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Samgina TY, Mazur DM, Lebedev AT. Assessing the Efficacy of Protease Inactivation for the Preservation of Bioactive Amphibian Skin Peptides. Int J Mol Sci 2024; 25:8759. [PMID: 39201446 PMCID: PMC11354720 DOI: 10.3390/ijms25168759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/03/2024] [Accepted: 08/08/2024] [Indexed: 09/02/2024] Open
Abstract
The skin of amphibians is a rich source of peptides with a wide range of biological activities. They are stored in secretory granules in an inactive form. Upon stimulation, they are secreted together with proteases into the skin. Once activated, they rapidly exert their biological effects, including fighting microorganisms and predators, while their excess is immediately destroyed by the released proteases. To keep bioactive peptides in their initial form, it is necessary to inhibit these enzymes. Several inhibitors for this purpose have previously been mentioned; however, there has not been any reliable comparison of their efficiency so far. Here, we studied the efficiency of methanol and hydrochloric and formic acids, as well as phenylmethylsulfonyl fluoride, in the inhibition of nine frog peptides with the known sequence, belonging to five families in the secretion of Pelophylax esculentus. The results demonstrated that methanol had the highest inhibitory efficiency, while phenylmethylsulfonyl fluoride was the least efficient, probably due to its instability in aqueous media. Possible cleavages between certain amino acid residues in the sequence were established for each of the inhibitors. These results may be helpful for future studies on the nature of proteases and on prediction of the possible cleavage sites in novel peptides.
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Affiliation(s)
- Tatiana Yu. Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China; (T.Y.S.); (D.M.M.)
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitrii M. Mazur
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China; (T.Y.S.); (D.M.M.)
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Albert T. Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China; (T.Y.S.); (D.M.M.)
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
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2
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Alahyaribeik S, Nazarpour M. Peptide recovery from chicken feather keratin and their anti-biofilm properties against methicillin-resistant Staphylococcus aureus (MRSA). World J Microbiol Biotechnol 2024; 40:123. [PMID: 38441817 DOI: 10.1007/s11274-024-03921-3] [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: 07/13/2023] [Accepted: 02/03/2024] [Indexed: 03/07/2024]
Abstract
Bacteria have the potential to adhere to abiotic surfaces, which has an undesirable effect in the food industry because they can survive for sustained periods through biofilm formation. In this study, an antibacterial peptide (ABP), with a molecular mass of 3861 Da, was purified from hydrolyzed chicken feathers using a locally isolated keratinolytic bacterium, namely Rhodococcus erythropolis, and its antibacterial and antibiofilm potential were investigated against planktonic and biofilm cells of Methicillin-Resistant Staphylococcus Aureus (MRSA). The results demonstrated that purified ABP showed the growth inhibition of MRSA cells with the minimum inhibitory concentration (MIC) of 45 µg/ml and disrupted MRSA biofilm formation at a concentration of 200 ug/ml, which results were confirmed by scanning electron micrograph (SEM). Moreover, the secondary structures of the peptide were assessed as part of the FTIR analysis to evaluate its mode of action. ExPASy tools were used to predict the ABP sequence, EPCVQUQDSRVVIQPSPVVVVTLPGPILSSFPQNTA, from a chicken feather keratin sequence database following in silico digestion by trypsin. Also, ABP had 54.29% hydrophobic amino acids, potentially contributing to its antimicrobial activity. The findings of toxicity prediction of the peptide by the ToxinPred tool revealed that ABP had non-toxic effects. Thus, these results support the potential of this peptide to be used as an antimicrobial agent for the treatment or prevention of MRSA biofilm formation in feed, food, or pharmaceutical applications.
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Affiliation(s)
- Samira Alahyaribeik
- Industrial and Environmental Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Madineh Nazarpour
- Industrial and Environmental Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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3
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Anooja VV, Archana K, Athira PP, Anju MV, Neelima S, Muhammed Musthafa S, Dhaneesha M, Sajeevan TP, Singh ISB, Philip R. Antibacterial activity and modes of action of a novel hepcidin isoform from the shrimp scad, Alepes djedaba (Forsskål, 1775). FISH & SHELLFISH IMMUNOLOGY 2024; 146:109406. [PMID: 38278338 DOI: 10.1016/j.fsi.2024.109406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Hepcidin, initially identified in human blood ultrafiltrate as cysteine rich Liver Expressed Antimicrobial Peptide (LEAP-1), is a core molecular conduit between iron trafficking and immune response. Though a great share of studies has been focused on the iron regulatory function of hepcidins, investigations on the antimicrobial aspects are relatively less. The present study is aimed at identification of hepcidin from a teleost fish, Alepes djedaba followed by its recombinant expression, testing antibacterial property, stability and evaluation of cytotoxicity. Modes of action on bacterial pathogens were also examined. A novel hepcidin isoform, Ad-Hep belonging to the HAMP1 (Hepcidin antimicrobial peptide 1) group of hepcidins was identified from the shrimp scad, Alepes djedaba. Ad-Hep with 2.9 kDa size was found to be a cysteine rich, cationic peptide (+4) with antiparallel beta sheet conformation, a furin cleavage site (RXXR) and 'ATCUN' motif. It was heterologously expressed in E. coli Rosettagami B(DE3)PLysS cells and the recombinant peptide, rAd-Hep was found to have significant antibacterial activity, especially against Edwardsiella tarda, Vibrio parahaemolyticus and Escherichia coli. Membrane depolarization followed by membrane permeabilization and Reactive Oxygen Species (ROS) production were found to be the modes of action of rAd-Hep on bacterial cells. Ad-Hep was found to be non-haemolytic to hRBC and non-cytotoxic in mammalian cell line. Stability of the peptide at varying temperature, pH and metal salts qualify them for applications in vivo. With significant bactericidal activity coupled with direct killing mechanisms, the rAd-Hep can be a promising drug candidate for therapeutic applications in medicine and fish culture systems.
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Affiliation(s)
- V V Anooja
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - K Archana
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - P P Athira
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - M V Anju
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - S Neelima
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - S Muhammed Musthafa
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - M Dhaneesha
- National Center for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - T P Sajeevan
- National Center for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - I S Bright Singh
- National Center for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India
| | - Rosamma Philip
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, 682016, Kerala, India.
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4
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Samgina TY, Vasileva ID, Trebše P, Torkar G, Surin AK, Meng Z, Zubarev RA, Lebedev AT. Tandem Mass Spectrometry de novo Sequencing of the Skin Defense Peptides of the Central Slovenian Agile Frog Rana dalmatina. Molecules 2023; 28:7118. [PMID: 37894596 PMCID: PMC10608968 DOI: 10.3390/molecules28207118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Peptides released on frogs' skin in a stress situation represent their only weapon against micro-organisms and predators. Every species and even population of frog possesses its own peptidome being appropriate for their habitat. Skin peptides are considered potential pharmaceuticals, while the whole peptidome may be treated as a taxonomic characteristic of each particular population. Continuing the studies on frog peptides, here we report the peptidome composition of the Central Slovenian agile frog Rana dalmatina population. The detection and top-down de novo sequencing of the corresponding peptides was conducted exclusively by tandem mass spectrometry without using any chemical derivatization procedures. Collision-induced dissociation (CID), higher energy collision-induced dissociation (HCD), electron transfer dissociation (ETD) and combined MS3 method EThcD with stepwise increase of HCD energy were used for that purpose. MS/MS revealed the whole sequence of the detected peptides including differentiation between isomeric Leu/Ile, and the sequence portion hidden in the disulfide cycle. The array of the discovered peptide families (brevinins 1 and 2, melittin-related peptides (MRPs), temporins and bradykinin-related peptides (BRPs)) is quite similar to that of R. temporaria. Since the genome of this frog remains unknown, the obtained results were compared with the recently published transcriptome of R. dalmatina.
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Affiliation(s)
- Tatiana Yu. Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Irina D. Vasileva
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Polonca Trebše
- Faculty of Health Sciences, University of Ljubljana Zdravstvena Pot 5, 1000 Ljubljana, Slovenia;
| | - Gregor Torkar
- Department for Biology, Chemistry and Home Economics, University of Ljubljana Faculty of Education, Kardeljeva Ploščad 16, 1000 Ljubljana, Slovenia;
| | - Alexey K. Surin
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, 142290 Moscow, Russia;
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (Z.M.); (R.A.Z.)
| | - Roman A. Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (Z.M.); (R.A.Z.)
- The National Medical Research Center for Endocrinology, 115478 Moscow, Russia
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Albert T. Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
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5
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Rollins-Smith LA. The importance of antimicrobial peptides (AMPs) in amphibian skin defense. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 142:104657. [PMID: 36754220 DOI: 10.1016/j.dci.2023.104657] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/20/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Antimicrobial peptides (AMPs) are produced for defense in nearly all taxa from simple bacteria to complex mammalian species. Some amphibian families have developed this defensive strategy to a high level of sophistication by loading the AMPs into specialized granular glands within the dermis. Enervated by the sympathetic nervous system, the granular glands are poised to deliver an array of AMPs to cleanse the wound and facilitate healing. There have been a number of excellent review publications in recent years that describe amphibian AMPs with an emphasis on their possible uses for human medicine. Instead, my aim here is to review what is known about the nature of amphibian AMPs, the diversity of amphibian AMPs, regulation of their production, and to provide the accumulated evidence that they do, indeed, play an important role in the protection of amphibian skin, vital for survival. While much has been learned about amphibian AMPs, there are still important gaps in our understanding of peptide synthesis, storage, and functions.
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Affiliation(s)
- Louise A Rollins-Smith
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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6
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Tuning the Anthranilamide Peptidomimetic Design to Selectively Target Planktonic Bacteria and Biofilm. Antibiotics (Basel) 2023; 12:antibiotics12030585. [PMID: 36978452 PMCID: PMC10044445 DOI: 10.3390/antibiotics12030585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
There is a pressing need to develop new antimicrobials to help combat the increase in antibiotic resistance that is occurring worldwide. In the current research, short amphiphilic antibacterial and antibiofilm agents were produced by tuning the hydrophobic and cationic groups of anthranilamide peptidomimetics. The attachment of a lysine cationic group at the tail position increased activity against E. coli by >16-fold (from >125 μM to 15.6 μM) and greatly reduced cytotoxicity against mammalian cells (from ≤20 μM to ≥150 μM). These compounds showed significant disruption of preformed biofilms of S. aureus at micromolar concentrations.
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7
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Stanovova MV, Gazizova GR, Gorbushin AM. Transcriptomic profiling of immune-associated molecules in the coelomocytes of lugworm Arenicola marina (Linnaeus, 1758). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:34-55. [PMID: 35438249 DOI: 10.1002/jez.b.23135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/04/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022]
Abstract
Organization and functioning of immune system remain unevenly studied in different taxa of lophotrochozoan animals. We analyzed transcriptomic data on coelomocytes of the lugworm Arenicola marina (Linnaeus, 1758; Annelida, Polychaeta) to gain insights into the molecular mechanisms involved in polychaete immunity. Coelomocytes are specialized motile cells populating coelomic fluid of annelids, responsible for cellular defense reactions and providing humoral immune factors. The transcriptome was enriched with immune-related transcripts by challenging the cells in vitro with lipopolysaccharides of Escherichia coli and Zymosan from Saccharomyces cerevisiae. Our analysis revealed a multifaceted and complex internal defense system of the lugworm. A. marina possesses orthologs of proto-complement-like factors: six thioester-containing proteins, a complement-like receptor, and a MASP-related serine protease (MReM2). A. marina coelomocytes employ pattern-recognition receptors to detect pathogens and regulate immune responses. Among them, there are 18 Toll-like receptors and various putative lectin-like proteins with evolutionary conserved and taxa-specific domains. C-type lectins and a novel family of Gal-binding and CUB domains containing receptors were the most abundant in the transcriptome. The array of pore-forming proteins in the coelomocytes was surprisingly reduced compared to that of other invertebrate species. We characterized a set of conserved proteins metabolizing reactive oxygen species and nitric oxide and expanded the arsenal of potential antimicrobial peptides. Phenoloxidase activity in immune cells of lugworm is mediated only by laccase enzyme. The described repertoire of immune-associated molecules provides valuable candidates for further functional and comparative research on the immunity of annelids.
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Affiliation(s)
- Maria V Stanovova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Guzel R Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Alexander M Gorbushin
- Sechenov Institute of Evolutionary Physiology and Biochemistry (IEPhB RAS), St. Petersburg, Russia
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8
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Zhang XJ, Zhong YQ, Ma ZY, Hu YZ, Su JG, Zhang YA. Insights into the Antibacterial Properties of Complement Peptides C3a, C4a, and C5a across Vertebrates. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:ji2101019. [PMID: 36280254 DOI: 10.4049/jimmunol.2101019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 09/30/2022] [Indexed: 02/17/2024]
Abstract
Complement peptides C3a, C4a, and C5a are important components of innate immunity in vertebrates. Although they diverged from a common ancestor, only C3a and C4a can act as antibacterial peptides in Homo sapiens, suggesting that C5a has evolved into a purely chemotactic molecule; however, the antibacterial properties of C3a, C4a, and C5a across vertebrates still require elucidation. In this article, we show that, unlike those in H. sapiens, Mus musculus C3a, C4a, and C5a all possess antibacterial activities, implying that the antibacterial properties of C3a, C4a, and C5a have evolved divergently in vertebrates. The extremely different net charge, a key factor determining the antibacterial activities of cationic antimicrobial peptides, of vertebrate C3a, C4a, and C5a supports this speculation. Moreover, the antibacterial activity of overlapping peptides covering vertebrate C3a, C4a, and C5a further strongly supports the speculation, because their activity is positively correlated with the net charge of source molecules. Notably, the structures of C3a, C4a, and C5a are conserved in vertebrates, and the inactive overlapping peptides can become antibacterial peptides if mutated to possess enough net positive charges, indicating that net charge is the only factor determining the antibacterial properties of vertebrate C3a, C4a, and C5a. More importantly, many vertebrate C3a-, C4a-, and C5a-derived peptides possess high antibacterial activities yet exhibit no hemolytic activities, suggesting the application potential in anti-infective therapy. Taken together, our findings reveal that vertebrate C3a, C4a, and C5a are all sources of antibacterial peptides that will facilitate the design of excellent peptide antibiotics.
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Affiliation(s)
- Xu-Jie Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China; and
| | - Ya-Qin Zhong
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zi-You Ma
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Ya-Zhen Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jian-Guo Su
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yong-An Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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9
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Anticancer peptides mechanisms, simple and complex. Chem Biol Interact 2022; 368:110194. [PMID: 36195187 DOI: 10.1016/j.cbi.2022.110194] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022]
Abstract
Peptide therapy has started since 1920s with the advent of insulin application, and now it has emerged as a new approach in treatment of diseases including cancer. Using anti-cancer peptides (ACPs) is a promising way of cancer therapy as ACPs are continuing to be approved and arrived at major pharmaceutical markets. Traditional cancer treatments face different problems like intensive adverse effects to patient's body, cell resistance to conventional chemical drugs and in some worse cases the occurrence of cell multidrug resistance (MDR) of cancerous tissues against chemotherapy. On the other hand, there are some benefits conceived for peptides usage in treatment of diseases specifically cancer, as these compounds present favorable characteristics such as smaller size, high activity, low immunogenicity, good biocompatibility in vivo, convenient and rapid way of synthesis, amenable to sequence modification and revision and there is no limitation for the type of cargo they carry. It is possible to achieve an optimum molecular and functional structure of peptides based on previous experience and bank of peptide motif data which may result in novel peptide design. Bioactive peptides are able to form pores in cell membrane and induce necrosis or apoptosis of abnormal cells. Moreover, recent researches have focused on the tumor recognizing peptide motifs with the ability to permeate to cancerous cells with the aim of cancer treatment at earlier stages. In this strategy the most important factors for addressing cancer are choosing peptides with easy accessibility to tumor cell without cytotoxicity effect towards normal cells. The peptides must also meet acceptable pharmacokinetic requirements. In this review, the characteristics of peptides and cancer cells are discussed. The various mechanisms of peptides' action proposed against cancer cells make the next part of discussion. It will be followed by giving information on peptides application, various methods of peptide designing along with introducing various databases. Future aspects of peptides for employing in area of cancer treatment come as conclusion at the end.
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10
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Jain A, Mittal S, Tripathi LP, Nussinov R, Ahmad S. Host-pathogen protein-nucleic acid interactions: A comprehensive review. Comput Struct Biotechnol J 2022; 20:4415-4436. [PMID: 36051878 PMCID: PMC9420432 DOI: 10.1016/j.csbj.2022.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/01/2022] [Accepted: 08/01/2022] [Indexed: 12/02/2022] Open
Abstract
Recognition of pathogen-derived nucleic acids by host cells is an effective host strategy to detect pathogenic invasion and trigger immune responses. In the context of pathogen-specific pharmacology, there is a growing interest in mapping the interactions between pathogen-derived nucleic acids and host proteins. Insight into the principles of the structural and immunological mechanisms underlying such interactions and their roles in host defense is necessary to guide therapeutic intervention. Here, we discuss the newest advances in studies of molecular interactions involving pathogen nucleic acids and host factors, including their drug design, molecular structure and specific patterns. We observed that two groups of nucleic acid recognizing molecules, Toll-like receptors (TLRs) and the cytoplasmic retinoic acid-inducible gene (RIG)-I-like receptors (RLRs) form the backbone of host responses to pathogen nucleic acids, with additional support provided by absent in melanoma 2 (AIM2) and DNA-dependent activator of Interferons (IFNs)-regulatory factors (DAI) like cytosolic activity. We review the structural, immunological, and other biological aspects of these representative groups of molecules, especially in terms of their target specificity and affinity and challenges in leveraging host-pathogen protein-nucleic acid interactions (HP-PNI) in drug discovery.
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Affiliation(s)
- Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shikha Mittal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Lokesh P. Tripathi
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
- Riken Center for Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa, Japan
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National, Laboratory for Cancer Research, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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11
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A Type Ib Crustin from Deep-Sea Shrimp Possesses Antimicrobial and Immunomodulatory Activity. Int J Mol Sci 2022; 23:ijms23126444. [PMID: 35742887 PMCID: PMC9223358 DOI: 10.3390/ijms23126444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Crustins are small antimicrobial proteins produced by crustaceans. Of the many reported crustins, very few are from deep sea environments. Crustins are categorized into several types. Recently, the Type I crustin has been further classified into three subtypes, one of which is Type Ib, whose function is unknown. Here, we studied the function of a Type Ib crustin (designated Crus2) identified from a deep-sea crustacean. Crus2 has a whey acidic protein (WAP) domain and a long C-terminal region (named P58). Recombinant Crus2 bound to peptidoglycan (PGN), lipoteichoic acid (LTA), and lipopolysaccharide (LPS), and killed Gram-positive and Gram-negative bacteria by permeabilizing the bacterial cytomembrane. Consistently, Crus2 dramatically attenuated the inflammatory response induced by LPS and LTA. Disruption of the disulfide bonds in the WAP domain abolished the bactericidal ability of Crus2, but had no effect on the bacterial binding ability of Crus2. Deletion of the C-terminal P58 region moderately affected the antimicrobial activity of Crus2 against some bacteria. P58 as a synthesized peptide could bind bacteria and inhibit the bactericidal activity of Crus2. Taken together, these results revealed different roles played by the WAP domain and the P58 region in Type Ib crustin, and provided new insights into the antimicrobial and immunomodulatory functions of crustins.
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12
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Evolving and assembling to pierce through: Evolutionary and structural aspects of antimicrobial peptides. Comput Struct Biotechnol J 2022; 20:2247-2258. [PMID: 35615024 PMCID: PMC9117813 DOI: 10.1016/j.csbj.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/27/2022] [Accepted: 05/01/2022] [Indexed: 11/24/2022] Open
Abstract
The burgeoning menace of antimicrobial resistance across the globe has necessitated investigations into other chemotherapeutic strategies to combat infections. Antimicrobial peptides, or host defense peptides, are a set of promising therapeutic candidates in this regard. Most of them cause membrane permeabilization and are a key component of the innate immune response to pathogenic invasion. It has also been reported that peptide self-assembly is a driving factor governing the microbicidal activity of these peptide candidates. While efforts have been made to develop novel synthetic peptides against various microbes, many clinical trials of such peptides have failed due to toxicity and hemolytic activity to the host. A function-guided rational peptide engineering, based on evolutionary principles, physicochemical properties and activity determinants of AMP activity, is expected to help in targeting specific microbes. Furthermore, it is important to develop a unified understanding of the evolution of AMPs in order to fully appreciate their importance in host defense. This review seeks to explore the evolution of AMPs and the physicochemical determinants of AMP activity. The specific interactions driving AMP self-assembly have also been reviewed, emphasizing implications of this self-assembly on microbicidal and immunomodulatory activity.
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13
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Isolation and Characterization of Antimicrobial Peptides Isolated from Fagonia bruguieri. Appl Biochem Biotechnol 2022; 194:4319-4332. [PMID: 35041129 DOI: 10.1007/s12010-022-03818-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2021] [Indexed: 01/08/2023]
Abstract
The majority of pathogenic microorganisms have developed resistance to commercial antibiotics. It causes the risk of illness relapse with current antimicrobial therapy regimens; additional and/or different antibacterial drugs are needed to treat diseases caused by these pathogenic microorganisms. The applied analysis in the present study was purification and characterization of plant peptides isolated from the leaves of Fagonia bruguieri as well as their antibacterial activities against Gram-positive bacteria, Staphylococcus aureus, Bacillus subtilis, Micrococcus luteus, and methicillin-resistant Staphylococcus aureus, in addition to Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa. The minimum inhibitory concentration for the isolated peptide ranges from 25 to 62.5 mg/mL. The methanolic solvent was used for the extraction followed by reversed-phase high-performance liquid chromatography for purification of peptides. Eventually, the peptide characterization and identification were also determined by MALDI-TOF/TOF and SEM analysis. This study paves a way to the effective antimicrobials from the plant resources.
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14
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Gubatan J, Holman DR, Puntasecca CJ, Polevoi D, Rubin SJS, Rogalla S. Antimicrobial peptides and the gut microbiome in inflammatory bowel disease. World J Gastroenterol 2021; 27:7402-7422. [PMID: 34887639 PMCID: PMC8613745 DOI: 10.3748/wjg.v27.i43.7402] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/13/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMP) are highly diverse and dynamic molecules that are expressed by specific intestinal epithelial cells, Paneth cells, as well as immune cells in the gastrointestinal (GI) tract. They play critical roles in maintaining tolerance to gut microbiota and protecting against enteric infections. Given that disruptions in tolerance to commensal microbiota and loss of barrier function play major roles in the pathogenesis of inflammatory bowel disease (IBD) and converge on the function of AMP, the significance of AMP as potential biomarkers and novel therapeutic targets in IBD have been increasingly recognized in recent years. In this frontier article, we discuss the function and mechanisms of AMP in the GI tract, examine the interaction of AMP with the gut microbiome, explore the role of AMP in the pathogenesis of IBD, and review translational applications of AMP in patients with IBD.
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Affiliation(s)
- John Gubatan
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Redwood City, CA 94063, United States
| | - Derek R Holman
- Department of Radiology, Molecular Imaging Program at Stanford , Stanford University, Stanford , CA 94305, United States
| | | | - Danielle Polevoi
- Stanford University School of Medicine, Stanford University, Stanford, CA 94063, United States
| | - Samuel JS Rubin
- Stanford University School of Medicine, Stanford University, Stanford, CA 94063, United States
| | - Stephan Rogalla
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Redwood City, CA 94063, United States
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15
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Fadaka AO, Sibuyi NRS, Madiehe AM, Meyer M. Nanotechnology-Based Delivery Systems for Antimicrobial Peptides. Pharmaceutics 2021; 13:pharmaceutics13111795. [PMID: 34834210 PMCID: PMC8620809 DOI: 10.3390/pharmaceutics13111795] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant threat to global health. The conventional antibiotic pool has been depleted, forcing the investigation of novel and alternative antimicrobial strategies. Antimicrobial peptides (AMPs) have shown potential as alternative diagnostic and therapeutic agents in biomedical applications. To date, over 3000 AMPs have been identified, but only a fraction of these have been approved for clinical trials. Their clinical applications are limited to topical application due to their systemic toxicity, susceptibility to protease degradation, short half-life, and rapid renal clearance. To circumvent these challenges and improve AMP’s efficacy, different approaches such as peptide chemical modifications and the development of AMP delivery systems have been employed. Nanomaterials have been shown to improve the activity of antimicrobial drugs by providing support and synergistic effect against pathogenic microbes. This paper describes the role of nanotechnology in the targeted delivery of AMPs, and some of the nano-based delivery strategies for AMPs are discussed with a clear focus on metallic nanoparticle (MNP) formulations.
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Affiliation(s)
| | | | | | - Mervin Meyer
- Correspondence: (A.O.F.); (N.R.S.S.); (A.M.M.); (M.M.)
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16
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Modification Strategy of D-leucine Residue Addition on a Novel Peptide from Odorrana schmackeri, with Enhanced Bioactivity and In Vivo Efficacy. Toxins (Basel) 2021; 13:toxins13090611. [PMID: 34564615 PMCID: PMC8473181 DOI: 10.3390/toxins13090611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 11/25/2022] Open
Abstract
Brevinins are a well-characterised, frog-skin-derived, antimicrobial peptide (AMP) family, but their applications are limited by high cytotoxicity. In this study, a wild-type des-Leu2 brevinin peptide, named brevinin-1OS (B1OS), was identified from Odorrana schmackeri. To explore the significant role of the leucine residue at the second position, two variants, B1OS-L and B1OS-D-L, were designed by adding L-leucine and D-leucine residues at this site, respectively. The antibacterial and anticancer activities of B1OS-L and B1OS-D-L were around ten times stronger than the parent peptide. The activity of B1OS against the growth of Gram-positive bacteria was markedly enhanced after modification. Moreover, the leucine-modified products exerted in vivo therapeutic potential in an methicillin-resistant Staphylococcus aureus (MRSA)-infected waxworm model. Notably, the single substitution of D-leucine significantly increased the killing speed on lung cancer cells, where no viable H838 cells survived after 2 h of treatment with B1OS-D-L at 10 μM with low cytotoxicity on normal cells. Overall, our study suggested that the conserved leucine residue at the second position from the N-terminus is vital for optimising the dual antibacterial and anticancer activities of B1OS and proposed B1OS-D-L as an appealing therapeutic candidate for development.
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17
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Calcino AD, Kenny NJ, Gerdol M. Single individual structural variant detection uncovers widespread hemizygosity in molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200153. [PMID: 33813894 PMCID: PMC8059565 DOI: 10.1098/rstb.2020.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans. Here, we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC, we also show how individual gene families are distributed within pan-genomes. This work suggests that extensive pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Andrew D. Calcino
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Nathan J. Kenny
- Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
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18
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Robles-Loaiza AA, Pinos-Tamayo EA, Mendes B, Teixeira C, Alves C, Gomes P, Almeida JR. Peptides to Tackle Leishmaniasis: Current Status and Future Directions. Int J Mol Sci 2021; 22:ijms22094400. [PMID: 33922379 PMCID: PMC8122823 DOI: 10.3390/ijms22094400] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/16/2022] Open
Abstract
Peptide-based drugs are an attractive class of therapeutic agents, recently recognized by the pharmaceutical industry. These molecules are currently being used in the development of innovative therapies for diverse health conditions, including tropical diseases such as leishmaniasis. Despite its socioeconomic influence on public health, leishmaniasis remains long-neglected and categorized as a poverty-related disease, with limited treatment options. Peptides with antileishmanial effects encountered to date are a structurally heterogeneous group, which can be found in different natural sources—amphibians, reptiles, insects, bacteria, marine organisms, mammals, plants, and others—or inspired by natural toxins or proteins. This review details the biochemical and structural characteristics of over one hundred peptides and their potential use as molecular frameworks for the design of antileishmanial drug leads. Additionally, we detail the main chemical modifications or substitutions of amino acid residues carried out in the peptide sequence, and their implications in the development of antileishmanial candidates for clinical trials. Our bibliographic research highlights that the action of leishmanicidal peptides has been evaluated mainly using in vitro assays, with a special emphasis on the promastigote stage. In light of these findings, and considering the advances in the successful application of peptides in leishmaniasis chemotherapy, possible approaches and future directions are discussed here.
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Affiliation(s)
- Alberto A. Robles-Loaiza
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Tena 150150, Ecuador; (A.A.R.-L.); (E.A.P.-T.)
| | - Edgar A. Pinos-Tamayo
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Tena 150150, Ecuador; (A.A.R.-L.); (E.A.P.-T.)
| | - Bruno Mendes
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, Brazil;
| | - Cátia Teixeira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; (C.T.); (C.A.); (P.G.)
| | - Cláudia Alves
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; (C.T.); (C.A.); (P.G.)
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; (C.T.); (C.A.); (P.G.)
| | - José R. Almeida
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Tena 150150, Ecuador; (A.A.R.-L.); (E.A.P.-T.)
- Correspondence:
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19
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Torres MDT, Cao J, Franco OL, Lu TK, de la Fuente-Nunez C. Synthetic Biology and Computer-Based Frameworks for Antimicrobial Peptide Discovery. ACS NANO 2021; 15:2143-2164. [PMID: 33538585 PMCID: PMC8734659 DOI: 10.1021/acsnano.0c09509] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Antibiotic resistance is one of the greatest challenges of our time. This global health problem originated from a paucity of truly effective antibiotic classes and an increased incidence of multi-drug-resistant bacterial isolates in hospitals worldwide. Indeed, it has been recently estimated that 10 million people will die annually from drug-resistant infections by the year 2050. Therefore, the need to develop out-of-the-box strategies to combat antibiotic resistance is urgent. The biological world has provided natural templates, called antimicrobial peptides (AMPs), which exhibit multiple intrinsic medical properties including the targeting of bacteria. AMPs can be used as scaffolds and, via engineering, can be reconfigured for optimized potency and targetability toward drug-resistant pathogens. Here, we review the recent development of tools for the discovery, design, and production of AMPs and propose that the future of peptide drug discovery will involve the convergence of computational and synthetic biology principles.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jicong Cao
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, DF 70790160, Brazil
- S-inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS 79117010, Brazil
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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20
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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: 35] [Impact Index Per Article: 11.7] [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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21
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Lee EY, Chan LC, Wang H, Lieng J, Hung M, Srinivasan Y, Wang J, Waschek JA, Ferguson AL, Lee KF, Yount NY, Yeaman MR, Wong GCL. PACAP is a pathogen-inducible resident antimicrobial neuropeptide affording rapid and contextual molecular host defense of the brain. Proc Natl Acad Sci U S A 2021; 118:e1917623117. [PMID: 33372152 PMCID: PMC7817161 DOI: 10.1073/pnas.1917623117] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Defense of the central nervous system (CNS) against infection must be accomplished without generation of potentially injurious immune cell-mediated or off-target inflammation which could impair key functions. As the CNS is an immune-privileged compartment, inducible innate defense mechanisms endogenous to the CNS likely play an essential role in this regard. Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide known to regulate neurodevelopment, emotion, and certain stress responses. While PACAP is known to interact with the immune system, its significance in direct defense of brain or other tissues is not established. Here, we show that our machine-learning classifier can screen for immune activity in neuropeptides, and correctly identified PACAP as an antimicrobial neuropeptide in agreement with previous experimental work. Furthermore, synchrotron X-ray scattering, antimicrobial assays, and mechanistic fingerprinting provided precise insights into how PACAP exerts antimicrobial activities vs. pathogens via multiple and synergistic mechanisms, including dysregulation of membrane integrity and energetics and activation of cell death pathways. Importantly, resident PACAP is selectively induced up to 50-fold in the brain in mouse models of Staphylococcus aureus or Candida albicans infection in vivo, without inducing immune cell infiltration. We show differential PACAP induction even in various tissues outside the CNS, and how these observed patterns of induction are consistent with the antimicrobial efficacy of PACAP measured in conditions simulating specific physiologic contexts of those tissues. Phylogenetic analysis of PACAP revealed close conservation of predicted antimicrobial properties spanning primitive invertebrates to modern mammals. Together, these findings substantiate our hypothesis that PACAP is an ancient neuro-endocrine-immune effector that defends the CNS against infection while minimizing potentially injurious neuroinflammation.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, CA 90095
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095
| | - Liana C Chan
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90509
- Division of Molecular Medicine, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
- Division of Infectious Diseases, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
| | - Huiyuan Wang
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90509
- Division of Molecular Medicine, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
| | - Juelline Lieng
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - Mandy Hung
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - Yashes Srinivasan
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - Jennifer Wang
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - James A Waschek
- Semel Institute for Neuroscience and Human Behavior, Intellectual Development and Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637
| | - Kuo-Fen Lee
- Peptide Biology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Nannette Y Yount
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90509
- Division of Molecular Medicine, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
| | - Michael R Yeaman
- Division of Molecular Medicine, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509;
- Division of Infectious Diseases, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
- Semel Institute for Neuroscience and Human Behavior, Intellectual Development and Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, CA 90095;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
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22
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Lei Y, Qiu R, Shen Y, Zhou Y, Cao Z, Sun Y. Molecular characterization and antibacterial immunity functional analysis of liver-expressed antimicrobial peptide 2 (LEAP-2) gene in golden pompano (Trachinotus ovatus). FISH & SHELLFISH IMMUNOLOGY 2020; 106:833-843. [PMID: 32891790 DOI: 10.1016/j.fsi.2020.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Liver-expressed antimicrobial peptide-2 (LEAP-2) is a member of the antimicrobial peptides family. Research has demonstrated that LEAP-2 contains a number of cations and plays a key role in the innate immune system of organism. In this study, we cloned and identified TroLEAP-2, from the golden pompano (Trachinotus ovatus), and analyzed its functions in vivo and in vitro. Results showed that TroLEAP-2 contains a 321 bp open reading frame (ORF) that encodes 106 putative amino acids with a molecular weight of 11.65 kDa. The mature TroLEAP-2 peptide possesses four conserved cysteine residues, which can form a core structure with two disulfide bonds between the cysteine residues in the relative 1-3 (Cys 77 and Cys 88) and 2-4 (Cys 83 and Cys 93) positions. It has a high amino acid sequence similarity (38.68%-83.02%) with the liver-expressed antimicrobial peptide -2 of other teleosts. Phylogenetic analysis showed that TroLEAP-2 clustered with the LEAP-2 of Paralichthys olivaceus and Miichthy milluy. TroLEAP-2 was most abundantly expressed in the liver, spleen, and kidney, and was significantly upregulated during Edwardsiella tarda and Streptococcus agalactiae infection. Purified recombinant TroLEAP-2 (rTroLEAP-2) could significantly inhibit the in vitro growth of E. tarda and S. agalactiae. Overexpression of TroLEAP-2 in vivo was shown to significantly reduce E. tarda and S. agalactiae colonization of tissues, whereas its knockdown resulted in an increase of bacteria in fish tissues. We also saw that TroLEAP-2 overexpression significantly improved macrophage activation in vivo. Moreover, TroLEAP-2 can induce the expression of nonspecific immune-related genes. These results showed that it might play a significant role in the innate immune system of golden pompano. In conclusion, our results indicate that TroLEAP-2 plays an important role in antibacterial immunity and provides a new avenue for protection against pathogenic infections in golden pompano.
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Affiliation(s)
- Yang Lei
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Reng Qiu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Yang Shen
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, PR China
| | - Yongcan Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, PR China
| | - Zhenjie Cao
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, PR China
| | - Yun Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, PR China.
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23
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Purification and characterization of antimicrobial peptide fractions of Junipers seravschanica. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Le Bloa S, Boidin-Wichlacz C, Cueff-Gauchard V, Rosa RD, Cuvillier-Hot V, Durand L, Methou P, Pradillon F, Cambon-Bonavita MA, Tasiemski A. Antimicrobial Peptides and Ectosymbiotic Relationships: Involvement of a Novel Type IIa Crustin in the Life Cycle of a Deep-Sea Vent Shrimp. Front Immunol 2020; 11:1511. [PMID: 32765521 PMCID: PMC7381244 DOI: 10.3389/fimmu.2020.01511] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/09/2020] [Indexed: 01/04/2023] Open
Abstract
The symbiotic shrimp Rimicaris exoculata dominates the macrofauna inhabiting the active smokers of the deep-sea mid Atlantic ridge vent fields. We investigated the nature of the host mechanisms controlling the vital and highly specialized ectosymbiotic community confined into its cephalothoracic cavity. R. exoculata belongs to the Pleocyemata, crustacean brooding eggs, usually producing Type I crustins. Unexpectedly, a novel anti-Gram-positive type II crustin was molecularly identified in R. exoculata. Re-crustin is mainly produced by the appendages and the inner surfaces of the cephalothoracic cavity, embedding target epibionts. Symbiosis acquisition and regulating mechanisms are still poorly understood. Yet, symbiotic communities were identified at different steps of the life cycle such as brooding stage, juvenile recruitment and molt cycle, all of which may be crucial for symbiotic acquisition and control. Here, we show a spatio-temporal correlation between the production of Re-crustin and the main ectosymbiosis-related life-cycle events. Overall, our results highlight (i) a novel and unusual AMP sequence from an extremophile organism and (ii) the potential role of AMPs in the establishment of vital ectosymbiosis along the life cycle of deep-sea invertebrates.
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Affiliation(s)
- Simon Le Bloa
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Céline Boidin-Wichlacz
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Valérie Cueff-Gauchard
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Rafael Diego Rosa
- Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Lucile Durand
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Pierre Methou
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Florence Pradillon
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Aurélie Tasiemski
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
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Yeoh YQ, Horsley JR, Yu J, Polyak SW, Jovcevski B, Abell AD. Short Photoswitchable Antibacterial Peptides. ChemMedChem 2020; 15:1505-1508. [DOI: 10.1002/cmdc.202000280] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Yuan Qi Yeoh
- Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - John R. Horsley
- Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Jingxian Yu
- Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Steven W. Polyak
- Department of Molecular and Cellular Biology The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Present address: UniSA: Clinical and Health Sciences University of South Australia North Terrace Adelaide SA 5000 Australia
| | - Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Andrew D. Abell
- Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
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26
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Yeoh YQ, Horsley JR, Polyak SW, Abell AD. A hypoxia-activated antibacterial prodrug. Bioorg Med Chem Lett 2020; 30:127140. [PMID: 32247730 DOI: 10.1016/j.bmcl.2020.127140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
A prodrug based on a known antibacterial compound is reported to target Staphylococcus aureus and Escherichia coli under reductive conditions. The prodrug was prepared by masking the N-terminus and side chain amines of a component lysine residue as 4-nitrobenzyl carbamates. Activation to liberate the antibacterial was demonstrated on treatment with a model reductant, tin(II) chloride. The bioactivity of 1 was confirmed in antibacterial susceptibility assays whereas prodrug 2 was inactive.
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Affiliation(s)
- Yuan Qi Yeoh
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - John R Horsley
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, Department of Molecular and Cellular Biology, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia.
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia.
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27
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Lazzaro BP, Zasloff M, Rolff J. Antimicrobial peptides: Application informed by evolution. Science 2020; 368:368/6490/eaau5480. [PMID: 32355003 DOI: 10.1126/science.aau5480] [Citation(s) in RCA: 499] [Impact Index Per Article: 124.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/25/2019] [Accepted: 03/09/2020] [Indexed: 12/13/2022]
Abstract
Antimicrobial peptides (AMPs) are essential components of immune defenses of multicellular organisms and are currently in development as anti-infective drugs. AMPs have been classically assumed to have broad-spectrum activity and simple kinetics, but recent evidence suggests an unexpected degree of specificity and a high capacity for synergies. Deeper evaluation of the molecular evolution and population genetics of AMP genes reveals more evidence for adaptive maintenance of polymorphism in AMP genes than has previously been appreciated, as well as adaptive loss of AMP activity. AMPs exhibit pharmacodynamic properties that reduce the evolution of resistance in target microbes, and AMPs may synergize with one another and with conventional antibiotics. Both of these properties make AMPs attractive for translational applications. However, if AMPs are to be used clinically, it is crucial to understand their natural biology in order to lessen the risk of collateral harm and avoid the crisis of resistance now facing conventional antibiotics.
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Affiliation(s)
- Brian P Lazzaro
- Department of Entomology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA
| | - Michael Zasloff
- MedStar Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, USA
| | - Jens Rolff
- Freie Universität Berlin, Evolutionary Biology, Institut für Biologie, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany. .,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
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28
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Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, Richter-Boix A, Laurila A, Höglund J. Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans. BMC Genet 2020; 21:38. [PMID: 32228443 PMCID: PMC7106915 DOI: 10.1186/s12863-020-00839-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns. RESULTS We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values. CONCLUSION Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
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Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.,Centre for Paleogenetics Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Tom Van der Valk
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Alex Richter-Boix
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
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29
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Wang Q, Xia R, Ji JJ, Zhu Q, Li XP, Ma Y, Xu YC. Diversity of Antimicrobial Peptides in Three Partially Sympatric Frog Species in Northeast Asia and Implications for Evolution. Genes (Basel) 2020; 11:E158. [PMID: 32024145 PMCID: PMC7073735 DOI: 10.3390/genes11020158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 01/31/2023] Open
Abstract
Antimicrobial peptides (AMPs) are evolutionarily ancient molecules that play an essential role in innate immunity across taxa from invertebrates to vertebrates. The evolution system of AMP system has not been well explained in the literature. In this study, we cloned and sequenced AMP transcriptomes of three frog species, namely Rana dybowskii, Rana amurensis, and Pelophylax nigromaculatus, which are partially sympatric in northeast Asia, but show different habitat preferences. We found that each species contained 7 to 14 families of AMPs and the diversity was higher in species with a large geographic range and greater habitat variation. All AMPs are phylogenetically related but not associated with the speciation process. Most AMP genes were under negative selection. We propose that the diversification and addition of novel functions and improvement of antimicrobial efficiency are facilitated by the expansion of family members and numbers. We also documented significant negative correlation of net charges and numbers of amino acid residues between the propiece and mature peptide segments. This supports the Net Charge Balance Hypothesis. We propose the Cut Point Sliding Hypothesis as a novel diversification mechanism to explain the correlation in lengths of the two segments.
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Affiliation(s)
- Qing Wang
- Department of Physiology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Q.W.); (R.X.); (J.J.J.); (Q.Z.); (X.P.L.); (Y.M.)
| | - Rui Xia
- Department of Physiology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Q.W.); (R.X.); (J.J.J.); (Q.Z.); (X.P.L.); (Y.M.)
- Department of Ecology, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jing Jing Ji
- Department of Physiology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Q.W.); (R.X.); (J.J.J.); (Q.Z.); (X.P.L.); (Y.M.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qian Zhu
- Department of Physiology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Q.W.); (R.X.); (J.J.J.); (Q.Z.); (X.P.L.); (Y.M.)
- Beijing E-young Technology Company Limited, Beijing 100021, China
| | - Xiao Ping Li
- Department of Physiology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Q.W.); (R.X.); (J.J.J.); (Q.Z.); (X.P.L.); (Y.M.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yue Ma
- Department of Physiology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Q.W.); (R.X.); (J.J.J.); (Q.Z.); (X.P.L.); (Y.M.)
- State Forestry and Grassland Administration Detecting Centre of Wildlife, Harbin 150040, China
| | - Yan Chun Xu
- Department of Physiology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Q.W.); (R.X.); (J.J.J.); (Q.Z.); (X.P.L.); (Y.M.)
- State Forestry and Grassland Administration Detecting Centre of Wildlife, Harbin 150040, China
- State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
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30
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Puthia M, Butrym M, Petrlova J, Strömdahl AC, Andersson MÅ, Kjellström S, Schmidtchen A. A dual-action peptide-containing hydrogel targets wound infection and inflammation. Sci Transl Med 2020; 12:12/524/eaax6601. [DOI: 10.1126/scitranslmed.aax6601] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
There is a clinical need for improved wound treatments that prevent both infection and excessive inflammation. TCP-25, a thrombin-derived peptide, is antibacterial and scavenges pathogen-associated molecular patterns (PAMPs), such as lipopolysaccharide, thereby preventing CD14 interaction and Toll-like receptor dimerization, leading to reduced downstream immune activation. Here, we describe the development of a hydrogel formulation that was functionalized with TCP-25 to target bacteria and associated PAMP-induced inflammation. In vitro studies determined the polymer prerequisites for such TCP-25–mediated dual action, favoring the use of noncharged hydrophilic hydrogels, which enabled peptide conformational changes and LPS binding. The TCP-25–functionalized hydrogels killed Gram-positive Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa bacteria in vitro, as well as in experimental mouse models of subcutaneous infection. The TCP-25 hydrogel also mediated reduction of LPS-induced local inflammatory responses, as demonstrated by analysis of local cytokine production and in vivo bioimaging using nuclear factor κB (NF-κB) reporter mice. In porcine partial thickness wound models, TCP-25 prevented infection with S. aureus and reduced concentrations of proinflammatory cytokines. Proteolytic fragmentation of TCP-25 in vitro yielded a series of bioactive TCP fragments that were identical or similar to those present in wounds in vivo. Together, the results demonstrate the therapeutic potential of TCP-25 hydrogel, a wound treatment based on the body’s peptide defense, for prevention of both bacterial infection and the accompanying inflammation.
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Affiliation(s)
- Manoj Puthia
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184 Lund, Sweden
| | - Marta Butrym
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184 Lund, Sweden
| | - Jitka Petrlova
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184 Lund, Sweden
| | - Ann-Charlotte Strömdahl
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184 Lund, Sweden
| | | | - Sven Kjellström
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, SE-22362 Lund, Sweden
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184 Lund, Sweden
- Copenhagen Wound Healing Center, Bispebjerg Hospital, Department of Biomedical Sciences, University of Copenhagen, DK-2400 Copenhagen, Denmark
- Dermatology, Skåne University Hospital, SE-22185 Lund, Sweden
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31
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Brady D, Grapputo A, Romoli O, Sandrelli F. Insect Cecropins, Antimicrobial Peptides with Potential Therapeutic Applications. Int J Mol Sci 2019; 20:E5862. [PMID: 31766730 PMCID: PMC6929098 DOI: 10.3390/ijms20235862] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
The alarming escalation of infectious diseases resistant to conventional antibiotics requires urgent global actions, including the development of new therapeutics. Antimicrobial peptides (AMPs) represent potential alternatives in the treatment of multi-drug resistant (MDR) infections. Here, we focus on Cecropins (Cecs), a group of naturally occurring AMPs in insects, and on synthetic Cec-analogs. We describe their action mechanisms and antimicrobial activity against MDR bacteria and other pathogens. We report several data suggesting that Cec and Cec-analog peptides are promising antibacterial therapeutic candidates, including their low toxicity against mammalian cells, and anti-inflammatory activity. We highlight limitations linked to the use of peptides as therapeutics and discuss methods overcoming these constraints, particularly regarding the introduction of nanotechnologies. New formulations based on natural Cecs would allow the development of drugs active against Gram-negative bacteria, and those based on Cec-analogs would give rise to therapeutics effective against both Gram-positive and Gram-negative pathogens. Cecs and Cec-analogs might be also employed to coat biomaterials for medical devices as an approach to prevent biomaterial-associated infections. The cost of large-scale production is discussed in comparison with the economic and social burden resulting from the progressive diffusion of MDR infectious diseases.
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Affiliation(s)
- Daniel Brady
- Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy; (D.B.); (A.G.); (O.R.)
| | - Alessandro Grapputo
- Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy; (D.B.); (A.G.); (O.R.)
| | - Ottavia Romoli
- Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy; (D.B.); (A.G.); (O.R.)
- Institut Pasteur de la Guyane, 23 Avenue Pasteur, 97306 Cayenne, French Guiana, France
| | - Federica Sandrelli
- Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy; (D.B.); (A.G.); (O.R.)
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Näpflin K, O’Connor EA, Becks L, Bensch S, Ellis VA, Hafer-Hahmann N, Harding KC, Lindén SK, Olsen MT, Roved J, Sackton TB, Shultz AJ, Venkatakrishnan V, Videvall E, Westerdahl H, Winternitz JC, Edwards SV. Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales. PeerJ 2019; 7:e8013. [PMID: 31720122 PMCID: PMC6839515 DOI: 10.7717/peerj.8013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.
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Affiliation(s)
- Kathrin Näpflin
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
| | - Emily A. O’Connor
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Lutz Becks
- Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany
| | - Staffan Bensch
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Vincenzo A. Ellis
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Nina Hafer-Hahmann
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Karin C. Harding
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Sara K. Lindén
- Department of Medical Chemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Morten T. Olsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Roved
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Timothy B. Sackton
- Informatics Group, Harvard University, Cambridge, MA, United States of America
| | - Allison J. Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Vignesh Venkatakrishnan
- Department of Medical Chemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Elin Videvall
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Jamie C. Winternitz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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Go HJ, Kim CH, Park JB, Kim TY, Lee TK, Oh HY, Park NG. Biochemical and molecular identification of a novel hepcidin type 2-like antimicrobial peptide in the skin mucus of the pufferfish Takifugu pardalis. FISH & SHELLFISH IMMUNOLOGY 2019; 93:683-693. [PMID: 31408729 DOI: 10.1016/j.fsi.2019.08.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/03/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
Fish skin mucus is considered to act as the first line of defense against waterborne pathogens and to be potential source of novel antimicrobial components. Here we report the purification and characterization of a novel hepcidin type 2-like antimicrobial peptide (TpHAMP2) from the skin mucus of the pufferfish Takifugu pardalis. The purified TpHAMP2 comprised of 23 amino acids (AAs) with eight Cys residues that form four intramolecular disulfide bonds. The TpHAMP2 gene shared overall structural characteristics with all known hepcidins, which have a tripartite exon-intron gene organization and three structural signatures in the precursor protein. Phylogenetically, TpHAMP2 was classified as HAMP2 class in acanthopterygian fish. Interestingly, the AA sequence of TpHAMP2 did not contain a proprotein cleavage site (RXXR motif) that conserved in most hepcidins and showed a highly positive charged (RKR-) short N-terminus and Val18 and Gly22 residues, which are distinctive structures compared to other known active hepcidins. Recombinant TpHAMP2 identical to the native form exhibited a broad spectrum and potent antimicrobial activity against tested gram-positive and -negative bacteria. Expression of TpHAMP2 mRNA was predominant in the liver and was upregulated in the liver, the spleen, the intestine, and the skin of T. pardalis post immune challenge. Thus, our findings suggests that TpHAMP2 might be of importance in the framework of discovering the fish hepcidins, especially type 2s, and provide noteworthy insight into its gene structure and expression and in the innate immunity as well as the mucosal immunity in regard to hepcidins' evolutionary history in fish species.
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Affiliation(s)
- Hye-Jin Go
- Department of Biotechnology, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| | - Chan-Hee Kim
- Department of Biotechnology, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| | - Ji Been Park
- Department of Biotechnology, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| | - Tae Young Kim
- Department of Biotechnology, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| | - Tae Kwan Lee
- Department of Biotechnology, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| | - Hye Young Oh
- Department of Biotechnology, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| | - Nam Gyu Park
- Department of Biotechnology, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea.
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35
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Sweidan A, Smida I, Chollet-Krugler M, Sauvager A, Vallet J, Gouault N, Oliviero N, Tamanai-Shacoori Z, Burel A, van de Weghe P, Chokr A, Tomasi S, Bousarghin L. Lichen butyrolactone derivatives disrupt oral bacterial membrane. Fitoterapia 2019; 137:104274. [DOI: 10.1016/j.fitote.2019.104274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/20/2019] [Accepted: 07/21/2019] [Indexed: 02/06/2023]
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36
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Saigo N, Izumi K, Kawano R. Electrophysiological Analysis of Antimicrobial Peptides in Diverse Species. ACS OMEGA 2019; 4:13124-13130. [PMID: 31460440 PMCID: PMC6705042 DOI: 10.1021/acsomega.9b01033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/24/2019] [Indexed: 05/25/2023]
Abstract
This study describes a technical platform that allows us to measure the pore-forming activity of antimicrobial peptides (AMPs) in the lipid bilayer and estimate antimicrobial activity. We selected six different AMPs of diverse species from urochordata to vertebrata and measured the channel current signals using a microfabricated lipid bilayer system. As a result of the electrophysiological measurements, we were able to estimate the pore-forming activity and roughly predict the antimicrobial activity although there was not a strong correlation between the pore-forming activity and the variety of species. Our method will be a unique tool for analyzing a wide variety of diverse AMPs.
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Affiliation(s)
- Naoki Saigo
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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Chen D, Zhou X, Chen X, Huang L, Xi X, Ma C, Zhou M, Wang L, Chen T. Evaluating the Bioactivity of a Novel Antimicrobial and Anticancer Peptide, Dermaseptin-PS4(Der-PS4), from the Skin Secretion of Phyllomedusa sauvagii. Molecules 2019; 24:molecules24162974. [PMID: 31426323 PMCID: PMC6719146 DOI: 10.3390/molecules24162974] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/11/2019] [Accepted: 08/15/2019] [Indexed: 12/15/2022] Open
Abstract
Dermaseptins belonging to a large family of cationic membrane-disruption antimicrobial peptides display extensive antibacterial and antiproliferative activities depending on a coil-to-helix transition and the specific structural parameters. Herein, a novel dermaseptin peptide named Der-PS4 was discovered from the skin secretion of the waxy monkey tree frog, Phyllomedusa sauvagii. The complementary DNA (cDNA)-encoding precursor was obtained relying on "shotgun" cloning, and afterwards, a mature peptide amino acid sequence was identified by reverse-phase high performance liquid chromatography (RP-HPLC) and MS/MS. Specimens were chemically synthesized and applied for further functional studies. Structural analysis demonstrated a higher α-helical content in the membrane-mimetic environment compared with that in the ammonium acetate/water circumstance. Der-PS4 displayed a broad spectrum of antimicrobial activities against tested pathogenic microorganisms, however, exhibiting slight membrane-damaging effectiveness towards horse red blood cells. Coincident with the inhibitory activities on pathogens, Der-PS4 also showed considerable biofilm eradicating impact. Also, Der-PS4 penetrated cell membrane in a relative short period under each minimum bactericidal concentration. In addition, Der-PS4 possessed antiproliferative capacity against five cancer cell lines, while presenting slight suppressing effect on human microvascular endothelial, HMEC-1. These findings provide a promising insight for the discovery and development of novel drugs from a natural source.
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Affiliation(s)
- Dong Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK
| | - Xiaowei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK
- Department of Nutrition, Henry Fok School of Food Science and Engineering, Shaoguan University, Shaoguan 512005, China
| | - Xi Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK
| | - Linyuan Huang
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK.
- School of Life Sciences and Technology, China Pharmaceutical University, Nanjing 211198, China.
| | - Xinping Xi
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK.
| | - Chengbang Ma
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK
| | - Mei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK
| | - Lei Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University, Belfast BT9 7BL, UK
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Shirdel I, Kalbassi MR, Hosseinkhani S, Paknejad H, Wink M. Cloning, characterization and tissue-specific expression of the antimicrobial peptide hepcidin from caspian trout (Salmo caspius) and the antibacterial activity of the synthetic peptide. FISH & SHELLFISH IMMUNOLOGY 2019; 90:288-296. [PMID: 31071462 DOI: 10.1016/j.fsi.2019.05.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/25/2019] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
Antimicrobial peptides have a wide range of antimicrobial activity and widely occur in different organisms including mollusks, crustaceans and vertebrates. Hepcidins are a group of cysteine-rich antimicrobial peptides that are active against a variety of pathogens including gram-positive and gram-negative bacteria, as well as viruses. In this study, the hepcidin gene of Caspian trout (CtHep) was identified and characterized. Our results showed that CtHep cDNA has a 267-bp Open Reading Frame (ORF), which is translated to 88 amino acids. The CtHep was classified in the HAMP1 class of hepcidins. Comparison of DNA and cDNA sequences showed that CtHep has 3 exons and 2 introns. The signal, prodomain and mature part of CtHep have 24, 39 and 25 amino acids, respectively. The mature peptide has a molecular weight of 2881.43 Da and a theoretical isoelectric point of 8.53. The expression of CtHep mRNA was detected in different tissues of healthy and infected fish. CtHep expression in the liver, head kidney, spleen and skin was significantly enhanced after bacterial challenge. Expression of CtHep in different embryonic development stages was also substantial. Antibacterial activity of synthetic CtHep peptides was investigated against a number of Gram-positive and Gram-negative bacteria. CtHep inhibited some pathogenic bacteria such as Streptococcus iniae and Aeromonas hydrophila. In the in vivo experiment, CtHep upregulated the cytokines IL-6 and TNF-α in both kidney and spleen tissues after 24 h of the peptide injection. In conclusion, our study showed that CtHep plays an important role in the immune system of Caspian trout and also in the embryonic stages. Moreover, CtHep peptide has a potential to be used as an antimicrobial therapeutic agent as well as an immunostimulant in aquaculture.
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Affiliation(s)
- Iman Shirdel
- Department of Fisheries, Marine Sciences Faculty, Tarbiat Modares University, Noor, Iran.
| | - Mohammad Reza Kalbassi
- Department of Fisheries, Marine Sciences Faculty, Tarbiat Modares University, Noor, Iran.
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Hamed Paknejad
- Department of Fisheries, Division of Genetics and Physiology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
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Comparative mode of action of the antimicrobial peptide melimine and its derivative Mel4 against Pseudomonas aeruginosa. Sci Rep 2019; 9:7063. [PMID: 31068610 PMCID: PMC6506473 DOI: 10.1038/s41598-019-42440-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/18/2019] [Indexed: 12/16/2022] Open
Abstract
Melimine and Mel4 are chimeric cationic peptides with broad-spectrum antimicrobial activity. They have been shown to be highly biocompatible in animal models and human clinical trials. The current study examined the mechanism of action of these two antimicrobial peptides against P. aeruginosa. The effect of the peptides of endotoxin neutralization, and their interactions with cytoplasmic membranes using DiSC(3)-5 and Sytox green, Syto-9 and PI dyes were analysed. Release of ATP and DNA/RNA were determined using ATP luminescence and increase in OD260 nm. The bacteriolytic ability of the peptides was determined by measuring decreases in OD620 nm. Both the peptides neutralized LPS suggesting their interaction with lipid A. Cytoplasmic membrane was disrupted within 30 seconds, which correlated with reductions in cellular viability. At 2 minutes melimine or Mel4, released 75% and 36% cellular ATP respectively (P < 0.001). Membrane permeabilization started 5 minutes with simultaneous release of DNA/RNA. Flow cytometry demonstrated 52% and 18% bacteria were stained with PI after 30 minutes. Overall, melimine showed higher capacity for membrane disruption compared to Mel4 (P < 0.001). The findings of this study have been summarized as a timeline of bactericidal activity, suggesting that the peptides permeabilized P. aeruginosa within 5 minutes, started lysis within 2 hours of exposure.
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40
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Unifying structural signature of eukaryotic α-helical host defense peptides. Proc Natl Acad Sci U S A 2019; 116:6944-6953. [PMID: 30877253 DOI: 10.1073/pnas.1819250116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Diversity of α-helical host defense peptides (αHDPs) contributes to immunity against a broad spectrum of pathogens via multiple functions. Thus, resolving common structure-function relationships among αHDPs is inherently difficult, even for artificial-intelligence-based methods that seek multifactorial trends rather than foundational principles. Here, bioinformatic and pattern recognition methods were applied to identify a unifying signature of eukaryotic αHDPs derived from amino acid sequence, biochemical, and three-dimensional properties of known αHDPs. The signature formula contains a helical domain of 12 residues with a mean hydrophobic moment of 0.50 and favoring aliphatic over aromatic hydrophobes in 18-aa windows of peptides or proteins matching its semantic definition. The holistic α-core signature subsumes existing physicochemical properties of αHDPs, and converged strongly with predictions of an independent machine-learning-based classifier recognizing sequences inducing negative Gaussian curvature in target membranes. Queries using the α-core formula identified 93% of all annotated αHDPs in proteomic databases and retrieved all major αHDP families. Synthesis and antimicrobial assays confirmed efficacies of predicted sequences having no previously known antimicrobial activity. The unifying α-core signature establishes a foundational framework for discovering and understanding αHDPs encompassing diverse structural and mechanistic variations, and affords possibilities for deterministic design of antiinfectives.
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Shelenkov AA, Slavokhotova AA, Odintsova TI. Cysmotif Searcher Pipeline for Antimicrobial Peptide Identification in Plant Transcriptomes. BIOCHEMISTRY (MOSCOW) 2018; 83:1424-1432. [PMID: 30482154 DOI: 10.1134/s0006297918110135] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this paper, we present the new Cysmotif searcher pipeline for identification of various antimicrobial peptides (AMPs), the most important components of innate immunity, in plant transcriptomes. Cysmotif searcher reveals and classifies short cysteine-rich amino acid sequences containing an open reading frame and a signal peptide cleavage site. Due to the combination of various search methods, Cysmotif searcher allows to obtain the most complete repertoire of AMPs for one or more transcriptomes in a short amount of time. The pipeline performance is estimated on the model plant Arabidopsis thaliana and nine other plants, including cultivated and wild species. The obtained results are compared to the existing annotation (A. thaliana) and results of conventional homology search (other plants). The comparison is carried out for known families of plant AMPs and newly discovered peptides that could not be assigned to existing families. The applicability of Cysmotif searcher in detecting new AMPs is discussed, and some practical recommendations on the pipeline usage for end users are given. The Cysmotif searcher pipeline is free for academic use and can be downloaded from Github (http://github.com/fallandar/cysmotifsearcher).
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Affiliation(s)
- A A Shelenkov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. .,Central Research Institute of Epidemiology, Rospotrebnadzor, Moscow, 111123, Russia
| | - A A Slavokhotova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - T I Odintsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
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42
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Yasir M, Willcox MDP, Dutta D. Action of Antimicrobial Peptides against Bacterial Biofilms. MATERIALS 2018; 11:ma11122468. [PMID: 30563067 PMCID: PMC6317029 DOI: 10.3390/ma11122468] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
Microbes are known to colonize surfaces and form biofilms. These biofilms are communities of microbes encased in a self-produced matrix that often contains polysaccharides, DNA and proteins. Antimicrobial peptides (AMPs) have been used to control the formation and to eradicate mature biofilms. Naturally occurring or synthetic antimicrobial peptides have been shown to prevent microbial colonization of surfaces, to kill bacteria in biofilms and to disrupt the biofilm structure. This review systemically analyzed published data since 1970 to summarize the possible anti-biofilm mechanisms of AMPs. One hundred and sixty-two published reports were initially selected for this review following searches using the criteria ‘antimicrobial peptide’ OR ‘peptide’ AND ‘mechanism of action’ AND ‘biofilm’ OR ‘antibiofilm’ in the databases PubMed; Scopus; Web of Science; MEDLINE; and Cochrane Library. Studies that investigated anti-biofilm activities without describing the possible mechanisms were removed from the analysis. A total of 17 original reports were included which have articulated the mechanism of antimicrobial action of AMPs against biofilms. The major anti-biofilm mechanisms of antimicrobial peptides are: (1) disruption or degradation of the membrane potential of biofilm embedded cells; (2) interruption of bacterial cell signaling systems; (3) degradation of the polysaccharide and biofilm matrix; (4) inhibition of the alarmone system to avoid the bacterial stringent response; (5) downregulation of genes responsible for biofilm formation and transportation of binding proteins.
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Affiliation(s)
- Muhammad Yasir
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia.
| | | | - Debarun Dutta
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia.
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43
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Yeoh YQ, Yu J, Polyak SW, Horsley JR, Abell AD. Photopharmacological Control of Cyclic Antimicrobial Peptides. Chembiochem 2018; 19:2591-2597. [DOI: 10.1002/cbic.201800618] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yuan Qi Yeoh
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)Department of ChemistryThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
| | - Jingxian Yu
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)Department of ChemistryThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
| | - Steven W. Polyak
- School of Biological SciencesDepartment of Molecular and Cellular BiologyThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
| | - John R. Horsley
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)Department of ChemistryThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
| | - Andrew D. Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)Department of ChemistryThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
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44
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Gu J, Gao B, Zhu S. Characterization of bi-domain drosomycin-type antifungal peptides in nematodes: An example of convergent evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:90-97. [PMID: 29894713 DOI: 10.1016/j.dci.2018.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/08/2018] [Accepted: 06/08/2018] [Indexed: 06/08/2023]
Abstract
Drosomycin-type antifungal peptides (DTAFPs) are natural effectors of the innate immune system, which are restrictedly distributed in plants and ecdysozoans. Mehamycin is a bi-domain DTAFP (abbreviated as bDTAFP) firstly found in the Northern root-knot nematode Meloidogyne hapla. Here, we report its structural and functional features and the evolution of bDTAFPs in nematodes. Different from classical DTAFPs, mehamycin contains an insertion, called single Disulfide Bridge-linked Domain (abbreviated as sDBD), located in a loop region of the drosomycin scaffold. Despite this, recombinant mehamycin likely adopts a similar fold to drosomycin, as revealed by the circular dichroism spectral analysis. Functionally, it showed some weak activity against three species of fungi but relatively stronger activity against seven species of Gram-positive bacteria, indicative of functional diversification between mehamycin and classical DTAFPs. By computational data mining of the nematode databases, we identified polymorphic genes encoding mehamycin and a new multigene family of bDTAFPs (named roremycins) from Rotylenchulus reniformis. A combination of data suggests that the origination of sDBDs from M. hapla and R. reniformis is a consequence of convergent evolution, in which some probably suffered positive selection during evolution. Our study may be valuable in understanding the role of these unique antimicrobial peptides in the innate immunity of nematodes.
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Affiliation(s)
- Jing Gu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
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45
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Guo Y, Xun M, Han J. A bovine myeloid antimicrobial peptide (BMAP-28) and its analogs kill pan-drug-resistant Acinetobacter baumannii by interacting with outer membrane protein A (OmpA). Medicine (Baltimore) 2018; 97:e12832. [PMID: 30334982 PMCID: PMC6211872 DOI: 10.1097/md.0000000000012832] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) exhibit multiple activities against bacteria and fungi. A bovine myeloid antimicrobial peptide (BMAP-28) belongs to the cathelicidin-derived AMPs and has antimicrobial activity. Due to the rapidly increasing number of infections and outbreaks caused by pan-drug-resistant Acinetobacter baumannii (PDRAB), we sought to determine whether BMAP-28 and its 4 analog peptides (A837, A838, A839, and A840) have antimicrobial activity against PDRAB. Furthermore, we clarified the possible mechanism of inhibition by which of BMAP-28 acts against PDRAB. In the current study, we examined the inhibitory effect of BMAP-28 and its 4 analog peptides on the growth of PDRAB through minimal inhibitory concentration (MIC) analysis and short time killing assays. We also evaluated the effects of BMAP-28 and its analogs on the bacterial cell surface through the use of field emission scanning electron microscopy (FE-SEM). In order to determine the inhibitory mechanism of BMAP-28, we examined the interaction between BMAP-28 and outer membrane proteins (OMPs), especially the interaction between BMAP-28 and A. baumannii OmpA (AbOmpA), which is the main component of OMPs, by using a quartz crystal microbalance (QCM). BMAP-28 and its 4 analogs were effective in inhibiting the growth of PDRAB and had rapid killing ability. BMAP-28 showed exceptionally strong and rapid inhibitory effects on PDRAB when compared to the other peptides and was also shown to cause damage to the cell surface of PDRAB. Moreover, QCM analysis provided evidence of potential interaction between BMAP-28 and AbOmpA. These data indicate that BMAP-28 is a promising candidate for the treatment of PDRAB infections and that its inhibitory effects were related with its binding to AbOmpA.
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Affiliation(s)
- Yijie Guo
- Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education of China
- Department of Pathogenic Biology and Immunology
| | - Meng Xun
- Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education of China
- Department of Pathogenic Biology and Immunology
| | - Jing Han
- Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education of China
- School of Public Health, Xi’an Jiaotong University, Health Science Center, Xi’an, China
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46
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Yoshida K, Ishikawa A, Toyoda A, Shigenobu S, Fujiyama A, Kitano J. Functional divergence of a heterochromatin‐binding protein during stickleback speciation. Mol Ecol 2018; 28:1563-1578. [DOI: 10.1111/mec.14841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Kohta Yoshida
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
| | - Asano Ishikawa
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory National Institute of Genetics Mishima Shizuoka Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities National Institute for Basic Biology Okazaki Aichi Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory National Institute of Genetics Mishima Shizuoka Japan
| | - Jun Kitano
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
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47
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Lyons DM, Lauring AS. Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses. Mol Biol Evol 2018; 34:3205-3215. [PMID: 29029187 PMCID: PMC5850290 DOI: 10.1093/molbev/msx251] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The substitution rates of transitions are higher than expected by chance relative to those of transversions. Many have argued that selection disfavors transversions, as nonsynonymous transversions are less likely to conserve biochemical properties of the original amino acid. Only recently has it become feasible to directly test this selective hypothesis by comparing the fitness effects of a large number of transition and transversion mutations. For example, a recent study of six viruses and one beta-lactamase gene did not find evidence supporting the selective hypothesis. Here, we analyze the relative fitness effects of transition and transversion mutations from our recently published genome-wide study of mutational fitness effects in influenza virus. In contrast to prior work, we find that transversions are significantly more detrimental than transitions. Using what we believe to be an improved statistical framework, we also identify a similar trend in two HIV data sets. We further demonstrate a fitness difference in transition and transversion mutations using four deep mutational scanning data sets of influenza virus and HIV, which provided adequate statistical power. We find that three of the most commonly cited radical/conservative amino acid categories are predictive of fitness, supporting their utility in studies of positive selection and codon usage bias. We conclude that selection is a major contributor to the transition:transversion substitution bias in viruses and that this effect is only partially explained by the greater likelihood of transversion mutations to cause radical as opposed to conservative amino acid changes.
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Affiliation(s)
- Daniel M Lyons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Adam S Lauring
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
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48
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Gerdol M, Luo YJ, Satoh N, Pallavicini A. Genetic and molecular basis of the immune system in the brachiopod Lingula anatina. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 82:7-30. [PMID: 29278680 DOI: 10.1016/j.dci.2017.12.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 06/07/2023]
Abstract
The extension of comparative immunology to non-model systems, such as mollusks and annelids, has revealed an unexpected diversity in the complement of immune receptors and effectors among evolutionary lineages. However, several lophotrochozoan phyla remain unexplored mainly due to the lack of genomic resources. The increasing accessibility of high-throughput sequencing technologies offers unique opportunities for extending genome-wide studies to non-model systems. As a result, the genome-based study of the immune system in brachiopods allows a better understanding of the alternative survival strategies developed by these immunologically neglected phyla. Here we present a detailed overview of the molecular components of the immune system identified in the genome of the brachiopod Lingula anatina. Our findings reveal conserved intracellular signaling pathways as well as unique strategies for pathogen detection and killing in brachiopods.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy.
| | - Yi-Jyun Luo
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy; Anton Dohrn Zoological Station, Villa Comunale, 80121 Napoli, Italy
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49
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Muncaster S, Kraakman K, Gibbons O, Mensink K, Forlenza M, Jacobson G, Bird S. Antimicrobial peptides within the Yellowtail Kingfish (Seriola lalandi). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 80:67-80. [PMID: 28433529 DOI: 10.1016/j.dci.2017.04.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/18/2017] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
A number of Seriola species are currently farmed or being investigated as future aquaculture species in countries around the world. However they face a number of issues and limitations which will need to be overcome to ensure future stability and growth, one of which are disease outbreaks. Despite this, very little has been done to understand the immune system of Seriola species and very few immune genes have been characterised. Antimicrobial peptides (AMP) are naturally occurring low molecular weight polypeptides that play a major role in an organism's immune system and act effectively as a first line of defence. This investigation isolates the full length cDNA sequences of two AMP's, piscidin and hepcidin from the yellowtail kingfish (Seriola lalandi). The full-length cDNA of the piscidin gene encodes a 65 amino acid prepropeptide, containing a 25-residue peptide, predicted to form an amphipathic helix-loop-helix structure. Phylogenetic analysis using fish piscidin sequences, showed that this AMP is only found in bony fish within the Acanthomorpha clade and that a possible three groups within the piscidin family exists, with S. lalandi belonging to a particular group. The full-length cDNA of the hepcidin gene encodes a 90 amino acid preprohepcidin, which contains a typical RX(R/K)R motif for cleavage of the mature peptide which comprises of eight conserved cysteine residues. Phylogenetic analysis of known vertebrate hepcidin antimicrobial peptide (HAMP) sequences, shows sequences from the Neoteleostei clade of bony fish form two very separate groups, HAMP1 and HAMP2, with the S. lalandi hepcidin gene grouped with the HAMP1 sequences. HAMP2 sequences are found to have multiple copies within fish and genome analysis showed very clearly that these two groups of genes are located on separate regions on the genome, with the multiple HAMP2 copies formed from tandem gene duplications. Lastly, using qPCR the expression of the S. lalandi piscidin gene within healthy fish was highest within, spleen and gills and lowest in liver, whereas hepcidin was highest in the liver with little or no expression in the spleen and gills.
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Affiliation(s)
- Simon Muncaster
- Marine and Environmental Group, School of Applied Science, Bay of Plenty Polytechnic, Tauranga, New Zealand
| | - Kirsty Kraakman
- Molecular Genetics, School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Olivia Gibbons
- Molecular Genetics, School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Koen Mensink
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Maria Forlenza
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Gregory Jacobson
- Molecular Genetics, School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Steve Bird
- Molecular Genetics, School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
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Kozic M, Fox SJ, Thomas JM, Verma CS, Rigden DJ. Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds. Proteins 2018; 86:548-565. [DOI: 10.1002/prot.25473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Mara Kozic
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
| | - Stephen J. Fox
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
| | - Jens M. Thomas
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
| | - Chandra S. Verma
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
- Department of Biological Sciences; National University of Singapore; Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
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