Maturation of the mammalian secretome

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Genome biology (Impact Factor: 10.81). 02/2007; 8(4):211. DOI: 10.1186/gb-2007-8-4-211
Source: PubMed


A recent use of quantitative proteomics to determine the constituents of the endoplasmic reticulum and Golgi complex is discussed in the light of other available methodologies for cataloging the proteins associated with the mammalian secretory pathway.

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Available from: Jeremy C Simpson
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    • "The term secretome is often used to refer to the complete set of secreted proteins in an organism (2,11,12). However, the term has also been used to include the set of proteins involved in the secretory pathway (13,14). In the work described here, the secretome only includes the secreted proteins in an organism. "
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    ABSTRACT: The Fungal Secretome KnowledgeBase (FunSecKB) provides a resource of secreted fungal proteins, i.e. secretomes, identified from all available fungal protein data in the NCBI RefSeq database. The secreted proteins were identified using a well evaluated computational protocol which includes SignalP, WolfPsort and Phobius for signal peptide or subcellular location prediction, TMHMM for identifying membrane proteins, and PS-Scan for identifying endoplasmic reticulum (ER) target proteins. The entries were mapped to the UniProt database and any annotations of subcellular locations that were either manually curated or computationally predicted were included in FunSecKB. Using a web-based user interface, the database is searchable, browsable and downloadable by using NCBI’s RefSeq accession or gi number, UniProt accession number, keyword or by species. A BLAST utility was integrated to allow users to query the database by sequence similarity. A user submission tool was implemented to support community annotation of subcellular locations of fungal proteins. With the complete fungal data from RefSeq and associated web-based tools, FunSecKB will be a valuable resource for exploring the potential applications of fungal secreted proteins. Database URL:
    Full-text · Article · Jan 2011 · Database The Journal of Biological Databases and Curation
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    • "In eukaryotes, the term secretome has been used to describe different subsets of the proteome, including (1) all the proteins processed through the secretory pathway (Klee, 2008), (2) the proteins processed through the secretory pathway that lack transmembrane domains and/or a glycosylphosphatidylinositol anchor signal (Grimmond et al., 2003; Lee et al., 2003), or (3) the subset of proteins identified in the extracellular proteome (Zwickl et al., 2005; Chevallet et al., 2007; Paper et al., 2007). From a proteomic perspective, the mammalian secretome was defined as the quantitative map for the distribution of all proteins and lipids in the classical secretory pathway (Simpson et al., 2007). These studies reveal that the term 'secretome' has been used (or misused) in a variety of ways. "
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    ABSTRACT: Parasitic protozoa of the genus Leishmania are the causative agents of leishmaniasis. Survival and transmission of these parasites in their different hosts require membrane-bound or extracellular factors to interact with and modify their host environments. Over the last decade, several approaches have been applied to study all the extracellular proteins exported by an organism at a particular time or stage in its life cycle and under defined conditions, collectively termed the secretome or the exoproteome. In this review, we focus on emerging data shedding light on the secretion mechanisms involved in the production of the Leishmania exoproteome. We also describe other methodologies currently available that could be used to analyse the Leishmania exoproteome. Understanding the complexity of the Leishmania exoproteome is a key component to elucidating the mechanisms used by these parasites for exporting proteins to the extracellular space during its life cycle. Given the importance of extracellular factors, a detailed knowledge of the Leishmania exoproteome may provide novel targets for rational drug design and/or a source of antigens for vaccine development.
    Full-text · Article · Sep 2009 · FEMS Immunology & Medical Microbiology
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