Characterization of an abaecin-like antimicrobial peptide identified from a Pteromalus puparum cDNA clone

De novo genome assembly and transcriptome sequencing in foot and mantle tissues of Megaustenia siamensis reveals components of adhesive substances

The semislug Megaustenia siamensis, commonly found in Thailand, is notable for its exceptional capacity to produce biological adhesives, enabling it to adhere to tree leaves even during heavy rainfall. In this study, we generated the first reference genome for M. siamensis using a combination of three sequencing technologies: Illumina's short-read, Pac-Bio's HIFI long-read, and Hi-C. The assembled genome size was 2593 billion base pairs (bp), containing 34,882 protein-coding genes. Our analysis revealed positive selection in pathways associated with the ubiquitin-proteasome system. Furthermore, RNA sequencing of foot and mantle tissues unveiled the primary constituents of the adhesive, including lectin-like proteins (C-lectin, H-lectin, and C1q) and matrilin-like proteins (VWA and EGF). Additionally, antimicrobial peptides were identified. The comprehensive M. siamensis genome and tissue-specific transcriptomic data provided here offer valuable resources for understanding its biology and exploring potential medical applications.

Evaluation of Potential DnaK Modulating Proline-Rich Antimicrobial Peptides Identified by Computational Screening

The day is rapidly approaching where current antibiotic therapies will no longer be effective due to the development of multi-drug resistant bacteria. Antimicrobial peptides (AMPs) are a promising class of therapeutic agents which have the potential to help address this burgeoning problem. Proline-rich AMPs (PrAMPs) are a sub-class of AMPs, that have multiple modes of action including modulation of the bacterial protein folding chaperone, DnaK. They are highly effective against Gram-negative bacteria and have low toxicity to mammalian cells. Previously we used an in silico approach to identify new potential PrAMPs from the DRAMP database. Four of these peptides, antibacterial napin, attacin-C, P9, and PP30, were each chemically assembled and characterized. Together with synthetic oncocin as a reference, each peptide was then assessed for antibacterial activity against Gram-negative/Gram-positive bacteria and for in vitro DnaK modulation activity. We observed that these peptides directly modulate DnaK activity independently of eliciting or otherwise an antibiotic effect. Based on our findings, we propose a change to our previously established PrAMP definition to remove the requirement for antimicrobial activity in isolation, leaving the following classifiers: >25% proline, modulation of DnaK AND/OR the 70S ribosome, net charge of +1 or more, produced in response to bacterial infection AND/OR with pronounced antimicrobial activity.

Using an Ensemble to Identify and Classify Macroalgae Antimicrobial Peptides

The rapid spread of multi-drug resistant microbes has lead researchers to discover natural alternative remedies such as antimicrobial peptides (AMPs). In the first line of defense, AMPs display a broad spectrum of potent activity against multi-resistant pathogenic bacteria, viruses, fungi, and even cancer. AMPs can be further characterised into families according to amino acid composition, secondary structure, and function. However, despite recent advancements in rapid computational methods for AMP prediction from various mammalian, aquatic, and terrestrial species, there is limited information regarding their presence, functional roles, and family type from marine macroalgae. In this paper, we present a promising two-tier ensemble of heterogeneous machine learning models that integrates seven well-known machine learning classifiers to predict AMPs from macroalgae. The first tier of the ensemble consists of a suite of binary classifiers that identify AMPs from protein sequence data which are then forwarded to a second-tier multi-class ensemble to characterise their functional family type. The two-tier ensemble was successfully used to identify 39 putative AMP sequences in 12 macroalgae species from three different phyla groups. The approach we describe is not limited to AMPs and can also be applied to search sequence data for other types of proteins.

(Re)Defining the Proline-Rich Antimicrobial Peptide Family and the Identification of Putative New Members

As we rapidly approach a post-antibiotic era in which multi-drug resistant bacteria are ever-pervasive, antimicrobial peptides (AMPs) represent a promising class of compounds to help address this global issue. AMPs are best-known for their membrane-disruptive mode of action leading to bacteria cell lysis and death. However, many AMPs are also known to be non-lytic and have intracellular modes of action. Proline-rich AMPs (PrAMPs) are one such class, that are generally membrane permeable and inhibit protein synthesis leading to a bactericidal outcome. PrAMPs are highly effective against Gram-negative bacteria and yet show very low toxicity against eukaryotic cells. Here, we review both the PrAMP family and the past and current definitions for this class of peptides. Computational analysis of known AMPs within the DRAMP database (http://dramp.cpu-bioinfor.org/) and assessment of their PrAMP-like properties have led us to develop a revised definition of the PrAMP class. As a result, we subsequently identified a number of unknown and unclassified peptides containing motifs of striking similarity to known PrAMP-based DnaK inhibitors and propose a series of new sequences for experimental evaluation and subsequent addition to the PrAMP family.

Biophysical approaches for exploring lipopeptide-lipid interactions

In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed.

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A brief overview of topics to understand the generalities of lipopeptide (LP) science.

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Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes.

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Guidelines for selecting of the most adequate membrane models for the given analytical technique.

Diversity, evolution and medical applications of insect antimicrobial peptides

Antimicrobial peptides (AMPs) are short proteins with antimicrobial activity. A large portion of known AMPs originate from insects, and the number and diversity of these molecules in different species varies considerably. Insect AMPs represent a potential source of alternative antibiotics to address the limitation of current antibiotics, which has been caused by the emergence and spread of multidrug-resistant pathogens. To get more insight into AMPs, we investigated the diversity and evolution of insect AMPs by mapping their phylogenetic distribution, allowing us to predict the evolutionary origins of selected AMP families and to identify evolutionarily conserved and taxon-specific families. Furthermore, we highlight the use of the nematode Caenorhabditis elegans as a whole-animal model in high-throughput screening methods to identify AMPs with efficacy against human pathogens, including Acinetobacter baumanii and methicillin-resistant Staphylococcus aureus. We also discuss the potential medical applications of AMPs, including their use as alternatives for conventional antibiotics in ectopic therapies, their combined use with antibiotics to restore the susceptibility of multidrug-resistant pathogens, and their use as templates for the rational design of peptidomimetic drugs that overcome the disadvantages of therapeutic peptides.

The article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.

Heterologous expression of abaecin peptide from Apis mellifera in Pichia pastoris

Background

Antimicrobial peptides (AMPs) are the first line of host immune defense against pathogens. Among AMPs from the honeybee Apis mellifera, abaecin is a major broad-spectrum antibacterial proline-enriched cationic peptide.

Results

For heterologous expression of abaecin in Pichia pastoris, we designed an ORF with HisTag, and the codon usage was optimized. The gene was chemically synthetized and cloned in the pUC57 vector. The new ORF was sub-cloned in the pPIC9 expression vector and transformed into P. pastoris. After selection of positive clones, the expression was induced by methanol. The supernatant was analyzed at different times to determine the optimal time for the recombinant peptide expression. As a proof-of-concept, Escherichia coli was co-incubated with the recombinant peptide to verify its antimicrobial potential.

Discussion

Briefly, the recombinant Abaecin (rAbaecin) has efficiently decreased E. coli growth (P < 0.05) through an in vitro assay, and may be considered as a novel therapeutic agent that may complement other conventional antibiotic therapies.

Peptides and Peptidomimetics for Antimicrobial Drug Design

The purpose of this paper is to introduce and highlight a few classes of traditional antimicrobial peptides with a focus on structure-activity relationship studies. After first dissecting the important physiochemical properties that influence the antimicrobial and toxic properties of antimicrobial peptides, the contributions of individual amino acids with respect to the peptides antibacterial properties are presented. A brief discussion of the mechanisms of action of different antimicrobials as well as the development of bacterial resistance towards antimicrobial peptides follows. Finally, current efforts on novel design strategies and peptidomimetics are introduced to illustrate the importance of antimicrobial peptide research in the development of future antibiotics.

Proline-rich antimicrobial peptides: potential therapeutics against antibiotic-resistant bacteria

The increasing resistance of pathogens to antibiotics causes a huge clinical burden that places great demands on academic researchers and the pharmaceutical industry for resolution. Antimicrobial peptides, part of native host defense, have emerged as novel potential antibiotic alternatives. Among the different classes of antimicrobial peptides, proline-rich antimicrobial peptides, predominantly sourced from insects, have been extensively investigated to study their specific modes of action. In this review, we focus on recent developments in these peptides. They show a variety of modes of actions, including mechanism shift at high concentration, non-lytic mechanisms, as well as possessing different intracellular targets and lipopolysaccharide binding activity. Furthermore, proline-rich antimicrobial peptides display the ability to not only modulate the immune system via cytokine activity or angiogenesis but also possess properties of penetrating cell membranes and crossing the blood brain barrier suggesting a role as potential novel carriers. Ongoing studies of these peptides will likely lead to the development of more potent antimicrobial peptides that may serve as important additions to the armoury of agents against bacterial infection and drug delivery.

Plant Essential Oils and Mastitis Disease: Their Potential Inhibitory Effects on Pro-inflammatory Cytokine Production in Response to Bacteria Related Inflammation

This paper highlights the role of plant volatile organic compounds, found in essential oils, for the treatment of bacteria related inflammation. This report is focused on tea tree oil, particularly its main compound terpinen-4-ol. Analysis of the published literature shows that many essential oils have significant antibacterial, antifungal and anti-inflammatory effects. Some of their major components, such as terpinen-4-ol, act by inhibiting pro-inflammatory cytokine expression while stimulating production of anti-inflammatory cytokines. Such observations may be exploited to encourage biotherapy against mastitis. The use of synthetic antibiotics is being increasingly discouraged because their presence in dairy milk may have potential downstream effects on population health and the agri-food chain. In the context of inflammation and related mammalian responses, understanding the interplay between volatile organic compounds, especially terpinen-4-ol, and cytokines during bacteria related inflammation should clarify their mode of action to control mastitis.