WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms

Chi, Sang-Mun; Nam, Dougu

doi:10.1093/bioinformatics/bts062

Cited by 52 publications

(32 citation statements)

References 18 publications

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“…This covered the cases where homologues of one or two of the A. pullulans varieties were not included in the original list due to annotation errors, or for other reasons. Clusters that contained less than half of the predicted secreted proteins (2274 proteins) were further analysed with online predictors CELLO [171] and WegoLoc [172], the latter with fungal BaCelLo and Höglund databases, with an e-value threshold of 1 × e -10 and a multiplex threshold of 1. The proteins were considered as secreted if they were predicted as such by at least three of four methods (our method described above, and three online predictors).…”

Section: Methodsmentioning

confidence: 99%

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species

et al. 2014

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BackgroundAureobasidium pullulans is a black-yeast-like fungus used for production of the polysaccharide pullulan and the antimycotic aureobasidin A, and as a biocontrol agent in agriculture. It can cause opportunistic human infections, and it inhabits various extreme environments. To promote the understanding of these traits, we performed de-novo genome sequencing of the four varieties of A. pullulans.ResultsThe 25.43-29.62 Mb genomes of these four varieties of A. pullulans encode between 10266 and 11866 predicted proteins. Their genomes encode most of the enzyme families involved in degradation of plant material and many sugar transporters, and they have genes possibly associated with degradation of plastic and aromatic compounds. Proteins believed to be involved in the synthesis of pullulan and siderophores, but not of aureobasidin A, are predicted. Putative stress-tolerance genes include several aquaporins and aquaglyceroporins, large numbers of alkali-metal cation transporters, genes for the synthesis of compatible solutes and melanin, all of the components of the high-osmolarity glycerol pathway, and bacteriorhodopsin-like proteins. All of these genomes contain a homothallic mating-type locus.ConclusionsThe differences between these four varieties of A. pullulans are large enough to justify their redefinition as separate species: A. pullulans, A. melanogenum, A. subglaciale and A. namibiae. The redundancy observed in several gene families can be linked to the nutritional versatility of these species and their particular stress tolerance. The availability of the genome sequences of the four Aureobasidium species should improve their biotechnological exploitation and promote our understanding of their stress-tolerance mechanisms, diverse lifestyles, and pathogenic potential.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-549) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species

et al. 2014

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“…28 Subcellular localizations were added in Table 1, if at least three programs predicted the same localization of a protein at subcellular level.…”

Section: Prediction Of Subcellular Localizationmentioning

confidence: 99%

Expression Profiling of Starchy Endosperm Metabolic Proteins at 21 Stages of Wheat Grain Development

Tasleem-Tahir

Nadaud

Chambon³

et al. 2012

J. Proteome Res.

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Proteomic analysis of albumins and globulins (alg) present in starchy endosperm of wheat (Triticum aestivum cv Récital), at 21 stages of grain development, led to the identification of 487 proteins. Four main developmental phases of these metabolic proteins, with three subphases in phase three and two in phase four, were shown. Hierarchical cluster analysis revealed nine major expression profiles throughout grain development. Classification of identified proteins in 17 different biochemical functions provided a uniform picture of temporal coordination among cellular processes. Proteins involved in cell division, transcription/translation, ATP interconversion, protein synthesis, protein transport, along with amino acid, lipid, carbohydrate and nucleotide metabolisms were highly expressed in early and early mid stages of development. Protein folding, cytoskeleton, and storage proteins peaked during the middle of grain development, while in later stages stress/defense, folic acid metabolism, and protein turn over were the abundant functional categories. Detailed analysis of stress/defense enzymes revealed three different evolutionary profiles. A global map with their predicted subcellular localizations and placement in grain developmental scale was constructed. The present study of complete grain development enriched our knowledge on proteome expression of alg, successively from endosperm cell division and differentiation to programmed cell death.

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“…Therefore, many programs have been developed to predict the function [6] and the subcellular localization of a targeted protein. [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] Some of these programs provide additional information, e.g., protein-protein interactions [14], [19] or three-dimensional structure comparisons [18], although most just attempt to determine the subcellular compartment of the targeted protein. Additionally, studies have found that the more similar protein sequences are, the greater the likelihood that proteins with similar sequences will be found in the same subcellular localization [17], [22].…”

Section: Introductionmentioning

confidence: 99%

“…A hybrid approach combining machine learning and homology searching also can provide accurate subcellular-localization predictions. [22] The reason why certain computational tools provide improved subcellular localization prediction appears to be that GO information [8], [9], [10], [12], [15], [20], [21] or a homology-based modular structure comparison [23] is included in the prediction routine. However, if homologs for the protein of interest are not GO annotated or if a signature(s) and sequences similar to that of the query protein are not found in a relevant, searched database, such as InterPro [24], then a prediction cannot made.…”

Section: Introductionmentioning

confidence: 99%

CELLO2GO: A Web Server for Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation

et al. 2014

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CELLO2GO (http://cello.life.nctu.edu.tw/cello2go/) is a publicly available, web-based system for screening various properties of a targeted protein and its subcellular localization. Herein, we describe how this platform is used to obtain a brief or detailed gene ontology (GO)-type categories, including subcellular localization(s), for the queried proteins by combining the CELLO localization-predicting and BLAST homology-searching approaches. Given a query protein sequence, CELLO2GO uses BLAST to search for homologous sequences that are GO annotated in an in-house database derived from the UniProt KnowledgeBase database. At the same time, CELLO attempts predict at least one subcellular localization on the basis of the species in which the protein is found. When homologs for the query sequence have been identified, the number of terms found for each of their GO categories, i.e., cellular compartment, molecular function, and biological process, are summed and presented as pie charts representing possible functional annotations for the queried protein. Although the experimental subcellular localization of a protein may not be known, and thus not annotated, CELLO can confidentially suggest a subcellular localization. CELLO2GO should be a useful tool for research involving complex subcellular systems because it combines CELLO and BLAST into one platform and its output is easily manipulated such that the user-specific questions may be readily addressed.

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WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms

Abstract: Supplementary data is available at http://www.btool.org/WegoLoc.

Cited by 52 publications

References 18 publications

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species

Expression Profiling of Starchy Endosperm Metabolic Proteins at 21 Stages of Wheat Grain Development

CELLO2GO: A Web Server for Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation

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