Improved Prediction of Signal Peptides: SignalP 3.0

Bendtsen, Jannick Dyrløv; Nielsen, Henrik; Heijne, Gunnar von; Brunak, Søren

doi:10.1016/j.jmb.2004.05.028

Cited by 5,767 publications

(1,721 citation statements)

References 43 publications

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“…In addition, classical excretorysecretory (ES) proteins of S. haematobium were predicted (on the basis of the presence of a signal peptide at the N terminus) using SignalP v.3.0 (ref. 40; using both the neural network and hidden Markov models) and the absence of a transmembrane domain using TMHMM 41 , and by BLASTp 42 homology-searching of the validated signal peptide database (SPD) 43 and an ES database containing published proteomic data for nematodes (Brugia malayi and Meloidogyne incognita) and trematodes (S. mansoni, S. japonicum, O. viverrini and F. hepatica) 13,14,[44][45][46][47][48][49][50] . The secondary structure of genes specific to S. haematobium were predicted using PSIPRED 51 .…”

Section: Methodsmentioning

confidence: 99%

Whole-genome sequence of Schistosoma haematobium

et al. 2012

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Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide 1 . No vaccines are available, and treatment relies on one drug, praziquantel 2 . Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer 1,3 and as a predisposing factor for HIV/AIDS 4,5 . The parasite is transmitted to humans from freshwater snails 1 . Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease 6 and induce squamous cell carcinoma 7 . Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites 8,9 . We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.

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Section: Methodsmentioning

confidence: 99%

Whole-genome sequence of Schistosoma haematobium

et al. 2012

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“…Partial sequences were excluded and the remaining genes were regarded as CRN proteins. Secretion signals of serine peptidases and CRN proteins were identified using three tools (SignalP [34], TargetP [35], and iPSORT [36]) with default settings. The conserved N-terminal profiles were generated using WebLogo http://weblogo.berkeley.edu.…”

Section: Methodsmentioning

confidence: 99%

Evidence for acquisition of virulence effectors in pathogenic chytrids

et al. 2011

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BackgroundThe decline in amphibian populations across the world is frequently linked to the infection of the chytrid fungus Batrachochytrium dendrobatidis (Bd). This is particularly perplexing because Bd was only recently discovered in 1999 and no chytrid fungus had previously been identified as a vertebrate pathogen.ResultsIn this study, we show that two large families of known virulence effector genes, crinkler (CRN) proteins and serine peptidases, were acquired by Bd from oomycete pathogens and bacteria, respectively. These two families have been duplicated after their acquisition by Bd. Additional selection analyses indicate that both families evolved under strong positive selection, suggesting that they are involved in the adaptation of Bd to its hosts.ConclusionsWe propose that the acquisition of virulence effectors, in combination with habitat disruption and climate change, may have driven the Bd epidemics and the decline in amphibian populations. This finding provides a starting point for biochemical investigations of chytridiomycosis.

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“…For tree reconstruction, we first applied PROTTEST (Abascal et al 2005) to estimate the optimal model of amino acid substitution (consistently found to be WAGCICG), then calculated a maximum likelihood tree using PHYML (Guindon & Gascuel 2003) with this model (the proportion of invariant sites calculated from the alignment, and four rate categories with a gamma distribution parameter estimated from the data). Signal sequences were predicted using SIGNALP v. 3.0 (http://www.cbs.dtu.dk/ services/SignalP-3.0/; Bendtsen et al 2004) and SIGCLEAVE (http://bioweb.pasteur.fr/seqanal/interfaces/sigcleave.html). Homopolymeric runs were accessed at the TRIPS database (http://www.ncl-india.org/trips/index.html; Katti et al 2000), compiled from SWISSPROT Release 38, followed by checking updated sequences in SWISSPROT Release 44.…”

Section: Methodsmentioning

confidence: 99%

An unusual choanoflagellate protein released by Hedgehog autocatalytic processing

Snell

Brooke

Taylor³

et al. 2005

Proc. R. Soc. B.

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Hedgehog proteins are important cell-cell signalling proteins utilized during the development of multicellular animals. Members of the hedgehog gene family have not been detected outside the Metazoa, raising unanswered questions about their evolutionary origin. Here we report a highly unusual hedgehog-related gene from a choanoflagellate, a close unicellular relative of the animals. The deduced C-terminal domain, Hoglet-C, is homologous to the autocatalytic domain of Hedgehog proteins and is predicted to function in autocatalytic cleavage of the precursor peptide. In contrast, the N-terminal Hoglet-N peptide has no similarity to the signalling peptide of Hedgehog (Hh-N). Instead, Hoglet-N is deduced to be a secreted protein with an enormous threonine-rich domain of unprecedented size and purity (over 200 threonine residues) and two polysaccharide-binding domains. Structural modelling reveals that these domains have a novel combination of features found in cellulose-binding domains (CBD) of types IIa and IIb, and are expected to bind cellulose. We propose that the two CBD domains enable Hoglet-N to bind to plant matter, tethering an amorphous nucleophilic anchor, facilitating transient adhesion of the choanoflagellate cell. Since Hh-C and Hoglet-C are homologous, but Hh-N and Hoglet-N are not, we argue that metazoan hedgehog genes evolved by fusion of two distinct genes.

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Improved Prediction of Signal Peptides: SignalP 3.0

Cited by 5,767 publications

References 43 publications

Whole-genome sequence of Schistosoma haematobium

Whole-genome sequence of Schistosoma haematobium

Evidence for acquisition of virulence effectors in pathogenic chytrids

An unusual choanoflagellate protein released by Hedgehog autocatalytic processing

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