PepSAVI-MS Reveals a Proline-rich Antimicrobial Peptide in Amaranthus tricolor

Peptidomics profiling and biological activities of grape pomace protein hydrolysates

Grape pomace protein isolate was hydrolysed by Alcalase, Flavourzyme and Protease either individually or in combination to produce hydrolysates with antihypertensive and antimicrobial properties. The degree of hydrolysis (DH) ranged between 22 and 52 % for Protease and Flavourzyme, respectively. Among all treatments, hydrolysates prepared using Flavourzyme exhibited the highest angiotensin-converting enzyme inhibitory (ACEi) activity, with an IC50 value of 91 μg/mL. The peptidomics analysis revealed that the peptides identified in Flavourzyme hydrolysate presented molecular features compatible with its bioactivity, like a high density of ACEi sequences per peptide. The hydrolysates were also able to inhibit the growth of Escherichia coli in a range between 9 and 54 % for Alcalase and Alcalase + Flavourzyme, respectively. Peptides in the most active hydrolysate evidenced a high occurrence of proline residues, which is a structural feature of some antimicrobial peptides.

Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides

Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.

Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies

Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.

Peptide-Membrane Docking and Molecular Dynamic Simulation of In Silico Detected Antimicrobial Peptides from Portulaca oleracea's Transcriptome

The main issue with clinical infections is multidrug resistance to traditional antibiotics. As they are essential to innate immunity, shielding hosts from pathogenic microbes, traditional herbal remedies are an excellent supplier of antimicrobial peptides (AMPs), vital parts of defensive systems. Nevertheless, little is known about the bioactive peptide components of most ethnobotanical species. Our goal in this study was to find new, likely AMPs from Portulaca oleracea (P. oleracea) using in silico studies. The P. oleracea transcriptome was gained from Sequence Read Archive (SRA) and quality controlled, then adapters and other low-quality reads were trimmed. Afterward, de novo assembled and translated open reading frames (ORFs) were determined. Next, the ORFs were filtered based on AMP physiochemical criteria and deep learning methods. Finally, the five selected putative AMPs docked with E. coli and S. aureus membranes that showed penetration in bilayers. In this step, PO2 was chosen as a candidate AMP to analyze with molecular dynamics (MD) simulations. Our data demonstrated that PO2 is more stable in E. coli than in S. aureus. Moreover, these predicted AMPs can be good candidates for in vitro and in vivo analysis.

Recent advances of bioactive proteins/polypeptides in the treatment of breast cancer

Proteins do not only serve as nutrients to fulfill the demand for food, but also are used as a source of bioactive proteins/polypeptides for regulating physical functions and promoting physical health. Female breast cancer has the highest incidence in the world and is a serious threat to women's health. Bioactive proteins/polypeptides exert strong anti-tumor effects and exhibit inhibition of multiple breast cancer cells. This review discussed the suppressing effects of bioactive proteins/polypeptides on breast cancer in vitro and in vivo, and their mechanisms of migration and invasion inhibition, apoptosis induction, and cell cycle arrest. This may contribute to providing a basis for the development of bioactive proteins/polypeptides for the treatment of breast cancer.

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Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis

Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor, the first reference genome for the subgenus Albersia, combining PacBio HiFi, Nanopore ultra-long and Hi-C data. The contig N50 size was 906 kb, and 99.58% of contig sequence was anchored to the 17 chromosomes, totalling 520 Mb. We annotated 27,813 protein-coding genes with an average 1.3 kb coding sequence and 5.3 exons. We inferred that A. tricolor underwent a whole-genome duplication (WGD) and that the WGD shared by amaranths occurred in the last common ancestor of subfamily Amaranthoideae. Moreover, we comprehensively identified candidate genes in betalain biosynthesis pathway. Among them, DODAα1 and CYP76ADα1, located in one topologically associated domain (TAD) of an active (A) compartment on chromosome 16, were more highly expressed in red leaves than in green leaves, and DODAα1 might be the rate-limiting enzyme gene in betalains biosynthesis. This study presents new genome resources and enriches our understanding of amaranth evolution, betalains production, facilitating molecular breeding improvements and the understanding of C4 plants evolution.

Colorant Pigments, Nutrients, Bioactive Components, and Antiradical Potential of Danta Leaves (Amaranthus lividus)

In the Indian subcontinent, danta (stems) of underutilized amaranth are used as vegetables in different culinary dishes. At the edible stage of the danta, leaves are discarded as waste in the dustbin because they are overaged. For the first time, we assessed the colorant pigments, bioactive components, nutrients, and antiradical potential (AP) of the leaves of danta to valorize the by-product (leaf) for antioxidant, nutritional, and pharmacological uses. Leaves of danta were analyzed for proximate and element compositions, colorant pigments, bioactive constituents, AP (DPPH), and AP (ABTS+). Danta leaves had satisfactory moisture, protein, carbohydrates, and dietary fiber. The chosen danta leaves contained satisfactory magnesium, iron, calcium, potassium, manganese, copper, and zinc; adequate bioactive pigments, such as betacyanins, carotenoids, betalains, β-carotene, chlorophylls, and betaxanthins; and copious bioactive ascorbic acid, polyphenols, flavonoids, and AP. The correlation coefficient indicated that bioactive phytochemicals and colorant pigments of the selected danta leaves had good AP as assessed via ABTS+ and DPPH assays. The selected danta leaves had good ROS-scavenging potential that could indicate massive possibilities for promoting the health of the nutraceutical- and antioxidant-deficit public. The findings showed that danta leaves are a beautiful by-product for contributing as an alternate origin of antioxidants, nutrients, and bioactive compounds with pharmacological use.

Amaranthus hypochondriacus seeds as a rich source of cysteine rich bioactive peptides

Amaranthus hypochondriacus is a nutritious alternative grain native to Central and South America. Increased interest in the impact of A. hypochondriacus on the human body has driven characterization of bioactive secondary metabolites. The seeds are known to contain bioactive small molecules but little is known regarding endogenous peptides. Cysteine-rich peptides (CRPs) in foodstuffs are particularly relevant because they are stabilized by disulfide bonds enhancing resistance to digestion. Here, in silico predictions, proteomics, and simulated gastrointestinal digestions are leveraged to identify digestion resistant CRPs within A. hypochondriacus seeds. Thirteen in silico predicted CRPs were detected in a seed extract providing evidence for the translation of five CRP families. Mature forms of six CRPs were characterized via top-down proteomics revealing multiple post-translational modifications. All six peptides demonstrated resistance to simulated gastrointestinal digestion, suggesting that A. hypochondriacus CRPs may exhibit bioactivity after consumption and should be prioritized for further characterization.

Phytonutrients, Colorant Pigments, Phytochemicals, and Antioxidant Potential of Orphan Leafy Amaranthus Species

The underutilized Amaranthus leafy vegetables are a unique basis of pigments such as β-cyanins, β-xanthins, and betalains with radical scavenging capacity (RSC). They have abundant phytonutrients and antioxidant components, such as pigments, vitamins, phenolics, and flavonoids. Eight selected genotypes (four genotypes from each species) of underutilized Amaranthus leafy vegetables were evaluated for phytonutrients, pigments, vitamins, phenolics, flavonoids, and antioxidants in a randomized complete block design under ambient field conditions with three replicates. The studied traits showed a wide range of variations across eight genotypes of two species of Amaranthus leafy vegetables. The highest fat, β-xanthins, K, dietary fiber, Mg, β-cyanins, Mn, chlorophyll ab, Zn, TP, TF, betalains, chlorophyll a content, and (RSC) (DPPH) and RSC (ABTS+) were obtained from A. tricolor accessions. Conversely, the highest protein, Cu, carbohydrates, Ca, and chlorophyll b content were obtained from A. lividus accessions. The highest dry matter, carotenoids, Fe, energy, and ash were obtained from A. tricolor and A. lividus. The accession AT2 confirmed the highest vit. C and RSC (DPPH) and RSC (ABTS+); AT5 had the highest TP content; and AT12 had the highest TF content. A. tricolor accessions had high phytochemicals across the two species, such as phytopigments, vitamins, phenolics, antioxidants, and flavonoids, with considerable nutrients and protein. Hence, A. tricolor accessions can be used as high-yielding cultivars comprising ample antioxidants. The correlation study revealed that vitamin C, pigments, flavonoids, β-carotene, and phenolics demonstrated a strong RSC, and showed a substantial contribution to the antioxidant potential (AP) of A. tricolor. The investigation exposed that the accessions displayed a plentiful origin of nutritional values, phytochemicals, and AP with good quenching ability of reactive oxygen species (ROS) that provide enormous prospects for nourishing the mineral-, antioxidant-, and vitamin-threatened community.

The Dual Nature of Amaranth-Functional Food and Potential Medicine

The beneficial health-promoting properties of plants have been known to mankind for generations. Preparations from them are used to create recipes for dietary supplements, functional food, and medicinal products. Recently, amaranth has become an area of increasing scientific and industrial interest. This is due to its valuable biological properties, rich phytochemical composition, and wide pharmacological activity. Amaranth is a pseudo-cereal crop with a dual character, combining the features of food and health-promoting product. This paper briefly and concisely reviews the current information on the chemical composition of amaranth, the value of its supplementation, the status of amaranth as a food ingredient as well as its key biological and pharmacological activities. The beneficial biological properties of amaranth preparations described in this paper may be an incentive to conduct further in-depth scientific research in this field and also to promote the development of innovative technologies in the food and cosmetics industry with the use of this plant.

A peptidoform based proteomic strategy for studying functions of post-translational modifications

Protein post-translational modifications (PTMs) generate an enormous, but as yet undetermined, expansion of the produced proteoforms. In this Viewpoint, we firstly reviewed the concepts of proteoform and peptidoform. We show that many of the current PTM biological investigation and annotation studies largely follow a PTM site-specific rather than proteoform-specific approach. We further illustrate a potentially useful matching strategy in which a particular "modified peptidoform" is matched to the corresponding "unmodified peptidoform" as a reference for the quantitative analysis between samples and conditions. We suggest this strategy has the potential to provide more directly relevant information to learn the PTM site-specific biological functions. Accordingly, we advocate for the wider use of the nomenclature "peptidoform" in future bottom-up proteomic studies.

Creating optimized peptide libraries for AMP discovery via PepSAVI-MS

Antimicrobial peptides (AMPs) are host defense peptides with a range of functions/activities/modes of action that are ubiquitously expressed across all forms of life. Continued discovery of novel AMPs presents exciting opportunities to address evolving resistance to existing treatments in multiple fields, including agricultural pathogens/pests as well as antimicrobial and chemotherapeutics for human health. However, typical discovery methods including bioassay-guided fractionation and genome mining generally lack the capacity for robust AMP discovery in non-model/unsequenced organisms. PepSAVI-MS (Statistically guided bioactive peptides prioritized via mass spectrometry) was developed as an AMP discovery approach that addresses some of the limitations associated with these standard methods. PepSAVI-MS is a multi-pronged pipeline that includes peptide library creation, bioactivity screening, LC-MS analysis, and statistical modeling for putative AMP identification. The original implementation of PepSAVI-MS outlined strategies for the fractionation of plant extracts with strong cation exchange chromatography (SCX). Herein, we elaborate on recent improvements to peptide library creation through the use of orthogonal fractionation methods, specifically crude SCX chromatography and reversed-phase liquid chromatography (RPLC). This optimization of the "peptide library creation" step has demonstrated improvements for processing and AMP identifications via PepSAVI-MS.

Antimicrobial peptides: mechanism of action, activity and clinical potential

The management of bacterial infections is becoming a major clinical challenge due to the rapid evolution of antibiotic resistant bacteria. As an excellent candidate to overcome antibiotic resistance, antimicrobial peptides (AMPs) that are produced from the synthetic and natural sources demonstrate a broad-spectrum antimicrobial activity with the high specificity and low toxicity. These peptides possess distinctive structures and functions by employing sophisticated mechanisms of action. This comprehensive review provides a broad overview of AMPs from the origin, structural characteristics, mechanisms of action, biological activities to clinical applications. We finally discuss the strategies to optimize and develop AMP-based treatment as the potential antimicrobial and anticancer therapeutics.

Too Hot to Handle: Antibacterial Peptides Identified in Ghost Pepper

Capsicum spp. (hot peppers) demonstrate a range of interesting bioactive properties spanning anti-inflammatory, antioxidant, and antimicrobial activities. While several species within the genus are known to produce antimicrobial peptides (AMPs), AMP sequence mining of genomic data indicates this space remains largely unexplored. Herein, in silico AMP predictions were paired with peptidomics to identify novel AMPs from the interspecific hybrid ghost pepper (Capsicum chinense × frutescens). AMP prediction algorithms revealed 115 putative AMPs within the Capsicum chinense genome, of which 14 were identified in the aerial tissue peptidome. PepSAVI-MS, de novo sequencing, and complementary approaches were used to fully molecularly characterize two novel AMPs, CC-AMP1 and CC-AMP2, including elucidation of a pyroglutamic acid post-translational modification of CC-AMP1 and disulfide bond connectivity of both. Both CC-AMP1 and CC-AMP2 have little homology with known AMPs and exhibited low μM antimicrobial activity against Gram-negative bacteria, including Escherichia coli. These findings demonstrate the complementary nature of peptidomics, bioactivity-guided discovery, and bioinformatics-based investigations to characterize plant AMP profiles.

Proteomic response of Escherichia coli to a membrane lytic and iron chelating truncated Amaranthus tricolor defensin

BACKGROUND

Plant defensins are a broadly distributed family of antimicrobial peptides which have been primarily studied for agriculturally relevant antifungal activity. Recent studies have probed defensins against Gram-negative bacteria revealing evidence for multiple mechanisms of action including membrane lysis and ribosomal inhibition. Herein, a truncated synthetic analog containing the γ-core motif of Amaranthus tricolor DEF2 (Atr-DEF2) reveals Gram-negative antibacterial activity and its mechanism of action is probed via proteomics, outer membrane permeability studies, and iron reduction/chelation assays.

RESULTS

Atr-DEF2(G39-C54) demonstrated activity against two Gram-negative human bacterial pathogens, Escherichia coli and Klebsiella pneumoniae. Quantitative proteomics revealed changes in the E. coli proteome in response to treatment of sub-lethal concentrations of the truncated defensin, including bacterial outer membrane (OM) and iron acquisition/processing related proteins. Modification of OM charge is a common response of Gram-negative bacteria to membrane lytic antimicrobial peptides (AMPs) to reduce electrostatic interactions, and this mechanism of action was confirmed for Atr-DEF2(G39-C54) via an N-phenylnaphthalen-1-amine uptake assay. Additionally, in vitro assays confirmed the capacity of Atr-DEF2(G39-C54) to reduce Fe3+ and chelate Fe2+ at cell culture relevant concentrations, thus limiting the availability of essential enzymatic cofactors.

CONCLUSIONS

This study highlights the utility of plant defensin γ-core motif synthetic analogs for characterization of novel defensin activity. Proteomic changes in E. coli after treatment with Atr-DEF2(G39-C54) supported the hypothesis that membrane lysis is an important component of γ-core motif mediated antibacterial activity but also emphasized that other properties, such as metal sequestration, may contribute to a multifaceted mechanism of action.

Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products

Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.

Multiple Classes of Antimicrobial Peptides in Amaranthus tricolor Revealed by Prediction, Proteomics, and Mass Spectrometric Characterization

Traditional medicinal plants are rich reservoirs of antimicrobial agents, including antimicrobial peptides (AMPs). Advances in genomic sequencing, in silico AMP predictions, and mass spectrometry-based peptidomics facilitate increasingly high-throughput bioactive peptide discovery. Herein, Amaranthus tricolor aerial tissue was profiled via MS-based proteomics/peptidomics, identifying AMPs predicted in silico. Bottom-up proteomics identified seven novel peptides spanning three AMP classes including lipid transfer proteins, snakins, and a defensin. Characterization via top-down peptidomic analysis of Atr-SN1, Atr-DEF1, and Atr-LTP1 revealed unexpected proteolytic processing and enumerated disulfide bonds. Bioactivity screening of isolated Atr-LTP1 showed activity against the high-risk ESKAPE bacterial pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter cloacae). These results highlight the potential for integrating AMP prediction algorithms with complementary -omics approaches to accelerate characterization of biologically relevant AMP peptidoforms.

Implementation of Microfluidics for Antimicrobial Susceptibility Assays: Issues and Optimization Requirements

Despite the continuous emergence of multi-drug resistant pathogens, the number of new antimicrobials reaching the market is critically low. Natural product peptides are a rich source of bioactive compounds, and advances in mass spectrometry have achieved unprecedented capabilities for the discovery and characterization of novel molecular species. However, traditional bioactivity assay formats hinder the discovery and biochemical characterization of natural product antimicrobial peptides (AMPs), necessitating large sample quantities and significant optimization of experimental parameters to achieve accurate/consistent activity measurements. Microfluidic devices offer a promising alternative to bulk assay systems. Herein, a microfluidics-based bioassay was compared to the traditional 96-well plate format in respective commercially-available hardware. Bioactivity in each assay type was compared using a Viola inconspicua peptide library screened against E. coli ATCC 25922. Brightfield microcopy was used to determine bioactivity in microfluidic channels while both common optical and fluorescence-based measurements of cell viability were critically assessed in plate-based assays. Exhibiting some variation in optical density and fluorescence-based measurements, all plate-based assays conferred bioactivity in late eluting V. inconspicua library fractions. However, significant differences in the bioactivity profiles of plate-based and microfluidic assays were found, and may be derived from the materials comprising each assay device or the growth/assay conditions utilized in each format. While new technologies are necessary to overcome the limitations of traditional bioactivity assays, we demonstrate that off-the-shelf implementation of microfluidic devices is non-trivial and significant method development/optimization is required before conventional use can be realized for sensitive and rapid detection of AMPs in natural product matrices.