Identification and functional characterization of an uncharacterized antimicrobial peptide from a ciliate Paramecium caudatum

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 zebrafish ELAVL1b as a new member of antimicrobial protein

Previous studies have shown that ELAVL1 play multiple roles and may be associated with immune response. However, it remains largely unknown about the direct roles of ELAVL1 during a bacterial infection. After reporting the zebrafish ELAVL1a is a maternal immune factor that can protect zebrafish embryos from bacterial infection, here we studied the immune function of zebrafish ELAVL1b. In this study, we showed that zebrafish elavl1b was markedly up-regulated by LTA and LPS treatment, suggesting it may be involved in anti-infectious responses. We also showed that zebrafish recombinant ELAVL1b (rELAVL1b) could bind to both the Gram-positive and negative bacteria M. luteus and S. aureus, E. coli and A. hydrophila as well as their signature molecules LTA and LPS, hinting it may act as a pattern recognition receptor, capable of identifying pathogens. In addition, rELAVL1b could directly kill the Gram-positive and negative bacteria tested via inducing membrane depolarization and intracellular ROS production. Collectively, our results indicate that zebrafish ELAVL1b plays an immune-relevant role as a newly-characterized antimicrobial protein. This work also provides further information to understand the biological roles of ELAVL family and the innate immunity in vertebrates.

In silico characterization of cysteine-stabilized αβ defensins from neglected unicellular microeukaryotes

BACKGROUND

The emergence of multi-resistant pathogens have increased dramatically in recent years, becoming a major public-health concern. Among other promising antimicrobial molecules with potential to assist in this worldwide struggle, cysteine-stabilized αβ (CS-αβ) defensins are attracting attention due their efficacy, stability, and broad spectrum against viruses, bacteria, fungi, and protists, including many known human pathogens.

RESULTS

Here, 23 genomes of ciliated protists were screened and two CS-αβ defensins with a likely antifungal activity were identified and characterized, using bioinformatics, from a culturable freshwater species, Laurentiella sp. (LsAMP-1 and LsAMP-2). Although any potential cellular ligand could be predicted for LsAMP-2; evidences from structural, molecular dynamics, and docking analyses suggest that LsAMP-1 may form stably associations with phosphatidylinositol 4,5-bisphosphates (PIP2), a phospholipid found on many eukaryotic cells, which could, in turn, represent an anchorage mechanism within plasma membrane of targeted cells.

CONCLUSION

These data stress that more biotechnology-oriented studies should be conducted on neglected protists, such ciliates, which could become valuable sources of novel bioactive molecules for therapeutic uses.

Fungicidal Activity of AP10W, a Short Peptide Derived from AP-2 Complex Subunit mu-A, In Vitro and In Vivo

With the increase in the incidence of fungal infections, and the restrictions of existing antifungal drugs, the development of novel antifungal agents is urgent. Here we prove that AP10W, a short peptide derived from AP-2 complex subunit mu-A, displays conspicuous antifungal activities against the main fungal pathogens of human infections Candida albicans and Aspergillus fumigatus. We also show that AP10W suppresses the fungal biofilm formation, and reduces the pre-established fungal biofilms. AP10W appears to exert its fungicidal activity through a mode of combined actions, including interaction with the fungal cell walls via laminarin, mannan and chitin, enhancement of cell wall permeabilization, induction of membrane depolarization, and increase in intracellular ROS generation. Importantly, we demonstrate that AP10W exhibits little toxicity towards mammalian fibroblasts, and effectively promotes the healing of wounded skins infected by C. albicans. These together indicate that AP10W is a new member of fungicidal agents. It also suggests that AP10W has a considerable potential for future development as a novel antifungal drug.

Antifungal Activity of NP20 Derived from Amphioxus Midkine/Pleiotrophin Homolog Against Aspergillus niger and Aspergillus fumigatus

With the emergence of antifungal resistance, systematic infections with Aspergillus are becoming the major cause of the clinical morbidity. The development of novel antifungal agents with high efficacy, low drug tolerance, and few side effects is urgent. In response to that need, we have identified NP20. Here we demonstrate clearly that NP20 has antifungal activity, capable of killing the spores of Aspergillus niger and Aspergillus fumigatus as well as causing direct damage to the surface, membrane, cytoplasm, organelle, and nucleus of the fungal spores. Interestingly, NP20 is active under temperature stress and a wide range of pH. Subsequently, MTT assay, assay for binding of NP20 to fungal cell wall components, membrane depolarization assay, confocal microscopy, ROS assay, DNA replication, and protein synthesis assay are performed to clarify the mechanisms underlying NP20 against Aspergillus. The results show that NP20 can bind with and pass through the fungal cell wall, and then interfere with the lipid membrane. Moreover, NP20 can induce intracellular ROS production, DNA fragmentation, and protein synthesis inhibition of the fungal cells. These together indicate that NP20 is a novel antifungal peptide, which has considerable potential for future development as novel peptide antibiotics against Aspergillus.

Identification and functional characterization of Cofilin-1 as a new member of antimicrobial protein

Cofilin-1 (Cfl1), a member of the ADF/cofilin family, has been identified as one of differentially expressed proteins in human dendritic cells challenged with lipopolysaccharide (LPS), suggesting that it may be involved in immune response. Here we showed that zebrafish cfl1 was markedly up-regulated by LPS and LTA treatment. We also showed that zebrafish recombinant Cfl1 (rCfl1) not only bound to the Gram-negative and positive bacteria A. hydrophila and S. aureus as well as their signature molecules LPS and LTA but also inhibited the growth of the bacteria. Moreover, we found that the heparin-binding motif-containing regions of Cfl1, i.e., Cfl1_9-25, Cfl1_34-51 and Cfl1_108-125, like rCfl1, were also able to bind to LPS and LTA and to inhibit the bacterial growth. rCfl1, Cfl1_9-25, Cfl1_34-51, and Cfl1_108-125 were all able to cause bacterial cell destruction, to induce membrane depolarization, and to stimulate intracellular ROS production. Finally, we showed that zebrafish Cfl1 could protect developing embryos/larvae against attack by the potential pathogen A. hydrophila. These data together indicate that zebrafish Cfl1 plays an immune-relevant role as a newly-characterized antimicrobial protein.

Identification of amphioxus protein disulfide isomerase as both an enzyme and an immunocompotent factor

Previous studies have shown that protein disulfide isomerase (PDI), a member of the thioredoxin (TRX) superfamily, are broadly associated with immune responses in a variety of animals. However, it remains largely unknown about the direct roles of PDIs during a bacterial infection. In this study, we identified the presence of a single pdi gene in the amphioxus Branchiostoma japonicum, Bjpdi. The deduced protein BjPDI is structurally characterized by the presence of four Trx-like domains in the order of a, b, b' and a' and a short acidic C-terminal tail, that are characteristic of PDIs. We demonstrated that rBjPDI displayed both thiol reductase and disulfide bond isomerase activities, indicating comparability of BjPDI with PDIs in term of enzymatic activities. We also showed that rBjPDI induced bacterial agglutination and exhibited a lectin-like activity capable of binding both bacteria (E. coli and S. aureus) and their signature molecules LPS and LTA. Furthermore, BjPDI could kill S. aureus via inducing membrane depolarization and intracellular ROS production in vitro, and treatment of amphioxus with a blocking anti-PDI antibody in vivo markedly reduced the survival rate of amphioxus following attack by S. aureus. Collectively, our study demonstrates that amphioxus protein disulfide isomerase acts as both an enzyme and an immunocompotent factor, and reports the specific function and mode of action of PDIs in immune responses.

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 AP-2 complex subunit mu-A as a new member of antimicrobial protein

AP-2 complex subunit mu-A (AP2M1A) is a component of the adaptor complexes that link clathrin to receptors in coated vesicles. It has recently been shown to be involved in the resistance to oxidative damage, challenging the conventional role of AP2M1A. Here we demonstrated that AP2M1A was a heparin-binding protein abundantly stored in eggs and embryos of zebrafish, and its gene expression was markedly up-regulated by LPS and LTA treatment. We also showed that recombinant AP2M1A (rAP2M1A) was not only able to interact with Gram-negative and Gram-positive bacteria as well as their signature molecules LPS and LTA, but also able to inhibit the growth of the bacteria. Additionally, we found that AP2M1A354-382 that contained 2 closely positioned heparin-binding motifs could also bind to LPS and LTA, and inhibit the bacterial growth. Both rAP2M1A and AP2M1A354-382 were shown to execute antibacterial activity by a combined action of destabilization/destruction of bacterial cell wall through interaction with LPS and LTA, disturbance of the usually polarized membrane through depolarization, and apoptosis/necrosis through intracellular ROS production. Finally, we showed that AP2M1A could protect zebrafish developing embryos/larvae against attack by the potential pathogen Aeromonas hydrophila. All these demonstrate for the first time that AP2M1A is a maternal antimicrobial protein previously uncharacterized. It also establishes a correlation between antibacterial activity and heparin-binding motifs.

Antimicrobial Peptides and Copper(II) Ions: Novel Therapeutic Opportunities

The emergence of new pathogens and multidrug resistant bacteria is an important public health issue that requires the development of novel classes of antibiotics. Antimicrobial peptides (AMPs) are a promising platform with great potential for the identification of new lead compounds that can combat the aforementioned pathogens due to their broad-spectrum antimicrobial activity and relatively low rate of resistance emergence. AMPs of multicellular organisms made their debut four decades ago thanks to ingenious researchers who asked simple questions about the resistance to bacterial infections of insects. Questions such as "Do fruit flies ever get sick?", combined with pioneering studies, have led to an understanding of AMPs as universal weapons of the immune system. This review focuses on a subclass of AMPs that feature a metal binding motif known as the amino terminal copper and nickel (ATCUN) motif. One of the metal-based strategies of hosts facing a pathogen, it includes wielding the inherent toxicity of copper and deliberately trafficking this metal ion into sites of infection. The sudden increase in the concentration of copper ions in the presence of ATCUN-containing AMPs (ATCUN-AMPs) likely results in a synergistic interaction. Herein, we examine common structural features in ATCUN-AMPs that exist across species, and we highlight unique features that deserve additional attention. We also present the current state of knowledge about the molecular mechanisms behind their antimicrobial activity and the methods available to study this promising class of AMPs.

Preserved antibacterial activity of ribosomal protein S15 during evolution

Conventional role of ribosomal proteins is ribosome assembly and protein translation, but some ribosomal proteins also show antimicrobial peptide (AMP) activity, though their mode of action remains ill-defined. Here we demonstrated for the first time that amphioxus RPS15, BjRPS15, was a previously uncharacterized AMP, which was not only capable of identifying Gram-negative and -positive bacteria via interaction with LPS and LTA but also capable of killing the bacteria. We also showed that both the sequence and 3D structure of RPS15 and its prokaryotic homologs were highly conserved, suggesting its antibacterial activity is universal across widely separated taxa. Actually this was supported by the facts that the residues positioned at 45-67 formed the core region for the antimicrobial activity of BjRPS15, and its prokaryotic counterparts, including Nitrospirae RPS19_33-55, Aquificae RPS19_33-55 and P. syringae RPS19_50-72, similarly displayed antibacterial activities. BjRPS15 functioned by both interaction with bacterial surface via LPS and LTA and membrane depolarization as well as induction of intracellular ROS. Moreover, we showed that RPS15 existed extracellularly in amphioxus, shrimp, zebrafish and mice, hinting it may play a critical role in systematic immunity in different animals. In addition, we found that neither BjRPS15 nor its truncated form BjRPS15_45-67 were toxic to mammalian cells, making them promising lead molecules for the design of novel AMPs against bacteria. Collectively, these indicate that RPS15 is a new member of AMP with ancient origin and high conservation throughout evolution.

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.

Overexpression of PtDefensin enhances resistance to Septotis populiperda in transgenic poplar

Plant defensins have been implicated in the plant defense system, but their role in poplar immunity is still unclear. In the present study, we present evidence that PtDefensin, a putative plant defensin, participates in the defense of poplar plants against Septotis populiperda infection. After the construction of recombinant plasmid PET-32a-PtDefensin, PtDefensin protein was expressed in Escherichia coli strain BL21 (DE3) and purified through Ni-IDA resin affinity chromatography. The Trx-PtDefensin fusion protein displayed no cytotoxic activity against RAW264.7 cells but had cytotoxic activity against E. coli K12D31 cells. Analyses of PtDefensin transcript abundance showed that the expression levels of PtDefensin responded to abiotic and biotic stresses. Overexpression of PtDefensin in 'Nanlin 895' poplars (Populus × euramericana cv 'Nanlin895') increased resistance to Septotis populiperda, coupled with upregulation of MYC2 (basic helix-loop-helix (bHLH) transcription factor) related to jasmonic acid (JA) signal transduction pathways and downregulation of Jasmonate-zim domain (JAZ), an inhibitor in the JA signal transduction pathway. We speculate that systemic acquired resistance (SAR) was activated in non-transgenic poplars after S. populiperda incubation, and that induced systemic resistance (ISR) was activated more obviously in transgenic poplars after S. populiperda incubation. Hence, overexpression of PtDefensin may improve the resistance of poplar plants to pathogens.

Epidemiology of Nucleus-Dwelling Holospora: Infection, Transmission, Adaptation, and Interaction with Paramecium

The chapter describes the exceptional symbiotic associations formed between the ciliate Paramecium and Holospora, highly infectious bacteria residing in the host nuclei. Holospora and Holospora-like bacteria (Alphaproteobacteria) are characterized by their ability for vertical and horizontal transmission in host populations, a complex biphasic life cycle, and pronounced preference for host species and colonized cell compartment. These bacteria are obligate intracellular parasites; thus, their metabolic repertoire is dramatically reduced. Nevertheless, they perform complex interactions with the host ciliate. We review ongoing efforts to unravel the molecular adaptations of these bacteria to their unusual lifestyle and the host's employment in the symbiosis. Furthermore, we summarize current knowledge on the genetic and genomic background of Paramecium-Holospora symbiosis and provide insights into the ecological and evolutionary consequences of this interaction. The diversity and occurrence of symbioses between ciliates and Holospora-like bacteria in nature is discussed in connection with transmission modes of symbionts, host specificity and compatibility of the partners. We aim to summarize 50 years of research devoted to these symbiotic systems and conclude trying to predict some perspectives for further studies.

About TFE: Old and New Findings

The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.

Identification and functional characterization of amphioxus Miple, ancestral type of vertebrate midkine/pleiotrophin homologues

Midkine (MK) and pleiotrophin (PTN) are the only two members of heparin-binding growth factor family. MK/PTN homologues found from Drosophila to humans are shown to have antibacterial activities and their antibacterial domains are conserved during evolution. However, little is known about MK/PTN homologue in the basal chordate amphioxus, and overall, information regarding MK/PTN homologues is rather limited in invertebrates. In this study, we identified a single MK/PTN homologue in Branchiostoma japonicum, termed BjMiple, which has a novel domain structure of PTN-PTNr1-PTNr2, and represents the ancestral form of vertebrate MK/PTN family proteins. BjMiple was expressed mainly in the ovary in a tissue-dependent fashion, and its expression was remarkably up-regulated following challenge with bacteria or their signature molecules LPS and LTA, suggesting its involvement in antibacterial responses. Functional assays revealed that BjMiple had strong antimicrobial activity, capable of killing a panel of Gram-negative and Gram-positive bacteria via a membranolytic mechanism, including interaction with bacterial membrane via LPS and LTA, membrane depolarization and high intracellular levels of ROS. Importantly, strong antibacterial activity was localized in PTN_42-61 and PTNr1_42-66. Additionally, BjMiple and its derived peptides PTN_42-61 and PTNr1_42-66 were not cytotoxic to human RBCs and mammalian cells. Taken together, our study suggests that amphioxus Miple is the ancestral type of vertebrate MK/PTN family homologues, and can play important roles as innate peptide antibiotics, which renders it a promising template for the design of novel peptide antibiotics against multi-drug resistant bacteria.

Identification and bioactivity analysis of a newly identified defensin from the oyster Magallana gigas

The relatively conserved sequences of signal peptides and proregions that antimicrobial peptides (AMPs) contain have been successfully used to search for and identify novel AMPs from databases within the same lineages of fish and amphibians and across different animal classes. If such an approach is applicable to invertebrate species such as oyster has not yet been tested so far. In this study, we found a cDNA from the digestive gland of the oyster Magallana gigas, designated Mgdefdg, which contains two exons interspaced by one intron. Mgdefdg coded for a protein with features characteristic of defensins. The mature peptide had the cysteine-stabilized α-helix/β-sheet motif (CSαβ) and the consensus pattern C-X_5-6-C-X₃-C-X_4-6-C-X_3-4-C-X_7-8-C-X-C-X₂-C forming potential disulfide linkages C1-C5, C2-C6, C3-C7 and C4-C8 in the predicted tertiary structure. Functional assays revealed that recombinant mature MgDefdg (rmMgDefdg) was able to kill the Gram-negative bacterium Aeromonas hydrophila and the Gram-positive bacterium Staphylococcus aureus, and to induce bacterial membrane/cytoplasmic damage. ELISA showed that rmMgDefdg had high affinity to both A. hydrophila and S. aureus as well as the microbe-associated molecular pattern molecules LPS and LTA. Moreover, rmMgDefdg was capable of causing bacterial membrane permeabilization and depolarization, and intracellular ROS increase. Additionally, rmMgDefdg was not cytotoxic to human red blood cells and murine RAW264.7 cells. Taken together, our results indicate that MgDefdg is a previously uncharacterized defensin with membrane selectivity towards bacterial cells. It also shows that the use of conserved sequences of signal peptides of defensins can be an effective tool to identify potential defensins across different animal genera in invertebrates.