Protter: interactive protein feature visualization and integration with experimental proteomic data

Omasits, Ulrich; Ahrens, Christian H.; Müller, Sebastian; Wollscheid, Bernd

doi:10.1093/bioinformatics/btt607

Cited by 1,135 publications

(919 citation statements)

References 26 publications

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“…1A) are similar to known proteins or contain any described motifs. Protter analysis (19) predicted that all genes of variable region 2 (V2) (Fig. 1A) of both strains encode transmembrane proteins, with either three or four predicted membrane spanning domains per protein (Fig.…”

Section: Resultsmentioning

confidence: 99%

Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species

Chatzidaki‐Livanis

Geva‐Zatorsky

Comstock

2016

Proc. Natl. Acad. Sci. U.S.A.

187

176

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Type VI secretion systems (T6SSs) are multiprotein complexes best studied in Gram-negative pathogens where they have been shown to inhibit or kill prokaryotic or eukaryotic cells and are often important for virulence. We recently showed that T6SS loci are also widespread in symbiotic human gut bacteria of the order Bacteroidales, and that these T6SS loci segregate into three distinct genetic architectures (GA). GA1 and GA2 loci are present on conserved integrative conjugative elements (ICE) and are transferred and shared among diverse human gut Bacteroidales species. GA3 loci are not contained on conserved ICE and are confined to Bacteroides fragilis. Unlike GA1 and GA2 T6SS loci, most GA3 loci do not encode identifiable effector and immunity proteins. Here, we studied GA3 T6SSs and show that they antagonize most human gut Bacteroidales strains analyzed, except for B. fragilis strains with the same T6SS locus. A combination of mutation analyses, trans-protection analyses, and in vitro competition assays, allowed us to identify novel effector and immunity proteins of GA3 loci. These proteins are not orthologous to known proteins, do not contain identified motifs, and most have numerous predicted transmembrane domains. Because the genes encoding effector and immunity proteins are contained in two variable regions of GA3 loci, GA3 T6SSs of the species B. fragilis are likely the source of numerous novel effector and immunity proteins. Importantly, we show that the GA3 T6SS of strain 638R is functional in the mammalian gut and provides a competitive advantage to this organism.Bacteroides | T6SS | gut microbiota | bacterial competition | type VI secretion

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Section: Resultsmentioning

confidence: 99%

Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species

Chatzidaki‐Livanis

Geva‐Zatorsky

Comstock

2016

Proc. Natl. Acad. Sci. U.S.A.

187

176

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“…Gene ontology was investigated with FunRich v3.1.3 using the Gene Ontology Database [24,25]. The peptides identified by mass spectrometry were visualised using Protter [26] with membrane orientations as specified in UniProt annotations [27]. Data has been uploaded to EVpedia [28].…”

Section: Methodsmentioning

confidence: 99%

Enrichment of extracellular vesicles from human synovial fluid using size exclusion chromatography

Foers

Chatfield

Dagley

et al. 2018

J of Extracellular Vesicle

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As a complex biological fluid, human synovial fluid (SF) presents challenges for extracellular vesicle (EV) enrichment using standard methods. In this study of human SF, a size exclusion chromatography (SEC)-based method of EV enrichment is shown to deplete contaminants that remain after standard ultracentrifugation-based enrichment methods. Specifically, considerable levels of serum albumin, the high-density lipoprotein marker, apolipoprotein A-I, fibronectin and other extracellular proteins and debris are present in EVs prepared by differential ultracentrifugation. While the addition of a sucrose density gradient purification step improved purification quality, some contamination remained. In contrast, using a SEC-based approach, SF EVs were efficiently separated from serum albumin, apolipoprotein A-I and additional contaminating proteins that co-purified with high-speed centrifugation. Finally, using high-resolution mass spectrometry analysis, we found that residual contaminants which remain after SEC, such as fibronectin and other extracellular proteins, can be successfully depleted by proteinase K. Taken together, our results highlight the limitations of ultracentrifugation-based methods of EV isolation from complex biological fluids and suggest that SEC can be used to obtain higher purity EV samples. In this way, SEC-based methods are likely to be useful for identifying EV-enriched components and improving understanding of EV function in disease.

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“…A, graphic depiction of recombinant CCL28 with cysteines highlighted. The image was generated in Protter (34). B, MS1 and MS2 spectra of the dipeptide resulting from a disulfide bridge between Cys-30 and Cys-80.…”

Section: Disulfide Bond Mapping Of Ccl28 By Mass Spectrometry-mentioning

confidence: 99%

Structure-Function Analysis of CCL28 in the Development of Post-viral Asthma

Thomas

Buelow

Nevins

et al. 2015

Journal of Biological Chemistry

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Background: CCL28 is associated with the pathogenesis of acute post-viral asthma. Results: In the absence of viral infection, natively folded CCL28 can induce asthma pathology, whereas unfolded CCL28 cannot. Conclusion:The structure of CCL28 is critical for its role in asthma pathogenesis. Significance: Inhibition of CCL28 presents a novel therapeutic option for the prevention of post-viral asthma.

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Protter: interactive protein feature visualization and integration with experimental proteomic data

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 1,135 publications

References 26 publications

Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species

Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species

Enrichment of extracellular vesicles from human synovial fluid using size exclusion chromatography

Structure-Function Analysis of CCL28 in the Development of Post-viral Asthma

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