Structural insight into the cooperation of chloroplast chaperonin subunits

Chaperonin: Co-chaperonin Interactions

Co-chaperonins function together with chaperonins to mediate ATP-dependent protein folding in a variety of cellular compartments. Chaperonins are evolutionarily conserved and form two distinct classes, namely, group I and group II chaperonins. GroEL and its co-chaperonin GroES form part of group I and are the archetypal members of this family of protein folding machines. The unique mechanism used by GroEL and GroES to drive protein folding is embedded in the complex architecture of double-ringed complexes, forming two central chambers that undergo conformational rearrangements that enable protein folding to occur. GroES forms a lid over the chamber and in doing so dislodges bound substrate into the chamber, thereby allowing non-native proteins to fold in isolation. GroES also modulates allosteric transitions of GroEL. Group II chaperonins are functionally similar to group I chaperonins but differ in structure and do not require a co-chaperonin. A significant number of bacteria and eukaryotes house multiple chaperonin and co-chaperonin proteins, many of which have acquired additional intracellular and extracellular biological functions. In some instances, co-chaperonins display contrasting functions to those of chaperonins. Human HSP60 (HSPD) continues to play a key role in the pathogenesis of many human diseases, in particular autoimmune diseases and cancer. A greater understanding of the fascinating roles of both intracellular and extracellular Hsp10 on cellular processes will accelerate the development of techniques to treat diseases associated with the chaperonin family.

Importation of taxadiene synthase into chloroplast improves taxadiene production in tobacco

MAIN CONCLUSION

Importation of taxadiene synthase into chloroplasts is important for the efficient heterologous production of taxadiene. Taxadiene, the first committed precursor to taxol, is synthesized from geranylgeranyl pyrophosphate (GGPP) by action of taxadiene synthase (TS). Heterologous production of taxadiene could potentially rely on both cytosolic mevalonic acid (MVA) pathway and the plastidic methylerythritol phosphate (MEP) pathway. We suggest the compartmentalized engineering in chloroplast as an efficient approach for taxadiene production. In this study, we directly introduced the TS gene from Taxus brevifolia into the tobacco chloroplast genome and found that the transplastomic plants accumulated a low content of taxadiene, ~ 5.6 μg/g dry weight (DW). Moreover, we tried a combination of MEP and MVA pathways for taxadiene synthesis by nuclear transformation with a truncated version of TS (without encoding a transit peptide) into the transplastomic plants. However, this did not further improve the taxadiene production. In contrast, we found that taxadiene could be produced up to 87.8 μg/g DW in leaves of transgenic plants expressing TS with a chloroplast transit peptide, which was significantly higher than that in leaves of transplastomic plants. Thus, this study highlights the importance of TS importation into chloroplast for production of taxadiene.

Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo

The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.

Hetero-oligomeric CPN60 resembles highly symmetric group-I chaperonin structure revealed by Cryo-EM

The chloroplast chaperonin system is indispensable for the biogenesis of Rubisco, the key enzyme in photosynthesis. Using Chlamydomonas reinhardtii as a model system, we found that in vivo the chloroplast chaperonin consists of CPN60α, CPN60β1 and CPN60β2 and the co-chaperonin of the three subunits CPN20, CPN11 and CPN23. In Escherichia coli, CPN20 homo-oligomers and all possible other chloroplast co-chaperonin hetero-oligomers are functional, but only that consisting of CPN11/20/23-CPN60αβ1β2 can fully replace GroES/GroEL under stringent stress conditions. Endogenous CPN60 was purified and its stoichiometry was determined to be 6:2:6 for CPN60α:CPN60β1:CPN60β2. The cryo-EM structures of endogenous CPN60αβ1β2/ADP and CPN60αβ1β2/co-chaperonin/ADP were solved at resolutions of 4.06 and 3.82 Å, respectively. In both hetero-oligomeric complexes the chaperonin subunits within each ring are highly symmetric. Through hetero-oligomerization, the chloroplast co-chaperonin CPN11/20/23 forms seven GroES-like domains, which symmetrically interact with CPN60αβ1β2. Our structure also reveals an uneven distribution of roof-forming domains in the dome-shaped CPN11/20/23 co-chaperonin and potentially diversified surface properties in the folding cavity of the CPN60αβ1β2 chaperonin that might enable the chloroplast chaperonin system to assist in the folding of specific substrates.

Complex Chaperone Dependence of Rubisco Biogenesis

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), a ∼530 kDa complex of 8 large (RbcL) and 8 small subunits (RbcS), mediates the fixation of atmospheric CO₂ into usable sugars during photosynthesis. Despite its fundamental role, Rubisco is a remarkably inefficient enzyme and thus is produced by plants in huge amounts. It has long been a key target for bioengineering with the goal to increase crop yields. However, such efforts have been hampered by the complex requirement of Rubisco biogenesis for molecular chaperones. Recent studies have identified an array of auxiliary factors needed for the folding and assembly of the Rubisco subunits. The folding of plant RbcL subunits is mediated by the cylindrical chloroplast chaperonin, Cpn60, and its cofactor Cpn20. Folded RbcL requires a number of additional Rubisco specific assembly chaperones, including RbcX, Rubisco accumulation factors 1 (Raf1) and 2 (Raf2), and the Bundle sheath defective-2 (BSD2), to mediate the assembly of the RbcL₈ intermediate complex. Incorporation of the RbcS and displacement of the assembly factors generates the active holoenzyme. An Escherichia coli strain expressing the chloroplast chaperonin and auxiliary factors now allows the expression of functional plant Rubisco, paving the way for Rubisco engineering by large scale mutagenesis. Here, we review our current understanding on how these chaperones cooperate to produce one of the most important enzymes in nature.

Rubisco Assembly in the Chloroplast

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step in the Calvin-Benson cycle, which transforms atmospheric carbon into a biologically useful carbon source. The slow catalytic rate of Rubisco and low substrate specificity necessitate the production of high levels of this enzyme. In order to engineer a more efficient plant Rubisco, we need to better understand its folding and assembly process. Form I Rubisco, found in green algae and vascular plants, is a hexadecamer composed of 8 large subunits (RbcL), encoded by the chloroplast genome and 8 small, nuclear-encoded subunits (RbcS). Unlike its cyanobacterial homolog, which can be reconstituted in vitro or in E. coli, assisted by bacterial chaperonins (GroEL-GroES) and the RbcX chaperone, biogenesis of functional chloroplast Rubisco requires Cpn60-Cpn20, the chloroplast homologs of GroEL-GroES, and additional auxiliary factors, including Rubisco accumulation factor 1 (Raf1), Rubisco accumulation factor 2 (Raf2) and Bundle sheath defective 2 (Bsd2). The discovery and characterization of these factors paved the way for Arabidopsis Rubisco assembly in E. coli. In the present review, we discuss the uniqueness of hetero-oligomeric chaperonin complex for RbcL folding, as well as the sequential or concurrent actions of the post-chaperonin chaperones in holoenzyme assembly. The exact stages at which each assembly factor functions are yet to be determined. Expression of Arabidopsis Rubisco in E. coli provided some insight regarding the potential roles for Raf1 and RbcX in facilitating RbcL oligomerization, for Bsd2 in stabilizing the oligomeric core prior to holoenzyme assembly, and for Raf2 in interacting with both RbcL and RbcS. In the long term, functional characterization of each known factor along with the potential discovery and characterization of additional factors will set the stage for designing more efficient plants, with a greater biomass, for use in biofuels and sustenance.

Reconstitution of Pure Chaperonin Hetero-Oligomer Preparations in Vitro by Temperature Modulation

Chaperonins are large, essential, oligomers that facilitate protein folding in chloroplasts, mitochondria, and eubacteria. Plant chloroplast chaperonins are comprised of multiple homologous subunits that exhibit unique properties. We previously characterized homogeneous, reconstituted, chloroplast-chaperonin oligomers in vitro, each composed of one of three highly homologous beta subunits from A. thaliana. In the current work, we describe alpha-type subunits from the same species and investigate their interaction with β subtypes. Neither alpha subunit was capable of forming higher-order oligomers on its own. When combined with β subunits in the presence of Mg-ATP, only the α2 subunit was able to form stable functional hetero-oligomers, which were capable of refolding denatured protein with native chloroplast co-chaperonins. Since β oligomers were able to oligomerize in the absence of α, we sought conditions under which αβ hetero-oligomers could be produced without contamination of β homo-oligomers. We found that β2 subunits are unable to oligomerize at low temperatures and used this property to obtain homogenous preparations of functional α2β2 hetero-oligomers. The results of this study highlight the importance of reaction conditions such as temperature and concentration for the reconstitution of chloroplast chaperonin oligomers in vitro.

Red algal Rubisco fails to accumulate in transplastomic tobacco expressing Griffithsia monilis RbcL and RbcS genes

In C3 plants, the carbon fixation step catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) represents a major rate-limiting step due to the competing oxygenation reaction, which leads to the energy-intensive photorespiration and lowers the overall photosynthetic efficiency. Hence, there is great biotechnological interest in replacing the Rubisco in C3 crops with a more efficient enzyme. The Rubisco enzymes from red algae are among the most attractive choices due to their remarkable preference for carboxylation over oxygenation reaction. However, the biogenesis of Rubisco is extremely complex. The Rubisco enzymes in plants, algae, and cyanobacteria are made up of eight large and eight small subunits. The folding of the large subunits and the assembly of the large subunits with the small subunits to form a functional holoenzyme require specific chaperonin complexes and assembly factors. As a result, previous success in expressing foreign Rubisco in plants has been limited to Rubisco large subunits from closely related plant species and simpler bacterial enzymes. In our previous work, we successfully replaced the Rubisco in tobacco with a cyanobacterial enzyme, which was able to support the phototrophic growth of the transgenic plants. In this work, we used the same approach to express the Rubisco subunits from the red alga Griffithsia monilis in tobacco chloroplasts in the absence of the tobacco Rubisco large subunit. Although the red algal Rubisco genes are being transcribed in tobacco chloroplasts, the transgenic plants lack functional Rubisco and can only grow in a medium containing sucrose. Our results suggest that co-expression of compatible chaperones will be necessary for successful assembly of red algal Rubisco in plants.

Chloroplast Chaperonin: An Intricate Protein Folding Machine for Photosynthesis

Group I chaperonins are large cylindrical-shaped nano-machines that function as a central hub in the protein quality control system in the bacterial cytosol, mitochondria and chloroplasts. In chloroplasts, proteins newly synthesized by chloroplast ribosomes, unfolded by diverse stresses, or translocated from the cytosol run the risk of aberrant folding and aggregation. The chloroplast chaperonin system assists these proteins in folding into their native states. A widely known protein folded by chloroplast chaperonin is the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), an enzyme responsible for the fixation of inorganic CO₂ into organic carbohydrates during photosynthesis. Chloroplast chaperonin was initially identified as a Rubisco-binding protein. All photosynthetic eucaryotes genomes encode multiple chaperonin genes which can be divided into α and β subtypes. Unlike the homo-oligomeric chaperonins from bacteria and mitochondria, chloroplast chaperonins are more complex and exists as intricate hetero-oligomers containing both subtypes. The Group I chaperonin requires proper interaction with a detachable lid-like co-chaperonin in the presence of ATP and Mg²⁺ for substrate encapsulation and conformational transition. Besides the typical Cpn10-like co-chaperonin, a unique co-chaperonin consisting of two tandem Cpn10-like domains joined head-to-tail exists in chloroplasts. Since chloroplasts were proposed as sensors to various environmental stresses, this diversified chloroplast chaperonin system has the potential to adapt to complex conditions by accommodating specific substrates or through regulation at both the transcriptional and post-translational levels. In this review, we discuss recent progress on the unique structure and function of the chloroplast chaperonin system based on model organisms Chlamydomonas reinhardtii and Arabidopsis thaliana. Knowledge of the chloroplast chaperonin system may ultimately lead to successful reconstitution of eukaryotic Rubisco in vitro.

Biogenesis and Metabolic Maintenance of Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) mediates the fixation of atmospheric CO₂ in photosynthesis by catalyzing the carboxylation of the 5-carbon sugar ribulose-1,5-bisphosphate (RuBP). Rubisco is a remarkably inefficient enzyme, fixing only 2-10 CO₂ molecules per second. Efforts to increase crop yields by bioengineering Rubisco remain unsuccessful, owing in part to the complex cellular machinery required for Rubisco biogenesis and metabolic maintenance. The large subunit of Rubisco requires the chaperonin system for folding, and recent studies have shown that assembly of hexadecameric Rubisco is mediated by specific assembly chaperones. Moreover, Rubisco function can be inhibited by a range of sugar-phosphate ligands, including RuBP. Metabolic repair depends on remodeling of Rubisco by the ATP-dependent Rubisco activase and hydrolysis of inhibitory sugar phosphates by specific phosphatases. Here, we review our present understanding of the structure and function of these auxiliary factors and their utilization in efforts to engineer more catalytically efficient Rubisco enzymes.

Proteome Profiling of Paulownia Seedlings Infected with Phytoplasma

Phytoplasma is an insect-transmitted pathogen that causes witches' broom disease in many plants. Paulownia witches' broom is one of the most destructive diseases threatening Paulownia production. The molecular mechanisms associated with this disease have been investigated by transcriptome sequencing, but changes in protein abundance have not been investigated with isobaric tags for relative and absolute quantitation. Previous results have shown that methyl methane sulfonate (MMS) can help Paulownia seedlings recover from the symptoms of witches' broom and reinstate a healthy morphology. In this study, a transcriptomic-assisted proteomic technique was used to analyze the protein changes in phytoplasma-infected Paulownia tomentosa seedlings, phytoplasma-infected seedlings treated with 20 and 60 mg·L^-1 MMS, and healthy seedlings. A total of 2,051 proteins were obtained, 879 of which were found to be differentially abundant in pairwise comparisons between the sample groups. Among the differentially abundant proteins, 43 were related to Paulownia witches' broom disease and many of them were annotated to be involved in photosynthesis, expression of dwarf symptom, energy production, and cell signal pathways.

Engineering chloroplasts to improve Rubisco catalysis: prospects for translating improvements into food and fiber crops

494 I. 495 II. 496 III. 496 IV. 499 V. 499 VI. 501 VII. 501 VIII. 502 IX. 505 X. 506 507 References 507 SUMMARY: The uncertainty of future climate change is placing pressure on cropping systems to continue to provide stable increases in productive yields. To mitigate future climates and the increasing threats against global food security, new solutions to manipulate photosynthesis are required. This review explores the current efforts available to improve carbon assimilation within plant chloroplasts by engineering Rubisco, which catalyzes the rate-limiting step of CO₂ fixation. Fixation of CO₂ and subsequent cycling of 3-phosphoglycerate through the Calvin cycle provides the necessary carbohydrate building blocks for maintaining plant growth and yield, but has to compete with Rubisco oxygenation, which results in photorespiration that is energetically wasteful for plants. Engineering improvements in Rubisco is a complex challenge and requires an understanding of chloroplast gene regulatory pathways, and the intricate nature of Rubisco catalysis and biogenesis, to transplant more efficient forms of Rubisco into crops. In recent times, major advances in Rubisco engineering have been achieved through improvement of our knowledge of Rubisco synthesis and assembly, and identifying amino acid catalytic switches in the L-subunit responsible for improvements in catalysis. Improving the capacity of CO₂ fixation in crops such as rice will require further advances in chloroplast bioengineering and Rubisco biogenesis.

Functional conservation and divergence of GmCHLI genes in polyploid soybean

Polyploidy is prevalent in nature. As the fate of duplicated genes becomes more complicated when the encoded proteins function as oligomers, functional investigations into duplicated oligomer-encoding genes in polyploid genomes will facilitate our understanding of how traits are expressed. In this study, we identified GmCHLI1, a gene encoding the I subunit of magnesium (Mg)-chelatase, which functions in hexamers as responsible for the semi-dominant etiolation phenotype in soybean. Four GmCHLI copies derived from two polyploidy events were identified in the soybean genome. Further investigation with regard to expression patterns indicated that these four copies have diverged into two pairs; mutation in the other copy of the pair that includes GmCHLI1 also resulted in a chlorophyll-deficient phenotype. Protein interaction assays showed that these four GmCHLIs can interact with each other, but stronger interactions were found with mutated subunits. The results indicate that, in polyploidy, deficiency in each copy of duplicated oligomer-encoding genes could result in a mutant phenotype due to hetero-oligomer formation, which is different from the model of allelic dosage or functional redundancy. In addition, we interestingly found an increase in isoflavonoids in the heterozygous etiolated plants, which might be useful for improving soybean seed quality.