PrediSi: prediction of signal peptides and their cleavage positions

Hiller, Karsten; Grote, Andreas; Scheer, Maurice; Münch, Richard; Jahn, Dieter

doi:10.1093/nar/gkh378

Cited by 445 publications

(350 citation statements)

References 11 publications

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“…It seems rather likely that the sequence following the pelB leader sequence in the anti-MUC1 fragment negatively influences transport and processing or gave rise to the production of insoluble anti-MUC1 in this experiment. The exact cleavage position as predicted by bioinformatics 25 was verified by N-terminal sequencing of the purified scFvs revealing the precise cleavage after amino acid 22, corresponding to the signal peptidase I recognition motiv AXA (AMA).…”

Section: Targeted Translocation To the Periplasma Of Pseudomonas Putimentioning

confidence: 94%

Biomedicals from a soil bug

Dammeyer

2012

Bioengineered

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Section: Targeted Translocation To the Periplasma Of Pseudomonas Putimentioning

confidence: 94%

Biomedicals from a soil bug

Dammeyer

2012

Bioengineered

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“…LOR-107 Overexpression-Sequence analysis of LOR_107 indicated the presence of a 31-amino acid signal peptide, with a cleavage site between a threonine at position 31 and an alanine at position 32 (when combining analysis of the SignalP and PrediSi software (16,17)). Heterologous expression was conducted using pET28a as the expression vector and the full LOR_107 (LOR_107) or truncated LOR_107 (LOR_107d), the latter with the signal peptide deleted.…”

Section: Table 2 Primers Used In This Studymentioning

confidence: 99%

New Family of Ulvan Lyases Identified in Three Isolates from the Alteromonadales Order

Kopel

Helbert

Belnik

et al. 2016

Journal of Biological Chemistry

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Ulvan is the main polysaccharide component of the Ulvales (green seaweed) cell wall. It is composed of disaccharide building blocks comprising 3-sulfated rhamnose linked to D-glucuronic acid (GlcUA), L-iduronic acid (IdoUA), or D-xylose (Xyl). The degradation of ulvan requires ulvan lyase, which catalyzes the endolytic cleavage of the glycoside bond between 3-sulfated rhamnose and uronic acid according to a ␤-elimination mechanism. The first characterized ulvan lyase was identified in Nonlabens ulvanivorans, an ulvanolytic bacterial isolate. In the current study, we have identified and biochemically characterized novel ulvan lyases from three Alteromonadales isolated bacteria. Two homologous ulvan lyases (long and short) were found in each of the bacterial genomes. The protein sequences have no homology to the previously reported ulvan lyases and therefore are the first representatives of a new family of polysaccharide lyases. The enzymes were heterologously expressed in Escherichia coli to determine their mode of action. The heterologous expressed enzymes were secreted into the milieu subsequent to their signal sequence cleavage. An endolytic mode of action was observed and studied using gel permeation chromatography and 1 H NMR. In contrast to N. ulvanivorans ulvan lyase, cleavage occurred specifically at the GlcUA residues. In light of the genomic context and modular structure of the ulvan lyase families identified to date, we propose that two ulvan degradation pathways evolved independently.

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“…Secreted proteins were predicted based on the presence of signal peptide or on non-classical secretion prediction. Signal peptide predictions were made using SignalP 4.1 [62], Phobius [55], and PrediSi [63]. Non-classical secretion was predicted using SecretomeP 1.0 [64].…”

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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PrediSi: prediction of signal peptides and their cleavage positions

Cited by 445 publications

References 11 publications

Biomedicals from a soil bug

Biomedicals from a soil bug

New Family of Ulvan Lyases Identified in Three Isolates from the Alteromonadales Order

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

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