scholarly journals Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host–Microbe Interactions by Revealing Diverse Antimicrobial Peptides

Marine Drugs ◽  
2020 ◽  
Vol 18 (7) ◽  
pp. 362
Author(s):  
Ana Matos ◽  
Dany Domínguez-Pérez ◽  
Daniela Almeida ◽  
Guillermin Agüero-Chapin ◽  
Alexandre Campos ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Marine Invertebrates ◽  
Shotgun Proteomics ◽  
Model Organisms ◽  
Developmental Studies ◽  
Orbitrap Mass Spectrometer ◽  
Proteome Discoverer ◽  
Eukaryotic Origin ◽  
Host Microbe Interactions ◽  
Catalytic Functions

Ascidians are marine invertebrates associated with diverse microbial communities, embedded in their tunic, conferring special ecological and biotechnological relevance to these model organisms used in evolutionary and developmental studies. Next-generation sequencing tools have increased the knowledge of ascidians’ associated organisms and their products, but proteomic studies are still scarce. Hence, we explored the tunic of three ascidian species using a shotgun proteomics approach. Proteins extracted from the tunic of Ciona sp., Molgula sp., and Microcosmus sp. were processed using a nano LC-MS/MS system (Ultimate 3000 liquid chromatography system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer). Raw data was searched against UniProtKB – the Universal Protein Resource Knowledgebase (Bacteria and Metazoa section) using Proteome Discoverer software. The resulting proteins were merged with a non-redundant Antimicrobial Peptides (AMPs) database and analysed with MaxQuant freeware. Overall, 337 metazoan and 106 bacterial proteins were identified being mainly involved in basal metabolism, cytoskeletal and catalytic functions. 37 AMPs were identified, most of them attributed to eukaryotic origin apart from bacteriocins. These results and the presence of “Biosynthesis of antibiotics” as one of the most highlighted pathways revealed the tunic as a very active tissue in terms of bioactive compounds production, giving insights on the interactions between host and associated organisms. Although the present work constitutes an exploratory study, the approach employed revealed high potential for high-throughput characterization and biodiscovery of the ascidians’ tunic and its microbiome.

scholarly journals Modulation of Human Complement System by Antimicrobial Peptide Arenicin-1 from Arenicola marina

Marine Drugs ◽  
2018 ◽  
Vol 16 (12) ◽  
pp. 480 ◽  
Author(s):  
Ekaterina Umnyakova ◽  
Nikolay Gorbunov ◽  
Alexander Zhakhov ◽  
Ilia Krenev ◽  
Tatiana Ovchinnikova ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Complement System ◽  
Complement Activation ◽  
Marine Invertebrates ◽  
Cytotoxic Agents ◽  
Arenicola Marina ◽  
Low Concentrations ◽  
Marine Polychaete ◽  
Hypothetical Mechanism

Antimicrobial peptides from marine invertebrates are known not only to act like cytotoxic agents, but they also can display some additional activities in mammalian organisms. In particular, these peptides can modulate the complement system as was described for tachyplesin, a peptide from the horseshoe crab. In this work, we investigated the influence on complement activation of the antimicrobial peptide arenicin-1 from the marine polychaete Arenicola marina. To study effects of arenicin on complement activation in human blood serum, we used hemolytic assays of two types, with antibody sensitized sheep erythrocytes and rabbit erythrocytes. Complement activation was also assessed, by the level of C3a production that was measured by ELISA. We found that the effect of arenicin depends on its concentration. At relatively low concentrations the peptide stimulates complement activation and lysis of target erythrocytes, whereas at higher concentrations arenicin acts as a complement inhibitor. A hypothetical mechanism of peptide action is proposed, suggesting its interaction with two complement proteins, C1q and C3. The results lead to the possibility of the development of new approaches for therapy of diseases connected with complement dysregulation, using peptide regulators derived from natural antimicrobial peptides of invertebrates.

scholarly journals Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database

Antibiotics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 757 ◽  
Author(s):  
Daniela Almeida ◽  
Dany Domínguez-Pérez ◽  
Ana Matos ◽  
Guillermin Agüero-Chapin ◽  
Hugo Osório ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Salivary Glands ◽  
Protein Identification ◽  
Inflammatory Responses ◽  
Shotgun Proteomics ◽  
Octopus Vulgaris ◽  
Protein Database ◽  
Venom Protein ◽  
Protein Toxin ◽  
Proteomics Approach

Cephalopods, successful predators, can use a mixture of substances to subdue their prey, becoming interesting sources of bioactive compounds. In addition to neurotoxins and enzymes, the presence of antimicrobial compounds has been reported. Recently, the transcriptome and the whole proteome of the Octopus vulgaris salivary apparatus were released, but the role of some compounds—e.g., histones, antimicrobial peptides (AMPs), and toxins—remains unclear. Herein, we profiled the proteome of the posterior salivary glands (PSGs) of O. vulgaris using two sample preparation protocols combined with a shotgun-proteomics approach. Protein identification was performed against a composite database comprising data from the UniProtKB, all transcriptomes available from the cephalopods’ PSGs, and a comprehensive non-redundant AMPs database. Out of the 10,075 proteins clustered in 1868 protein groups, 90 clusters corresponded to venom protein toxin families. Additionally, we detected putative AMPs clustered with histones previously found as abundant proteins in the saliva of O. vulgaris. Some of these histones, such as H2A and H2B, are involved in systemic inflammatory responses and their antimicrobial effects have been demonstrated. These results not only confirm the production of enzymes and toxins by the O. vulgaris PSGs but also suggest their involvement in the first line of defense against microbes.

Ontogenetic development of the otic region in the new model organism, Leucoraja erinacea (Chondrichthyes; Rajidae)

2018 ◽  
Vol 109 (1-2) ◽  
pp. 105-114 ◽  
Author(s):  
Cathrin PFAFF ◽  
Jürgen KRIWET ◽  
Kyle MARTIN ◽  
Zerina JOHANSON
Keyword(s):  
Soft Tissues ◽  
Developmental Stages ◽  
Model Organism ◽  
Model Organisms ◽  
Biological Research ◽  
Developmental Studies ◽  
Micro Computed Tomography ◽  
Computed Tomography Scanning ◽  
Cartilaginous Fishes ◽  
Tomography Scanning

ABSTRACTCartilaginous fishes have a long evolutionary history dating back 440 million years and include model organisms in a number of fields of biological research. However, comparative developmental studies of these organisms, particularly neuroanatomical investigations, still remain sparse. Here, pre-hatching to adult developmental stages of the Little Skate, Leucoraja erinacea, are investigated using micro-computed tomography scanning in conjunction with staining procedures designed to improve visualisation of soft tissues. Within the ear, the anatomy of the skeletal labyrinth changes during ontogeny and differs substantially from the underlying membranous system, contrary to previous observations in sharks. Additionally, substantial morphological remodelling characterises the parietal fossa, which appears initially as a massive and hook-like structure and subsequently becomes slender and surrounded by soft tissue. The sizes of the vestibular system and neurocranium increase isometrically from pre- to post-hatching phases, and then exponentially after the post-hatching stages.

scholarly journals Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

2020 ◽  
Vol 19 (7) ◽  
pp. 1088-1103 ◽  
Author(s):  
Lindsay K. Pino ◽  
Seth C. Just ◽  
Michael J. MacCoss ◽  
Brian C. Searle
Keyword(s):  
Gas Phase ◽  
Best Practice ◽  
Shotgun Proteomics ◽  
Small Sample ◽  
Attractive Alternative ◽  
Sequence Variants ◽  
Data Independent Acquisition ◽  
Orbitrap Mass Spectrometer ◽  
Practice Methods ◽  
Splice Junctions

Data independent acquisition (DIA) is an attractive alternative to standard shotgun proteomics methods for quantitative experiments. However, most DIA methods require collecting exhaustive, sample-specific spectrum libraries with data dependent acquisition (DDA) to detect and quantify peptides. In addition to working with non-human samples, studies of splice junctions, sequence variants, or simply working with small sample yields can make developing DDA-based spectrum libraries impractical. Here we illustrate how to acquire, queue, and validate DIA data without spectrum libraries, and provide a workflow to efficiently generate DIA-only chromatogram libraries using gas-phase fractionation (GPF). We present best-practice methods for collecting DIA data using Orbitrap-based instruments and develop an understanding for why DIA using an Orbitrap mass spectrometer should be approached differently than when using time-of-flight instruments. Finally, we discuss several methods for analyzing DIA data without libraries.

scholarly journals Host-Microbe Interactions in Caenorhabditis elegans

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Rui Zhang ◽  
Aixin Hou
Keyword(s):  
Life Cycle ◽  
Microbial Pathogens ◽  
Model Organisms ◽  
Short Life ◽  
C Elegans ◽  
Complex Microbial Community ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Laboratory Maintenance ◽  
Genetic Mutants

A good understanding of how microbes interact with hosts has a direct bearing on our capability of fighting infectious microbial pathogens and making good use of beneficial ones. Among the model organisms used to study reciprocal actions among microbes and hosts, C. elegans may be the most advantageous in the context of its unique attributes such as the short life cycle, easiness of laboratory maintenance, and the availability of different genetic mutants. This review summarizes the recent advances in understanding host-microbe interactions in C. elegans. Although these investigations have greatly enhanced our understanding of C. elegans-microbe relationships, all but one of them involve only one or few microbial species. We argue here that more research is needed for exploring the evolution and establishment of a complex microbial community in the worm’s intestine and its interaction with the host.

scholarly journals The Vibrio cholerae T6SS is Dispensable for Colonization but Affects Pathogenesis and the Structure of Zebrafish Intestinal Microbiome

2021 ◽  
Author(s):  
Paul Breen ◽  
Andrew D. Winters ◽  
Kevin R. Theis ◽  
Jeffrey H. Withey
Keyword(s):  
Vibrio Cholerae ◽  
Model Organism ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Model Organisms ◽  
Rrna Gene ◽  
Composition And Structure ◽  
Aquatic Microbes ◽  
Host Microbe Interactions ◽  
Rrna Gene Sequencing

Zebrafish ( Danio rerio ) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae , an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was essential for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.

scholarly journals AdpA Positively Regulates Morphological Differentiation and Chloramphenicol Biosynthesis in Streptomyces venezuelae

2021 ◽  
Author(s):  
Małgorzata Płachetka ◽  
Michał Krawiec ◽  
Jolanta Zakrzewska-Czerwińska ◽  
Marcin Wolański
Keyword(s):  
Secondary Metabolites ◽  
Morphological Differentiation ◽  
Transcriptional Regulator ◽  
Pleiotropic Effect ◽  
Model Organisms ◽  
Developmental Studies ◽  
Streptomyces Venezuelae ◽  
Cellular Processes

Streptomyces are well-known producers of valuable secondary metabolites which include a large variety of antibiotics and important model organisms for developmental studies in multicellular bacteria. The conserved transcriptional regulator AdpA of Streptomyces exerts a pleiotropic effect on cellular processes, including the morphological differentiation and biosynthesis of secondary metabolites.

scholarly journals Bioadhesion in ascidians: a developmental and functional genomics perspective

2015 ◽  
Vol 5 (1) ◽  
pp. 20140061 ◽  
Author(s):  
Roberta Pennati ◽  
Ute Rothbächer
Keyword(s):  
Functional Genomics ◽  
Marine Invertebrates ◽  
Marine Species ◽  
Sister Group ◽  
Model Organisms ◽  
Phylogenetic Position ◽  
Adhesive Properties ◽  
Marine Animals ◽  
Fouling Organism ◽  
Adhesive Organs

The development of bioadhesives inspired from marine animals is a promising approach to generate new tissue-compatible medical components. A number of marine species, through their adhesive properties, also represent significant foulers that become increasingly problematic to aquaculture, shipping or local biodiversity. In order to develop more sophisticated man-made glues and/or efficient fouling resistant surfaces, it is important to understand the mechanical, structural and molecular properties of adhesive organs in selected species. Ascidians are marine invertebrates with larvae that opportunistically attach to almost any type of submerged surface to undergo metamorphosis into permanently sessile adults. Not only do they represent a globally important fouling organism, but they are becoming increasingly popular as model organisms for developmental biology. The latter is due to their phylogenetic position as the sister group to the vertebrates and their cellular and molecular accessibility for experimentation. In this paper, we review the mechanisms of larval adhesion in ascidians and draw conclusions from comparative analyses of selected species. We further discuss how knowledge from a developmental and functional genomics point of view can advance our understanding of cellular and molecular signatures and their hierarchical usage in animal adhesive organs.

scholarly journals Drosophila Antimicrobial Peptides and Lysozymes Regulate Gut Microbiota Composition and Abundance

mBio ◽  
2021 ◽  
Author(s):  
A. Marra ◽  
M. A. Hanson ◽  
S. Kondo ◽  
B. Erkosar ◽  
B. Lemaitre
Keyword(s):  
Gut Microbiota ◽  
Antimicrobial Peptides ◽  
Current Knowledge ◽  
Microbiota Composition ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Gut Microbiota Composition

This study advances current knowledge in the field of host-microbe interactions by demonstrating that the two families of immune effectors, antimicrobial peptides and lysozymes, actively regulate the gut microbiota composition and abundance. Consequences of the loss of these antimicrobial peptides and lysozymes are exacerbated during aging, and their loss contributes to increased microbiota abundance and shifted composition in old flies.

scholarly journals In Vitro or In Vivo Models, the Next Frontier for Unraveling Interactions between Malassezia spp. and Hosts. How Much Do We Know?

2020 ◽  
Vol 6 (3) ◽  
pp. 155
Author(s):  
Maritza Torres ◽  
Hans de Cock ◽  
Adriana Marcela Celis Ramírez
Keyword(s):  
Galleria Mellonella ◽  
Fungal Infections ◽  
Model Organisms ◽  
In Vivo Models ◽  
Alternative Models ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Malassezia Spp

Malassezia is a lipid-dependent genus of yeasts known for being an important part of the skin mycobiota. These yeasts have been associated with the development of skin disorders and cataloged as a causal agent of systemic infections under specific conditions, making them opportunistic pathogens. Little is known about the host–microbe interactions of Malassezia spp., and unraveling this implies the implementation of infection models. In this mini review, we present different models that have been implemented in fungal infections studies with greater attention to Malassezia spp. infections. These models range from in vitro (cell cultures and ex vivo tissue), to in vivo (murine models, rabbits, guinea pigs, insects, nematodes, and amoebas). We additionally highlight the alternative models that reduce the use of mammals as model organisms, which have been gaining importance in the study of fungal host–microbe interactions. This is due to the fact that these systems have been shown to have reliable results, which correlate with those obtained from mammalian models. Examples of alternative models are Caenorhabditis elegans, Drosophila melanogaster, Tenebrio molitor, and Galleria mellonella. These are invertebrates that have been implemented in the study of Malassezia spp. infections in order to identify differences in virulence between Malassezia species.

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