The multifaceted role of Lon proteolysis in seedling establishment and maintenance of plant organelle function: living from protein destruction

Regulation of chloroplast protein degradation

Chloroplasts are unique organelles that not only provide sites for photosynthesis and many metabolic processes, but also are sensitive to various environmental stresses. Chloroplast proteins are encoded by genes from both nuclear and chloroplast genomes. During chloroplast development and responses to stresses, the robust protein quality control systems are essential for regulation of protein homeostasis and the integrity of chloroplast proteome. In this review, we summarize the regulatory mechanisms of chloroplast protein degradation refer to protease system, ubiquitin-proteasome system, and the chloroplast autophagy. These mechanisms symbiotically play a vital role in chloroplast development and photosynthesis under both normal or stress conditions.

Functional verification and screening of protein interacting with the slPHB3

slPHB3 was cloned from Salix linearistipularis, the amino acid sequence blast and phylogenetic tree analysis showed that slPHB3 has the most similarity with PHB3 from Populus trichocarpa using DNAMAN software and MEGA7 software. RT-qPCR results confirmed that the expression of slPHB3 was induced obviously under stress treatments. The growth of recombinant yeast cells was better than that of the control group under the stress treatment, indicating that slPHB3 may be involved in the stress response of yeast cells. The transgenic tobacco was treated with different concentrations of NaCl, NaHCO3 and H2O2, fresh weigh of overexpression tobacco were heavier than wild-types. The results showed that transgenic tobacco was more tolerant to salt and oxidation than wild-type tobacco. Expression of important genes including NHX1 and SOS1 in salt stress response pathways are steadily higher in overexpression tobacco than that in wild-types. We identified 17 proteins interacting with slPHB3 by yeast two-hybrid technique, most of these proteins were relation to the stresses. The salt tolerance of slPHB3 expressing yeast and slPHB3 overexpressing plants were better than that of the control. Ten stress-related proteins may interact with slPHB3, which preliminarily indicated that slPHB3 had a certain response relationship with salt stress. The study of slPHB3 under abiotic stress can improve our understanding of PHB3 gene function.

Organismal and Cellular Stress Responses upon Disruption of Mitochondrial Lonp1 Protease

Cells engage complex surveillance mechanisms to maintain mitochondrial function and protein homeostasis. LonP1 protease is a key component of mitochondrial quality control and has been implicated in human malignancies and other pathological disorders. Here, we employed two experimental systems, the worm Caenorhabditis elegans and human cancer cells, to investigate and compare the effects of LONP-1/LonP1 deficiency at the molecular, cellular, and organismal levels. Deletion of the lonp-1 gene in worms disturbed mitochondrial function, provoked reactive oxygen species accumulation, and impaired normal processes, such as growth, behavior, and lifespan. The viability of lonp-1 mutants was dependent on the activity of the ATFS-1 transcription factor, and loss of LONP-1 evoked retrograde signaling that involved both the mitochondrial and cytoplasmic unfolded protein response (UPR^mt and UPR^cyt) pathways and ensuing diverse organismal stress responses. Exposure of worms to triterpenoid CDDO-Me, an inhibitor of human LonP1, stimulated only UPR^cyt responses. In cancer cells, CDDO-Me induced key components of the integrated stress response (ISR), the UPR^mt and UPR^cyt pathways, and the redox machinery. However, genetic knockdown of LonP1 revealed a genotype-specific cellular response and induced apoptosis similar to CDDO-Me treatment. Overall, the mitochondrial dysfunction ensued by disruption of LonP1 elicits adaptive cytoprotective mechanisms that can inhibit cancer cell survival but diversely modulate organismal stress response and aging.

Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events

The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.

Changes in specific protein degradation rates in Arabidopsis thaliana reveal multiple roles of Lon1 in mitochondrial protein homeostasis

Mitochondrial Lon1 loss impairs oxidative phosphorylation complexes and TCA enzymes and causes accumulation of specific mitochondrial proteins. Analysis of over 400 mitochondrial protein degradation rates using ¹⁵ N labelling showed that 205 were significantly different between wild type (WT) and lon1-1. Those proteins included ribosomal proteins, electron transport chain subunits and TCA enzymes. For respiratory complexes I and V, decreased protein abundance correlated with higher degradation rate of subunits in total mitochondrial extracts. After blue native separation, however, the assembled complexes had slow degradation, while smaller subcomplexes displayed rapid degradation in lon1-1. In insoluble fractions, a number of TCA enzymes were more abundant but the proteins degraded slowly in lon1-1. In soluble protein fractions, TCA enzymes were less abundant but degraded more rapidly. These observations are consistent with the reported roles of Lon1 as a chaperone aiding the proper folding of newly synthesized/imported proteins to stabilise them and as a protease to degrade mitochondrial protein aggregates. HSP70, prohibitin and enzymes of photorespiration accumulated in lon1-1 and degraded slowly in all fractions, indicating an important role of Lon1 in their clearance from the proteome.

Essentials of Proteolytic Machineries in Chloroplasts

Plastids are unique organelles that can alter their structure and function in response to environmental and developmental stimuli. Chloroplasts are one type of plastid and are the sites for various metabolic processes, including photosynthesis. For optimal photosynthetic activity, the chloroplast proteome must be properly shaped and maintained through regulated proteolysis and protein quality control mechanisms. Enzymatic functions and activities are conferred by protein maturation processes involving consecutive proteolytic reactions. Protein abundances are optimized by the balanced protein synthesis and degradation, which is depending on the metabolic status. Malfunctioning proteins are promptly degraded. Twenty chloroplast proteolytic machineries have been characterized to date. Specifically, processing peptidases and energy-driven processive proteases are the major players in chloroplast proteome biogenesis, remodeling, and maintenance. Recently identified putative proteases are potential regulators of photosynthetic functions. Here we provide an updated, comprehensive overview of chloroplast protein degradation machineries and discuss their importance for photosynthesis. Wherever possible, we also provide structural insights into chloroplast proteases that implement regulated proteolysis of substrate proteins/peptides.

Specific Hsp100 Chaperones Determine the Fate of the First Enzyme of the Plastidial Isoprenoid Pathway for Either Refolding or Degradation by the Stromal Clp Protease in Arabidopsis

The lifespan and activity of proteins depend on protein quality control systems formed by chaperones and proteases that ensure correct protein folding and prevent the formation of toxic aggregates. We previously found that the Arabidopsis thaliana J-protein J20 delivers inactive (misfolded) forms of the plastidial enzyme deoxyxylulose 5-phosphate synthase (DXS) to the Hsp70 chaperone for either proper folding or degradation. Here we show that the fate of Hsp70-bound DXS depends on pathways involving specific Hsp100 chaperones. Analysis of individual mutants for the four Hsp100 chaperones present in Arabidopsis chloroplasts showed increased levels of DXS proteins (but not transcripts) only in those defective in ClpC1 or ClpB3. However, the accumulated enzyme was active in the clpc1 mutant but inactive in clpb3 plants. Genetic evidence indicated that ClpC chaperones might be required for the unfolding of J20-delivered DXS protein coupled to degradation by the Clp protease. By contrast, biochemical and genetic approaches confirmed that Hsp70 and ClpB3 chaperones interact to collaborate in the refolding and activation of DXS. We conclude that specific J-proteins and Hsp100 chaperones act together with Hsp70 to recognize and deliver DXS to either reactivation (via ClpB3) or removal (via ClpC1) depending on the physiological status of the plastid.

In this paper we report a relatively simple mechanism by which plant chloroplasts deal with inactive forms of DXS, the main rate-determining enzyme for the production of plastidial isoprenoids relevant for photosynthesis and development. We provide evidence supporting that particular members of the Hsp100 chaperone family contribute to either refold or degrade inactive DXS proteins specifically recognized by the J-protein adaptor J20 and delivered to Hsp70 chaperones. Our results also unveil a J-protein-based mechanism for substrate delivery to the Clp complex, the main protease in the chloroplast stroma. Together, this work allows a better understanding of how chloroplasts get rid of damaged DXS (and potentially other proteins), which should contribute to take more informed decisions in future approaches aimed to manipulate the levels of plastidial metabolites of interest (including vitamins, biofuels, or drugs against cancer and malaria) in crop plants.

Protein maturation and proteolysis in plant plastids, mitochondria, and peroxisomes

Plastids, mitochondria, and peroxisomes are key organelles with dynamic proteomes in photosynthetic eukaryotes. Their biogenesis and activity must be coordinated and require intraorganellar protein maturation, degradation, and recycling. The three organelles together are predicted to contain ∼200 presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar proteins, such as N-end degrons and tagging systems, have not been identified, but the substrate recognition mechanisms likely share similarities between organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, 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.

Shredding the signal: targeting peptide degradation in mitochondria and chloroplasts

The biogenesis and functionality of mitochondria and chloroplasts depend on the constant turnover of their proteins. The majority of mitochondrial and chloroplastic proteins are imported as precursors via their N-terminal targeting peptides. After import, the targeting peptides are cleaved off and degraded. Recent work has elucidated a pathway involved in the degradation of targeting peptides in mitochondria and chloroplasts, with two proteolytic components: the presequence protease (PreP) and the organellar oligopeptidase (OOP). PreP and OOP are specialized in degrading peptides of different lengths, with the substrate restriction being dictated by the structure of their proteolytic cavities. The importance of the intraorganellar peptide degradation is highlighted by the fact that elimination of both oligopeptidases affects growth and development of Arabidopsis thaliana.

Alternative transcription initiation and the AUG context configuration control dual-organellar targeting and functional competence of Arabidopsis Lon1 protease

Cellular homeostasis relies on components of protein quality control including chaperones and proteases. In bacteria and eukaryotic organelles, Lon proteases play a critical role in removing irreparably damaged proteins and thereby preventing the accumulation of deleterious degradation-resistant aggregates. Gene expression, live-cell imaging, immunobiochemical, and functional complementation approaches provide conclusive evidence for Lon1 dual-targeting to chloroplasts and mitochondria. Dual-organellar deposition of Lon1 isoforms depends on both transcriptional regulation and alternative translation initiation via leaky ribosome scanning from the first AUG sequence context that deviates extensively from the optimum Kozak consensus. Organelle-specific Lon1 targeting results in partial complementation of Arabidopsis lon1-1 mutants, whereas full complementation is solely accomplished by dual-organellar targeting. Both the optimal and non-optimal AUG sequence contexts are functional in yeast and facilitate leaky ribosome scanning complementing the pim1 phenotype when the mitochondrial presequence is used. Bioinformatic search identified a limited number of Arabidopsis genes with Lon1-type dual-targeting sequence organization. Lon4, the paralog of Lon1, has an ambiguous presequence likely evolved from the twin presequences of an ancestral Lon1-like gene, generating a single dual-targeted protein isoform. We postulate that Lon1 and its subfunctional paralog Lon4 evolved complementary subsets of transcriptional and posttranscriptional regulatory components responsive to environmental cues for dual-organellar targeting.

Evolution and significance of the Lon gene family in Arabidopsis organelle biogenesis and energy metabolism

Lon is the first identified ATP-dependent protease highly conserved across all kingdoms. Model plant species Arabidopsis thaliana has a small Lon gene family of four members. Although these genes share common structural features, they have distinct properties in terms of gene expression profile, subcellular targeting and substrate recognition motifs. This supports the notion that their functions under different environmental conditions are not necessarily redundant. This article intends to unravel the biological role of Lon proteases in energy metabolism and plant growth through an evolutionary perspective. Given that plants are sessile organisms exposed to diverse environmental conditions and plant organelles are semi-autonomous, it is tempting to suggest that Lon genes in Arabidopsis are paralogs. Adaptive evolution through repetitive gene duplication events of a single archaic gene led to Lon genes with complementing sets of subfunctions providing to the organism rapid adaptability for canonical development under different environmental conditions. Lon1 function is adequately characterized being involved in mitochondrial biogenesis, modulating carbon metabolism, oxidative phosphorylation and energy supply, all prerequisites for seed germination and seedling establishment. Lon is not a stand-alone proteolytic machine in plant organelles. Lon in association with other nuclear-encoded ATP-dependent proteases builds up an elegant nevertheless, tight interconnected circuit. This circuitry channels properly and accurately, proteostasis and protein quality control among the distinct subcellular compartments namely mitochondria, chloroplasts, and peroxisomes.

The proteasome and the degradation of oxidized proteins: Part II - protein oxidation and proteasomal degradation

Here, we review the role of oxidative protein modification as a signal for recognition and degradation of proteins. It was clearly demonstrated that the ATP- and ubiquitin-independent 20S proteasome is playing a key role in the selective removal of oxidized proteins. Furthermore, the current knowledge of the substrate susceptibility on the degradation of oxidized proteins and the role of the immunoproteasome will be highlighted.

Interplay between protein carbonylation and nitrosylation in plants

ROS and reactive nitrogen species (RNS) are key regulators of redox homeostasis in living organisms including plants. As control of redox homeostasis plays a central function in plant biology, redox proteomics could help in characterizing the potential roles played by ROS/RNS-induced posttranslational modification in plant cells. In this review, we focus on two posttranslational modifications: protein carbonylation (a marker of protein oxidation) and protein S-nitrosylation, both of which having recently emerged as important regulatory mechanisms during numerous fundamental biological processes. Here, we describe the recent progress in proteomic analysis of carbonylated and nitrosylated proteins and highlight the achievements made in understanding the physiological basis of these oxy/nitro modifications in plants. In addition, we document the existence of a relationship between ROS-based carbonylation and RNS-based nitrosylation thus supporting the finding that crosstalk between cellular signaling stress pathways induced by ROS and RNS could be mediated by specific protein modifications.

A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts

Over 100 proteins are found in both mitochondria and chloroplasts, via a variety of processes known generally as 'dual-targeting'. Dual-targeting has attracted interest from many different research groups because of its profound implications concerning the mechanisms of protein import into these organelles and the evolution of both the protein import machinery and the targeting sequences within the imported proteins. Beyond these aspects, dual-targeting is also interesting for its implications concerning shared functions between mitochondria and chloroplasts, and especially the control of the activities of these two very different energy organelles. We discuss each of these points in the light of the latest relevant research findings and make some suggestions for where research might be most illuminating in the near future. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.