PP66CH04-VanWijk ARI 30 March 2015 20:57 Protein Maturation and Proteolysis in Plant Plastids, Mitochondria, and Peroxisomes Klaas J. van Wijk Department of Plant Biology, Cornell University, Ithaca, New York 14853; email: [email protected] Annu. Rev. Plant Biol. 2015. 66:75–111 Keywords First published online as a Review in Advance on proteome remodeling, endosymbiotic organelle, degron, proteostasis, January 12, 2015 degradomics, autophagy The Annual Review of Plant Biology is online at plant.annualreviews.org Abstract This article’s doi: Plastids, mitochondria, and peroxisomes are key organelles with dynamic 10.1146/annurev-arplant-043014-115547 proteomes in photosynthetic eukaryotes. Their biogenesis and activity must Copyright c 2015 by Annual Reviews. be coordinated and require intraorganellar protein maturation, degradation, All rights reserved and recycling. The three organelles together are predicted to contain ∼200 Annu. Rev. Plant Biol. 2015.66:75-111. Downloaded from www.annualreviews.org presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar pro- teins, such as N-end degrons and tagging systems, have not been identi- fied, but the substrate recognition mechanisms likely share similarities be- tween organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, Access provided by Chinese Academy of Agricultural Sciences (Agricultural Information Institute) on 05/10/16. For personal use only. degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome. This review summarizes (putative) plant organellar protease functions and substrate-protease relationships. Examples illustrate key proteolytic events. 75 PP66CH04-VanWijk ARI 30 March 2015 20:57 Contents WHY DO ORGANELLES NEED PROTEOLYSIS? . 76 COMMONALITIES BETWEEN PLASTIDIAL, MITOCHONDRIAL, AND PEROXISOMAL PROTEOLYSIS AND ORGANELLE TURNOVER . 77 SCOPE OF THIS REVIEW, KEY QUESTIONS, AND NEW FRONTIERS IN ORGANELLAR PROTEOLYSIS. 78 ORGANELLAR PROTEASE INVENTORY, CLASSIFICATION, ANDCHARACTERIZATION................................................ 78 Presequence Cleavage, Protein Maturation, Stabilization, and Recycling. 83 ATP-Dependent Proteases of the AAA+ Family: LON, CLP, and FTSH . 85 TheATP-IndependentDEGProteaseFamily................................... 90 Intramembrane Cleaving Proteases of the Rhomboid and S2P Families in the Organelles. 92 Recent Discoveries and Functional Analysis of Other Organellar Proteases . 93 PROTEASE NETWORKS, PROTEOSTASIS, AND RETROGRADESIGNALING................................................. 93 SUBSTRATE SELECTION, PROTEIN LIFETIME DETERMINANTS, DEGRONS, AND POSTTRANSLATIONAL MODIFICATIONS . 95 TheN-EndRuleandN-Degrons............................................... 96 Posttranslational Modifications Can Affect Proteolysis . 96 INVOLVEMENT OF UBIQUITINATION AND THE PROTEASOME IN ORGANELLE BIOGENESIS AND DIFFERENTIATION . 97 ORGANELLE PROTEOME TURNOVER THROUGH AUTOPHAGY ANDTARGETEDVESICLETRANSPORT.................................. 98 Pexophagy..................................................................... 98 Mitophagy..................................................................... 98 Chlorophagy and Targeted Chloroplast Protein Removal by Rubisco-Containing Bodies and Senescence-Associated Vacuoles. 99 ORGANELLAR PROTEOLYSIS IN CROP PLANTS, BIOTECHNOLOGY, ANDSYNTHETICBIOLOGY................................................ 99 DEGRADOMICS: SYSTEMS ANALYSIS OF PROTEOLYSIS ANDPROTEINLIFETIME.................................................. 100 Identification of Cleavage Sites and Degradation Products Through Annu. Rev. Plant Biol. 2015.66:75-111. Downloaded from www.annualreviews.org Large-ScaleN-orC-TerminalLabelingandEnrichment..................... 101 ComparativeProteomicsofProteaseMutants.................................... 101 ProteinLifetimeAnalysisUsingStableIsotopes.................................. 101 WHY DO ORGANELLES NEED PROTEOLYSIS? Access provided by Chinese Academy of Agricultural Sciences (Agricultural Information Institute) on 05/10/16. For personal use only. Plastids, mitochondria, and peroxisomes each have their own complement of proteins, referred to as their proteomes. Most of these proteins are encoded by nuclear genes, but plastids and mito- chondria also contain a set of ∼85 and ∼50 organelle-encoded proteins, respectively. To generate and maintain fully functional organelles, these proteomes require the activity of processing pep- tidases, proteases, and aminopeptidases for a broad range of functions, including (a) removal 76 van Wijk PP66CH04-VanWijk ARI 30 March 2015 20:57 of presequences of nucleus-encoded organellar proteins; (b) N-terminal methionine cleavage of organelle-encoded proteins; (c) additional N- or C-terminal cleavages for the maturation, stabi- lization, and possibly activation of proteins; (d ) removal of misfolded, damaged, or aggregated proteins; (e) removal of unwanted proteins in response to environmental or developmental transi- tions (e.g., from glyoxysome to peroxisome or chloroplast to chromoplast) and during senescence; ( f ) release of membrane-bound proteins (e.g., transcription factors); and ( g) generation of protein degradation products as a respiratory substrate for stressed plants. The objective of this review is not only to summarize information about intraorganellar pro- teases, but also to identify principles that may govern substrate-protease relationships and protein lifetime as well as commonalities and differences in protease function and operation among the organelles. Over the last decade or so, there has been excellent progress in localizing and identi- fying organellar proteases. Loss-of-function mutants for many proteases have been identified in Arabidopsis and recently also in rice and maize. Furthermore, several proteases have been shown to be part of oligomeric structures, and for a handful there is (tentative) evidence for substrates. However, understanding of the role and mechanisms of proteolysis within plant organelles is lim- ited, and many basic questions remain to be answered. Furthermore, intraorganellar proteolysis is complemented in surprising ways by autophagy of chloroplasts, mitochondria, and peroxisomes. Now that it is more widely appreciated that mRNA is an imperfect proxy for protein abundance (136 and references therein), it is essential to turn our attention to plant proteolysis. Proteolysis (and autophagy) must be viewed as part of proteome homeostasis, now referred to as proteostasis. Understanding the contributions of protein preprocessing, proteolysis, and autophagy to organel- lar proteostasis will allow us to better understand plant development and function, but will also require systems-based approaches. COMMONALITIES BETWEEN PLASTIDIAL, MITOCHONDRIAL, AND PEROXISOMAL PROTEOLYSIS AND ORGANELLE TURNOVER There are multiple reasons why it is beneficial to review proteolysis in plastids, mitochondria, and peroxisomes together. First of all, both plastids and mitochondria have an endosymbiotic origin, and they are derived respectively from cyanobacteria and α-proteobacteria. Indeed, their gene expression machineries, their protein-folding and maturation factors, and many of their proteases are of prokaryotic origin. Furthermore, more than 100 proteins are dually targeted to both chloroplasts and mitochondria (22), including several proteases, such as LON1 (34), PREP1 (85), FTSH11 (169), α-MPP2 (15), and OOP (84). (Please note that throughout this review, Annu. Rev. Plant Biol. 2015.66:75-111. Downloaded from www.annualreviews.org all plant protein names are capitalized, as is the convention for several plant journals; similarly, all gene names are in italics and capitalized.) It is therefore likely that mechanisms for protease substrate recognition also have similarities. Although peroxisomes are unlikely to have an en- dosymbiotic origin (58), members of the prokaryotic-type protease families found in plastids and mitochondria, such as LON2 and DEG15, are also found in peroxisomes (58). Furthermore, sev- eral peroxisomal division proteins are shared with plastids and/or mitochondria, perhaps aiding in the coordination of biogenesis between these three organelles (58, 112). Particularly in leaves, Access provided by Chinese Academy of Agricultural Sciences (Agricultural Information Institute) on 05/10/16. For personal use only. chloroplasts, mitochondria, and peroxisomes are functionally coupled through various metabolic pathways, such as photorespiration (between all three organelles) (16, 58), biotin synthesis (be- tween peroxisomes and mitochondria) (110), and jasmonate biosynthesis (between peroxisomes and plastids). Therefore, coordination of their proteome compositions is needed and requires proteolysis. www.annualreviews.org • Plant Organelle Proteolysis 77 PP66CH04-VanWijk ARI 30 March 2015 20:57 SCOPE OF THIS REVIEW, KEY QUESTIONS, AND NEW FRONTIERS IN ORGANELLAR PROTEOLYSIS Degradomics: the Since 2010, reviews have been published on plastid proteases (73), mitochondrial proteases (67, systematic large-scale 90, 113), degradation of photosystem II (29, 194), and specific protease families in plants and or- analysis of protein