SignalP 4.0: discriminating signal peptides from transmembrane regions

Whipworms are parasitic nematodes that live in the gut of more than 500 million people worldwide. Owing to the difficulty in obtaining parasite material, the mouse whipworm Trichuris muris has been extensively used as a model to study human whipworm infections. These nematodes secrete a multitude of compounds that interact with host tissues where they orchestrate a parasitic existence. Herein we provide the first comprehensive characterization of the excretory/secretory products of T. muris. We identify 148 proteins secreted by T. muris and show for the first time that the mouse whipworm secretes exosome-like extracellular vesicles (EVs) that can interact with host cells. We use an Optiprep® gradient to purify the EVs, highlighting the suitability of this method for purifying EVs secreted by a parasitic nematode. We also characterize the proteomic and genomic content of the EVs, identifying >350 proteins, 56 miRNAs (22 novel) and 475 full-length mRNA transcripts mapping to T. muris gene models. Many of the miRNAs putatively mapped to mouse genes are involved in regulation of inflammation, implying a role in parasite-driven immunomodulation. In addition, for the first time to our knowledge, colonic organoids have been used to demonstrate the internalization of parasite EVs by host cells. Understanding how parasites interact with their host is crucial to develop new control measures. This first characterization of the proteins and EVs secreted by T. muris provides important information on whipworm–host communication and forms the basis for future studies.

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“…Putative signal peptides and transmembrane domain(s) were predicted using the programs CD-Search tool [29] and SignalP [30]. …”

Section: Methodsmentioning

confidence: 99%

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Eichenberger

Talukder

Field

et al. 2018

J of Extracellular Vesicle

112

145

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“…The theoretical exoproteome of the eight Synechococcus strains used in the experimental study plus four Prochlorococcus strains (MED4, MIT9303, MIT9312 and MIT9313) and SAR11 ( Pelagibacter ubique HTCC1062) was determined based on three prediction tools: (i) the S ignal P 4.0 server for predicting N‐terminal signal peptides for secretion (Petersen et al ., 2011), (ii) the S ecretome P 2.0 server for predicting proteins exported by non‐classical systems (Bendtsen et al ., 2005) and (iii) the L ipo P server for predicting lipoproteins (Juncker et al ., 2003). PSORT b 3.0 was used to determine subcellular location of the proteins (Yu et al ., 2010).…”

Section: Methodsmentioning

confidence: 99%

Functional distinctness in the exoproteomes of marine Synechococcus

Christie-Oleza

Armengaud

Guérin

et al. 2015

Environmental Microbiology

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SummaryThe exported protein fraction of an organism may reflect its life strategy and, ultimately, the way it is perceived by the outside world. Bioinformatic prediction of the exported pan‐proteome of P rochlorococcus and S ynechococcus lineages demonstrated that (i) this fraction of the encoded proteome had a much higher incidence of lineage‐specific proteins than the cytosolic fraction (57% and 73% homologue incidence respectively) and (ii) exported proteins are largely uncharacterized to date (54%) compared with proteins from the cytosolic fraction (35%). This suggests that the genomic and functional diversity of these organisms lies largely in the diverse pool of novel functions these organisms export to/through their membranes playing a key role in community diversification, e.g. for niche partitioning or evading predation. Experimental exoproteome analysis of marine S ynechococcus showed transport systems for inorganic nutrients, an interesting array of strain‐specific exoproteins involved in mutualistic or hostile interactions (i.e. hemolysins, pilins, adhesins), and exoenzymes with a potential mixotrophic goal (i.e. exoproteases and chitinases). We also show how these organisms can remodel their exoproteome, i.e. by increasing the repertoire of interaction proteins when grown in the presence of a heterotroph or decrease exposure to prey when grown in the dark. Finally, our data indicate that heterotrophic bacteria can feed on the exoproteome of S ynechococcus.

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“…Additionally, the application of refolding strategies to solubilize inclusion bodies, which were formed in significant amounts, were not successful. The key to success was finally to design E. coli optimized DNA sequences devoid of the inherent signal peptide15, 16 but including an N‐terminal His 6 ‐tag, which were expressed using E. coli Shuffle T7LysY as the expression host for promoting disulfide bond formation, and performing the expression in TB medium by a careful selection of the expression conditions. This approach finally led to clear detectable enzyme expression and up to 100‐fold improvement in activity per mg cell‐free extract when employing the natural substrates (Figure S1 and Table S6).…”

mentioning

confidence: 99%

Asymmetric Synthesis of (R)‐1‐Alkyl‐Substituted Tetrahydro‐ß‐carbolines Catalyzed by Strictosidine Synthases

et al. 2018

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Stereoselective methods for the synthesis of tetrahydro‐ß‐carbolines are of significant interest due to the broad spectrum of biological activity of the target molecules. In the plant kingdom, strictosidine synthases catalyze the C−C coupling through a Pictet–Spengler reaction of tryptamine and secologanin to exclusively form the (S)‐configured tetrahydro‐ß‐carboline (S)‐strictosidine. Investigating the biocatalytic Pictet–Spengler reaction of tryptamine with small‐molecular‐weight aliphatic aldehydes revealed that the strictosidine synthases give unexpectedly access to the (R)‐configured product. Developing an efficient expression method for the enzyme allowed the preparative transformation of various aldehydes, giving the products with up to >98 % ee. With this tool in hand, a chemoenzymatic two‐step synthesis of (R)‐harmicine was achieved, giving (R)‐harmicine in 67 % overall yield in optically pure form.

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SignalP 4.0: discriminating signal peptides from transmembrane regions

Cited by 8,260 publications

References 15 publications

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Functional distinctness in the exoproteomes of marine Synechococcus

Asymmetric Synthesis of (R)‐1‐Alkyl‐Substituted Tetrahydro‐ß‐carbolines Catalyzed by Strictosidine Synthases

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