Extensive feature detection of N-terminal protein sorting
  signals

Bannai, Hideo; Tamada, Yoshinori; Maruyama, Osamu; Nakai, Kenta; Miyano, Satoru

doi:10.1093/bioinformatics/18.2.298

Cited by 677 publications

(513 citation statements)

References 18 publications

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“…Another possibility is that they have distinct functions reflected by different spatial and temporal regulation. 71,72 It would be of interest to investigate the spatial and temporal regulation of AtBAG6 paralogues to elucidate their specific molecular functions.…”

Section: Discussionmentioning

confidence: 99%

AtBAG6, a novel calmodulin-binding protein, induces programmed cell death in yeast and plants

et al. 2005

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Calmodulin (CaM) influences many cellular processes by interacting with various proteins. Here, we isolated AtBAG6, an Arabidopsis CaM-binding protein that contains a central BCL-2-associated athanogene (BAG) domain. In yeast and plants, overexpression of AtBAG6 induced cell death phenotypes consistent with programmed cell death (PCD). Recombinant AtBAG6 had higher affinity for CaM in the absence of free Ca 2 þ than in its presence. An IQ motif (IQXXXRGXXXR, where X denotes any amino-acid) was required for Ca 2 þ -independent CaM complex formation and single amino-acid changes within this motif abrogated both AtBAG6-activated CaM-binding and cell death in yeast and plants. A 134-amino-acid stretch, encompassing both the IQ motif and BAG domain, was sufficient to induce cell death. Agents generating oxygen radicals, which are known to be involved in plant PCD, specifically induced the AtBAG6 transcript. Collectively, these results suggest that AtBAG6 is a stress-upregulated CaM-binding protein involved in plant PCD.

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Section: Discussionmentioning

confidence: 99%

AtBAG6, a novel calmodulin-binding protein, induces programmed cell death in yeast and plants

et al. 2005

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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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“…The sets of protein sequences encoded in the nuclear genomes of Arabidopsis and rice were analyzed using each of the four predictors iPSORT (Bannai et al, 2002), TargetP (Emanuelsson et al, 2000), PCLR (Schein et al, 2001) and Predotar (http://www.inra.fr/ predotar/). Sensitivity and specificity of cTP predictions were examined by using the 4500 protein test set described above.…”

Section: Identification Of Ctps and Evaluation Of The Accuracy Of Prementioning

confidence: 99%

“…The specificity and sensitivity of the four cTP predictors iPSORT (Bannai et al, 2002), TargetP (Emanuelsson et al, 2000), PCLR (Schein et al, 2001) and Predotar (http:// www.inra.fr/predotar/) have been determined based on a test set of 4500 proteins whose subcellular localization has been experimentally determined (see http://www.mpiz-koeln. mpg.de/~leister/chloroplast _ 2.html).…”

Section: Accuracy Of Ctp Predictors and Of Their Combinationsmentioning

confidence: 99%

“…Furthermore, their secondary structure is not well characterized, and the degree of sequence conservation observed around the site cleaved by the stromal processing peptidase is quite low (Gavel and von Heijne, 1990;Emanuelsson et al, 1999). Previous approaches to the prediction of cTPs have employed the expert systems PSORT (Nakai and Kanehisa, 1992;Nakai and Horton, 1999) and iPSORT (Bannai et al, 2002), neural networks (ChloroP: Emanuelsson et al, 1999;TargetP: Emanuelsson et al, 2000; and Predotar: http:// www.inra.fr/predotar/) or principal component analysis (PCLR: Schein et al, 2001), but more sophisticated systems should improve the accuracy of cTP prediction.…”

Section: Introductionmentioning

confidence: 99%

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An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice

Richly¹,

Leister²

2004

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Proteins that form part of the chloroplast proteome can be identified by computational prediction of the N-terminal presequences (chloroplast transit peptides, cTPs) of their cytoplasmic precursor proteins. The accuracy of four different cTP predictors has been evaluated on a test set of 4500 proteins whose subcellular localization is known, and was found to be substantially lower than previously reported. A combination of cTP prediction programs was superior to any one of the predictors alone. This combination was employed to estimate the size and composition of the chloroplast proteomes of Arabidopsis and rice, and about 2,100 (Arabidopsis thaliana) and 4800 (Oryza sativa) different chloroplast proteins with a cTP are predicted to be encoded by their nuclear genomes. A subset of around 900 chloroplast proteins, predominantly derived from the cyanobacterial endosymbiont and with functions mostly related to metabolism, energy and transcription, is shared by the two species. This points to the existence of both conserved nucleus-encoded chloroplast proteins that are predominantly of prokaryotic origin, and a large fraction of taxon-specific chloroplast-targeted proteins, in flowering plants. D

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Extensive feature detection of N-terminal protein sorting signals

Abstract: We have succeeded in finding rules whose prediction accuracies come close to that of TargetP, while still retaining a very simple and interpretable form. We also discuss and interpret the discovered rules.

Cited by 677 publications

References 18 publications

AtBAG6, a novel calmodulin-binding protein, induces programmed cell death in yeast and plants

AtBAG6, a novel calmodulin-binding protein, induces programmed cell death in yeast and plants

Evidence for acquisition of virulence effectors in pathogenic chytrids

An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice

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