Note: Intro -- Preface -- References -- Contents -- Mass Spectrometry-Based Organelle Proteomics -- 1 Proteome of Plant Peroxisomes -- Abstract -- 1 Introduction -- 2 MS-Based Peroxisome Proteome Studies in Plants -- 3 An Update on Arabidopsis Peroxisome Proteins and Their Functions -- 3.1 Biogenesis and Dynamics of Peroxisomes -- 3.2 Fatty Acid Catabolism and Hormone Biosynthesis -- 3.3 Photorespiration -- 3.4 The Glyoxylate Cycle -- 3.5 Detoxification of ROS and Methylglyoxal -- 3.6 Biosynthesis of Phylloquinone, Biotin and CoA -- 3.7 The Mevalonic Acid (MVA) Pathway -- 3.8 Catabolism of Polyamines, Urate, Pseudouridine and Sulfite -- 3.9 Amino Acid Metabolism -- 3.10 Pathogen Response -- 3.11 Metabolism of NADPH and NADH -- 3.12 Peroxisomal Transporters for Metabolites and Cofactors -- 3.13 Nucleotide Homeostasis -- 3.14 Phosphoregulation -- 3.15 Molecular Chaperones and Proteases -- 3.16 Other Peroxisomal Proteins -- 4 Conclusions and Perspectives -- Acknowledgements -- References -- 2 Defining the Mammalian Peroxisomal Proteome -- Abstract -- 1 Introduction -- 2 Mass Spectrometry-Based Studies of Mammalian Peroxisomes -- 3 Definition of the Mammalian Peroxisomal Proteome -- 3.1 Proteins That Are Detected in High Frequency in Peroxisomal Fractions -- 3.2 Proteins That Are Detected in Low Frequency in Peroxisomal Fractions -- 4 Conclusions -- Acknowledgements -- References -- 3 Fungal Peroxisomes Proteomics -- Abstract -- 1 Introduction -- 2 Organellar Proteomics on Peroxisomes in Fungi -- 2.1 Organellar Proteomics on Peroxisomes from S. Cerevisiae -- 2.2 The Proteome of Peroxisomes in N. Crassa -- 2.3 Identification of Peroxisomal Matrix Proteins in P. Chrysogenum -- 3 Perspectives -- Acknowledgements -- References -- 4 The Craft of Peroxisome Purification-A Technical Survey Through the Decades -- Abstract -- 1 Introduction. , 2 Isolation of PO from Liver and Kidney -- 2.1 Liver Peroxisomes -- 2.2 Kidney Peroxisomes -- 3 Peroxisome Isolation from Brain Tissue-A Still Unsolved Problem -- 4 Peroxisome Isolation from Yeast and Other Fungi -- 5 Peroxisome/Glyoxysome Purification from Plants -- 6 The Limits of Density Gradient Centrifugation-The Development of Alternative Purification Techniques -- 7 The Era of Proteomics-Opposing Approaches to Characterize Organelle Proteomes -- 8 Challenges for the Future -- Acknowledgements -- References -- Predicting Peroxisomal Proteomes -- 5 Prediction of Peroxisomal Matrix Proteins in Plants -- Abstract -- 1 Prediction of PTS1 Proteins -- 1.1 Canonical Versus Non-canonical PTS1s -- 1.2 Prediction Algorithms for PTS1 Proteins -- 1.3 Prediction and Analysis of Peroxisome Targeting Efficiency -- 2 PTS2 Nonapeptide Definition and Prediction of PTS2 Proteins -- 3 Conclusions and Future Perspectives -- References -- 6 The Obvious and the Hidden: Prediction and Function of Fungal Peroxisomal Matrix Proteins -- Abstract -- 1 Peroxisomes in Fungi -- 2 Predicting Peroxisomal Proteins -- 3 Cryptic Peroxisomal Proteins -- 3.1 Weak Peroxisomal Targeting Signals Promote Dual Targeting -- 3.2 Differential Splicing and More: Alternative Transcripts Encoding Peroxisomal Isoforms -- 3.3 Translational Stop Codon Readthrough: A Widely Conserved Mechanism to Create Peroxisomal Isoforms -- 3.4 Peroxisomal Matrix Proteins Without PTS: The Really Hidden Ones -- 4 Dual Targeting Reveals a Broader Metabolic Capacity of Fungal Peroxisomes -- References -- 7 Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals -- Abstract -- 1 Introduction -- 2 Elucidation of the Peroxisomal Proteome -- 3 Predicting the Peroxisomal Proteome -- 3.1 Concept -- 3.2 Peroxisomal Protein Transport -- 3.3 Peroxisomal Targeting Signals. , 3.3.1 Targeting Signals for Matrix Proteins -- 3.3.2 Targeting Signals for Membrane Proteins -- 3.4 Computational Algorithms to Predict the Subcellular Localization of Proteins -- 3.4.1 Prediction Algorithms to Identify Targeting Signals -- Prediction Algorithms Based on the Conservation Pattern at Individual Positions of the Targeting Signal -- Generating Prediction Algorithms for Targeting Signals by Combining Various Properties and Considering the Context -- 3.4.2 Prediction Algorithms to Classify Proteins into Groups Sharing the Same Subcellular Compartment -- 3.5 Available Prediction Algorithms for the Identification of Peroxisomal Proteins -- 3.5.1 Prediction Algorithms for Targeting Signals -- 3.5.2 Prediction Algorithms Based on Classifiers Using General Properties of Peroxisomal Proteins -- 4 Strengths and Weaknesses of Prediction Algorithms -- 4.1 General Considerations -- 4.2 Incorrect Predictions Based on the Limitations of the Algorithm -- 4.3 Biological Background of the Misevaluation -- 4.4 Evaluation of the Quality of Prediction Algorithms -- 5 Prediction of the Peroxisomal Proteome -- 6 Summary and Outlook -- Acknowledgements -- References -- 8 Multiple Localization by Functional Translational Readthrough -- Abstract -- 1 Dual and Multiple Targeting of Proteins -- 2 Dual and Multiple Targeting to the Peroxisome and Other Organelles -- 3 Identifying the PTS1ome by Bioinformatics -- 4 The Hierarchy of Targeting Signals -- 5 Translational Readthrough -- 6 Functional Translational Readthrough Diversifies Protein Function -- 7 Functional Translational Readthrough Diversifies Protein Targeting -- 8 Omics Approaches for the Identification of Readthrough Proteins -- 9 Readthrough-Omics in Silico -- 10 Translational Readthrough as a Modification of the Genetic Code -- 11 The Physiology of Peroxisomal Malate and Lactate Dehydrogenases. , Acknowledgements -- References -- 9 Evolution of the Peroxisomal Proteome -- Abstract -- 1 Introduction -- 2 Functional Diversity of Extant Peroxisomes -- 3 Diverse but All the Same -- 4 Evolutionary Origin of Peroxisomes -- 5 Current Hypotheses on the Origin of the Peroxisome -- 6 Shaping the Peroxisomal Proteome Through Subcellular Retargeting -- 7 Secondary Loss of Peroxisomes -- 8 Concluding Remarks -- Acknowledgements -- References -- 10 Peroxisome Protein Prediction in Drosophila melanogaster -- Abstract -- 1 Introduction: Drosophila Has Been Used in the Laboratory for over 100 Years -- 2 Early Studies of Drosophila Peroxisomal Proteins -- 2.1 Analysis of Potential Peroxisome Enzymes in Drosophila Organs -- 2.2 Release of the Drosophila Genome Sequence and Peroxisome Protein Predictions -- 3 Systematic Analysis of the Drosophila Peroxisome Proteome -- 3.1 Identification of Drosophila Peroxisome Biogenesis Protein Homologs -- 3.2 Functional Characterization of Predicted Drosophila Pex Proteins -- 3.3 Drosophila Does not Seem to Employ PTS2 Mediated Protein Trafficking -- 3.4 Conservation of Drosophila Peroxisome Membrane Protein (PMP) Trafficking -- 3.5 Drosophila Peroxisome Matrix Proteins -- 4 The Effects of Overexpressing Drosophila Peroxisome Proteins -- 5 Screening for Peroxisome-Associated Proteins  in Drosophila -- 5.1 Large Scale Screens for Novel Protein Interactions -- 5.2 Proteins Regulating Peroxisome Dynamics in Drosophila S2 Cells -- 6 Developing Drosophila as a Model for Human Peroxisome Biogenesis Disorders -- 6.1 Phenotypes Associated with Defective Peroxisome Biogenesis in Drosophila -- 6.2 Analysis of the Drosophila Whole-Animal Response to Pex1 Deficiency -- 6.3 Modelling Single Peroxisome Enzyme Deficiencies Using Drosophila -- 7 Identification of Novel Peroxisome Functions Using Drosophila -- 8 Summary -- References. , Analysis of Peroxisome Proteome Interaction Networks -- 11 Using Pull Down Strategies to Analyze the Interactome of Peroxisomal Membrane Proteins in Human Cells -- Abstract -- 1 Membrane Protein Complexes in Human Peroxisomes -- 1.1 Biogenesis I-de Novo Formation, Proliferation and Division -- 1.2 Biogenesis II-Membrane and Matrix Protein Import -- 1.3 PMPs with Other Functions -- 1.3.1 Metabolite Transport -- 1.3.2 Inter-Organelle Contact Sites -- 1.3.3 Novel Functions of PMPs -- 2 Proteomic Strategies Applied to the Characterization of PMPs from Human Cells -- 2.1 MS-Based Methods for the Characterization of Human PMP Complexes -- 2.1.1 Affinity Purification Combined with High-Resolution Mass Spectrometry (AP-MS) -- 2.1.2 Proximity-Dependent Biotin Identification (BioID) -- 2.2 Critical Aspects to Consider for Experimental Design -- 3 Towards a PMP Interactome -- 3.1 The PEX14 Complex Analysis Revisited -- 3.2 PEX16 Interactome Defined by BioID -- 3.3 Comparing the Peroxin Network of Yeast and Man -- 4 Outlook -- Acknowledgements -- References -- 12 Identification of Peroxisomal Protein Complexes with PTS Receptors, Pex5 and Pex7, in Mammalian Cells -- Abstract -- 1 Introduction -- 2 Approaches to Identifying Peroxisomal Protein Import Complexes in Mammalian Cells -- 3 Identification of Peroxisomal Protein Complexes by Immunoprecipitation -- 3.1 Complexes with PTS1 Receptor Pex5 -- 3.2 Complexes with PTS2 Receptor Pex7 -- 3.3 Substrates of Intraperoxisomal Processing Enzyme, Tysnd1 -- 4 Biochemical Purification of Awp1 -- 5 Concluding Remarks -- Acknowledgements -- References -- 13 Unraveling of the Structure and Function of Peroxisomal Protein Import Machineries -- Abstract -- 1 Peroxisomal Protein Import -- 2 Peroxisomal Matrix Protein Import -- 2.1 Cargo Recognition -- 2.1.1 Pre-import Complexes -- 2.2 Docking at the Peroxisomal Membrane. , 2.3 Peroxisomal Import Pores.

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