Protein-based stable isotope probing (protein-SIP) in functional metaproteomics

Authors

  • Jana Seifert,

    1. Department of Proteomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
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  • Martin Taubert,

    1. Department of Proteomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
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  • Nico Jehmlich,

    1. Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15a, D-17487 Greifswald, Germany
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  • Frank Schmidt,

    1. Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15a, D-17487 Greifswald, Germany
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  • Uwe Völker,

    1. Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15a, D-17487 Greifswald, Germany
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  • Carsten Vogt,

    1. Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research—UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
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  • Hans-Hermann Richnow,

    1. Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research—UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
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  • Martin von Bergen

    Corresponding author
    1. Department of Proteomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
    2. Department of Metabolomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
    • Helmholtz Centre for Environmental Research—UFZ, Department of Proteomics, Department of Metabolomics, Permoserstrasse 15, D-04318 Leipzig, Germany.
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Abstract

The community phenotype as the sum of molecular functions of organisms living in consortia strongly depends on interactions within these communities. Therefore, the analyses of the most significant molecules in terms of the phenotype, the proteins, have to be performed on samples without disrupting the meta-species environment. Due to the increasing genomic information, proteins provide insights into a potential molecular function and the phylogenetic structure of the community. Unfortunately, the lists of identified proteins are often based first on the technical capacity of the used methods or instruments, and second on the interpretation of them by the assignment of molecular functions to proteins in databases. Especially in non-model organisms the functions of many proteins are often not known and an increasing number of studies indicate a significant amount of uncertainty. To decrease the dependency on assumptions and to enable functional insights by metaproteome approaches, the metabolic labeling from an isotopically labeled substrate can be used. Since the metabolites deriving from the substrate are very rarely species-specific, the incorporation of the stable isotope into proteins can be used as a surrogate marker for metabolic activity. The degree of incorporation can be determined accurately on the peptide level by mass spectrometry; additionally, the peptide sequence provides information on the metabolic active species. Thereby, protein-stable isotope probing (protein-SIP) adds functional information to metaproteome approaches. The classical metaproteome approaches will be reviewed with an emphasis on their attempts towards functional interpretation. The gain from functional insights into metaproteomics by using metabolic labeling of stable isotopes of carbon, nitrogen, and sulfur is reviewed with a focus on the techniques of measurement, calculation of incorporation and data processing. © 2012 Wiley Periodicals, Inc. Mass Spec Rev 31:683–697, 2012

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