Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts

The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas

Tomato (Solanum lycopersicum) is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato's world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,278 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 545 and 92 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 91 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.

Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21

Triose phosphates (TPs) are the primary products of photosynthetic CO₂ fixation in chloroplasts, which need to be exported into the cytosol across the chloroplast inner envelope (IE) and outer envelope (OE) membranes to sustain plant growth. While transport across the IE is well understood, the mode of action of the transporters in the OE remains unclear. Here we present the high-resolution nuclear magnetic resonance (NMR) structure of the outer envelope protein 21 (OEP21) from garden pea, the main exit pore for TPs in C₃ plants. OEP21 is a cone-shaped β-barrel pore with a highly positively charged interior that enables binding and translocation of negatively charged metabolites in a competitive manner, up to a size of ~1 kDa. ATP stabilizes the channel and keeps it in an open state. Despite the broad substrate selectivity of OEP21, these results suggest that control of metabolite transport across the OE might be possible.

Reconstruction of the Native Biosynthetic System of Carotenoids in E. coli─Biosynthesis of a Series of Carotenoids Specific to Paprika Fruit

Capsanthin, capsorubin, cucurbitaxanthin A, and capsanthin 3,6-epoxide, a series of carotenoids specific to the red fruit of paprika (Capsicum annuum), were produced in pathway-engineered Escherichia coli cells. These cells functionally expressed multiple genes for eight carotenogenic enzymes, two of which, paprika capsanthin/capsorubin synthase (CaCCS) and zeaxanthin epoxidase (CaZEP), were designed to be located adjacently. The biosynthesis of these carotenoids, except for capsanthin, was the first successful attempt in E. coli. In a previous study, the levels of capsanthin synthesized were low despite the high expression of the CaCCS gene, which may have been due to the dual activity of CaCCS as a lycopene β-cyclase and CCS. An enhanced interaction between CaCCS and CaZEP that supplies antheraxanthin and violaxanthin, substrates for CaCCS, was considered to be crucial for an efficient reaction. To achieve this, we adapted S·tag and S-protein binding. The S·tag Thrombin Purification Kit (Novagen) is merchandized for in vitro affinity purification, and S·tag-fused proteins in the E. coli lysate are specifically trapped by S-proteins fixed on the agarose carrier. Furthermore, S-proteins have been reported to oligomerize via C-terminal swapping. In the present study, CaCCS and CaZEP were individually fused to the S·tag and designed to interact on oligomerized S-protein scaffolds in E. coli, which led to the biosynthesis of not only capsanthin and capsorubin but also cucurbitaxanthin A and capsanthin 3,6-epoxide. The latter reaction by CaCCS was assigned for the first time. This approach reinforces the scaffold's importance for multienzyme pathways when native biosynthetic systems are reconstructed in microorganisms.

Plant environmental sensing relies on specialized plastids

In plants, plastids are thought to interconvert to various forms that are specialized for photosynthesis, starch and oil storage, and diverse pigment accumulation. Post-endosymbiotic evolution has led to adaptations and specializations within plastid populations that align organellar functions with different cellular properties in primary and secondary metabolism, plant growth, organ development, and environmental sensing. Here, we review the plastid biology literature in light of recent reports supporting a class of 'sensory plastids' that are specialized for stress sensing and signaling. Abundant literature indicates that epidermal and vascular parenchyma plastids display shared features of dynamic morphology, proteome composition, and plastid-nuclear interaction that facilitate environmental sensing and signaling. These findings have the potential to reshape our understanding of plastid functional diversification.

Molecular studies of cellulose synthase supercomplex from cotton fiber reveal its unique biochemical properties

Cotton fiber is a highly elongated and thickened single cell that produces large quantities of cellulose, which is synthesized and assembled into cell wall microfibrils by the cellulose synthase complex (CSC). In this study, we report that in cotton (Gossypium hirsutum) fibers harvested during secondary cell wall (SCW) synthesis, GhCesA 4, 7, and 8 assembled into heteromers in a previously uncharacterized 36-mer-like cellulose synthase supercomplex (CSS). This super CSC was observed in samples prepared using cotton fiber cells harvested during the SCW synthesis period but not from cotton stem tissue or any samples obtained from Arabidopsis. Knock-out of any of GhCesA 4, 7, and 8 resulted in the disappearance of the CSS and the production of fiber cells with no SCW thickening. Cotton fiber CSS showed significantly higher enzyme activity than samples prepared from knock-out cotton lines. We found that the microfibrils from the SCW of wild-type cotton fibers may contain 72 glucan chains in a bundle, unlike other plant materials studied. GhCesA4, 7, and 8 restored both the dwarf and reduced vascular bundle phenotypes of their orthologous Arabidopsis mutants, potentially by reforming the CSC hexamers. Genetic complementation was not observed when non-orthologous CesA genes were used, indicating that each of the three subunits is indispensable for CSC formation and for full cellulose synthase function. Characterization of cotton CSS will increase our understanding of the regulation of SCW biosynthesis.

The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource

We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.

TGD5 is required for normal morphogenesis of non-mesophyll plastids, but not mesophyll chloroplasts, in Arabidopsis

Stromules are dynamic membrane-bound tubular structures that emanate from plastids. Stromule formation is triggered in response to various stresses and during plant development, suggesting that stromules may have physiological and developmental roles in these processes. Despite the possible biological importance of stromules and their prevalence in green plants, their exact roles and formation mechanisms remain unclear. To explore these issues, we obtained Arabidopsis thaliana mutants with excess stromule formation in the leaf epidermis by microscopy-based screening. Here, we characterized one of these mutants, stromule biogenesis altered 1 (suba1). suba1 forms plastids with severely altered morphology in a variety of non-mesophyll tissues, such as leaf epidermis, hypocotyl epidermis, floral tissues, and pollen grains, but apparently normal leaf mesophyll chloroplasts. The suba1 mutation causes impaired chloroplast pigmentation and altered chloroplast ultrastructure in stomatal guard cells, as well as the aberrant accumulation of lipid droplets and their autophagic engulfment by the vacuole. The causal defective gene in suba1 is TRIGALACTOSYLDIACYLGLYCEROL5 (TGD5), which encodes a protein putatively involved in the endoplasmic reticulum (ER)-to-plastid lipid trafficking required for the ER pathway of thylakoid lipid assembly. These findings suggest that a non-mesophyll-specific mechanism maintains plastid morphology. The distinct mechanisms maintaining plastid morphology in mesophyll versus non-mesophyll plastids might be attributable, at least in part, to the differential contributions of the plastidial and ER pathways of lipid metabolism between mesophyll and non-mesophyll plastids.

Molecular changes of Arabidopsis thaliana plastoglobules facilitate thylakoid membrane remodeling under high light stress

Plants require rapid responses to adapt to environmental stresses. This includes dramatic changes in the size and number of plastoglobule lipid droplets within chloroplasts. Although the morphological changes of plastoglobules are well documented, little is known about the corresponding molecular changes. To address this gap, we have compared the quantitative proteome, oligomeric state, prenyl-lipid content and kinase activities of Arabidopsis thaliana plastoglobules under unstressed and 5-day light-stressed conditions. Our results show a specific recruitment of proteins related to leaf senescence and jasmonic acid biosynthesis under light stress, and identify nearly half of the plastoglobule proteins in high native molecular weight masses. Additionally, a specific increase in plastoglobule carotenoid abundance under the light stress was consistent with enhanced thylakoid disassembly and leaf senescence, supporting a specific role for plastoglobules in senescence and thylakoid remodeling as an intermediate storage site for photosynthetic pigments. In vitro kinase assays of isolated plastoglobules demonstrated kinase activity towards multiple target proteins, which was more pronounced in the plastoglobules of unstressed than light-stressed leaf tissue, and which was diminished in plastoglobules of the abc1k1/abc1k3 double-mutant. These results strongly suggest that plastoglobule-localized ABC1 kinases hold endogenous kinase activity, as these were the only known or putative kinases identified in the isolated plastoglobules by deep bottom-up proteomics. Collectively, our study reveals targeted changes to the protein and prenyl-lipid composition of plastoglobules under light stress that present strategies by which plastoglobules appear to facilitate stress adaptation within chloroplasts.

A Review of Starch Biosynthesis in Relation to the Building Block-Backbone Model

Starch is a water-insoluble polymer of glucose synthesized as discrete granules inside the stroma of plastids in plant cells. Starch reserves provide a source of carbohydrate for immediate growth and development, and act as long term carbon stores in endosperms and seed tissues for growth of the next generation, making starch of huge agricultural importance. The starch granule has a highly complex hierarchical structure arising from the combined actions of a large array of enzymes as well as physicochemical self-assembly mechanisms. Understanding the precise nature of granule architecture, and how both biological and abiotic factors determine this structure is of both fundamental and practical importance. This review outlines current knowledge of granule architecture and the starch biosynthesis pathway in relation to the building block-backbone model of starch structure. We highlight the gaps in our knowledge in relation to our understanding of the structure and synthesis of starch, and argue that the building block-backbone model takes accurate account of both structural and biochemical data.

A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses

COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.

Cellular Organization and Regulation of Plant Glycerolipid Metabolism

Great strides have been made in understanding how membranes and lipid droplets are formed and maintained in land plants, yet much more is to be learned given the complexity of plant lipid metabolism. A complicating factor is the multi-organellar presence of biosynthetic enzymes and unique compositional requirements of different membrane systems. This necessitates a rich network of transporters and transport mechanisms that supply fatty acids, membrane lipids and storage lipids to their final cellular destination. Though we know a large number of the biosynthetic enzymes involved in lipid biosynthesis and a few transport proteins, the regulatory mechanisms, in particular, coordinating expression and/or activity of the majority remain yet to be described. Plants undergoing stress alter their membranes' compositions, and lipids such as phosphatidic acid have been implicated in stress signaling. Additionally, lipid metabolism in chloroplasts supplies precursors for jasmonic acid (JA) biosynthesis, and perturbations in lipid homeostasis has consequences on JA signaling. In this review, several aspects of plant lipid metabolism are discussed that are currently under investigation: cellular transport of lipids, regulation of lipid biosynthesis, roles of lipids in stress signaling, and lastly the structural and oligomeric states of lipid enzymes.

Consequences of impaired 1-MDa TIC complex assembly for the abundance and composition of chloroplast high-molecular mass protein complexes

We report a systematic analysis of chloroplast high-molecular mass protein complexes using a combination of native gel electrophoresis and absolute protein quantification by MS^E. With this experimental setup, we characterized the effect of the tic56-3 mutation in the 1-MDa inner envelope translocase (TIC) on the assembly of the chloroplast proteome. We show that the tic56-3 mutation results in a reduction of the 1-MDa TIC complex to approximately 10% of wildtype levels. Hierarchical clustering confirmed the association of malate dehydrogenase (MDH) with an envelope-associated FtsH/FtsHi complex and suggested the association of a glycine-rich protein with the 1-MDa TIC complex. Depletion of this complex leads to a reduction of chloroplast ATPase to approx. 75% of wildtype levels, while the abundance of the FtsH/FtsHi complex is increased to approx. 140% of wildtype. The accumulation of the major photosynthetic complexes is not affected by the mutation, suggesting that tic56-3 plants can sustain a functional photosynthetic machinery despite a significant reduction of the 1-MDa TIC complex. Together our analysis expands recent efforts to catalogue the native molecular masses of chloroplast proteins and provides information on the consequences of impaired accumulation of the 1-MDa TIC translocase for chloroplast proteome assembly.

Starch granule initiation and morphogenesis-progress in Arabidopsis and cereals

Starch, the major storage carbohydrate in plants, is synthesized in plastids as semi-crystalline, insoluble granules. Many organs and cell types accumulate starch at some point during their development and maturation. The biosynthesis of the starch polymers, amylopectin and amylose, is relatively well understood and mostly conserved between organs and species. However, we are only beginning to understand the mechanism by which starch granules are initiated, and the factors that control the number of granules per plastid and the size/shape of granules. Here, we review recent progress in understanding starch granule initiation and morphogenesis. In Arabidopsis, granule initiation requires several newly discovered proteins with specific locations within the chloroplast, and also on the availability of maltooligosaccharides which act as primers for initiation. We also describe progress in understanding granule biogenesis in the endosperm of cereal grains-within which there is large interspecies variation in granule initiation patterns and morphology. Investigating whether this diversity results from differences between species in the functions of known proteins, and/or from the presence of novel, unidentified proteins, is a promising area of future research. Expanding our knowledge in these areas will lead to new strategies for improving the quality of cereal crops by modifying starch granule size and shape in vivo.

Chloroplast function revealed through analysis of GreenCut2 genes

Chloroplasts are the green plastids responsible for light-powered photosynthetic reactions and carbon assimilation in the plant cell. Our knowledge of chloroplast functions is constantly increasing and we now know this plastid is predicted to house around 3000 proteins. However, even with generous estimates, we do not know the function of more than 10-15% of these proteins. The next frontier in chloroplast research is to identify and characterize the function of the whole chloroplast proteome, a challenging task due to the inherent complexity a proteome possesses. A logical starting point is to identify and study proteins that have been determined experimentally to be localized in the chloroplast, conserved only among the photosynthetic lineage. These are the proteins with the most probable and important roles in chloroplast function. This review gives an introduction to the GreenCut2, a collection of proteins present only in photosynthetic organisms. By using recent large scale proteomics data, this cut was narrowed to include only those proteins experimentally verified to be localized in the chloroplast, and more specifically to the photosynthetic thylakoid membrane. By using highly informative bioinformatic approaches, the theoretical functional prediction for several of these uncharacterized GreenCut2 proteins is discussed.