- Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
J Mol Biol 305:567-80. 2001
..We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/...
- Improved prediction of signal peptides: SignalP 3.0
Jannick Dyrløv Bendtsen
Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
J Mol Biol 340:783-95. 2004
..The new method has been benchmarked against other available methods. Predictions can be made at the publicly available web server..
- Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
Stockholm Bioinformatics Center, Department of Biochemistry, Stockholm University, Stockholm, S 106 91, Sweden
J Mol Biol 300:1005-16. 2000
..TargetP is available as a web-server at http://www.cbs.dtu.dk/services/TargetP/...
- WoLF PSORT: protein localization predictor
Computational Biology Research Center, AIST, Tokyo, Japan
Nucleic Acids Res 35:W585-7. 2007
..Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org...
- CRM1 is an export receptor for leucine-rich nuclear export signals
European Molecular Biology Laboratory, Heidelberg, Germany
Cell 90:1051-60. 1997
..We conclude that CRM1 is an export receptor for leucine-rich nuclear export signals and discuss a model for the role of RanGTP in CRM1 function and in nuclear export in general...
- Computational method to predict mitochondrially imported proteins and their targeting sequences
M G Claros
Laboratoire de Genetique Moleculaire, CNRS URA 1302, Ecole Normale Superieure, Paris, France or
Eur J Biochem 241:779-86. 1996
..As a practical application, the number of unknown yeast open reading frames that might be mitochondrial proteins has been predicted, which revealed that many of them are clustered...
- Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence
Research Institute of Molecular Pathology, Dr Bohrgasse 7, A 1030 Vienna, Austria
J Mol Biol 328:581-92. 2003
..The predicted presence of a PTS1 signal implies peroxisomal localisation in the absence of N-terminal targeting sequences such as the mitochondrial import signal...
- A combined transmembrane topology and signal peptide prediction method
Center for Genomics and Bioinformatics, Karolinska Institutet, SE 17 177 Stockholm, Sweden
J Mol Biol 338:1027-36. 2004
..The method is available at as well as at..
- Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems
Department of Microbiology, University of Washington, Seattle, Washington, United States of America
PLoS Pathog 5:e1000375. 2009
..This approach provides a new way to identify secreted effectors in a broad range of pathogenic bacteria for further experimental characterization and provides insight into the nature of the type III secretion signal...
- PrediSi: prediction of signal peptides and their cleavage positions
Institut fur Mikrobiologie, Technische Universitat Braunschweig, Spielmannstrasse 7, D 38106 Braunschweig, Germany
Nucleic Acids Res 32:W375-9. 2004
..PrediSi is accessible via a web interface. An extra Java package was designed for the integration of PrediSi into other software projects. The tool is freely available on the World Wide Web at http://www.predisi.de...
- Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli
Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
Cell 121:235-45. 2005
..These genetic interactions suggest a role for YfgL, one of the lipoprotein components of the protein assembly complex, in a homeostatic control mechanism that coordinates the overall OM assembly process...
- Characterization and prediction of protein nucleolar localization sequences
Michelle S Scott
Division of Biological Chemistry and Drug Discovery and Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
Nucleic Acids Res 38:7388-99. 2010
..NoLSs are a prevalent type of targeting motif that is distinct from nuclear localization signals and that can be computationally predicted...
- Signals for sorting of transmembrane proteins to endosomes and lysosomes
Juan S Bonifacino
Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
Annu Rev Biochem 72:395-447. 2003
..This complex array of signals and recognition proteins ensures the dynamic but accurate distribution of transmembrane proteins to different compartments of the endosomal-lysosomal system...
- Transmembrane protein topology prediction using support vector machines
Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
BMC Bioinformatics 10:159. 2009
..In the absence of structural data, sequence-based prediction methods allow TM protein topology to be investigated...
- Protein targeting and degradation are coupled for elimination of mislocalized proteins
Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
Nature 475:394-7. 2011
..We propose that such coupling allows the fast tracking of MLPs for degradation without futile engagement of the cytosolic folding machinery...
- Interaction of tyrosine-based sorting signals with clathrin-associated proteins
Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
Science 269:1872-5. 1995
..The interaction was confirmed by in vitro binding assays. Thus, it is likely that the medium chains serve as signal-binding components of the clathrin-dependent sorting machinery...
- Structural analysis of a monomeric form of the twin-arginine leader peptide binding chaperone Escherichia coli DmsD
Charles M Stevens
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
J Mol Biol 389:124-33. 2009
..coli DmsA and the most conserved regions on the surface of EcDmsD...
- PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization
Institute for Molecular and Cellular Biology, Osaka University, Japan
Trends Biochem Sci 24:34-6. 1999
- Extensive feature detection of N-terminal protein sorting signals
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
Bioinformatics 18:298-305. 2002
..We adopt an approach which consists of an extensive search for simple rules and various attributes which is partially guided by human intuition...
- The Tat protein export pathway
B C Berks
Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
Mol Microbiol 35:260-74. 2000
..Here, we review recent progress on the characterization of the Tat system and critically discuss the structure and operation of this major new bacterial protein export pathway...
- Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
Center for Genomics and Bioinformatics, Karolinska Institutet, S 17177 Stockholm, Sweden
Nucleic Acids Res 35:W429-32. 2007
..We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius...
- Proteomics of protein secretion by Bacillus subtilis: separating the "secrets" of the secretome
Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Kerklaan 30, 9751 NN Haren, The Netherlands
Microbiol Mol Biol Rev 68:207-33. 2004
..subtilis and other gram-positive bacteria. Ultimately, such leads will serve to increase our understanding of virulence factor biogenesis in gram-positive pathogens, which is likely to be of high medical relevance...
- Prediction of subcellular locations of proteins: where to proceed?
Computational Biology Research Center, AIST, Tokyo, Japan
Proteomics 10:3970-83. 2010
..Recent advances on the study of protein sorting signals will hopefully be incorporated into future prediction methods...
- ABI domain-containing proteins contribute to surface protein display and cell division in Staphylococcus aureus
Matthew B Frankel
Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
Mol Microbiol 78:238-52. 2010
- Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane--distinct translocases and mechanisms
Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
Biochim Biophys Acta 1778:1735-56. 2008
..Although the targeting signals that direct secretory proteins to these pathways show a high degree of similarity, the translocation mechanisms and translocases involved are vastly different...
- Features of a twin-arginine signal peptide required for recognition by a Tat proofreading chaperone
Division of Molecular and Environmental Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
FEBS Lett 582:3979-84. 2008
..Screening of a random torD mutant library identified a variant TorD protein (Q7L) that displayed increased binding affinity for the TorA signal peptide...
- Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall
S K Mazmanian
Department of Microbiology and Immunology, UCLA School of Medicine, University of California, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
Science 285:760-3. 1999
..The protein specified by srtA, sortase, may be a useful target for the development of new antimicrobial drugs...
- Differential interactions between a twin-arginine signal peptide and its translocase in Escherichia coli
Institut für Biochemie und Molekularbiologie and Universität Freiburg, Hermann Herder Strasse 7, D 79104, Freiburg, Germany
Mol Cell 12:937-46. 2003
- A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins
M Madan Babu
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
J Bacteriol 188:2761-73. 2006
..The website, along with additional information on the biosynthetic pathway, statistics on predicted lipoproteins, and related figures, is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop/...
- A substrate-specific inhibitor of protein translocation into the endoplasmic reticulum
Jennifer L Garrison
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94107, USA
Nature 436:285-9. 2005
..Thus, the range of substrates accommodated by the channel can be specifically and reversibly modulated by a cell-permeable small molecule that alters the interaction between signal sequences and the Sec61 complex...
- Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides
Kuo Chen Chou
Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA
Biochem Biophys Res Commun 357:633-40. 2007
..Signal-CF is freely available as a web-server at http://chou.med.harvard.edu/bioinf/Signal-CF/ or http://188.8.131.52/bioinf/Signal-CF/...
- A proteomic view on genome-based signal peptide predictions
Institut fur Mikrobiologie und Molekularbiologie, Ernst Moritz Arndt Universiät Greifswald, D 17487 Greifswald, Germany
Genome Res 11:1484-502. 2001
..Major problems are currently encountered with the prediction of extracellular proteins lacking signal peptides (including cytoplasmic proteins) and lipoproteins...
- Prediction of lipoprotein signal peptides in Gram-negative bacteria
Agnieszka S Juncker
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark
Protein Sci 12:1652-62. 2003
..A neural network-based predictor was developed for comparison, and it gave very similar results. LipoP is available as a Web server at www.cbs.dtu.dk/services/LipoP/...
- Architects at the bacterial surface - sortases and the assembly of pili with isopeptide bonds
Antoni P A Hendrickx
Department of Microbiology, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Rev Microbiol 9:166-76. 2011
..Together, these isopeptide bonds endow these sortase products with adhesive properties and resistance to host proteases...
- Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences
Research Institute of Molecular Pathology, Dr Bohrgasse 7, A 1030 Vienna, Austria
J Mol Biol 328:567-79. 2003
..Specificity differences are confined to taxonomic subgroups (metazoa and fungi) and are connected with amino acid type preferences in region 1 and deviating hydrophobicity patterns in region 2...
- Signal peptidases
Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
Chem Rev 102:4549-80. 2002
- Trafficking of STEVOR to the Maurer's clefts in Plasmodium falciparum-infected erythrocytes
Jude M Przyborski
Hygiene Institut, Abteilung Parasitologie, Universitatsklinikum Heidelberg, Heidelberg, Germany
EMBO J 24:2306-17. 2005
..Our data suggest general principles for transport of transmembrane proteins to the Maurer's clefts and provide new insights into protein sorting and trafficking processes in P. falciparum...
- Locating proteins in the cell using TargetP, SignalP and related tools
Stockholm Bioinformatics Center, AlbaNova, Stockholm University, SE 10691 Stockholm, Sweden
Nat Protoc 2:953-71. 2007
..In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular...
- A new method for predicting signal sequence cleavage sites
G von Heijne
Nucleic Acids Res 14:4683-90. 1986
..The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins...
- The signal sequence coding region promotes nuclear export of mRNA
Alexander F Palazzo
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS Biol 5:e322. 2007
..The discovery of an SSCR-mediated pathway explains the previously noted amino acid bias in signal sequences and suggests a link between nuclear export and membrane targeting of mRNAs...
- Targeting malaria virulence and remodeling proteins to the host erythrocyte
Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
Science 306:1930-3. 2004
..The conservation of this signal across Plasmodium species has implications for the development of new antimalarials...
- A host-targeting signal in virulence proteins reveals a secretome in malarial infection
N Luisa Hiller
Departments of Pathology and Microbiology Immunology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
Science 306:1934-7. 2004
..Erythrocyte modification by the parasite may involve plasmodial heat shock proteins and be vastly more complex than hitherto realized...
- The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment
Hilary F Clark
Departments of Bioinformatics, Molecular Biology and Protein Chemistry, Genentech, Inc, South San Francisco, California 94080, USA
Genome Res 13:2265-70. 2003
..The SPDI collection should facilitate efforts to better understand intercellular communication, may lead to new understandings of human diseases, and provides potential opportunities for the development of therapeutics...
- An investigation of the role of transmembrane domains in Golgi protein retention
MRC Laboratory of Molecular Biology, Cambridge, UK
EMBO J 14:4695-704. 1995
..These observations are more consistent with lipid-based sorting of ST TMD, but they also allow for reconciliation with the kin recognition model which appears to act on sequences outside of the TMD...
- A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins
J H Weiner
Department of Biochemistry, University of Alberta, Edmonton, Canada
Cell 93:93-101. 1998
..Proteins with a Sec-dependent leader or which assemble spontaneously in the membrane are not affected by this mutation. MttA, B, and C are members of a large family of related sequences extending from archaebacteria to higher eukaryotes...
- C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis
Patricia A Digiuseppe Champion
Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Campus Box 2200, San Francisco, CA 94143 2200, USA
Science 313:1632-6. 2006
..Attachment of the signal to yeast ubiquitin was sufficient for secretion from M. tuberculosis cells, demonstrating that this ESX-1 signal is portable...
- Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic
Daniel H Haft
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville MD 20850, USA
BMC Biol 4:29. 2006
..Detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families...
- A comprehensive assessment of N-terminal signal peptides prediction methods
Khar Heng Choo
Institute for Infocomm Research, 1 Fusionopolis Way, 21 01 Connexis, Singapore
BMC Bioinformatics 10:S2. 2009
..Of the myriad software prediction tools developed to automate the task of assigning the SP cleavage site of these new sequences, we review here, the performance and reliability of commonly used SP prediction tools...
- Conservation and diversification of dileucine signal recognition by adaptor protein (AP) complex variants
Cell Biology and Metabolism Program, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
J Biol Chem 286:2022-30. 2011
..However, the characteristics of the binding site on each complex vary, providing for the specific recognition of a diverse repertoire of (D/E)XXXL(L/I) signals...
- Selective inhibition of cotranslational translocation of vascular cell adhesion molecule 1
Novartis Institutes for BioMedical Research, Brunner Strasse 59, A 1235 Vienna, Austria
Nature 436:290-3. 2005
..In addition, they highlight cotranslational translocation at the ER membrane as a potential target for drug discovery...
- The signal peptide of the rat corticotropin-releasing factor receptor 1 promotes receptor expression but is not essential for establishing a functional receptor
Forschungsinstitut für Molekulare Pharmakologie FMP, Robert Rossle Str 10, 13125 Berlin, Germany
Biochem J 390:455-64. 2005
..Thus the signal peptide of the CRF-R1 promotes an early step of receptor biogenesis, such as targeting of the nascent chain to the ER membrane and/or the gating of the protein-conducting translocon of the ER membrane...
- Free-energy cost for translocon-assisted insertion of membrane proteins
Department of Physics, Beckman Institute, University of Illinois at Urbana Champaign, Urbana Champaign, IL 61801, USA
Proc Natl Acad Sci U S A 108:3596-601. 2011
- Chloroplast transit peptide prediction: a peek inside the black box
A I Schein
University of Pennsylvania Department of Computer and Information Science, 556 Moore Building, 200 S 33rd Street, Philadelphia, PA 19104 6389, USA
Nucleic Acids Res 29:E82. 2001
..Our most accurate predictor combines principal component analysis and logistic regression. Web-based prediction using this method is available online at http://apicoplast.cis.upenn.edu/pclr/...
- Two proteases, trypsin domain-containing 1 (Tysnd1) and peroxisomal lon protease (PsLon), cooperatively regulate fatty acid β-oxidation in peroxisomal matrix
Department of Biology, Faculty of Sciences, Kyushu University Graduate School, 6 10 1 Hakozaki, Higashi ku, Fukuoka 812 8581, Japan
J Biol Chem 286:44367-79. 2011
..The proteolytic activity of oligomeric Tysnd1 is in turn controlled by self-cleavage of Tysnd1 and degradation of Tysnd1 cleavage products by PsLon...
- Genetic evidence for a tight cooperation of TatB and TatC during productive recognition of twin-arginine (Tat) signal peptides in Escherichia coli
Institut für Bio und Geowissenschaften 1, Biotechnologie, Forschungszentrum Julich GmbH, Julich, Germany
PLoS ONE 7:e39867. 2012
- How tails guide tail-anchored proteins to their destinations
National Research Council Institute for Neuroscience and Department of Medical Pharmacology, University of Milan, Via Vanvitelli 32, 20129 Milano, Italy
Curr Opin Cell Biol 19:368-75. 2007
..Unravelling these pathways will shed light on the biosynthesis and regulation of an important group of membrane proteins and is likely to lead to new concepts in the field of membrane biogenesis...
- Cell wall antibiotics provoke accumulation of anchored mCherry in the cross wall of Staphylococcus aureus
Microbial Genetics, University of Tubingen, Tubingen, Germany
PLoS ONE 7:e30076. 2012
..The effect is most likely due to antibiotic mediated increase of free anchoring sites (Lipid II) at the cross wall, the substrate of SrtA, leading to a preferential incorporation of anchored proteins at the cross wall...
- Mechanisms of regulated unconventional protein secretion
Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
Nat Rev Mol Cell Biol 10:148-55. 2009
- Widespread expression of BORIS/CTCFL in normal and cancer cells
Tania A Jones
Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
PLoS ONE 6:e22399. 2011
..While BORIS transcript levels are low compared to CTCF, its protein levels are readily detectable. These findings show that BORIS expression is more widespread than previously believed, and suggest a role for BORIS in nucleolar function...
- Structure of a complex of the ATPase SecA and the protein-translocation channel
Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
Nature 455:936-43. 2008
..SecA binding generates a 'window' at the lateral gate of the SecY channel and it displaces the plug domain, preparing the channel for signal sequence binding and channel opening...
- A signature in HIV-1 envelope leader peptide associated with transition from acute to chronic infection impacts envelope processing and infectivity
Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS ONE 6:e23673. 2011
..These results support the potential utility of using a computational approach to examine large viral sequence data sets for functional signatures and indicate the importance of Envelope expression levels for efficient HIV transmission...
- A conserved tripeptide sorts proteins to peroxisomes
S J Gould
Department of Biology and Center for Molecular Genetics, University of California, La Jolla, California 92093
J Cell Biol 108:1657-64. 1989
..These results indicate that peroxisomal protein import, unlike other types of transmembrane translocation, is dependent upon a conserved amino acid sequence...
- The thylakoid proton gradient promotes an advanced stage of signal peptide binding deep within the Tat pathway receptor complex
Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611, USA
J Biol Chem 282:5263-72. 2007
..This implies that translocation involves a very intimate association of the signal peptide with the receptor complex binding site...
- Dissection of the role of the stable signal peptide of the arenavirus envelope glycoprotein in membrane fusion
Emily L Messina
Montana Biotechnology Center, The University of Montana, Missoula, Montana, USA
J Virol 86:6138-45. 2012
..Our studies suggest that interactions of SSP TM1 with the transmembrane domain of G2 may be important for GPC-mediated membrane fusion and its inhibition...
- Interconvertibility of lipid- and translocon-bound forms of the bacterial Tat precursor pre-SufI
Umesh K Bageshwar
Department of Molecular and Cellular Medicine, College of Medicine, Texas A and M Health Science Center, College Station, TX 77843, USA
Mol Microbiol 74:209-26. 2009
..Thus, the non-Tat bound form of the precursor is a functional intermediate in the transport cycle. This intermediate appears to directly equilibrate with the translocon-bound form of the precursor...
- The curious case of arenavirus entry, and its inhibition
Jack H Nunberg
Montana Biotechnology Center, The University of Montana, Missoula, MT 59812, USA
Viruses 4:83-101. 2012
..This unusual solution to maintaining the metastable prefusion state of GPC on the virion and activating the class I fusion cascade at acidic pH provides novel targets for antiviral intervention...
- Genetic analysis of pathway specificity during posttranslational protein translocation across the Escherichia coli plasma membrane
Institut für Biotechnologie 1, Forschungszentrum Julich GmbH, D 52425 Julich, Germany
J Bacteriol 185:2811-9. 2003
- Gaa1p and gpi8p are components of a glycosylphosphatidylinositol (GPI) transamidase that mediates attachment of GPI to proteins
Department of Immunoregulation, Research Institute for Microbial Diseases, Osaka University, Osaka 565 0871, Japan
Mol Biol Cell 11:1523-33. 2000
..Moreover, Gaa1p and Gpi8p are associated with each other. Therefore, Gaa1p and Gpi8p constitute a GPI transamidase and cooperate in generating a carbonyl intermediate, a prerequisite for GPI attachment...
- Reverse genetics generation of chimeric infectious Junin/Lassa virus is dependent on interaction of homologous glycoprotein stable signal peptide and G2 cytoplasmic domains
Cesar G Albarino
Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G 14, Atlanta, GA 30329, USA
J Virol 85:112-22. 2011
..These recombinant chimeric viruses shed light on the fundamental requirements of arenavirus GPC maturation and may serve as a strategy for the development of bivalent JUNV and LASV vaccine candidates...
- Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif
Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
PLoS Biol 4:e377. 2006
..coli outer membrane was accomplished after adapting its signature sequence. These results demonstrate that the Omp85 assembly machinery recognizes OMPs by virtue of their C-terminal signature sequence...
- Structure of a zinc-binding domain in the Junin virus envelope glycoprotein
Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, USA
J Biol Chem 286:1528-36. 2011
..Our studies describe the structural basis for retention of the unique SSP subunit and suggest a mechanism whereby SSP is positioned in the GPC complex to modulate pH-dependent membrane fusion...
- The yeast deubiquitinating enzyme Ubp16 is anchored to the outer mitochondrial membrane
Institut fur Mikrobiologie, Heinrich Heine Universitat Dusseldorf, Geb 26 12 01, Universitatsstr 1, D 40225 Dusseldorf, Germany
FEBS Lett 549:135-40. 2003
- A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins
Garry W Buchko
Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Mol Biosyst 6:2448-58. 2010
..Typhimurium effectors SptP, SopD-2, GtgE, and the Yersinia pestis effector YopH...
- TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes
Centre for Biotechnology, Anna University, Chennai 600 025, Tamil Nadu, India
J Mol Evol 70:359-70. 2010
..The role of the TAT pathway in the export of folded-lipoproteins and in niche-specific adaptation for survival has important implications not only in lipoprotein biosynthesis, but also for protein and metabolic engineering applications...
- Signal sequences specify the targeting route to the endoplasmic reticulum membrane
D T Ng
Department of Biochemistry and Biophysics, University of California, School of Medicine, San Francisco 94143 0448, USA
J Cell Biol 134:269-78. 1996
..Our studies show a previously unrecognized diversity in ER-directed signal sequences, that carry structural information that serves to identify the route taken...
- Design of a protein-targeting system for lactic acid bacteria
, INRA, 78352 Jouy-en-Josas Cedex, France
J Bacteriol 183:4157-66. 2001
..These results provide the first report of a targeting system in lactic acid bacteria in which the final location of a protein is controlled and biological activity is maintained...
- SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology
Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE 10691 Stockholm, Sweden
Bioinformatics 24:2928-9. 2008
..We provide a description of the SPOCTOPUS algorithm together with a performance evaluation where SPOCTOPUS compares favorably with state-of-the-art methods for signal peptide and topology predictions...
- A cathepsin L isoform that is devoid of a signal peptide localizes to the nucleus in S phase and processes the CDP/Cux transcription factor
Department of Biochemistry, McGill University, 687 Pine Avenue West, Montreal H3A 1A1, Canada
Mol Cell 14:207-19. 2004
..Overall, these results uncover an as yet unsuspected role for cysteine proteases in the control of cell cycle progression...
- Peroxisomal membrane proteins contain common Pex19p-binding sites that are an integral part of their targeting signals
Institut fur Physiologische Chemie, Ruhr Universitat Bochum, 44780 Bochum, Germany
Mol Biol Cell 15:3406-17. 2004
..By adding the heterologous binding site of Pex11p, peroxisomal targeting of the Pex13p fragment was restored. We conclude that Pex19p-binding sites are well-defined entities that represent an essential part of the mPTS...
- Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1
Research Institute of Molecular Pathology, Dr Bohr Gasse 7, A 1030 Vienna, Republic of Austria
Nucleic Acids Res 31:3631-4. 2003
..Guidelines for application of the three WWW-based predictors (http://mendel.imp.univie.ac.at/) and for the interpretation of their output are described...
- Unexpected deposition patterns of recombinant proteins in post-endoplasmic reticulum compartments of wheat endosperm
Institute for Molecular Biotechnology, Rheinische Westfälische Technische Hochschule Aachen, 52074 Aachen, Germany
Plant Physiol 136:3457-66. 2004
..Our data also confirm that recombinant proteins are invaluable tools for the analysis of protein trafficking in cereals...
- Secretion of anti-Plasmodium effector proteins from a natural Pantoea agglomerans isolate by using PelB and HlyA secretion signals
Dawn C Bisi
Duquesne University, Department of Biological Sciences, 600 Forbes Ave, Pittsburgh, PA 15282, USA
Appl Environ Microbiol 77:4669-75. 2011
..Importantly, those strains that secreted efficiently grew as well as wild-type strains under laboratory conditions and, thus, may be expected to be competitive with the native microbiota in the environment of the mosquito midgut...
- Sorting signals, N-terminal modifications and abundance of the chloroplast proteome
Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
PLoS ONE 3:e1994. 2008
..This study provides the most comprehensive chloroplast proteome analysis to date and an expanded Plant Proteome Database (PPDB) in which all MS data are projected on identified gene models...
- Remnant signal peptides on non-exported enzymes: implications for the evolution of prokaryotic respiratory chains
School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
Microbiology 155:3992-4004. 2009
..These data highlight an intimate genetic and evolutionary link between some non-exported redox enzymes and those transported across membranes by the Tat translocation system...
- An E. coli ribonucleoprotein containing 4.5S RNA resembles mammalian signal recognition particle
M A Poritz
Department of Biochemistry and Biophysics, University of California Medical School, San Francisco 94143 0448
Science 250:1111-7. 1990
..Protein synthesis did not cease until very late, an indication that 4.5S RNA probably does not have a direct role in this process...
- Identification of Lassa virus glycoprotein signal peptide as a trans-acting maturation factor
Institut für Virologie der Philipps Universität Marburg, Robert Koch Strasse 17, D 35037 Marburg, Germany
EMBO Rep 4:1084-8. 2003
..To our knowledge, this is the first report on a signal peptide that is essential for proteolytic processing of a secretory pathway protein...
- A twin arginine signal peptide and the pH gradient trigger reversible assembly of the thylakoid [Delta]pH/Tat translocase
Horticultural Sciences and Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA
J Cell Biol 157:205-10. 2002
..It also explains in part how the system can exist in the membrane without compromising its ion and proton permeability barrier...
- Signal peptides direct surface proteins to two distinct envelope locations of Staphylococcus aureus
Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
EMBO J 27:2656-68. 2008
- Bitopic membrane topology of the stable signal peptide in the tripartite Junín virus GP-C envelope glycoprotein complex
Sudhakar S Agnihothram
Montana Biotechnology Center, The University of Montana, Science Complex, Room 221, Missoula, MT 59812, USA
J Virol 81:4331-7. 2007
..Taken together, our results suggest that bitopic membrane insertion of SSP is centrally important in the assembly and function of the tripartite GP-C complex...
- Targeting of proteins derived from self-processing polyproteins containing multiple signal sequences
Pablo de Felipe
School of Biology, Centre for Biomolecular Sciences, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
Traffic 5:616-26. 2004
..The inclusion of a fluorescent reporter enables visualisation of expression levels, whilst inclusion of a selectable marker enables stable cell-lines to be established rapidly...
- Protein translocation is mediated by oligomers of the SecY complex with one SecY copy forming the channel
Andrew R Osborne
Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
Cell 129:97-110. 2007
..Oligomeric channels with only one active pore likely mediate protein translocation in all organisms...
- 454 Genome sequencing of Pseudoperonospora cubensis reveals effector proteins with a QXLR translocation motif
Department of Plant Pathology, Michigan State University, East Lansing, MI 48824, USA
Mol Plant Microbe Interact 24:543-53. 2011
..cubensis. Furthermore, the massive duplication of PcQNE suggests that they might play pivotal roles in pathogen fitness and pathogenicity...
- Sequence-based prediction of type III secreted proteins
Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, Freising, Germany
PLoS Pathog 5:e1000376. 2009
..Our findings will facilitate further studies on and improve our understanding of type III secretion and its role in pathogen-host interactions...
- Transmembrane topology and signal peptide prediction using dynamic bayesian networks
Sheila M Reynolds
Department of Electrical Engineering, University of Washington, Seattle, Washington, United States of America
PLoS Comput Biol 4:e1000213. 2008
..gs.washington.edu/proj/philius. A Philius Web server is available at http://www.yeastrc.org/philius, and the predictions on the YRC database are available at http://www.yeastrc.org/pdr...
- A particle-associated glycoprotein signal peptide essential for virus maturation and infectivity
Institut fur Virologie und Immunbiologie, Universitat Wurzburg, Versbacher Str 7, 97078 Wurzburg, 01307 Dresden, Germany
J Virol 75:5762-71. 2001
..While the SP N terminus was found to mediate the specificity of FV Env to interact with FV capsids, it was dispensable for Env targeting to the secretory pathway and FV envelope-mediated infectivity of murine leukemia virus pseudotypes...
- Nucleus-to-nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms
Sven B Gould
Philipps Universitat Marburg, Marburg, Germany
Mol Biol Evol 23:2413-22. 2006
..tricornutum. Furthermore, the described cryptophyte PPC proteins possibly allow the elucidation of the processes by which proteins are involved in different levels of host control over its eukaryotic organelle...
- Plasmepsin V licenses Plasmodium proteins for export into the host erythrocyte
Howard Hughes Medical Institute, Washington University School of Medicine, Department of Molecular Microbiology, St Louis, Missouri 63110, USA
Nature 463:632-6. 2010
..This enzyme is essential for parasite viability and ER residence is essential for its function. We propose that plasmepsin V is the PEXEL protease and is an attractive enzyme for antimalarial drug development...
- Stepwise insertion and inversion of a type II signal anchor sequence in the ribosome-Sec61 translocon complex
Prasanna K Devaraneni
Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, Portland, OR 97239, USA
Cell 146:134-47. 2011
..Thus, the RTC coordinates SA topogenesis within a protected environment via sequential energetic transitions of the TM segment...
- Sequential checkpoints govern substrate selection during cotranslational protein targeting
Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
Science 328:757-60. 2010
..Thus, high fidelity of substrate selection is achieved through the cumulative effect of multiple checkpoints; this principle may be generally applicable to other pathways involving selective signal recognition...
- A profile hidden Markov model for signal peptides generated by HMMER
Department of Bioinformatics, Genentech Inc, South San Francisco, CA 94080, USA
Bioinformatics 19:307-8. 2003
..Here we describe an approach for building a complex model of eukaryotic signal peptides by the standard HMMER package. Signal peptide prediction with this model gives a 95.6% sensitivity and 95.7% specificity...
- Plastid ultrastructure defines the protein import pathway in dinoflagellates
Departement de sciences biologiques, Universite de Montreal, 4101 Sherbrooke est, Montreal, Quebec, Canada H1X 2B2
J Cell Sci 116:2867-74. 2003
..We conclude that the protein import mechanism is dictated by plastid ultrastructure rather than by the evolutionary history of the cell...