The Clp protease system; a central component of the chloroplast protease network

Intra-plastid proteases play crucial and diverse roles in the development and maintenance of non-photosynthetic plastids and chloroplasts. Formation and maintenance of a functional thylakoid electron transport chain requires various protease activities, operating in parallel, as well as in series. This review first provides a short, referenced overview of all experimentally identified plastid proteases in Arabidopsis thaliana. We then focus on the Clp protease system which constitutes the most abundant and complex soluble protease system in the plastid, consisting of 15 nuclear-encoded members and one plastid-encoded member in Arabidopsis. Comparisons to the simpler Clp system in photosynthetic and non-photosynthetic bacteria will be made and the role of Clp proteases in the green algae Chlamydomonas reinhardtii will be briefly reviewed. Extensive molecular genetics has shown that the Clp system plays an essential role in Arabidopsis chloroplast development in the embryo as well as in leaves. Molecular characterization of the various Clp mutants has elucidated many of the consequences of loss of Clp activities. We summarize and discuss the structural and functional aspects of the Clp machinery, including progress on substrate identification and recognition. Finally, the Clp system will be evaluated in the context of the chloroplast protease network. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.     

Cytosolic Ca2+ pulses and protein kinase activation in the signal transduction pathways leading to the plant oxidative burst

The oxidative burst, the rapid production of O₂- and H₂O₂ by plant cells in response to pathogens and Stressors, is a critical step in plant disease resistance and is controlled by several different elicitor-initiated signaling pathways. While different defense elicitors appear to activate disparate initial steps in signaling the oxidative burst, all of the elicitors tested thus far appear to stimulate pathways that converge on the same three core signaling intermediates: 1) the Ca₂₊-independent activation of a mitogen-activated protein kinase (MAPK) family member, 2) the influx of Ca₂₊ into the cytosol, deriving most critically from an internal compartment, and 3) the Ca²⁺-dependent activation of additional protein kinases including a second MAPK homologue and possibly calcium dependent protein kinases (CDPKs). Data from several recent reports are summarized to place these signaling events into a complete and updated model of signaling to the plant oxidative burst.     

A salt stress-activated mitogen-activated protein kinase in soybean is regulated by phosphatidic acid in early stages of the stress response

Salt stress inhibits plant growth and development and plants activate kinase-dependent survival pathways in response to salt stress. However, the role of soybean mitogenactivated protein kinases (MAPKs) in salt stress response has yet to be characterized. In this study, we found that salt stress activates Glycine max MAP kinase 1 (GMK1), a soybean MAPK. The activity of GMK1 induced with increasing salt concentrations, up to 300 mM NaCl, after 5 min of the treatment and was regulated by post-translational modification. We found that mastoparan, a heteromeric G-protein activator, also activated GMK1, and that n-butanol, a phospholipase D inhibitor, and neomycin, a phospholipase C inhibitor, inhibited its activity. Moreover, GMK1 activity was reduced by suramin, a heteromeric G-protein inhibitor, and by two inhibitors of phosphatidic acid (PA) generation after 5 min of 300 mM NaCl treatment. Endogenous PA levels were highest 5 min after induction of salt stress, and exogenous PA directly activated GMK1. From these data, we propose that salt stress signaling is transduced from heteromeric G-protein to GMK1 via phospholipases in the early stages of the response to salt stress in soybean.     

ClpS1 Is a Conserved Substrate Selector for the Chloroplast Clp Protease System in Arabidopsis

Whereas the plastid caseinolytic peptidase (Clp) P protease system is essential for plant development, substrates and substrate selection mechanisms are unknown. Bacterial ClpS is involved in N-degron substrate selection and delivery to the ClpAP protease. Through phylogenetic analysis, we show that all angiosperms contain ClpS1 and some species also contain ClpS1-like protein(s). In silico analysis suggests that ClpS1 is the functional homolog of bacterial ClpS. We show that Arabidopsis thaliana ClpS1 interacts with plastid ClpC1,2 chaperones. The Arabidopsis ClpS1 null mutant (clps1) lacks a visible phenotype, and no genetic interactions with ClpC/D chaperone or ClpPR core mutants were observed. However, clps1, but not clpc1-1, has increased sensitivity to the translational elongation inhibitor chloramphenicol suggesting a link between translational capacity and ClpS1. Moreover, ClpS1 was upregulated in clpc1-1, and quantitative proteomics of clps1, clpc1, and clps1 clpc1 showed specific molecular phenotypes attributed to loss of ClpC1 or ClpS1. In particular, clps1 showed alteration of the tetrapyrrole pathway. Affinity purification identified eight candidate ClpS1 substrates, including plastid DNA repair proteins and Glu tRNA reductase, which is a control point for tetrapyrrole synthesis. ClpS1 interaction with five substrates strictly depended on two conserved ClpS1 residues involved in N-degron recognition. ClpS1 function, substrates, and substrate recognition mechanisms are discussed.     

The Arabidopsis Chloroplast Stromal N-Terminome: Complexities of Amino-Terminal Protein Maturation and Stability

Protein amino (N) termini are prone to modifications and are major determinants of protein stability in bacteria, eukaryotes, and perhaps also in chloroplasts. Most chloroplast proteins undergo N-terminal maturation, but this is poorly understood due to insufficient experimental information. Consequently, N termini of mature chloroplast proteins cannot be accurately predicted. This motivated an extensive characterization of chloroplast protein N termini in Arabidopsis (Arabidopsis thaliana) using terminal amine isotopic labeling of substrates and mass spectrometry, generating nearly 14,000 tandem mass spectrometry spectra matching to protein N termini. Many nucleus-encoded plastid proteins accumulated with two or three different N termini; we evaluated the significance of these different proteoforms. Alanine, valine, threonine (often in N-α-acetylated form), and serine were by far the most observed N-terminal residues, even after normalization for their frequency in the plastid proteome, while other residues were absent or highly underrepresented. Plastid-encoded proteins showed a comparable distribution of N-terminal residues, but with a higher frequency of methionine. Infrequent residues (e.g. isoleucine, arginine, cysteine, proline, aspartate, and glutamate) were observed for several abundant proteins (e.g. heat shock proteins 70 and 90, Rubisco large subunit, and ferredoxin-glutamate synthase), likely reflecting functional regulation through their N termini. In contrast, the thylakoid lumenal proteome showed a wide diversity of N-terminal residues, including those typically associated with instability (aspartate, glutamate, leucine, and phenylalanine). We propose that, after cleavage of the chloroplast transit peptide by stromal processing peptidase, additional processing by unidentified peptidases occurs to avoid unstable or otherwise unfavorable N-terminal residues. The possibility of a chloroplast N-end rule is discussed.Following synthesis, most proteins undergo various N-terminal (Nt) protein modifications, including removal of the Nt Met and signal peptide, N-terminal α-acetylation (NAA), ubiquitination, and acylations. These Nt modifications play an important role in the regulation of cellular functions. The N terminus of proteins has also been shown to be a major determinant of protein stability in bacteria (Varshavsky, 2011), eukaryotes (Graciet et al., 2009), mitochondria, and perhaps in plastids/chloroplasts (Apel et al., 2010; Nishimura et al., 2013; van Wijk, 2015). The role of the N terminus in protein stability is conceptualized in the N-end rule, which states that certain amino acids, when exposed at the N terminus of a protein, act as triggers for degradation (Bachmair et al., 1986; Dougan et al., 2012; Tasaki et al., 2012; Gibbs et al., 2014).Most of the approximately 3,000 plastid proteins are nucleus encoded (n-encoded) and are targeted to the plastid through an Nt chloroplast transit peptide (cTP). After import, the cTP is cleaved by the stromal processing peptidase (SPP; Richter and Lamppa, 1998; Trösch and Jarvis, 2011). The consensus site of cTP cleavage by SPP is only loosely defined, and the rules, mechanisms, and enzymes for possible subsequent processing, stabilization, and other posttranslational modifications (PTMs) are not well characterized (for discussion, see van Wijk, 2015). The exact N terminus is unknown for many chloroplast proteins and cannot be accurately predicted, because SPP specificity is not sufficiently understood (Emanuelsson et al., 2000; Zybailov et al., 2008) and probably also because additional Nt processing occurs for many chloroplast proteins (Fig. 1A). The approximately 85 plastid-encoded (p-encoded) proteins typically first undergo cotranslational Nt deformylation, followed by N-terminal Met excision (NME; Giglione et al., 2009; Fig. 1B); both these PTMs are required for normal plastid/chloroplast development and protein stability (Dirk et al., 2001, 2002; Giglione et al., 2003; Meinnel et al., 2006). Both n-encoded and p-encoded proteins can undergo NAA inside the plastid (Zybailov et al., 2008; Fig. 1). Postulated functions of NAA in eukaryotes include the mediation of protein location, assembly, and stability (Jones and O’Connor, 2011; Starheim et al., 2012; Hoshiyasu et al., 2013; Xu et al., 2015), thereby affecting a variety of processes, including drought tolerance in Arabidopsis (Arabidopsis thaliana; Linster et al., 2015).Open in a separate windowFigure 1.Conceptual illustration of Nt maturation of n-encoded and p-encoded proteins. Ac, Acetylated; MAP, Met amino peptidase; NAT, N-acetyltransferase; N-term, N-terminal; PDF, peptide deformylase. A, Nt maturation of n-encoded plastid proteins including removal of cTP by SPP and potential subsequent Nt modifications. B, Nt maturation of p-encoded proteins. *, The removal depends on the penultimate residue, generally following the N-terminal Met Excision (NME) rule; **, N-terminal acetylation typically occurs only for selected residues; “Results”).Typical proteomics work flows generally yield only partial coverage of protein sequences, and it is often difficult to know which peptides represent the true N termini (Nti) or C termini. Systematic identification of Nti or C termini requires specific labeling and enrichment strategies, such as combined fractional diagonal chromatography, developed by Gevaert and colleagues (Staes et al., 2011), and terminal amine isotopic labeling of substrates (TAILS), developed by the group of Overall (Kleifeld et al., 2011; Lange and Overall, 2013). These strategies allow the identification of different Nt proteoforms and were recently also applied to plants (Tsiatsiani et al., 2013; Carrie et al., 2015; Kohler et al., 2015; Zhang et al., 2015) and diatoms (Huesgen et al., 2013). We previously reported on Nti of chloroplast proteins based on tandem mass spectrometry (MS/MS) analysis, but because no Nt enrichment/labeling technique was used, only those that underwent NAA could be considered bona fide Nti (Zybailov et al., 2008). Nt Edman degradation sequencing was systematically carried out for thylakoid lumen proteins (Peltier et al., 2000, 2002) but not for stromal proteins or chloroplast membrane proteins with their Nti exposed to the stroma. The Nti of thylakoid lumen proteins are mostly generated by lumenal peptidases (Hsu et al., 2011; Midorikawa et al., 2014), and the thylakoid lumen contains a different set of peptidases than the stroma; hence, rules for Nt maturation and stability are likely different than those for stroma-exposed proteins.The objective of this study was to systematically determine the Nti of stroma-exposed chloroplast proteins of Arabidopsis (the N-terminome) and to provide a baseline for understanding Nt protein maturation and protein stability in the chloroplast stroma. To that end, we applied the TAILS technique and determined the Nti of approximately 250 chloroplast proteins by mass spectrometry (MS). We observed that many n-encoded plastid proteins accumulated with two or even three different Nt residues, in many cases both with and without NAA. The extent of accumulation of different Nt proteoforms is surprising and will be discussed. The p-encoded proteins generally showed very similar Nt residues as compared with the n-encoded proteins, with the exception of Met. Our data show that small, apolar, or hydroxylated residues (Ala, Val, Ser, and Thr) are the most frequent Nt residues of stromal proteins, whereas other residues are strictly avoided or are only present for very specific proteins likely to aid in their function. Chloroplast protein degradation products were also detected, with enrichment for peptides generated by cleavage between Arg and Thr residues. We present testable hypotheses for understanding Nt processing and maturation, stability, and a possible N-end rule in chloroplast stroma.     

Discovery of a Unique Clp Component,ClpF, in Chloroplasts: A Proposed Binary ClpF-ClpS1 Adaptor Complex Functions in Substrate Recognition and Delivery

Clp proteases are found in prokaryotes, mitochondria, and plastids where they play crucial roles in maintaining protein homeostasis (proteostasis). The plant plastid Clp machinery comprises a hetero-oligomeric ClpPRT proteolytic core, ATP-dependent chaperones ClpC and ClpD, and an adaptor protein, ClpS1. ClpS1 selects substrates to the ClpPR protease-ClpC chaperone complex for degradation, but the underlying substrate recognition and delivery mechanisms are currently unclear. Here, we characterize a ClpS1-interacting protein in Arabidopsis thaliana, ClpF, which can interact with the Clp substrate glutamyl-tRNA reductase. ClpF and ClpS1 mutually stimulate their association with ClpC. ClpF, which is only found in photosynthetic eukaryotes, contains bacterial uvrB/C and YccV protein domains and a unique N-terminal domain. We propose a testable model in which ClpS1 and ClpF form a binary adaptor for selective substrate recognition and delivery to ClpC, reflecting an evolutionary adaptation of the Clp system to the plastid proteome.     

Large Scale Comparative Proteomics of a Chloroplast Clp Protease Mutant Reveals Folding Stress, Altered Protein Homeostasis, and Feedback Regulation of Metabolism

The clpr2-1 mutant is delayed in development due to reduction of the chloroplast ClpPR protease complex. To understand the role of Clp proteases in plastid biogenesis and homeostasis, leaf proteomes of young seedlings of clpr2-1 and wild type were compared using large scale mass spectrometry-based quantification using an LTQ-Orbitrap and spectral counting with significance determined by G-tests. Virtually only chloroplast-localized proteins were significantly affected, indicating that the molecular phenotype was confined to the chloroplast. A comparative chloroplast stromal proteome analysis of fully developed plants was used to complement the data set. Chloroplast unfoldase ClpB3 was strongly up-regulated in both young and mature leaves, suggesting widespread and persistent protein folding stress. The importance of ClpB3 in the clp2-1 mutant was demonstrated by the observation that a CLPR2 and CLPB3 double mutant was seedling-lethal. The observed up-regulation of chloroplast chaperones and protein sorting components further illustrated destabilization of protein homeostasis. Delayed rRNA processing and up-regulation of a chloroplast DEAD box RNA helicase and polynucleotide phosphorylase, but no significant change in accumulation of ribosomal subunits, suggested a bottleneck in ribosome assembly or RNA metabolism. Strong up-regulation of a chloroplast translational regulator TypA/BipA GTPase suggested a specific response in plastid gene expression to the distorted homeostasis. The stromal proteases PreP1,2 were up-regulated, likely constituting compensation for reduced Clp protease activity and possibly shared substrates between the ClpP and PreP protease systems. The thylakoid photosynthetic apparatus was decreased in the seedlings, whereas several structural thylakoid-associated plastoglobular proteins were strongly up-regulated. Two thylakoid-associated reductases involved in isoprenoid and chlorophyll synthesis were up-regulated reflecting feedback from rate-limiting photosynthetic electron transport. We discuss the quantitative proteomics data and the role of Clp proteolysis using a “systems view” of chloroplast homeostasis and metabolism and provide testable hypotheses and putative substrates to further determine the significance of Clp-driven proteolysis.Intracellular proteolysis is important for regulation of metabolic and signaling pathways as well as protein homeostasis and viability of cells and organelles. Chloroplasts contain multiple soluble and membrane-bound proteases and processing peptidases (1) presumably with partially overlapping substrates. These include stromal processing peptidase (2) and stromal PreP1,2 involved in degradation of cleaved transit peptides (3); various amino peptidases (4, 5); the thylakoid processing peptidases cTPA (6), TPP (7), and thylakoid/envelope signal peptidase I (8); and thylakoid-bound proteases SppA (9) and Egy1 (10) as well as stromal and thylakoid members of the Deg, FtsH, and Clp families (11–13). Together with several chaperone systems, including CPN60/CPN10, HSP70/DnaJ, HSP90, and ClpB3 (14), these proteases are part of the chloroplast protein homeostasis network. Importantly the connectivity and overlap of proteins within this homeostasis network is poorly understood; in particular it is unclear how protease substrates are recognized by the different proteolytic systems. Several suppressors of variegated FtsH protease mutants in Arabidopsis have elegantly demonstrated that the balance between protein synthesis and degradation plays an important role in chloroplast homeostasis (15–17). Comparative proteome analysis of chloroplast homeostasis mutants will provide insights in this homeostasis network as we recently showed for a protein sorting mutant (18), and it will identify candidate protease substrates.The Clp proteins form the largest plastid localized protease family with five serine-type ClpP (P1,P3–6) proteases, four non-catalytic ClpR (R1–4) proteins, three Clp AAA⁺ chaperones (C1,C2, and D), and several additional members (ClpT1,T2,S) with unknown functions (1, 13, 19). We note that we renamed Arabidopsis ClpS1,S2 and ClpT as ClpT1,T2 and ClpS to be consistent with the Escherichia coli nomenclature for ClpS (20). The ClpR proteins lack the three catalytic amino acid residues that are conserved across ClpP proteins (21). All proteins of the Arabidopsis Clp proteolytic system have been identified by mass spectrometry (13), including a potential substrate affinity regulator, ClpS.¹Recent evidence shows that the Clp proteolytic system plays a critical role in plant growth, development, and protein homeostasis. ClpP1 is plastid-encoded and was shown to be essential for shoot development in tobacco (22, 23). Down-regulation of the plastid-encoded CLPP1 gene in the green algae Chlamydomonas reinhardtii suggested that ClpP1 is involved in the degradation of the thylakoid-bound subunits of cytochrome b₆f and photosystem II (PSII)² complex (24, 25). Arabidopsis mutant clpr1-1 carries a premature stop codon in the CLPR1 gene and showed a virescent phenotype and delayed chloroplast development and differentiation (26). Maturation of 23 and 4.5 S chloroplast ribosomal RNA (rRNA) is delayed in clpr1-1 (26), but it is not clear how this is related to the loss of ClpR1 protein. Phenotypes of Arabidopsis antisense lines against CLPP4 (27) and CLPP6 (28) also showed delayed chloroplast and plant development as well as reduced accumulation of other ClpP,R subunits. Based on two-dimensional gel analysis, several chloroplast proteins were suggested to be substrates of the Clp machinery (28–30), but direct evidence is lacking. A null mutant for the CLPC1 chaperone (also named HSP93-V) resulted in reduced plant growth, chloroplast development, and protein import rates, but homozygous plants are autotrophic and seeds are viable (31–33). A null mutant for chaperone CLPC2 has no visible phenotype, whereas lack of both CLPC1 and CLPC2 prevents embryogenesis (34). Interestingly ClpC1 is also involved in accumulation of chlorophyll a oxygenase, which is responsible for conversion of chlorophyll a to chlorophyll b (35).In a previous study, we identified and characterized a T-DNA-tagged Arabidopsis thaliana mutant with reduced expression of CLPR2; this mutant was named clpr2-1 (36). Accumulation of the assembled 325-kDa ClpPRT complex was 2–3-fold reduced and resulted in delayed chloroplast and plant development with small chloroplasts and a pale green phenotype. The clpr2-1 mutant shows the strongest visible phenotype when seedlings are young. To better understand the role of the Clp machinery in chloroplast biogenesis and homeostasis and to discover potential Clp substrates, a comprehensive proteome analysis at different points in leaf development of the clpr2-1 mutant is presented in the current study. The methods to quantitatively analyze differences in protein accumulation have greatly improved over the last decade and have shifted from gel image-based quantification to quantification within the mass spectrometer (37–39). Taking advantage of these new developments and opportunities, we compared the leaf proteome of clpr2-1 and wt seedlings early in development using spectral counting. This was complemented with a comparative analysis of the chloroplast soluble proteome of fully developed leaf rosettes. The seedling proteome analysis showed that the strongest effects occurred within the chloroplast. The functional significance of one of the most up-regulated proteins, ClpB3, was confirmed by additional mutant analysis. Putative substrates for the Clp system suggested in recent studies (28–30, 35) are reviewed in the context of our findings. This study provides testable hypotheses to further determine the significance of Clp-driven proteolysis and provides new insights in the plastid protein homeostasis network and how secondary metabolism is intertwined with photosynthetic capacity. We show that a systems view of chloroplast biogenesis and proteome homeostasis is needed to identify putative protease substrates and to understand the role of proteolysis in chloroplast biology. Finally we believe that the experimental setup described in this study provides an attractive template for comparative proteome analysis of other (chloroplast) mutants.