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PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization

Nakai, Kenta, Horton, Paul·1999·Trends in Biochemical Sciences

DOI 10.1016/s0968-0004(98)01336-x

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A new method for predicting signal sequence cleavage sites
von HEIJNE, G. (1986) · Nucleic Acids Research · doi:10.1093/nar/14.11.4683 · Cited by 4,473
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The detection and classification of membrane-spanning proteins
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Using neural networks for prediction of the subcellular location of proteins
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Research works printed but not linked: 4

Horton, 1996, Intelligent Systems for Molecular Biology, 4, 109
Horton, 1997, Intelligent Systems for Molecular Biology, 5, 147
Nakai, K.(1996) in Genome Informatics 1996 (Vol. 7) (Akutsu, T. et al.., eds), pp. 72-81, Universal Academy Press
Bairoch, 1997, Nucleic Acids Res., 25, 217, 10.1093/nar/25.1.217 · DOI

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“The PSORT program, which was developed to predict subcellular localization of proteins by Nakai and Horton (1999), predicts that the shep-GRP is localized to the vacuole with a certainty of 0.90 and contains a cleavable N-terminal signal sequence.”
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“This number is considerably higher than the 76 PSORT I-predicted lipoproteins (Nakai and Horton 1999) annotated at http://www.pseudomonas.com, likely due to the improved identification algorithm of LipoP.”
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“This is in agreement with the prediction of the PSORT algorithm (27), which suggests a type Ib orientation for MAHRP1.”
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“Analysis of proteins was carried out using previously described web-based analysis tools (28, 29, 43 , 46, 60).”
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“The sequence of the predicted proteins encoded by these 21 full-length cDNAs were analyzed by BLASTP for similarity to known proteins, Signal P (Nielsen et al. 1997) for the presence of signal peptides, and PSORT II (Nakai and Horton 1999) to predict subcellular localizations.”
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“The prediction methods in this group focus on mining informative features consisting of GO terms [2-5], sorting signals [6,7], amino acid composition (AAC) [8-10], k -peptide encoding vector [7,11-14], physicochemical properties of amino acids [15-17], and fusing AAC and physicochemical properties…”
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“Prediction of subcellular localization of these proteins using pSORT and TargetP programmes [34–36] indicated that 13 sHsp proteins are located in the cytoplasm and one each in the mitochondria, ER, plastid and peroxisome.”
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“The SP cleavage site was predicted using both ‘‘PSORT II’’ (http://psort.ims.u-tokyo.ac.jp/) (Nakai and Horton 1999) and ‘‘SignalP 3.0’’ (http:// www.cbs.dtu.dk/services/SignalP/; hidden Markov model) (Emanuelsson et al. 2007).”
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Background
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“Our first hierarchal method, LocTree (Nair and Rost, 2005), used a concept initially introduced by the work on PSORT carried by Paul Horton and initiated by Kenta Nakai and Minoru Kanehisa (Horton et al., 2007; Nakai and Horton, 1999; Nakai and Kanehisa, 1991).”
Method
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Method
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Method
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An overview on predicting the subcellular location of a protein.
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“According to the prediction of protein localisation in cells (Nakai and Horton, 1999), Pse1p is localised in the ER, which is in agreement with the microsomal localisation of fatty acid elongation.”
Result
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“analyzed using the programs BLAST (3), PSORT (44), InterProScan (43), and”
Method
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“A prediction program for protein localization, PSORT, indicated that all three contain signal peptides for secretion and up to five potential N-glycosylation sites.”
Method
Human secretory signal peptide description by hidden Markov model and generation of a strong artificial signal peptide for secreted protein expression
Barash, S., Wang, W., & Shi, Y. (2002) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(02)00566-1 · Cited by 108
5 S rRNA and tRNA Import into Human Mitochondria
Entelis, N., Kolesnikova, O., Dogan, S., Martin, R. P., & Tarassov, I. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m103906200 · Cited by 113
High performance system for signal peptide prediction: SOSUIsignal
Gomi, M., Sonoyama, M., & Mitaku, S. (2004) · Chem-Bio Informatics Journal · doi:10.1273/cbij.4.142 · Cited by 108
d ‐Glucose sensing by a plasma membrane regulator of G signaling protein, AtRGS1
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“jp/) to localize to the plasma membrane or extracellularly [48–55].”
Background
Genome-Based Bioinformatic Selection of ChromosomalBacillus anthracisPutative Vaccine Candidates Coupled with Proteomic Identification of Surface-Associated Antigens
Ariel, N., Zvi, A., Makarova, K. S., Chitlaru, T., Elhanany, E., Velan, B., Cohen, S. B., Friedlander, A. M., & Shafferman, A. (2003) · Infection and Immunity · doi:10.1128/iai.71.8.4563-4579.2003 · Cited by 107
RECQL4 is essential for the transport of p53 to mitochondria in normal human cells in the absence of exogenous stress
De, S., Kumari, J., Mudgal, R., Modi, P., Gupta, S., Futami, K., Goto, H., Lindor, N. M., Furuichi, Y., Mohanty, D., et al. (2012) · Journal of Cell Science · doi:10.1242/jcs.101501 · Cited by 107
“Web-based tools Four web-based tools: Target P (Emanuelsson et al., 2007), PSORT (Nakai and Horton, 1999), MitoProt (Claros and Vincens, 1996) and iPSORT (Bannai et al., 2002) were used to predict the MLS in RECQL4.”
BackgroundMethod
Rice Ovate Family Protein 2 ( OFP2 ) alters hormonal homeostasis and vasculature development
Schmitz, A. J., Begcy, K., Sarath, G., et al. (2015) · Plant Science · doi:10.1016/j.plantsci.2015.10.011 · Cited by 107
Identification of a novel mouse membrane-bound family 1 glycosidase-like protein, which carries an atypical active site structure
Ito, S., Fujimori, T., Hayashizaki, Y., & Nabeshima, Y. (2002) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/s0167-4781(02)00281-6 · Cited by 108
Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments
Tanaka, N., Fujita, M., Handa, H., et al. (2004) · Molecular Genetics and Genomics · doi:10.1007/s00438-004-1002-z · Cited by 107
“In the mitochondrial proteome of Arabidopsis, a comparison of the performance of the prediction programs Mitoprot (Claros and Vincens 1996), PSORT (Nakai and Horton 1999) and TargetP suggested that no one program provided a complete, high-confidence analysis of the nucleus-encoded fractions of the plant mitochondrial…”
ResultInfluential
Functional Identification of Conjugation and Replication Regions of the Tetracycline Resistance Plasmid pCW3 fromClostridium perfringens
Bannam, T. L., Teng, W. L., Bulach, D., et al. (2006) · Journal of Bacteriology · doi:10.1128/jb.00298-06 · Cited by 107
“Sequence data were analyzed using Sequencher version 3.0 (Gene Codes Corporation), and potential genes were identified using Gene-MarkS (11), in conjunction with the Sanger Institute freeware Artemis, release 6. Putative gene products were analyzed using PSI-BLAST (6, 7), TopPred (14), and PSORT Prediction ( 38 ).”
MethodInfluential
Screen for ISG15-crossreactive Deubiquitinases
Catic, A., Fiebiger, E., Korbel, G. A., Blom, D., Galardy, P. J., & Ploegh, H. L. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000679 · Cited by 108
“USP3 is predicted to be a nuclear protein [34] and USP36 was Figure 4.”
TARGET: a new method for predicting protein subcellular localization in eukaryotes
Guda, C., & Subramaniam, S. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti650 · Cited by 106
A dual positional specific lipoxygenase functions in the generation of flavor compounds during climacteric ripening of apple
Schiller, D., Contreras, C., Vogt, J., et al. (2015) · Horticulture Research · doi:10.1038/hortres.2015.3 · Cited by 106
A H2O2-producing glyoxal oxidase is required for filamentous growth and pathogenicity in Ustilago maydis
Leuthner, B., Aichinger, C., Oehmen, E., et al. (2004) · Molecular Genetics and Genomics · doi:10.1007/s00438-004-1085-6 · Cited by 106
“Interestingly, for Glo3 the iPSORT algorithm (Nakai and Horton 1999) predicted a cytoplasmic localization of the catalytic domain, while the catalytic portion of Glo1 is most probably extracellular.”
Method
Functional Analysis of the Purified Anandamide-generating Phospholipase D as a Member of the Metallo-β-lactamase Family
Wang, J., Okamoto, Y., Morishita, J., Tsuboi, K., Miyatake, A., & Ueda, N. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m512359200 · Cited by 106
Plant organelle proteomics: Collaborating for optimal cell function
Agrawal, G. K., Bourguignon, J., Rolland, N., Ephritikhine, G., Ferro, M., Jaquinod, M., Alexiou, K. G., Chardot, T., Chakraborty, N., Jolivet, P., et al. (2010) · Mass Spectrometry Reviews · doi:10.1002/mas.20301 · Cited by 111
Identification and characterization of human cardiolipin synthase
Houtkooper, R. H., Akbari, H., van LENTHE, H., Kulik, W., Wanders, R. J. A., Frentzen, M., & Vaz, F. M. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.04.054 · Cited by 106
“jp) [27] and belongs to the CDPalcohol phosphatidyltransferase class-I family like the CLS”
Background
Predicting Protein Cellular Localization Using a Domain Projection MethodPreprint
Mott, R., Schultz, J., Bork, P., & Ponting, C. P. (2002) · Genome Research · doi:10.1101/gr.96802 · Cited by 105
Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features
Zhou, H., Yang, Y., & Shen, H. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw723 · Cited by 105
Molecular Cloning and Characterization of β-Expansin Gene Related to Root Hair Formation in Barley
Kwaśniewski, M., & Szarejko, I. (2006) · PLANT PHYSIOLOGY · doi:10.1104/pp.106.078626 · Cited by 105
“Plant Physiol 123: 563–573 Nakai K, Horton P (1999) PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization.”
Method
Contribution of Peroxisomes to Secondary Metabolism and Pathogenicity in the Fungal Plant Pathogen Alternaria alternata
Imazaki, A., Tanaka, A., Harimoto, Y., et al. (2010) · Eukaryotic Cell · doi:10.1128/ec.00369-09 · Cited by 105
“A PSORT II (40) analysis of the amino acid sequences of Akt1, Akt2, and Akt3 identified PTS1-like tripeptides SKI, SKL, and PKL, respectively, at the C-terminal ends of these proteins, suggesting that these enzymes are located in peroxisomes (55, 56).”
Characterization of seed‐specific benzoyloxyglucosinolate mutations in Arabidopsis thaliana
Kliebenstein, D. J., D’Auria, J. C., Behere, A. S., et al. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03205.x · Cited by 104
“Moreover, the protein targeting prediction programs PSORT (Nakai and Horton, 1999) and TARGETP (Emanuelsson et al.”
Comparative Proteomics Profiling of a Phospholamban Mutant Mouse Model of Dilated Cardiomyopathy Reveals Progressive Intracellular Stress Responses
Gramolini, A. O., Kislinger, T., Alikhani‐Koupaei, R., Fong, V., Thompson, N. J., Isserlin, R., Sharma, P., Oudit, G. Y., Trivieri, M. G., Fagan, A., et al. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700245-mcp200 · Cited by 104
“Cross-referencing On-line Data Sets—Protein predictions for secretion were made according to the on-line predication algorithm PSort II (27) and the Secreted Protein Database (28) available publicly.”
BackgroundMethod
Nuclear Translocated Ehrlichia chaffeensis Ankyrin Protein Interacts with a Specific Adenine-Rich Motif of Host Promoter and Intronic Alu Elements
Zhu, B., Nethery, K. A., Kuriakose, J. A., et al. (2009) · Infection and Immunity · doi:10.1128/iai.00376-09 · Cited by 104
“chaffeensis p200 protein lacks a classical monopartite or bipartite nuclear localization signal (NLS) according to the predictNLS (13) and PSORT software programs (45); thus, its method of entry into the nucleus is not clear.”
Method
Physical Features of Intracellular Proteins that Moonlight on the Cell Surface
Amblee, V., & Jeffery, C. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130575 · Cited by 103
Investigation into the use of C‐ and N‐terminal GFP fusion proteins for subcellular localization studies using reverse transfection microarrays
Palmer, E., & Freeman, T. C. (2004) · Comparative and Functional Genomics · doi:10.1002/cfg.405 · Cited by 103
Membrane Localization of Cyclic Nucleotide Phosphodiesterase 3 (PDE3)
Shakur, Y., Takeda, K., Kenan, Y., Yu, Z., Rena, G., Brandt, D., Houslay, M. D., Degerman, E., Ferrans, V. J., & Manganiello, V. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m001734200 · Cited by 103
Hantaan Virus Nucleocapsid Protein Binds to Importin α Proteins and Inhibits Tumor Necrosis Factor Alpha-Induced Activation of Nuclear Factor Kappa B
Taylor, S. L., Frias‐Staheli, N., García‐Sastre, A., & Schmaljohn, C. S. (2008) · Journal of Virology · doi:10.1128/jvi.00986-08 · Cited by 102
“Using the algorithm PSORT II (31), we were able to identify a putative, monopartite NLS within the HTNV N protein, beginning at amino acid position 172.”
Systematic characterization of the peroxidase gene family provides new insights into fungal pathogenicity in Magnaporthe oryzae
Mir, A. A., Park, S., Sadat, M. A., Kim, S., Choi, J., Jeon, J., & Lee, Y. (2015) · Scientific Reports · doi:10.1038/srep11831 · Cited by 101
Inosine 5′-monophosphate dehydrogenase binds nucleic acids in vitro and in vivo
McLean, J. E., Hamaguchi, N., Belenky, P. A., MORTIMER, S. E., Stanton, M. J., & Hedstrom, L. (2004) · Biochemical Journal · doi:10.1042/bj20031585 · Cited by 102
ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes
King, B. R., & Guda, C. (2007) · Genome biology · doi:10.1186/gb-2007-8-5-r68 · Cited by 102
“For our first test, we compared ngLOC against two existing methods, namely PSORT [24] and pTARGET [11].”
Method
An SVM-based system for predicting protein subnuclear localizations
Lei, Z., & Dai, Y. D. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-291 · Cited by 101
IGFBP-2 nuclear translocation is mediated by a functional NLS sequence and is essential for its pro-tumorigenic actions in cancer cells
Azar, W. J., Zivkovic, S., Werther, G. A., et al. (2013) · Oncogene · doi:10.1038/onc.2012.630 · Cited by 99
Prediction of subcellular locations of proteins: Where to proceed?
Imai, K., & Nakai, K. (2010) · PROTEOMICS · doi:10.1002/pmic.201000274 · Cited by 99
“Since then the PSORT program has been available through the Internet [12, 13].”
BackgroundMethodInfluentialSelf-citation
Fasciola hepatica leucine aminopeptidase, a promising candidate for vaccination against ruminant fasciolosis☆
Acosta, D., Cancela, M., Piacenza, L., et al. (2007) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2007.11.011 · Cited by 99
Spatial Organisation of Four Enzymes from Stevia rebaudiana that are Involved in Steviol Glycoside Synthesis
Humphrey, T., Richman, A. S., Menassa, R., et al. (2006) · Plant Molecular Biology · doi:10.1007/s11103-005-5966-9 · Cited by 99
“The subcellular location prediction program PSORT (Nakai and Horton, 1999) suggested that SrKO1 was localised to the membrane of the endoplasmic reticulum (ER)(p=0.640).”
BackgroundInfluential
Recent Horizontal Transfer of Mellifera Subfamily Mariner Transposons into Insect Lineages Representing Four Different Orders Shows that Selection Acts Only During Horizontal Transfer
Lampe, D. J. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg069 · Cited by 99
UNC-80 and the NCA Ion Channels Contribute to Endocytosis Defects in Synaptojanin Mutants
Jospin, M., Watanabe, S., Joshi, D., Young, S., Hamming, K. S. C., Thacker, C. M., Snutch, T. P., Jørgensen, E. M., & Schuske, K. R. (2007) · Current Biology · doi:10.1016/j.cub.2007.08.036 · Cited by 98
Neuroglobin, cytoglobin, and a novel, eye-specific globin from chicken
Kugelstadt, D., Haberkamp, M., Hankeln, T., & Burmester, T. (2004) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.10.080 · Cited by 94
Characterization of a hydroperoxide lyase gene and effect of C6-volatiles on expression of genes of the oxylipin metabolism in Citrus
Gomi, K., Yamasaki, Y., Yamamoto, H., & Akimitsu, K. (2003) · Journal of Plant Physiology · doi:10.1078/0176-1617-01177 · Cited by 99
RNase T2 genes from rice and the evolution of secretory ribonucleases in plants
MacIntosh, G. C., Hillwig, M. S., Meyer, A., & Flagel, L. (2010) · Molecular Genetics and Genomics · doi:10.1007/s00438-010-0524-9 · Cited by 97
A putative multicopper protein secreted by an atypical type II secretion system involved in the reduction of insoluble electron acceptors in Geobacter sulfurreducens
Mehta, T., Childers, S. E., Glaven, S. M., Lovley, D. R., & Mester, T. (2006) · Microbiology · doi:10.1099/mic.0.28864-0 · Cited by 99
“This gene was designated oxide reducing pathway protein G (oxpG) because PSORT analysis (Nakai & Horton, 1999) and FingerPRINTScan (http://www.bioinf. man.ac.uk/fingerPRINTScan/) suggested that this ORF is similar to the genes for a general secretion pathway protein G related to type II general…”
Method

Authors: Nakai, K., & Horton, P.
Affiliations: The University of Osaka (JP)
Corresponding author: Nakai, Kenta
ORCID: Nakai, Kenta
Horton, Paul
Venue: Trends in Biochemical Sciences
Publisher: Elsevier BV
Published: 1999-01
Volume: 24
Issue: 1
Pages: 34-35
ISSN: 0968-0004 (ISSN-L)
DOI: 10.1016/s0968-0004(98)01336-x
OpenAlex: W2006211612
Cited by: 2,181
References: 13
Citations by year: 2026: 25 · 2025: 26 · 2024: 43 · 2023: 33 · 2022: 23 · 2021: 31 · 2020: 36 · 2019: 53 · 2018: 59 · 2017: 46 · 2016: 59 · 2015: 69 · 2014: 76 · 2013: 89 · 2012: 105
FWCI: 27.84
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
Locations: Trends in Biochemical Sciences (publishedVersion)
PubMed (publishedVersion)
Funders: Ministry of Education, Culture, Sports, Science and Technology
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: protein sorting signals, subcellular localization prediction, protein localization, signal peptide, amino acid composition, protein function prediction
MeSH terms: Algorithms, Proteins, Software, Subcellular Fractions, Protein Sorting Signals

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