PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

Yu, Nancy; Wagner, James; Laird, Matthew R.; Melli, Gabor; Rey, Sébastien; Lo, Raymond; Dao, Phuong; Sahinalp, S. Cenk; Ester, Martin; Foster, Leonard J.; Brinkman, Fiona S. L.

doi:10.1093/bioinformatics/btq249

Cited by 2,149 publications

(1,730 citation statements)

References 33 publications

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“…PSORT b 3.0 was used to determine subcellular location of the proteins (Yu et al ., 2010). Local BLASTp analyses were done with the B io E dit BLAST tool v.7.0.5.3 (Hall, 1999) using default parameters and an E‐value cut‐off < 10 −20 .…”

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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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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“…Non-lipoproteins were then analyzed for transmembrane domain prediction using TMHMM v.2.0 [54], Phobius [55], HMMTOP [56], CW-PRED [57], and HMM-TM [58]. Non-transmembrane proteins were further analyzed for subcellular localization using PSORTb v. 3.0.2 [59], iLoc-Gpos [60], and CELLO v.2.5 [61]. …”

Section: Methodsmentioning

confidence: 99%

Comparative proteomics of twoMycoplasma hyopneumoniaestrains andMycoplasma flocculareidentified potential porcine enzootic pneumonia determinants

et al. 2018

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Mycoplasma hyopneumoniae and Mycoplasma flocculare are genetically similar bacteria, which coinhabit the porcine respiratory tract. These mycoplasmas share most of the known virulence factors, but, while M. hyopneumoniae causes porcine enzootic pneumonia (PEP), M. flocculare is a commensal species. To identify potential PEP determinants and provide novel insights on mycoplasma-host interactions, the whole cell proteomes of two M. hyopneumoniae strains, one pathogenic (7448) and other non-pathogenic (J), and M. flocculare were compared. A cell fractioning approach combined with mass spectrometry (LC-MS/MS) proteomics was used to analyze cytoplasmic and surface-enriched protein fractions. Average detection of ~ 50% of the predicted proteomes of M. hyopneumoniae 7448 and J, and M. flocculare was achieved. Many of the identified proteins were differentially represented in M. hyopneumoniae 7448 in comparison to M. hyopneumoniae J and M. flocculare, including potential PEP determinants, such as adhesins, proteases, and redox-balancing proteins, among others. The LC-MS/MS data also provided experimental validation for several genes previously regarded as hypothetical for all analyzed mycoplasmas, including some coding for proteins bearing virulence-related functional domains. The comprehensive proteome profiling of two M. hyopneumoniae strains and M. flocculare provided tens of novel candidates to PEP determinants or virulence factors, beyond those classically described.

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“…The bacterial localization prediction tool, PSORTb version 3.0.2 (http://www.psort.org/psortb/) [35], was used to determine the topology and domain structure of SpsQ and SpsP. SpsQ modeling and binding site prediction were performed using Protein Homology/analogY Recognition Engine V 2.0 (Phyre 2 ) (http://www.sbg.bio.ic.ac.uk/phyre2) [36], and the 3DLigandSite (http://www.sbg.bio.ic.ac.uk/3dligandsite/) [37], using SpA as a basis to predict the IgBDs in each domain.…”

Section: Methodsmentioning

confidence: 99%

Characterization of recombinant wild-type and nontoxigenic protein A from Staphylococcus pseudintermedius

2018

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Background: Staphylococcus pseudintermedius is an opportunistic pathogen that is the major cause of pyoderma affecting dogs. Conventional antimicrobial treatment for infections caused by this organism have failed in recent years due to widespread resistance and alternative treatment strategies are a high priority. Protein A encoded in Staphylococcus aureus by spa protects the bacterium by binding IgG and acts as a superantigen. Staphylococcus pseudintermedius possess two genes orthologous to S. aureus spa, spsP, and spsQ. Methods: SpsQ and SpsQ-M, a non-toxigenic SpsQ, were cloned and expressed as recombinant proteins and their cytotoxic effect on canine B cells was measured. The neutralizing ability of antibody raised against them in clinically healthy dogs was evaluated. Results: S. pseudintermedius SpsQ induced apoptosis of canine B cells. Specific amino acid substitutions diminished SpsQ-M binding to immunoglobulin and its super-antigenic activity, while its antigenicity was maintained. This recombinant, non-toxigenic S. pseudintermedius SpsQ stimulated the production of antibodies in dogs that specifically reacted with SpsQ and greatly diminished its cytotoxic effect on canine B cells. Conclusions: The production of neutralizing antibody suggests that attenuated, non-toxic SpsQ produced in this study is a good candidate for inclusion in a vaccine for use in the treatment and prevention of S. pseudintermedius infections.Abbreviations: SpA: Staphylococcus aureus protein A; SpsP: Staphylococcus pseudintermedius protein A; SpsQ: Staphylococcus pseudintermedius protein A; SpsQ-M: attenuated Staphylococcus pseudintermedius protein A; MRSP: methicillin resistant Staphylococcus pseudintermedius; IgA: immunoglobulin A; IgG: immunoglobulin G; IgM: immunoglobulin M; VH: variable region of immunoglobulin heavy chain; IgBD: immunoglobulin binding domains; MFI: mean fluorescent intensity; SEM: standard error of the mean; PBMC: Peripheral blood mononuclear cells; CD21: complement receptor type 2; ST: Sequence type; OD: Optical density; ORF: open reading frame; PBS: Phosphate buffered saline; Tween 20: Polyethylene glycol sorbitan monolaurate 20; HRP: horseradish peroxidase; TMB- 3,3',5,5'-Tetramethylbenzidine

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PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

Cited by 2,149 publications

References 33 publications

Functional distinctness in the exoproteomes of marine Synechococcus

Functional distinctness in the exoproteomes of marine Synechococcus

Comparative proteomics of twoMycoplasma hyopneumoniaestrains andMycoplasma flocculareidentified potential porcine enzootic pneumonia determinants

Characterization of recombinant wild-type and nontoxigenic protein A from Staphylococcus pseudintermedius

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