Organelle Proteomics

Department Biology I, University Munich, LMU, Menzingerstr. 67, 80638, Munich.
Methods in Molecular Biology (Impact Factor: 1.29). 02/2009; 519:65-82. DOI: 10.1007/978-1-59745-281-6_5
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The proteome of the cell is at the frontier of being too complex for proteomic analysis. Organelles provide a step up. Organelles compartmentalize the cell enabling a proteome, physiology and metabolism analysis in time and in space. Protein complexes separated by electrophoresis have been identified as the next natural level to characterize the organelles' compartmentalized membrane and soluble proteomes by mass spectrometry. Work on mitochondria and chloroplasts has shown where we are in the characterization of complex proteomes to understand the network of endogenous and extrinsic factors which regulate growth and development, adaptation and evolution.

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    • "precomplexes . PsbN was absent in the mutants and could only be found in the free fraction of thylakoid proteins in the wild type , confirming previous databases on mass spectrometric analysis ( Plöscher et al . , 2009 ) . This strongly indicates that PsbN is not or only loosely and / or transiently associated with other proteins or complexes . The immunological data using antisera for PSII pro - teins also confirmed the lack of PSII supercomplexes and dimers in ΔpsbN - F and ΔpsbN - R ( Figure 6B ) . It appeared that the ratios of pre - CP43 / PSII m"
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    ABSTRACT: The chloroplast-encoded low molecular weight protein PsbN is annotated as a photosystem II (PSII) subunit. To elucidate the localization and function of PsbN, encoded on the opposite strand to the psbB gene cluster, we raised antibodies and inserted a resistance cassette into PsbN in both directions. Both homoplastomic tobacco (Nicotiana tabacum) mutants psbN-F and psbN-R show essentially the same PSII deficiencies. The mutants are extremely light sensitive and failed to recover from photoinhibition. Although synthesis of PSII proteins was not altered significantly, both mutants accumulated only ∼25% of PSII proteins compared with the wild type. Assembly of PSII precomplexes occurred at normal rates, but heterodimeric PSII reaction centers (RCs) and higher order PSII assemblies were not formed efficiently in the mutants. The psbN-R mutant was complemented by allotopic expression of the PsbN gene fused to the sequence of a chloroplast transit peptide in the nuclear genome. PsbN represents a bitopic trans-membrane peptide localized in stroma lamellae with its highly conserved C terminus exposed to the stroma. Significant amounts of PsbN were already present in dark-grown seedling. Our data prove that PsbN is not a constituent subunit of PSII but is required for repair from photoinhibition and efficient assembly of the PSII RC.
    The Plant Cell 03/2014; 26(3). DOI:10.1105/tpc.113.120444 · 9.34 Impact Factor
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    ABSTRACT: In the last decade, proteomic technologies have been increasingly used in fish biology research. Proteomics has been applied primarily to investigate the physiology, development biology and the impact of contaminants in fish model organisms, such as zebrafish (Danio rerio), as well as in some commercial species produced in aquaculture, mainly salmonids and cyprinids. However, the lack of previous genetic information on most fish species has been a major drawback for a more general application of the different proteomic technologies currently available. Also, many teleosts of interest in biological research and with potential application in aquaculture hold unique physiological characteristics that cannot be directly addressed from the study of small laboratory fish models. This review describes proteomic approaches that have been used to investigate diverse biological questions in model and non-model fish species. We will also evaluate the current possibilities to integrate fish proteomics with other "omic" approaches, as well as with additional complementary techniques, in order to address the future challenges in fish biology research.
    Proteomics 02/2010; 10(4):858-72. DOI:10.1002/pmic.200900609 · 3.81 Impact Factor
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    ABSTRACT: Organelle proteomics allows the characterization of complex proteomes to understand the protein networks which regulate growth and development, as well as adaptation and evolution. Purification of organelles is of paramount importance and diverse protocols are published. Some organelles such as chloroplasts, mitochondria, and the nucleus are surrounded by membranes which facilitate their purification. Others have membranes easily disrupted (vacuoles and peroxisomes), or are complex systems for protein trafficking (endoplasmic reticulum, Golgi, and secretory vesicles). The cell walls present different difficulties since they have no physical limits allowing purification. The purity of the targeted cell compartment is usually evaluated by biochemical and/or immunological methods. Nevertheless, in any sub-cellular proteomic analysis, proteins from a different compartment can be detected and the difficulty is to decide whether it is a contamination, or the unexpected location is real and has a functional significance. Software to predict sub-cellular location of proteins is available. However, since not all the targeting signals are known at present, carefulness in the use of such tools is recommended. Different tactics to solve this puzzle are discussed in this commentary.
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