killing. They are released or secreted at epithelial surfaces, and in some cases, from immune cells in response to infection and inflammation. Defensins have been described as endogenous alarmins, alerting the body to danger and responding to inflammatory signals by promoting both local innate and adaptive systemic immune responses. However, there is now increasing evidence that they exert variable control on the response to danger; creating a dichotomous response that can suppress inflammation in some circumstances but exacerbate the response to danger and damage in others and, at higher levels, lead to a cytotoxic effect. Focussing in this review on human β-defensins, we discuss the evidence for their functions as proinflammatory, immune activators amplifying the response to infection or damage signals and/or as mediators of resolution of damage, contributing to a return to homeostasis. Finally, we consider their involvement in the development of autoimmune diseases.
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Affiliation(s)
- Jennifer R Shelley
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh BioQuarter, Edinburgh, Scotland
| | - Donald J Davidson
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh BioQuarter, Edinburgh, Scotland
| | - Julia R Dorin
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh BioQuarter, Edinburgh, Scotland
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15
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Shafee T, Bacic A, Johnson K. Evolution of Sequence-Diverse Disordered Regions in a Protein Family: Order within the Chaos. Mol Biol Evol 2020; 37:2155-2172. [DOI: 10.1093/molbev/msaa096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Approaches for studying the evolution of globular proteins are now well established yet are unsuitable for disordered sequences. Our understanding of the evolution of proteins containing disordered regions therefore lags that of globular proteins, limiting our capacity to estimate their evolutionary history, classify paralogs, and identify potential sequence–function relationships. Here, we overcome these limitations by using new analytical approaches that project representations of sequence space to dissect the evolution of proteins with both ordered and disordered regions, and the correlated changes between these. We use the fasciclin-like arabinogalactan proteins (FLAs) as a model family, since they contain a variable number of globular fasciclin domains as well as several distinct types of disordered regions: proline (Pro)-rich arabinogalactan (AG) regions and longer Pro-depleted regions.
Sequence space projections of fasciclin domains from 2019 FLAs from 78 species identified distinct clusters corresponding to different types of fasciclin domains. Clusters can be similarly identified in the seemingly random Pro-rich AG and Pro-depleted disordered regions. Sequence features of the globular and disordered regions clearly correlate with one another, implying coevolution of these distinct regions, as well as with the N-linked and O-linked glycosylation motifs. We reconstruct the overall evolutionary history of the FLAs, annotated with the changing domain architectures, glycosylation motifs, number and length of AG regions, and disordered region sequence features. Mapping these features onto the functionally characterized FLAs therefore enables their sequence–function relationships to be interrogated. These findings will inform research on the abundant disordered regions in protein families from all kingdoms of life.
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Affiliation(s)
- Thomas Shafee
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, China
| | - Kim Johnson
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, China
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16
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Kalina RS, Peigneur S, Zelepuga EA, Dmitrenok PS, Kvetkina AN, Kim NY, Leychenko EV, Tytgat J, Kozlovskaya EP, Monastyrnaya MM, Gladkikh IN. New Insights into the Type II Toxins from the Sea Anemone Heteractis crispa. Toxins (Basel) 2020; 12:E44. [PMID: 31936885 PMCID: PMC7020476 DOI: 10.3390/toxins12010044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/23/2022] Open
Abstract
Toxins modulating NaV channels are the most abundant and studied peptide components of sea anemone venom. Three type-II toxins, δ-SHTX-Hcr1f (= RpII), RTX-III, and RTX-VI, were isolated from the sea anemone Heteractis crispa. RTX-VI has been found to be an unusual analog of RTX-III. The electrophysiological effects of Heteractis toxins on nine NaV subtypes were investigated for the first time. Heteractis toxins mainly affect the inactivation of the mammalian NaV channels expressed in the central nervous system (NaV1.1-NaV1.3, NaV1.6) as well as insect and arachnid channels (BgNaV1, VdNaV1). The absence of Arg13 in the RTX-VI structure does not prevent toxin binding with the channel but it has changed its pharmacological profile and potency. According to computer modeling data, the δ-SHTX-Hcr1f binds within the extracellular region of the rNaV1.2 voltage-sensing domain IV and pore-forming domain I through a network of strong interactions, and an additional fixation of the toxin at the channel binding site is carried out through the phospholipid environment. Our data suggest that Heteractis toxins could be used as molecular tools for NaV channel studies or insecticides rather than as pharmacological agents.
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Affiliation(s)
- Rimma S. Kalina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg, O&N 2, Herestraat~49, P.O. Box 922, 3000 Leuven, Belgium
| | - Elena A. Zelepuga
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
| | - Pavel S. Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
| | - Aleksandra N. Kvetkina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
| | - Natalia Y. Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
| | - Elena V. Leychenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg, O&N 2, Herestraat~49, P.O. Box 922, 3000 Leuven, Belgium
| | - Emma P. Kozlovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
| | - Margarita M. Monastyrnaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
| | - Irina N. Gladkikh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.Z.); (P.S.D.); (A.N.K.); (N.Y.K.); (E.V.L.); (E.P.K.); (M.M.M.)
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17
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Sintsova O, Gladkikh I, Kalinovskii A, Zelepuga E, Monastyrnaya M, Kim N, Shevchenko L, Peigneur S, Tytgat J, Kozlovskaya E, Leychenko E. Magnificamide, a β-Defensin-Like Peptide from the Mucus of the Sea Anemone Heteractis magnifica, Is a Strong Inhibitor of Mammalian α-Amylases. Mar Drugs 2019; 17:md17100542. [PMID: 31546678 PMCID: PMC6835510 DOI: 10.3390/md17100542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 01/07/2023] Open
Abstract
Sea anemones’ venom is rich in peptides acting on different biological targets, mainly on cytoplasmic membranes and ion channels. These animals are also a source of pancreatic α-amylase inhibitors, which have the ability to control the glucose level in the blood and can be used for the treatment of prediabetes and type 2 diabetes mellitus. Recently we have isolated and characterized magnificamide (44 aa, 4770 Da), the major α-amylase inhibitor of the sea anemone Heteractis magnifica mucus, which shares 84% sequence identity with helianthamide from Stichodactyla helianthus. Herein, we report some features in the action of a recombinant analog of magnificamide. The recombinant peptide inhibits porcine pancreatic and human saliva α-amylases with Ki’s equal to 0.17 ± 0.06 nM and 7.7 ± 1.5 nM, respectively, and does not show antimicrobial or channel modulating activities. We have concluded that the main function of magnificamide is the inhibition of α-amylases; therefore, its functionally active recombinant analog is a promising agent for further studies as a potential drug candidate for the treatment of the type 2 diabetes mellitus.
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Affiliation(s)
- Oksana Sintsova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Irina Gladkikh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Aleksandr Kalinovskii
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
- School of Natural Sciences, Far Eastern Federal University, 8, Sukhanova St, Vladivostok 690090, Russia.
| | - Elena Zelepuga
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Margarita Monastyrnaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Natalia Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Lyudmila Shevchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg, O&N2, Herestraat 49, P.O. Box 922, Leuven B-3000, Belgium.
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg, O&N2, Herestraat 49, P.O. Box 922, Leuven B-3000, Belgium.
| | - Emma Kozlovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Elena Leychenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
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18
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Zuo Y, Chang Y, Huang S, Zheng L, Yang L, Cao G. iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor. Evol Bioinform Online 2019; 15:1176934319867088. [PMID: 31391777 PMCID: PMC6669840 DOI: 10.1177/1176934319867088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 11/18/2022] Open
Abstract
Defensins as 1 of major classes of host defense peptides play a significant role in the innate immunity, which are extremely evolved in almost all living organisms. Developing high-throughput computational methods can accurately help in designing drugs or medical means to defense against pathogens. To take up such a challenge, an up-to-date server based on rigorous benchmark dataset, referred to as iDEF-PseRAAC, was designed for predicting the defensin family in this study. By extracting primary sequence compositions based on different types of reduced amino acid alphabet, it was calculated that the best overall accuracy of the selected feature subset was achieved to 92.38%. Therefore, we can conclude that the information provided by abundant types of amino acid reduction will provide efficient and rational methodology for defensin identification. And, a free online server is freely available for academic users at http://bioinfor.imu.edu.cn/idpf. We hold expectations that iDEF-PseRAAC may be a promising weapon for the function annotation about the defensins protein.
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Affiliation(s)
- Yongchun Zuo
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China.,State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yu Chang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Shenghui Huang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Lei Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Guifang Cao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
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