Embracing the era of antimicrobial peptides with marine organisms.

Covering: 2018 to Jun of 2023The efficiency of traditional antibiotics has been undermined by the proliferation of antibiotic-resistant pathogenic microorganisms, necessitating the pursuit of innovative therapeutic agents. Antimicrobial peptides (AMPs), which are part of host defence peptides found ubiquitously in nature, exhibiting a wide range of activity towards bacteria, fungi, and viruses, offer a highly promising candidate solution. The efficacy of AMPs can frequently be augmented via alterations to their amino acid sequences or structural adjustments. Given the vast reservoir of marine life forms and their distinctive ecosystems, marine AMPs stand as a burgeoning focal point in the quest for alternative peptide templates extracted from natural sources. Advances in identification and characterization techniques have accelerated the discoveries of marine AMPs, thereby stimulating AMP customization, optimization, and synthesis research endeavours. This review presents an overview of recent discoveries related to the intriguing qualities of marine AMPs. Emphasis will be placed upon post-translational modifications (PTMs) of marine AMPs and how they may impact functionality and potency. Additionally, this review considers ways in which marine PTM might support larger-scale, heterologous AMP manufacturing initiatives, providing insights into translational applications of these important biomolecules.

Integrated physiological, biochemical, and transcriptomic analyses of Bruguiera gymnorhiza leaves under long-term copper stress: Stomatal size, wax crystals and composition.

Copper (Cu) is a necessary mineral nutrient for plant growth and development and is involved in several morphological, physiological, and biochemical processes; however, high concentrations of Cu can negatively impact these processes. The role of stomata in responding to various biotic and abiotic stimuli has not been studied in Bruguiera gymnorhiza, particularly in terms of their coordinated interactions at the molecular, physiological, and biochemical levels. Moreover, numerous plants employ strategies such as the presence of thick waxy cuticles on their leaf epidermis and the closing of stomata to reduce water loss. Thus, this study investigates the accumulation of Cu in B. gymnorhiza and its effect on leaf morphology and the molecular response under different Cu treatments (0, 200, and 400 mg L⁻¹, Cu0, Cu200, and Cu400, respectively) during a two years stress period. The results show that Cu stress affected accumulation and transport, increased the activities of peroxidase and ascorbate peroxidase, concentrations of soluble sugar, proline, and H2O2, and decreased the activity of catalase and content of malondialdehyde. Also, Cu-induced stress decreased the uptake of phosphorus and nitrogen and inhibited plant photosynthesis, which consequently led to reduced plant growth. Scanning electron microscopy combined with gas chromatography-mass spectrometry showed that B. gymnorhiza leaves had higher wax crystals and compositions under increased Cu stress, which forced the leaf's stomata to be closed. Also, the contents of alkanes, alcohols, primary alcohol levels (C26:0, C28:0, C30:0, and C32:0), n-Alkanes (C29 and C30), and other wax loads were significantly higher, while fatty acid (C12, C16, and C18) was lower in Cu200 and Cu400 compared to Cu0. Furthermore, the transcriptomic analyses revealed 1240 (771 up- and 469 downregulated), 1000 (723 up- and 277 down-regulated), and 1476 (808 up- and 668 downregulated) differentially expressed genes in Cu0 vs Cu200, Cu0 vs Cu400, and Cu200 vs Cu400, respectively. RNA-seq analyses showed that Cu mainly affected eight pathways, including photosynthesis, cutin, suberin, and wax biosynthesis. This study provides a reference for understanding mangrove response to heavy metal stress and developing novel management practices.

Antibiotics soil-solution chemistry: A review of environmental behavior and uptake and transformation by plants.

The increased use of antibiotics by humans for various purposes has left the environment polluted. Antibiotic pollution remediation is challenging because antibiotics exist in trace amounts and only highly sensitive detection techniques could be used to quantify them. Nevertheless, their trace quantity is not a hindrance to their transfer along the food chain, causing sensitization and the development of antibiotic resistance. Despite an increase in the literature on antibiotic pollution and the development and transfer of antibiotic-resistant genes (ARGs), little attention has been given to the behavior of antibiotics at the soil-solution interface and how this affects antibiotic adsorption-desorption interactions and subsequent uptake and transformation by plants. Thus, this review critically examines the interactions and possible degradation mechanisms of antibiotics in soil and the link between antibiotic soil-solution chemistry and uptake by plants. Also, different factors influencing antibiotic mobility in soil and the transfer of ARGs from one organism to another were considered. The mechanistic and critical analyses revealed that: (a) the charge characteristics of antibiotics at the soil-root interface determine whether they are adsorbed to soil or taken up by plants; (b) antibiotics that avoid soil colloids and reach soil pore water can be absorbed by plant roots, but their translocation to the stem and leaves depends on the ionic state of the molecule; (c) few studies have explored how plants adapt to antibiotic pollution and the transformation of antibiotics in plants; and (d) the persistence of antibiotics in cropland soils can be influenced by the content of soil organic matter, coexisting ions, and fertilization practices. Future research should focus on the soil/solution-antibiotic-plant interactions to reveal detailed mechanisms of antibiotic transformation by plants and whether plant-transformed antibiotics could be of environmental risk.

Genome-Wide Identification and Expression Analysis of the Copper Transporter (COPT/Ctr) Gene Family in Kandelia obovata, a Typical Mangrove Plant.

The copper transporter (COPT/Ctr) gene family plays a critical part in maintaining the balance of the metal, and many diverse species depend on COPT to move copper (Cu) across the cell membrane. In Arabidopsis thaliana, Oryza sativa, Medicago sativa, Zea mays, Populus trichocarpa, Vitis vinifera, and Solanum lycopersicum, a genome-wide study of the COPT protein family was performed. To understand the major roles of the COPT gene family in Kandelia obovata (Ko), a genome-wide study identified four COPT genes in the Kandelia obovata genome for the first time. The domain and 3D structural variation, phylogenetic tree, chromosomal distributions, gene structure, motif analysis, subcellular localization, cis-regulatory elements, synteny and duplication analysis, and expression profiles in leaves and Cu were all investigated in this research. Structural and sequence investigations show that most KoCOPTs have three transmembrane domains (TMDs). According to phylogenetic research, these KoCOPTs might be divided into two subgroups, just like Populus trichocarpa. KoCOPT gene segmental duplications and positive selection pressure were discovered by universal analysis. According to gene structure and motif analysis, most KoCOPT genes showed consistent exon-intron and motif organization within the same group. In addition, we found five hormones and four stress- and seven light-responsive cis-elements in the KoCOPTs promoters. The expression studies revealed that all four genes changed their expression levels in response to copper (CuCl2) treatments. In summary, our study offers a thorough overview of the Kandelia obovata COPT gene family's expression pattern and functional diversity, making it easier to characterize each KoCOPT gene's function in the future.

Genome-Wide Identification, Characterization, and Expression Analysis of the Copper-Containing Amine Oxidase Gene Family in Mangrove Kandelia obovata.

Copper-containing amine oxidases (CuAOs) are known to have significant involvement in the process of polyamine catabolism, as well as serving crucial functions in plant development and response to abiotic stress. A genome-wide investigation of the CuAO protein family was previously carried out in sweet orange (Citrus sinensis) and sweet cherry (Prunus avium L.). Six CuAO (KoCuAO1-KoCuAO6) genes were discovered for the first time in the Kandelia obovata (Ko) genome through a genome-wide analysis conducted to better understand the key roles of the CuAO gene family in Kandelia obovata. This study encompassed an investigation into various aspects of gene analysis, including gene characterization and identification, subcellular localization, chromosomal distributions, phylogenetic tree analysis, gene structure analysis, motif analysis, duplication analysis, cis-regulatory element identification, domain and 3D structural variation analysis, as well as expression profiling in leaves under five different treatments of copper (CuCl2). Phylogenetic analysis suggests that these KoCuAOs, like sweet cherry, may be subdivided into three subgroups. Examining the chromosomal location revealed an unequal distribution of the KoCuAO genes across four out of the 18 chromosomes in Kandelia obovata. Six KoCuAO genes have coding regions with 106 and 159 amino acids and exons with 4 and 12 amino acids. Additionally, we discovered that the 2.5 kb upstream promoter region of the KoCuAOs predicted many cis elements linked to phytohormones and stress responses. According to the expression investigations, CuCl2 treatments caused up- and downregulation of all six genes. In conclusion, our work provides a comprehensive overview of the expression pattern and functional variety of the Kandelia obovata CuAO gene family, which will facilitate future functional characterization of each KoCuAO gene.

A novel yeast strain Geotrichum sp. CS-67 capable of accumulating heavy metal ions.

Bioremediation, which has several advantages over traditional methods, represents an alternative means of dealing with heavy metal pollution. We screened for microorganisms showing heavy metal tolerance in polluted mangrove soils. A novel yeast, Geotrichum sp. CS-67, was discovered and tested for tolerance of Cu2+, Zn2+, and Ni2+. Zn2+ was the most efficiently sequestered by Geotrichum sp. CS-67 followed by Ni2+ and Cu2+. Zn2+ and Ni2+ were actively taken up into the cell, while Cu2+ was adsorbed to the cell wall. We used RNA-Seq to show that a large number of genes involved in the physiological and biochemical processing of heavy metals were differentially expressed in this yeast when it was subjected to Zn2+ and Ni2+ stress. From this panel, we selected the SED1, GDI1 and ZRT1 genes for validation by qRT-PCR and discovered that, during Zn2+ and Ni2+ stress, SED1 and GDI1 were upregulated, while ZRT1 was downregulated, which was consistent with the RNA-Seq results and the biochemical function of these genes. In conclusion, the novel yeast Geotrichum sp. CS-67 has a marked ability to accumulate heavy metal ions, making it of great interest as a possible microbial agent for heavy metal pollution remediation in the future.

A simple transmission dynamics model for predicting the evolution of COVID-19 under control measures in China.

Epidemic forecasting provides an opportunity to predict geographic disease spread and counts when an outbreak occurs and plays a key role in preventing or controlling their adverse impact. However, conventional prediction models based on complex mathematical modelling rely on the estimation of model parameters, which yields unreliable and unsustainable results. Herein, we proposed a simple model for predicting the epidemic transmission dynamics based on nonlinear regression of the epidemic growth rate and iterative methods, which is applicable to the progression of the COVID-19 outbreak under the strict control measures of the Chinese government. Our model yields reliable and accurate results as confirmed by the available data: we predicted that the total number of infections in mainland China would be 91 253, and the maximum number of beds required for hospitalised patients would be 62 794. We inferred that the inflection point (when the growth rate turns from positive to negative) of the epidemic across China would be mid-February, and the end of the epidemic would be in late March. This model is expected to contribute to resource allocation and planning in the health sector while providing a theoretical basis for governments to respond to future global health crises or epidemics.

Jannaschia marina sp. nov., isolated from the gut of a gastropod, Onchidium reevesii.

A taxonomic study was carried out on strain SHC163T, which was isolated from the gut of Onchidium reevesii. The bacterium was Gram-stain-negative, oxidase-positive, catalase-negative and rod-shaped. Growth was observed at salinities of 0-4.0 % NaCl and at temperatures of 15-35 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SHC163T belonged to the genus Jannaschia, with the highest sequence similarity to Jannaschia seosinensis CL-SP26T (97.9%), followed by Jannaschia faecimaris DSM 100420T (97.8 %), Jannaschia rubra CECT 5088T (97.5%) and eight species of the genus Jannaschia (94.7-97.1 %). The average amino acid identity, average nucleotide identity and the digital DNA-DNA hybridization estimate values between strain SHC163T and the type strains of the genus Jannaschia were 64.33-79.78 %, 71.0-78.4 % and 19.2-21.0%, respectively. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c, 56.5 %), C18 : 1 ω7c 11-methyl (23.1 %), C18 : 0 (8.7 %). The G+C content of the chromosomal DNA was 67.8 mol%. The respiratory quinone was determined to be Q-10 (100 %). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and aminophospholipid. The combined genotypic and phenotypic data show that strain SHC163T represents a novel species within the genus Jannaschia, for which the name Jannaschia marina sp. nov. is proposed, with the type strain SHC163T (=MCCC 1K04032T=KCTC 72524T).

Inhibition of Tomato Early Blight Disease by Culture Extracts of a Streptomyces puniceus Isolate from Mangrove Soil.

This study investigates the potential of natural products derived from a mangrove rhizosphere bacterium in tomato early blight management. A Streptomyces puniceus strain L75 was isolated from the rhizosphere of Acanthus ilicifolius Linn in the Mai Po Reserve, Hong Kong. The crude ethyl acetate (EA) extract of L75 fermentation cultures has broad-spectrum antifungal bioactivities. L75 EA extract was significantly more effective in Alternaria solani growth inhibition at 25 µg/ml or lower compared with Mancozeb, with no observable negative impacts on tomato leaves or root development. Furthermore, L75 EA extract had significantly lower aquatic toxicity than Mancozeb at the same concentrations. L75 EA extract targets germ tube elongation of A. solani conidia, with a fungistatic mode of action. Liquid chromatography-quadrupole time-of-flight mass spectrometry analysis identified two possible antifungal compounds, Alteramide A and the Heat-Stable Antifungal Factor, which together contribute partially to the bioactivity of L75 EA extract. On detached tomato leaves, coinoculation of A. solani with L75 EA extract of 50, 25, or 5 µg/ml reduced diseased areas by ∼98, ∼90, and ∼48%, respectively, relative to the control after 5 days. This study demonstrates the potential of natural products from mangrove rhizosphere bacteria in agricultural applications.

Ribosome Inactivating Proteins from Rosaceae.

Ribosome-inactivating proteins (RIPs) are widespread among higher plants of different taxonomic orders. In this study, we report on the RIP sequences found in the genome/transcriptome of several important Rosaceae species, including many economically important edible fruits such as apple, pear, peach, apricot, and strawberry. All RIP domains from Rosaceae share high sequence similarity with conserved residues in the catalytic site and the carbohydrate binding sites. The genomes of Malus domestica and Pyrus communis contain both type 1 and type 2 RIP sequences, whereas for Prunus mume, Prunus persica, Pyrus bretschneideri, and Pyrus communis a complex set of type 1 RIP sequences was retrieved. Heterologous expression and purification of the type 1 as well as the type 2 RIP from apple allowed to characterize the biological activity of the proteins. Both RIPs from Malus domestica can inhibit protein synthesis. Furthermore, molecular modelling suggests that RIPs from Rosaceae possess three-dimensional structures that are highly similar to the model proteins and can bind to RIP substrates. Screening of the recombinant type 2 RIP from apple on a glycan array revealed that this type 2 RIP interacts with terminal sialic acid residues. Our data suggest that the RIPs from Rosaceae are biologically active proteins.

Comparative analysis of carbohydrate binding properties of Sambucus nigra lectins and ribosome-inactivating proteins.

In the past three decades a lot of research has been done on the extended family of carbohydrate-binding proteins from Sambucus nigra, including several so-called type 2 RIPs as well as hololectins. Although all these proteins have been studied for their carbohydrate-binding properties using hapten inhibition assays, detailed carbohydrate specificity studies have only been performed for a few Sambucus proteins. In particular SNA-I, has been studied extensively. Because of its unique binding characteristics this lectin was developed as an important tool in glycoconjugate research to detect sialic acid containing glycoconjugates. At present much less information is available with respect to the detailed carbohydrate binding specificity of other S. nigra lectins and RIPs, and as a consequence their applications remain limited. In this paper we report a comparative analysis of several lectins from S. nigra using the glycan microarray technology. Ultimately a better understanding of the ligands for each lectin can contribute to new/more applications for these lectins in glycoconjugate research. Furthermore, the data from glycan microarray analyses combined with the previously obtained sequence information can help to explain how evolution within a single lectin family eventually yielded a set of carbohydrate-binding proteins with a very broad specificity range.

Biochemical and multi-omics analyses of response mechanisms of rhizobacteria to long-term copper and salt stress: Effect on soil physicochemical properties and growth of Avicennia marina.

Mangroves are of important economic and environmental value and research suggests that their carbon sequestration and climate change mitigation potential is significantly larger than other forests. However, increasing salinity and heavy metal pollution significantly affect mangrove ecosystem function and productivity. This study investigates the tolerance mechanisms of rhizobacteria in the rhizosphere of Avicennia marina under salinity and copper (Cu) stress during a 4-y stress period. The results exhibited significant differences in antioxidant levels, transcripts, and secondary metabolites. Under salt stress, the differentially expressed metabolites consisted of 30% organic acids, 26.78% nucleotides, 16.67% organic heterocyclic compounds, and 10% organic oxides as opposed to 27.27% organic acids, 24.24% nucleotides, 15.15% organic heterocyclic compounds, and 12.12% phenyl propane and polyketides under Cu stress. This resulted in differential regulation of metabolic pathways, with phenylpropanoid biosynthesis being unique to Cu stress and alanine/aspartate/glutamate metabolism and α-linolenic acid metabolism being unique to salt stress. The regulation of metabolic pathways enhanced antioxidant defenses, nutrient recycling, accumulation of osmoprotectants, stability of plasma membrane, and chelation of Cu, thereby improving the stress tolerance of rhizobacteria and A. marina. Even though the abundance and community structure of rhizobacteria were significantly changed, all the samples were dominated by Proteobacteria, Chloroflexi, Actinobacteriota, and Firmicutes. Since the response mechanisms were unbalanced between treatments, this led to differential growth trends for A. marina. Our study provides valuable inside on variations in diversity and composition of bacterial community structure from mangrove rhizosphere subjected to long-term salt and Cu stress. It also clarifies rhizobacterial adaptive mechanisms to these stresses and how they are important for mitigating abiotic stress and promoting plant growth. Therefore, this study can serve as a reference for future research aimed at developing long-term management practices for mangrove forests.

Genome-Wide Identification and Bioinformatics Analyses of Host Defense Peptides Snakin/GASA in Mangrove Plants.

Host defense peptides (HDPs) are components of plant defensive barriers that resist microbial infection. Members of the Snakin/GASA protein family in plants have functions of regulating plant growth, defense, and bacteriostasis. Most mangrove plants grow in coastal zones. In order to survive in harsh environments, mangrove plants have evolved complex adaptations against microbes. In this study, Snakin/GASA family members were identified and analyzed in the genomes of three mangrove species. Twenty-seven, thirteen, and nine candidate Snakin/GASA family members were found in Avicennia marina, Kandelia obovata, and Aegiceras corniculatum, respectively. These Snakin/GASA family members were identified and categorized into three subfamilies via phylogenetic analysis. The genes coding for the Snakin/GASA family members were unevenly distributed on chromosomes. Collinearity and conservative motif analyses showed that the Snakin/GASA family members in K. obovata and A. corniculatum underwent multiple gene duplication events. Snakin/GASA family member expression in normal leaves and leaves infected with pathogenic microorganisms of the three mangrove species was verified using real-time quantitative polymerase chain reaction. The expression of KoGASA3 and 4, AcGASA5 and 10, and AmGASA1, 4, 5, 15, 18, and 23 increased after microbial infection. This study provides a research basis for the verification of HDPs from mangrove plants and suggests directions for the development and utilization of marine biological antimicrobial peptides.

NRAMP gene family in Kandelia obovata: genome-wide identification, expression analysis, and response to five different copper stress conditions.

Natural resistance-associated macrophage proteins (NRAMPs) are a class of metal transporters found in plants that exhibit diverse functions across different species. Transporter proteins facilitate the absorption, distribution, and sequestration of metallic elements within various plant tissues. Despite the extensive identification of NRAMP family genes in various species, a full analysis of these genes in tree species is still necessary. Genome-wide identification and bioinformatics analysis were performed to understand the roles of NRAMP genes in copper (CuCl2) stress in Kandelia obovata (Ko). In Arachis hypogaea L., Populus trichocarpa, Vitis vinifera, Phaseolus vulgaris L., Camellia sinensis, Spirodela polyrhiza, Glycine max L. and Solanum lycopersicum, a genome-wide study of the NRAMP gene family was performed earlier. The domain and 3D structural variation, phylogenetic tree, chromosomal distributions, gene structure, motif analysis, subcellular localization, cis-regulatory elements, synteny and duplication analysis, and expression profiles in leaves and CuCl2 were all investigated in this research. In order to comprehend the notable functions of the NRAMP gene family in Kandelia obovata, a comprehensive investigation was conducted at the genomic level. This study successfully found five NRAMP genes, encompassing one gene pair resulting from whole-genome duplication and a gene that had undergone segmental duplication. The examination of chromosomal position revealed an unequal distribution of the KoNRAMP genes across chromosomes 1, 2, 5, 7, and 18. The KoNRAMPs can be classified into three subgroups (I, II, and SLC) based on phylogeny and synteny analyses, similar to Solanum lycopersicum. Examining cis-regulatory elements in the promoters revealed five hormone-correlated responsive elements and four stress-related responsive elements. The genomic architecture and properties of 10 highly conserved motifs are similar among members of the NRAMP gene family. The conducted investigations demonstrated that the expression levels of all five genes exhibited alterations in response to different levels of CuCl2 stress. The results of this study offer crucial insights into the roles of KoNRAMPs in the response of Kandelia obovata to CuCl2 stress.

Discovery and Characterization of a New Crustin Antimicrobial Peptide from Amphibalanus amphitrite.

Crustins are an antimicrobial peptide (AMP) family that plays an important role in innate immunity in crustaceans. It is important to discover new AMPs from natural sources to expand the current database. Here, we identified and characterized a new crustin family member, named AaCrus1, from Amphibalanus amphitrite. AaCrus1 shares high identity (48.10%) with PvCrus, a Type I crustin of Penaeus vannamei that possesses a whey acidic protein (WAP) domain. AaCrus1 contains 237 amino acids and eight cysteine residues forming conserved 'four-disulfide core' structure. Our recombinant AaCrus1 (rAaCrus 1) could inhibit the growth of two Gram-positive bacteria (Staphylococcus aureus, Bacillus sp. T2) and four Gram-negative bacteria (Vibrio parahaemolyticus, Vibrio harveyi, Vibrio anguillarum, Vibrio alginolyticus) with a minimum inhibitory concentration of 3.5-28 µM. It can further induce agglutination of both Gram-positive and Gram-negative bacteria. rAaCrus1 can bind to bacteria and damage bacterial cell membranes. Furthermore, rAaCrus1 disrupted biofilm development of S. aureus and V. parahaemolyticus. Our discovery and characterization of this new crustin can be further optimized as a good alternative to antibiotics.

The Cytotoxicity of Elderberry Ribosome-Inactivating Proteins Is Not Solely Determined by Their Protein Translation Inhibition Activity.

Although the protein translation inhibition activity of ribosome inactivating proteins (RIPs) is well documented, little is known about the contribution of the lectin chain to the biological activity of these proteins. In this study, we compared the in vitro and intracellular activity of several S. nigra (elderberry) RIPs and non-RIP lectins. Our data demonstrate that RIPs from elderberry are much more toxic to HeLa cells than to primary fibroblasts. Differences in the cytotoxicity between the elderberry proteins correlated with differences in glycan specificity of their lectin domain, cellular uptake efficiency and intracellular destination. Despite the fact that the bulk of the RIPs accumulated in the lysosomes and partly in the Golgi apparatus, we could demonstrate effective inhibition of protein synthesis in cellula. As we also observed cytotoxicity for non-RIP lectins, it is clear that the lectin chain triggers additional pathways heralding cell death. Our data suggest that one of these pathways involves the induction of autophagy.

The role of thionins in rice defence against root pathogens.

Thionins are antimicrobial peptides that are involved in plant defence. Here, we present an in-depth analysis of the role of rice thionin genes in defence responses against two root pathogens: the root-knot nematode Meloidogyne graminicola and the oomycete Pythium graminicola. The expression of rice thionin genes was observed to be differentially regulated by defence-related hormones, whereas all analysed genes were consistently down-regulated in M. graminicola-induced galls, at least until 7 days post-inoculation (dpi). Transgenic lines of Oryza sativa cv. Nipponbare overproducing OsTHI7 revealed decreased susceptibility to M. graminicola infection and P. graminicola colonization. Taken together, these results demonstrate the role of rice thionin genes in defence against two of the most damaging root pathogens attacking rice.