ATP-dependent association between subunits of Clp protease in pea chloroplasts.

The chloroplast ATP-dependent Clp protease (EC 3.4.21.92) is composed of the proteolytic subunit ClpP and the regulatory ATPase, ClpC. Although both subunits are found in the stroma, the interaction between the two is dynamic. When immunoprecipitation with antibodies against ClpC was performed on stroma from dark-adapted pea (Pisum sativum L. cv. Alaska) chloroplasts, ClpC but not ClpP was precipitated. However, when stroma was supplemented with ATP, both ClpC and ClpP were precipitated. Co-immunoprecipitation was even more efficient in the presence of ATP-gamma-S, suggesting that the association between regulatory and proteolytic subunits is dependent on binding of ATP to ClpC, but not its hydrolysis. To further test this association, stroma was fractionated by column chromatography, and the presence of Clp subunits in the different fractions was monitored immunologically. When stroma depleted of ATP was fractionated on an ion-exchange column, ClpP and ClpC migrated separately, whereas in the presence of ATP-gamma-S both subunits co-migrated. Similar results were observed in size-exclusion chromatography. To further characterize the precipitated enzyme, its proteolytic activity was assayed by testing its ability to degrade beta-casein. No degradation was observed in the absence of ATP, and degradation was inhibited in the presence of phenylmethylsulfonyl fluoride, consistent with Clp being an ATP-dependent serine protease. The activity of the isolated enzyme was further tested using chimeric OE33 as a model substrate. This protein was also degraded in an ATP-dependent manner, supporting the suggested role of Clp protease as a major housekeeping protease in the stroma.

Degradation of unassembled and damaged thylakoid proteins.

To study protein degradation in thylakoid membranes we identified, characterized and cloned thylakoid proteases, and then linked them to known proteolytic processes. Several families of chloroplast proteases were identified and characterized to different extents. FtsH, an ATP-dependent metalloprotease that belongs to the AAA-protein family, was found to be integral to the thylakoid membrane, facing the stroma. It is involved in both the degradation of unassembled subunits of membrane complexes, such as the Rieske Fe-S protein of the cytochrome complex, and the degradation of oxidatively damaged proteins such as the D1 protein of the photosystem II (PS II) reaction centre. Plant genomes contain multiple isomers of this protease but the functional significance of this multiplication is not clear yet. A second protease, the serine ATP-independent DegP, was found to be strongly associated with the luminal side of the thylakoid membrane. Although a specific role has not yet assigned for it, its location suggests that it can degrade luminal soluble proteins as well as luminally exposed regions of thylakoid membrane proteins.

Chloroplast and mitochondrial proteases in Arabidopsis. A proposed nomenclature.

The identity and scope of chloroplast and mitochondrial proteases in higher plants has only started to become apparent in recent years. Biochemical and molecular studies suggested the existence of Clp, FtsH, and DegP proteases in chloroplasts, and a Lon protease in mitochondria, although currently the full extent of their role in organellar biogenesis and function remains poorly understood. Rapidly accumulating DNA sequence data, especially from Arabidopsis, has revealed that these proteolytic enzymes are found in plant cells in multiple isomeric forms. As a consequence, a systematic approach was taken to catalog all these isomers, to predict their intracellular location and putative processing sites, and to propose a standard nomenclature to avoid confusion and facilitate scientific communication. For the Clp protease most of the ClpP isomers are found in chloroplasts, whereas one is mitochondrial. Of the ATPase subunits, the one ClpD and two ClpC isomers are located in chloroplasts, whereas both ClpX isomers are present in mitochondria. Isomers of the Lon protease are predicted in both compartments, as are the different forms of FtsH protease. DegP, the least characterized protease in plant cells, has the most number of isomers and they are predicted to localize in several cell compartments. These predictions, along with the proposed nomenclature, will serve as a framework for future studies of all four families of proteases and their individual isomers.

The protein disulfide isomerase-like RB60 is partitioned between stroma and thylakoids in Chlamydomonas reinhardtii chloroplasts.

Translation of psbA mRNA in Chlamydomonas reinhardtii chloroplasts is regulated by a redox signal(s). RB60 is a member of a protein complex that binds with high affinity to the 5'-untranslated region of psbA mRNA. RB60 has been suggested to act as a redox-sensor subunit of the protein complex regulating translation of chloroplast psbA mRNA. Surprisingly, cloning of RB60 identified high homology to the endoplasmic reticulum-localized protein disulfide isomerase, including an endoplasmic reticulum-retention signal at its carboxyl terminus. Here we show, by in vitro import studies, that the recombinant RB60 is imported into isolated chloroplasts of C. reinhardtii and pea in a transit peptide-dependent manner. Subfractionation of C. reinhardtii chloroplasts revealed that the native RB60 is partitioned between the stroma and the thylakoids. The nature of association of native RB60, and imported recombinant RB60, with thylakoids is similar and suggests that RB60 is tightly bound to thylakoids. The targeting characteristics of RB60 and the potential implications of the association of RB60 with thylakoids are discussed.

Light-stimulated degradation of an unassembled Rieske FeS protein by a thylakoid-bound protease: the possible role of the FtsH protease.

Unassembled subunits of the cytochrome b6f complex as well as components of other unassembled chloroplastic complexes are rapidly degraded within the organelle. However, the mechanisms involved in these proteolytic processes are obscure. When the Rieske FeS protein (RISP) is imported into isolated chloroplasts in vitro, some of the protein does not property assemble with the cytochrome complex, as determined by its sensitivity to exogenous protease. When assayed in intact, lysed, or fractionated chloroplasts, the imported RISP was found to be sensitive to endogenous proteases as well. The activity responsible for degradation of the unassembled protein was localized to the thylakoid membrane and characterized as a metalloprotease requiring zinc ions for its activity. The degradation rate was stimulated by light, but no involvement of ATP or redox control was observed. Instead, when the RISP that was attached to thylakoid membranes was first illuminated on ice, degradation proceeded in either light or darkness at equal rates suggesting a light-induced conformational change making the protein prone to degradation. Antibodies raised against native FtsH, a bacterial, membrane-bound, ATP-dependent, zinc-stimulated protease, effectively inhibited degradation of the unassembled RISP, suggesting a role for the chloroplastic FtsH in this process.

Effects of light and temperature on expression of ClpC, the regulatory subunit of chloroplastic Clp protease, in pea seedlings.

Chloroplasts contain homologues to the proteolytic and regulatory subunits of bacterial ATP-dependent Clp protease. We tested the effects of light and temperature on the expression of ClpC, the chloroplastic homologue of the regulatory subunit. ClpC mRNA was present in all tissues of pea seedlings, most abundantly in leaves. Higher levels of the message were found in green leaves than in etiolated ones. Exposure of etiolated seedlings to light resulted in further accumulation of the transcript. Similarly, ClpC protein level was lower in etiolated leaves, and increased upon exposure to light. Transferring seedlings from 25 degrees C to either 17 or 37 degrees C resulted in a decrease in both ClpC mRNA and protein, with the lower temperature being the most effective.

Immunological detection of proteins similar to bacterial proteases in higher plant chloroplasts.

Despite numerous demonstrations of protein degradation in chloroplasts of higher plants, little is known about the identity of the proteases involved in these reactions. To identify chloroplast proteases by immunological means, we investigated two proteins: ClpP, a protein similar to the proteolytic subunit of the bacterial ATP-dependent Clp protease, for which a gene is found in the chloroplast genome [Maurizi, M.R., Clark, W.P., Kim, S. H. & Gottesman, S. (1990) J. Biol. Chem. 265, 12546-12552] and PrcA, a cyanobacterial Ca2+-stimulated protease [Maldener, I., Lockau, W., Cai, Y. & Wolk, P. (1991) Mol. & Gen. Genet. 225, 113-120]. We expressed the clpP gene from rice in Escherichia coli, purified its product, and generated antibodies against the product. Western blot analysis revealed the ClpP protein in different leaf extracts. Analysis of fractionated barley chloroplasts revealed that the protein was associated with the stromal fraction. The expression of ClpP is light independent and tissue specific, as it was found in green and etiolated barley leaves, but not in roots. A second protein, similar to the cyanobacterial protease PrcA, was also detected in chloroplasts. Antibody against this protease recognized proteins in various leaf extracts. When pea chloroplasts were fractionated, the antibody only recognized a stromal protein. The expression of this protein is regulated by light, as it was found in green leaves, but not in etiolated leaves. The tissue specificity of PrcA was similar to that of ClpP in that it could not be detected in root extracts.

Cross-linking of the ryanodine receptor/Ca2+ release channel from skeletal muscle.

The relationship between the tetrameric organization of the ryanodine receptor (RyR) and its activity in binding of ryanodine was approached through cross-linking studies using several bifunctional reagents, differing in their linear dimensions and flexibility, as well as in the reactivity of the active groups. Cross-linking with: 1,5-difluoro-2,4-dinitrobenzene (DFDNB); di(fluoro-3-nitrophenyl)sulfone (DFNPS), 1-ethyl-3-(3-dimethylamino)propyl)carbodiimide (EDC); dimethyl suberimidate (DMS); ethylene glycol bis(succinimidylsuccinate) (EGS); and glutaraldehyde resulted in the disappearance of the, 470 kDa, RyR monomer protein band with concomitant appearance of additional bands of molecular masses higher than the monomer. At the relatively low concentrations of the reagents and the conditions used, RyR is the only cross-linked protein of SR membranes. The 'new' protein bands cross-react with antibodies against the RyR and correspond to dimers and tetramers of the RyR subunits while trimers were not detectable. DFDNB and DFNPS produced also a 560 kDa protein band which probably represents an intramolecular cross-linked monomer. The SDS-electrophoretic patterns of the cross-linked purified RyR resemble those of the membrane-bound receptor. Ryanodine binding to the high-affinity site was inhibited by modification of SR membranes with DFDNB and DFNPS, but not with DMS, EDC, EGS and glutaraldehyde, although RyR was completely cross-linked. The inhibition by DFDNB and DFNPS is due to modification of a specific lysyl residue which is also involved in the control of Ca2+ release. On the other hand, cross linking of the RyR with glutaraldehyde or EGS resulted in inhibition of ryanodine binding to the low-affinity, but not to the high-affinity binding sites. Thus, the cross-linking of two or more sites in each monomer (which lead to fixation of dimers or tetramers) did not prevent the conformational changes involved in the binding and occlusion of ryanodine at the high-affinity site, but inhibited its binding to the low-affinity sites.