Identification of Ly2 members as antimicrobial peptides from zebrafish Danio rerio

Ribosomal protein L17 functions as an antimicrobial protein in amphioxus

Antimicrobial peptides (AMPs), characterized by their cationic nature and amphiphilic properties, play a pivotal role in inhibiting the biological activity of microbes. Currently, only a fraction of the antimicrobial potential within the ribosomal protein family has been explored, despite its extensive membership and resemblance to AMPs. Herein we demonstrated that amphioxus RPL17 (BjRPL17) exhibited not only upregulated expression upon bacterial stimulation but also possessed bactericidal capabilities against both Gram-negative and -positive bacteria through combined action mechanisms including interaction with cell surface molecules LPS, LTA, and PGN, disruption of cell membrane integrity, promotion of membrane depolarization, and induction of intracellular ROS production. Furthermore, a peptide derived from residues 127-141 of BjRPL17 (termed BjRPL17-1) showed antibacterial activity against Staphylococcus aureus and its methicillin-resistant strain via the same mechanism observed for the full-length protein. Additionally, the rpl17 gene was highly conserved in Metazoa, hinting it may play a universal role in the antibacterial defense system in different animals. Importantly, neither BjRPL17 nor peptide BjRPL17-1 exhibited toxicity towards mammalian cells thereby offering prospects for designing novel AMP agents based on these findings. Collectively, our results establish RPL17 as a novel member of AMPs with remarkable evolutionary conservation.

Identification and functional characterization of bactericidal permeability/increasing protein (BPI) from frog Nanorana yunnanensis (Paa yunnanensis)

Bactericidal permeability/increasing protein (BPI) and lipopolysaccharide-binding protein (LBP) have been most extensively studied in mammals, but little information is available regarding BPI and LBP in Amphibia. In this study we showed that the cDNA of BPI in the frog N. yunnanensis (P. yunnanensis) encoded a 490-amino-acid-long protein, the predicted tertiary structure appears closely similar to mammalian BPIs in terms of sequence and structure. Like mammalian BPI gene, the frog gene nybpi was widely expressed in various tissues and was inducible by challenge with LPS or Gram-negative bacterium. We also showed that recombinant NyBPI, resembling mammalian BPIs, specifically binds with LPS. In addition, the recombinant NyBPI displayed antibacterial activity against Gram-negative bacteria Vibrio anguillarum in a dose-dependent manner. These results indicate that NyBPI may play an important role in an immune response against bacteria in amphibians.

GluR2Q and GluR2R AMPA Subunits are not Targets of lypd2 Interaction

A large family of prototoxin-like molecules endogenous to mammals, Ly6 proteins have been implicated in the regulation of cell signaling processes across multiple species. Previous work has shown that certain members of the Ly6 family are expressed in the brain and target nicotinic acetylcholine receptor and potassium channel function. Structural similarities between Ly6 proteins and alpha-neurotoxins suggest the possibility of additional ionotropic receptor targets. Here, we investigated the possibility of lypd2 as a novel regulator of AMPA receptor (AMPAR) function. In particular, we focused on potential interactions with the Q/R isoforms of the GluR2 subunit, which have profound impacts on AMPAR permeability to calcium during neuronal stimulation. We find that although lypd2 and GluR2 share overlapping expression patterns in the mouse hippocampus, there was no interaction between lypd2 and either GluR2Q or GluR2R isoform. These results underscore the importance of continuing to investigate novel targets for Ly6 interaction and regulation.

New Three-Finger Protein from Starfish Asteria rubens Shares Structure and Pharmacology with Human Brain Neuromodulator Lynx2

Three-finger proteins (TFPs) are small proteins with characteristic three-finger β-structural fold stabilized by the system of conserved disulfide bonds. These proteins have been found in organisms from different taxonomic groups and perform various important regulatory functions or act as components of snake venoms. Recently, four TFPs (Lystars 1–4) with unknown function were identified in the coelomic fluid proteome of starfish A. rubens. Here we analyzed the genomes of A. rubens and A. planci starfishes and predicted additional five and six proteins containing three-finger domains, respectively. One of them, named Lystar5, is expressed in A. rubens coelomocytes and has sequence homology to the human brain neuromodulator Lynx2. The three-finger structure of Lystar5 close to the structure of Lynx2 was confirmed by NMR. Similar to Lynx2, Lystar5 negatively modulated α4β2 nicotinic acetylcholine receptors (nAChRs) expressed in X. laevis oocytes. Incubation with Lystar5 decreased the expression of acetylcholine esterase and α4 and α7 nAChR subunits in the hippocampal neurons. In summary, for the first time we reported modulator of the cholinergic system in starfish.

A cell atlas of microbe-responsive processes in the zebrafish intestine

Gut microbial products direct growth, differentiation, and development in animal hosts. However, we lack system-wide understanding of cell-specific responses to the microbiome. We profiled cell transcriptomes from the intestine, and associated tissue, of zebrafish larvae raised in the presence or absence of a microbiome. We uncovered extensive cellular heterogeneity in the conventional zebrafish intestinal epithelium, including previously undescribed cell types with known mammalian homologs. By comparing conventional to germ-free profiles, we mapped microbial impacts on transcriptional activity in each cell population. We revealed intricate degrees of cellular specificity in host responses to the microbiome that included regulatory effects on patterning and on metabolic and immune activity. For example, we showed that the absence of microbes hindered pro-angiogenic signals in the developing vasculature, causing impaired intestinal vascularization. Our work provides a high-resolution atlas of intestinal cellular composition in the developing fish gut and details the effects of the microbiome on each cell type.

Supplementation of zebrafish (Danio rerio) diet using a short antimicrobial peptide: Evaluation of growth performance, immunomodulatory function, antioxidant activity, and disease resistance

Short-chain bioactive peptides are new and promising antimicrobial, immune moderating, and antioxidant agents. Therefore, the present study was conducted to evaluate in vitro antibacterial activity of CM11, a short antimicrobial peptide (AMP), against Streptococcus iniae and Yersinia ruckeri as fish pathogenic bacteria using standard disk diffusion and microdilution assays. In addition, in vivo effects of CM11 on fish growth, immunity, antioxidant activity, and disease resistance were evaluated using zebrafish (Danio rerio) as an animal model. For in vivo study, based on in vitro susceptibility results, four diets were designed to include zero (as control), 10, 20, and 50 μg of CM11 per g diet referred to as control, P1, P2, and P3 treatments, respectively. After eight weeks of dietary trial, fish were challenged with Streptococcus iniae, and the survival rate was calculated for a period of two weeks. Results showed that CM11 effectively inhibited the growth of S. iniae and Y. ruckeri on agar plates at a concentration of eight μg/ml. Minimum inhibitory and minimum bactericidal concentrations of CM11 were measured at 8 and 32 μg/ml for S. iniae and 16 and 64 μg/ml Y. ruckeri, respectively. In vivo results showed no noticeable effects on fish growth parameters, however, feed conversion ratio (FCR) was found lower in P3 and P2 compared to control (P < 0.05). Immunological and antioxidant responses were found strongly affected by CM11 in all treatment groups in which the highest values were found in the P3 treated group. Key immune and antioxidant genes were up-regulated particularly in fish receiving the highest level of CM11 (P3). Fish receiving the CM11 peptide showed better survival when challenged with S. iniae. These findings suggest the potential of CM11 for use in aquaculture as an antibacterial and immunostimulant agent.

The Bioactivity Prediction of Peptides from Tuna Skin Collagen Using Integrated Method Combining In Vitro and In Silico

The hydrolysates and peptide fractions of bigeye tuna (Thunnus obesus) skin collagen have been successfully studied. The hydrolysates (HPA, HPN, HPS, HBA, HBN, HBS) were the result of the hydrolysis of collagen using alcalase, neutrase, and savinase. The peptide fractions (PPA, PPN, PPS, PBA, PBN, PBS) were the fractions obtained following ultrafiltration of the hydrolysates. The antioxidant activities of the hydrolysates and peptide fractions were studied using the DPPH method. The effects of collagen types, enzymes, and molecular sizes on the antioxidant activities were analyzed using profile plots analysis. The amino acid sequences of the peptides in the fraction with the highest antioxidant activity were analyzed using LC-MS/MS. Finally, their bioactivity and characteristics were studied using in silico analysis. The hydrolysates and peptide fractions provided antioxidant activity (6.17-135.40 µmol AAE/g protein). The lower molecular weight fraction had higher antioxidant activity. Collagen from pepsin treatment produced higher activity than that of bromelain treatment. The fraction from collagen hydrolysates by savinase treatment had the highest activity compared to neutrase and alcalase treatments. The peptides in the PBN and PPS fractions of <3 kDa had antidiabetic, antihypertensive and antioxidant activities. In conclusion, they have the potential to be used in food and health applications.

Improving the Activity of Antimicrobial Peptides Against Aquatic Pathogen Bacteria by Amino Acid Substitutions and Changing the Ratio of Hydrophobic Residues

With the increasing number of drug-resistant bacteria, there is an urgent need for new antimicrobial agents, and antimicrobial peptides (AMPs), which exist in the human non-specific immune system, are one of the most promising candidates. It is an effective optimization strategy to modify antimicrobial peptides (AMPs) according to the distribution of amino acids and hydrophobic characteristics. The addition of bacterial pheromones to the N short peptide can increase the ability to recognize bacteria. In this study, we designed and synthesized AMP1–6 by amino acid substitution of mBjAMP1. Additionally, P-6, S-6, and L-6 were designed and synthesized by adding bacterial pheromones based on 1–6. Functional tests showed that the four AMPs had the ability to kill Gram-negative Vibrio anguillarum, Pseudomonas mendocina, and Vibrio parahaemolyticus, and Gram-positive Micrococcus luteus and Listeria monocytogenes. Additionally, all four AMPs induced permeabilization and depolarization of bacterial cell membranes and increased intracellular reactive oxygen species (ROS) levels. Importantly, they had little or no mammalian cytotoxicity. At the same time, 1–6 and L-6 protected the stability of intestinal flora in Sebastes schlegelii and increased the relative abundance of Lactobacillaceae. In summary, our results indicate that the designed AMPs have broad application prospects as a new type of polypeptide antimicrobial agent.

Identification and functional characterization of ribosomal protein S23 as a new member of antimicrobial protein

Previous studies show that some ribosomal proteins possess antimicrobial peptide (AMP) activity. However, information as such remains rather fragmentary and rather limited. We showed here for the first time that amphioxus RPS23, BjRPS23, was a previously uncharacterized AMP. It not only acted as a pattern recognition receptor, capable of identifying LPS, LTA and PGN, but also an effector, capable of killing the Gram-negative and -positive bacteria. We also showed that the residues positioned at 67-84 formed the core region for the antimicrobial activity of BjRPS23, and its orthologues Verrucomicrobia RPS12_68-85 and Thermotoga RPS12_65-82 similarly displayed some antibacterial activities. BjRPS23 functioned by a combined action of membranolytic mechanisms including interaction with bacterial membrane via LPS, LTA and PGN, and membrane depolarization. BjRPS23 also stimulated production of intracellular ROS in bacteria. Moreover, we demonstrated that RPS23 existed across widely separated taxa, and might play a universal role in protection against bacterial infection in different animals. In addition, we found that neither BjRPS23 nor its truncated form BjRPS23_67-84 were cytotoxic to mammalian cells, making them promising lead molecules for the design of novel peptide antibiotics against bacteria. Collectively, these indicate that RPS23 is a new member of AMP with ancient origin and high conservation.

Injury affects coelomic fluid proteome of the common starfish, Asterias rubens

Echinoderms, possessing outstanding regenerative capabilities, provide a unique model system for the study of response to injury. However, little is known about the proteomic composition of coelomic fluid, an important biofluid circulating throughout the animal's body and reflecting the overall biological status of the organism. In this study, we used LC-MALDI tandem mass spectrometry to characterize the proteome of the cell-free coelomic fluid of the starfish Asterias rubens and to follow the changes occurring in response to puncture wound and blood loss. In total, 91 proteins were identified, of which 61 were extracellular soluble and 16 were bound to the plasma membrane. The most represented functional terms were 'pattern recognition receptor activity' and 'peptidase inhibitor activity'. A series of candidate proteins involved in early response to injury was revealed. Ependymin, β-microseminoprotein, serum amyloid A and avidin-like proteins, which are known to be involved in intestinal regeneration in the sea cucumber, were also identified as injury-responsive proteins. Our results expand the list of proteins potentially involved in defense and regeneration in echinoderms and demonstrate dramatic effects of injury on the coelomic fluid proteome.

Antimicrobial peptides from different plant sources: Isolation, characterisation, and purification

Antimicrobial peptides (AMPs), the self-defence products of organisms, are extensively distributed in plants. They can be classified into several groups, including thionins, defensins, snakins, lipid transfer proteins, glycine-rich proteins, cyclotides and hevein-type proteins. AMPs can be extracted and isolated from different plants and plant organs such as stems, roots, seeds, flowers and leaves. They perform various physiological defensive mechanisms to eliminate viruses, bacteria, fungi and parasites, and so could be used as therapeutic and preservative agents. Research on AMPs has sought to obtain more detailed and reliable information regarding the selection of suitable plant sources and the use of appropriate isolation and purification techniques, as well as examining the mode of action of these peptides. Well-established AMP purification techniques currently used include salt precipitation methods, absorption-desorption, a combination of ion-exchange and reversed-phase C18 solid phase extraction, reversed-phase high-performance liquid chromatography (RP-HPLC), and the sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) method. Beyond these traditional methods, this review aims to highlight new and different approaches to the selection, characterisation, isolation, purification, mode of action and bioactivity assessment of a range of AMPs collected from plant sources. The information gathered will be helpful in the search for novel AMPs distributed in the plant kingdom, as well as providing future directions for the further investigation of AMPs for possible use on humans.

Augmentation of the antibacterial activities of Pt5-derived antimicrobial peptides (AMPs) by amino acid substitutions: Design of novel AMPs against MDR bacteria

The ever-growing concerns on multi-drug resistant (MDR) bacteria lead to urgent demands for novel antibiotics including antimicrobial peptides (AMPs). Pt5, a peptide consisting of the C-terminal 55 residues of zebrafish phosvitin, has been shown to function as an antibacterial agent. Here we used Pt5 as a template to design new AMPs by shortening the sequence and substituting with tryptophan (W) and lysine (K) at selected positions. Among the resultant Pt5-derived peptides, Pt5-1c showed the strongest antimicrobial activity against both Gram-negative and Gram-positive bacteria, including MDR bacteia, with the minimum inhibitory concentrations (MICs) ranging from 1.2 μM to 4.8 μM. Electron microscopic examination showed that Pt5-1c was able to kill the bacteria directly. ELISA revealed that Pt5-1c possessed high affinity to lipopolysaccharide (LPS), lipoteichoic acid (LTA) and peptidoglycan (PGN). Importantly, Pt5-1c was able to disrupt the bacterial membrane by a combined action of membrane depolarization and permeabilization, with little cytotoxicity to mammalian cells. Taken together, these findings suggest that Pt5-1c has considerable potential for future development as novel peptide antibiotics against MDR bacteria.