Post-translational protein deimination signatures in sea lamprey (Petromyzon marinus) plasma and plasma-extracellular vesicles

Rast, Jonathan P.; D’Alessio, Stefania; Kraev, Igor; Lange, Sigrun

doi:10.1016/j.dci.2021.104225

Cited by 6 publications

(14 citation statements)

References 210 publications

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“…Protein interaction networks for deiminated proteins revealed nine KEGG pathways relating to immune (phagosome) and metabolic (glycolysis/gluconeogenesis, pentose phosphate pathway, biosynthesis of amino acids, fructose and mannose metabolism, carbon metabolism, ribosome biogenesis, protein processing in ER, metabolic pathways) functions in coelomic fluid, and two of these KEGG pathways were also found in the EVs and related to immune function (phagosome) and metabolic (protein processing) function. Compared with KEGG pathways identified for deiminated proteins in other species, the glycolysis/gluconeogenesis pathway was previously identified in cetacean sera [50], in plasma-EVs from naked mole-rat [48], in alligator plasma-EVs [25], in lamprey plasma and plasma-EVs [41], and in lobster and horseshoe crab haemolymph [39,40], as well as in alveolates [31]. The KEGG pentose phosphate pathway was previously identified for deiminated proteins from cetacean sera [50] and in alveolates [31].…”

Section: Discussionmentioning

confidence: 99%

“…The KEGG pentose phosphate pathway was previously identified for deiminated proteins from cetacean sera [50] and in alveolates [31]. The biosynthesis of amino acids KEGG pathway was previously identified for deiminated proteins from bovine plasma and plasma-EVs [52], plasma and plasma-EVs of reindeer [53], naked mole-rats [48], and lampreys [41], from cetacean sera [50], and lobster haemolymph [39]. The fructose and mannose metabolism KEGG pathway was identified for deiminated proteins in cetacean sera [50], lamprey plasma [41], and in alveolates [31].…”

Section: Discussionmentioning

confidence: 99%

“…The biosynthesis of amino acids KEGG pathway was previously identified for deiminated proteins from bovine plasma and plasma-EVs [52], plasma and plasma-EVs of reindeer [53], naked mole-rats [48], and lampreys [41], from cetacean sera [50], and lobster haemolymph [39]. The fructose and mannose metabolism KEGG pathway was identified for deiminated proteins in cetacean sera [50], lamprey plasma [41], and in alveolates [31]. The carbon metabolism KEGG pathway has been identified for deiminated proteins in lamprey plasma [41], in lobster and horseshoe crab haemolymph [39,40], as well as in alveolates [31].…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, antibodies against the other four human PAD isozymes were also tested for cross-reaction with sea urchin coelomic fluid (PAD1 (ab181762, 1/1000 in TBS-T), PAD3 (ab50246, 1/1000 in TBS-T), PAD4 (ab50247, 1/1000 in TBS-T), and PAD6 (PA5-72059, Thermo Fisher Scientific, Hemel Hempstead, UK, 1/1000 in TBS-T; results are shown in Supplementary Figure S2). For characterisation of coelomic fluid EVs, two phylogenetically conserved EV markers were used: CD63 (ab68418; diluted 1/1000) and Flotillin-1 (ab41927; diluted 1/2000), which have, besides in human, been previously shown to cross-react with EVs from other taxa [24,25,[39][40][41]48]. Primary antibody incubation was carried out on a shaking platform overnight at 4 • C. The nitrocellulose membranes were thereafter washed at room temperature in TBS-T for 3 × 10 min and then incubated with HRP-conjugated secondary anti-rabbit IgG antibody (BioRad), diluted 1/3000 in TBS-T, for 1 h at room temperature.…”

Section: Western Blotting Analysismentioning

confidence: 99%

“…A recent comparative body of research has focused on identifying putative roles for PADs/ADI and downstream deimination of proteins involved in shaping immunity and metabolism in a wide range of taxa throughout the phylogenetic tree, including Alveolata [31], Mollusca [38], Crustacea [39], Merostomata [40], Agnatha [41], Chondrichthyes [24], Teleosts [23,[42][43][44][45][46], Reptilia [25], Aves [47], Rodents [48,49], and sea and land mammals including Cetaceans [50], Pinnipeds [51], Artiodactyla [52,53], and Camelidae [54]. Through these studies, our group has particularly focused on identifying deimination signatures in circulatory fluid (e.g., plasma, serum, haemolymph or coelomic fluid, depending on species) and on characterising circulating extracellular vesicles (EVs), including with respect to their protein, including deiminated protein (and in some cases microRNA) cargos.…”

Section: Introductionmentioning

confidence: 99%

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Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin (Strongylocentrotus purpuratus) Coelomic Fluid—Novel Insights into Echinodermata Biology

D’Alessio

Buckley

Kraev

et al. 2021

Biology

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The purple sea urchin (Strongylocentrotus purpuratus) is a marine invertebrate of the class Echinoidea that serves as an important research model for developmental biology, cell biology, and immunology, as well as for understanding regenerative responses and ageing. Peptidylarginine deiminases (PADs) are calcium-dependent enzymes that mediate post-translational protein deimination/citrullination. These alterations affect protein function and may also play roles in protein moonlighting. Extracellular vesicles (EVs) are membrane-bound vesicles that are released from cells as a means of cellular communication. Their cargo includes a range of protein and RNA molecules. EVs can be isolated from many body fluids and are therefore used as biomarkers in physiological and pathological responses. This study assessed EVs present in the coelomic fluid of the purple sea urchin (Strongylocentrotus purpuratus), and identified both total protein cargo as well as the deiminated protein cargo. Deiminated proteins in coelomic fluid EVs were compared with the total deiminated proteins identified in coelomic fluid to assess putative differences in deiminated protein targets. Functional protein network analysis for deiminated proteins revealed pathways for immune, metabolic, and gene regulatory functions within both total coelomic fluid and EVs. Key KEGG and GO pathways for total EV protein cargo furthermore showed some overlap with deimination-enriched pathways. The findings presented in this study add to current understanding of how post-translational deimination may shape immunity across the phylogeny tree, including possibly via PAD activity from microbiota symbionts. Furthermore, this study provides a platform for research on EVs as biomarkers in sea urchin models.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Western Blotting Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin (Strongylocentrotus purpuratus) Coelomic Fluid—Novel Insights into Echinodermata Biology

D’Alessio

Buckley

Kraev

et al. 2021

Biology

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Application of Extracellular Vesicles in Aquatic Animals: A Review of the Latest Decade

Zhao

Deng

Zhu

et al. 2021

Reviews in Fisheries Science & Aquaculture

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Extracellular vesicles: an emerging tool for wild immunology

Espejo,

Ezenwa

2024

Discovery Immunology

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The immune system is crucial for defending organisms against pathogens and maintaining health. Traditionally, research in immunology has relied on laboratory animals to understand how the immune system works. However, there is increasing recognition that wild animals, due to their greater genetic diversity, lifespan, and environmental exposures, have much to contribute to basic and translational immunology. Unfortunately, logistical challenges associated with collecting and storing samples from wildlife and the lack of commercially available species-specific reagents have hindered the advancement of immunological research on wild species. Extracellular vesicles (EVs) are cell-derived nanoparticles present in all body fluids and tissues of organisms spanning from bacteria to mammals. Human and lab animal studies indicate that EVs are involved in a range of immunological processes, and recent work shows that EVs may play similar roles in diverse wildlife species. Thus, EVs can expand the toolbox available for wild immunology research, helping to overcome some of the challenges associated with this work. In this paper, we explore the potential application of EVs to wild immunology. First, we review current understanding of EV biology across diverse organisms. Next, we discuss key insights into the immune system gained from research on EVs in human and laboratory animal models and highlight emerging evidence from wild species. Finally, we identify research themes in wild immunology that can immediately benefit from the study of EVs and describe practical considerations for using EVs in wildlife research.

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Post-translational protein deimination signatures in sea lamprey (Petromyzon marinus) plasma and plasma-extracellular vesicles

Cited by 6 publications

References 210 publications

Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin (Strongylocentrotus purpuratus) Coelomic Fluid—Novel Insights into Echinodermata Biology

Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin (Strongylocentrotus purpuratus) Coelomic Fluid—Novel Insights into Echinodermata Biology

Application of Extracellular Vesicles in Aquatic Animals: A Review of the Latest Decade

Extracellular vesicles: an emerging tool for wild immunology

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