Subcellular Biochemistry 89 Luis A. del Río · Michael Schrader Editors Proteomics of Peroxisomes Identifying Novel Functions and Regulatory Networks Subcellular Biochemistry Volume 89 Series editor J. Robin Harris, Mainz, Germany More information about this series at http://www.springer.com/series/6515 í Luis A. del R o Michael Schrader (cid:129) Editors Proteomics of Peroxisomes Identifying Novel Functions and Regulatory Networks 123 Editors LuisA.del Río Michael Schrader Department ofBiochemistry, Department ofBiosciences CellandMolecular Biology ofPlants University of Exeter EstaciónExperimental del Zaidín,CSIC Exeter, UK Granada, Spain ISSN 0306-0225 Subcellular Biochemistry ISBN978-981-13-2232-7 ISBN978-981-13-2233-4 (eBook) https://doi.org/10.1007/978-981-13-2233-4 LibraryofCongressControlNumber:2018951704 ©SpringerNatureSingaporePteLtd.2018 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission orinformationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. 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Dariush Fahimi, who has made very important contributions to the understanding of the biology of mammalian peroxisomes, on the occasion of his 85th birthday. Preface Peroxisomes are a class of ubiquitous and essential single membrane-bound cell organelles,devoidofDNA,withanessentiallyoxidativetypeofmetabolism.When these organelles were first isolated from mammalian tissues and characterized by Christian de Duve in the 1960s, it was thought that their main function was the removal, by peroxisomal catalase, of toxic hydrogen peroxide generated in the peroxisomal respiratory pathway through different oxidases (De Duve and Baudhuin 1966). However, in recent years it has become progressively clear that peroxisomes are involved in several important cellular functions in almost all eukaryoticcells(Erdmann2016;Reumannetal.2016;delRío2013;delRíoetal. 2006; del Río and López-Huertas 2016; Wanders and Waterham 2006; Wanders 2013; Islinger et al. 2012; Baker and Graham 2002). Themainfunctionsofperoxisomesknownsofarwereelucidatedonthebasisof peroxisome purification and analysis by classical cell biology and biochemical methods (del Río and López-Huertas 2016; del Río 2013; Wanders and Waterham 2006; Baker and Graham 2002; Palma et al. 2009). However, in recent years a proteomic “burst” has taken place in peroxisome biology. Proteome analysis has confirmed the presence of many proteins previously described in peroxisomes by classical methods, but has also revealed many new peroxisomal proteins, and thus increased our knowledge of peroxisome functions and their metabolic and regu- latorynetworks(Erdmann2016;Reumann2011;Reumannetal.2016;Palmaetal. 2009; Saleem et al. 2006; Schuldiner and Zalckvar 2015; Camões et al. 2015; Gronemeyeretal.2013;KaurandHu2011;Eubeletal.2008;Islingeretal.2007; Kikuchi et al. 2004; Ho et al. 2002; Costello et al. 2017). Proteome studies of peroxisomes have been conducted mainly in organelles from human, animal, plant, and fungal origin. The development of sensitive pro- teomics andmass spectrometry(MS) technologiesnow allowstheidentificationof low-abundance and transient peroxisomal proteins and constantly increases our knowledge of the metabolic and regulatory networks of these important cellular organelles(Saleemetal.2006;SchuldinerandZalckvar2015;Islingeretal.2007). Additionally, the combination of experimental proteomics with bioinformatics vii viii Preface approaches now allows to identify the complete proteome of peroxisomes (Reumann 2011; Gronemeyer et al. 2013). Thisvolumeisorganizedinfourpartswhichpresentcomprehensivelytheactual stateoftheartinproteomicsofperoxisomesfrommultipleorigins.Inthefirstpart, an updated view of mass spectrometry-based proteomics using peroxisomes from mammalian, fungal, and plant origin is presented; and given the importance of having reliable high-yield methods for the purification of peroxisomes available, areviewarticleondifferentmethodsfortheisolationofperoxisomesfrommultiple sources is included. InPartII,differentapproachesforthepredictionofperoxisomalproteomesfrom mammals, Drosophila, fungi, and plants using bioinformatics approaches are pre- sented, and mechanisms by which proteins can be targeted to multiple organelles with a focus on functional translational readthrough, a novel gene regulatory mechanism,arediscussed. Thispartiscomplemented with areviewonthecurrent knowledge of the diversity, origin, and evolution of the peroxisomal proteome. Research conducted on different peroxisome–proteome interaction networks is presented in Part III, including Pull Down strategies to analyze the interactome of peroxisomal membrane proteins in human cells, the identification of peroxisomal protein complexes in mammalian cells and the structure and function of peroxi- somal protein import machineries. Studies of the proteome of peroxisomes from a fruit (sweet pepper), particularly the reactive oxygen species (ROS) proteome, and its relationship with the overall metabolism of the fruit are presented. The importance of the connections between peroxisomes and other subcellular compartments are addressed in Part IV. Knowledge of the central role of peroxi- somesinmetabolicinteractionnetworksinhumansandthecharacterizationofthese regulation networks that can be useful for the treatment of peroxisomal biogenesis disordersandotherdiseaseslinkedtoperoxisomesisreviewed.Themulti-localized proteinswhichareshared byperoxisomesandmitochondriainmammalsandtheir keyrolesinthecooperativefunctionsbetweenthesetwoorganelles thatimpact on humanhealthanddiseasearereviewed.Likewise,peroxisomesandmitochondriain plants also have a considerable overlap in their proteins, responses, and functions, and the interrelations between these two organelles are presented with results suggesting a more dynamic nature of their interactivity. The potential role of mammal peroxisomes as an intracellular redox signaling platform both in health and disease, and how protein redox modifications due to changes in the oxidant/antioxidant balance can impact on inter-organelle communication are examined.Thecelldeathorsurvivalagainstoxidativestressinmammaliancellsis addressed in the light of the recent peroxisomal localization of BAK, apro-apoptoticmember oftheBcl-2 familyproteins, which canreleasecatalase to the cytosol to eliminate extra-peroxisomal hydrogen peroxide. Finally, the meta- bolism of reactive nitrogen species (RNS) in plant peroxisomes is reviewed and a role for peroxisome-derived RNS in the communication with other cellular orga- nelles as well as in plant defense mechanisms is postulated. Preface ix We would like to thank all contributing colleagues for their enthusiastic collaborationandkeeninterest,aswellasthereviewersofthedifferentchaptersfor their valuable comments and suggestions. The helpful suggestions of Dr. Markus Islinger on theorganizationofthis book are appreciated. Weare convinced that in theupcoming years we will experienceimportant methodological developmentsin proteomics and will witness its increasing importance to reveal novel peroxisomal functions and advance in the understanding of regulatory networks of these most intriguing subcellular organelles. 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