The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis

Multiscale physiological responses to nitrogen supplementation of maize hybrids

Maize (Zea mays) production systems are heavily reliant on the provision of managed inputs such as fertilizers to maximize growth and yield. Hence, the effective use of nitrogen (N) fertilizer is crucial to minimize the associated financial and environmental costs, as well as maximize yield. However, how to effectively utilize N inputs for increased grain yields remains a substantial challenge for maize growers that requires a deeper understanding of the underlying physiological responses to N fertilizer application. We report a multiscale investigation of five field-grown maize hybrids under low or high N supplementation regimes that includes the quantification of phenolic and prenyl-lipid compounds, cellular ultrastructural features, and gene expression traits at three developmental stages of growth. Our results reveal that maize perceives the lack of supplemented N as a stress and, when provided with additional N, will prolong vegetative growth. However, the manifestation of the stress and responses to N supplementation are highly hybrid-specific. Eight genes were differentially expressed in leaves in response to N supplementation in all tested hybrids and at all developmental stages. These genes represent potential biomarkers of N status and include two isoforms of Thiamine Thiazole Synthase involved in vitamin B1 biosynthesis. Our results uncover a detailed view of the physiological responses of maize hybrids to N supplementation in field conditions that provides insight into the interactions between management practices and the genetic diversity within maize.

Cell-free translation system with artificial lipid-monolayer particles as a unique tool for characterizing lipid-monolayer binding proteins

Methods for functional analysis of proteins specifically localizing to lipid monolayers such as rubber particles and lipid droplets are limited. We have succeeded in establishing a system in which artificially prepared lipid monolayer particles are added to a cell-free translation system to confirm the properties of proteins that specifically bind to lipid monolayers in a translation-coupled manner.

The kiwifruit amyloplast proteome (kfALP): a resource to better understand the mechanisms underlying amyloplast biogenesis and differentiation

The biogenesis and differentiation (B&D) of amyloplasts contributes to fruit flavor and color. Here, remodeling of starch granules, thylakoids and plastoglobules was observed during development and ripening in two kiwifruit (Actinidia spp.) cultivars - yellow-fleshed 'Hort16A' and green-fleshed 'Hayward'. A protocol was developed to purify starch-containing plastids with a high degree of intactness, and amyloplast B&D was studied using label-free-based quantitative proteomic analyses in both cultivars. Over 3000 amyloplast-localized proteins were identified, of which >98% were quantified and defined as the kfALP (kiwifruit amyloplast proteome). The kfALP data were validated by Tandem-Mass-Tag (TMT) labeled proteomics in 'Hort16A'. Analysis of the proteomic data across development and ripening revealed: 1) a conserved increase in the abundance of proteins participating in starch synthesis/degradation during both amyloplast B&D; 2) up-regulation of proteins for chlorophyll degradation and of plastoglobule-localized proteins associated with chloroplast breakdown and plastoglobule formation during amyloplast differentiation; 3) constitutive expression of proteins involved in ATP supply and protein import during amyloplast B&D. Interestingly, two different pathways of amyloplast B&D were observed in the two cultivars. In 'Hayward', significant increases in abundance of photosynthetic- and tetrapyrrole metabolism-related proteins were observed, but the opposite trend was observed in 'Hort16A'. In conclusion, analysis of the kfALP provides new insights into the potential mechanisms underlying amyloplast B&D with relevance to key fruit quality traits in contrasting kiwifruit cultivars.

Dalbergia odorifera undergoes massive molecular shifts in response to waterlogging combined with salinity

Field and greenhouse studies attempting to describe the molecular responses of plant species under waterlogging (WL) combined with salinity (ST) are almost nonexistent. We integrated transcriptional, metabolic, and physiological responses involving several crucial transcripts and common differentially expressed genes and metabolites in fragrant rosewood (Dalbergia odorifera) leaflets to dissect plant-specific molecular responses and patterns under WL combined with ST (SWL). We discovered that the synergistic pattern of the transcriptional response of fragrant rosewood under SWL was exclusively characterized by the number of regulated transcripts. The response patterns under SWL based on transcriptome and metabolome regulation statuses revealed different patterns (additive, dominant, neutral, minor, unilateral, and antagonistic) of transcripts or metabolites that were commonly regulated or expressed uniquely under SWL. Under SWL, the synergistic transcriptional response of several functional gene subsets was positively associated with several metabolomic and physiological responses related to the shutdown of the photosynthetic apparatus and the extensive degradation of starch into saccharides through α-amylase, β-amylase, and α-glucosidase or plastoglobuli accumulation. The dissimilarity between the regulation status and number of transcripts in plants under combined stresses led to nonsynergistic responses in several physiological and phytohormonal traits. As inferred from the impressive synergistic transcriptional response to morpho-physiological changes, combined stresses exhibited a gradually decreasing effect on the changes observed at the molecular level compared to those in the morphological one. Here, by characterizing the molecular responses and patterns of plant species under SWL, our study considerably improves our understanding of the molecular mechanisms underlying combined stress.

Arabidopsis FIBRILLIN6 influences carotenoid biosynthesis by directly promoting phytoene synthase activity

Carotenoids are health-promoting plastidial isoprenoids with essential functions in plants as photoprotectants and photosynthetic pigments in chloroplasts. They also accumulate in specialized plastids named chromoplasts, providing color to non-photosynthetic tissues such as flower petals and ripe fruit. Carotenoid accumulation in chromoplasts requires specialized structures and proteins such as fibrillins (FBNs). The FBN family includes structural components of carotenoid sequestering structures in chromoplasts and members with metabolic roles in chloroplasts and other plastid types. However, the association of FBNs with carotenoids in plastids other than chromoplasts has remained unexplored. Here, we show that Arabidopsis (Arabidopsis thaliana) FBN6 interacts with phytoene synthase (PSY), the first enzyme of the carotenoid pathway. FBN6, but not FBN4 (a FBN that does not interact with PSY), enhances the activity of plant PSY (but not of the bacterial PSY crtB) in Escherichia coli cells. Overexpression of FBN6 in Nicotiana benthamiana leaves results in a higher production of phytoene, the product of PSY activity, whereas loss of FBN6 activity in Arabidopsis mutants dramatically reduces the production of carotenoids during seedling de-etiolation and after exposure to high light. Our work hence demonstrates that FBNs promote not only the accumulation of carotenoids in chromoplasts but also their biosynthesis in chloroplasts.

Multi-omics analyses reveal the importance of chromoplast plastoglobules in carotenoid accumulation in citrus fruit

Chromoplasts act as a metabolic sink for carotenoids, in which plastoglobules serve as versatile lipoprotein particles. PGs in chloroplasts have been characterized. However, the features of PGs from non-photosynthetic plastids are poorly understood. We found that the development of chromoplast plastoglobules (CPGs) in globular and crystalloid chromoplasts of citrus is associated with alterations in carotenoid storage. Using Nycodenz density gradient ultracentrifugation, an efficient protocol for isolating highly purified CPGs from sweet orange (Citrus sinensis) pulp was established. Forty-four proteins were defined as likely comprise the core proteome of CPGs using comparative proteomics analysis. Lipidome analysis of different chromoplast microcompartments revealed that the nonpolar microenvironment within CPGs was modified by 35 triacylglycerides, two sitosterol esters, and one stigmasterol ester. Manipulation of the CPG-localized gene CsELT1 (esterase/lipase/thioesterase) in citrus calli resulted in increased lipids and carotenoids, which is further evidence that the nonpolar microenvironment of CPGs contributes to carotenoid accumulation and storage in the chromoplasts. This multi-feature analysis of CPGs sheds new light on the role of chromoplasts in carotenoid metabolism, paving the way for manipulating carotenoid content in citrus fruit and other crops.

Dynamic adaptation of the extremophilic red microalga Cyanidioschyzon merolae to high nickel stress

The order of Cyanidiales comprises seven acido-thermophilic red microalgal species thriving in hot springs of volcanic origin characterized by extremely low pH, moderately high temperatures and the presence of high concentrations of sulphites and heavy metals that are prohibitive for most other organisms. Little is known about the physiological processes underlying the long-term adaptation of these extremophiles to such hostile environments. Here, we investigated the long-term adaptive responses of a red microalga Cyanidioschyzon merolae, a representative of Cyanidiales, to extremely high nickel concentrations. By the comprehensive physiological, microscopic and elemental analyses we dissected the key physiological processes underlying the long-term adaptation of this model extremophile to high Ni exposure. These include: (i) prevention of significant Ni accumulation inside the cells; (ii) activation of the photoprotective response of non-photochemical quenching; (iii) significant changes of the chloroplast ultrastructure associated with the formation of prolamellar bodies and plastoglobuli together with loosening of the thylakoid membranes; (iv) activation of ROS amelioration machinery; and (v) maintaining the efficient respiratory chain functionality. The dynamically regulated processes identified in this study are discussed in the context of the mechanisms driving the remarkable adaptability of C. merolae to extremely high Ni levels exceeding by several orders of magnitude those found in the natural environment of the microalga. The processes identified in this study provide a solid basis for the future investigation of the specific molecular components and pathways involved in the adaptation of Cyanidiales to the extremely high Ni concentrations.

Diversification of Plastid Structure and Function in Land Plants

Plastids represent a largely diverse group of organelles in plant and algal cells that have several common features but also a broad spectrum of morphological, ultrastructural, biochemical, and physiological differences. Plastids and their structural and metabolic diversity significantly contribute to the functionality and developmental flexibility of the plant body throughout its lifetime. In addition to the multiple roles of given plastid types, this diversity is accomplished in some cases by interconversions between different plastids as a consequence of developmental and environmental signals that regulate plastid differentiation and specialization. In addition to basic plastid structural features, the most important plastid types, the newly characterized peculiar plastids, and future perspectives in plastid biology are also provided in this chapter.

Prospects of chloroplast metabolic engineering for developing nutrient-dense food crops

Addressing nutritional deficiencies in food crops through biofortification is a sustainable approach to tackling malnutrition. Biofortification is continuously being attempted through conventional breeding as well as through various plant biotechnological interventions, ranging from molecular breeding to genetic engineering and genome editing for enriching crops with various health-promoting metabolites. Genetic engineering is used for the rational incorporation of desired nutritional traits in food crops and predominantly operates through nuclear and chloroplast genome engineering. In the recent past, chloroplast engineering has been deployed as a strategic tool to develop model plants with enhanced nutritional traits due to the various advantages it offers over nuclear genome engineering. However, this approach needs to be extended for the nutritional enhancement of major food crops. Further, this platform could be combined with strategies, such as synthetic biology, chloroplast editing, nanoparticle-mediated rapid chloroplast transformation, and horizontal gene transfer through grafting for targeting endogenous metabolic pathways for overproducing native nutraceuticals, production of biopharmaceuticals, and biosynthesis of designer nutritional compounds. This review focuses on exploring various features of chloroplast genome engineering for nutritional enhancement of food crops by enhancing the levels of existing metabolites, restoring the metabolites lost during crop domestication, and introducing novel metabolites and phytonutrients needed for a healthy daily diet.

Xanthophyll esterases in association with fibrillins control the stable storage of carotenoids in yellow flowers of rapeseed (Brassica juncea)

Biosynthesis, stabilization, and storage of carotenoids are vital processes in plants that collectively contribute to the vibrant colors observed in flowers and fruits. Despite its importance, the carotenoid storage pathway remains poorly understood and lacks thorough characterization. We identified two homologous genes, BjA02.PC1 and BjB04.PC2, belonging to the esterase/lipase/thioesterase (ELT) family of acyltransferases. We showed that BjPCs in association with fibrillin gene BjFBN1b control the stable storage of carotenoids in yellow flowers of Brassica juncea. Through genetic, high-resolution mass spectrometry and transmission electron microscopy analyses, we demonstrated that both BjA02.PC1 and BjB04.PC2 can promote the accumulation of esterified xanthophylls, facilitating the formation of carotenoid-enriched plastoglobules (PGs) and ultimately producing yellow pigments in flowers. The elimination of BjPCs led to the redirection of metabolic flux from xanthophyll ester biosynthesis to lipid biosynthesis, resulting in white flowers for B. juncea. Moreover, we genetically verified the function of two fibrillin genes, BjA01.FBN1b and BjB05.FBN1b, in mediating PG formation and demonstrated that xanthophyll esters must be deposited in PGs for stable storage. These findings identified a previously unknown carotenoid storage pathway that is regulated by BjPCs and BjFBN1b, while offering unique opportunities for improving the stability, deposition, and bioavailability of carotenoids.

A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways

Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.

OsFBN7-OsKAS I module promotes formation of plastoglobules clusters in rice chloroplasts

Plastoglobules (PGs) contiguous with the outer leaflets of thylakoid membranes regulate lipid metabolism, plastid developmental transitions, and responses to environmental stimuli. However, the function of OsFBN7, a PG-core fibrillin gene in rice, has not been elucidated. Using molecular genetics and physiobiochemical approaches, we observed that OsFBN7 overexpression promoted PG clustering in rice chloroplasts. OsFBN7 interacted with two KAS I enzymes, namely OsKAS Ia and OsKAS Ib, in rice chloroplasts. Lipidomic analysis of chloroplast subcompartments, including PGs in the OsFBN7 overexpression lines, confirmed that levels of diacylglycerol (DAG), a chloroplast lipid precursor and monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), the main chloroplast membrane lipids, were increased in PGs and chloroplasts. Furthermore, OsFBN7 enhanced the abundances of OsKAS Ia/Ib in planta and their stability under oxidative and heat stresses. In addition, RNA sequencing and real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analyses showed that the expression of the DAG synthetase gene PAP1 and MGDG synthase gene MDG2 was upregulated by OsFBN7. In conclusion, this study proposes a new model in which OsFBN7 binds to OsKAS Ia/Ib in chloroplast and enhances their abundance and stability, thereby regulating the chloroplast and PG membrane lipids involved in the formation of PG clusters.

Lipid droplets are versatile organelles involved in plant development and plant response to environmental changes

Since decades plant lipid droplets (LDs) are described as storage organelles accumulated in seeds to provide energy for seedling growth after germination. Indeed, LDs are the site of accumulation for neutral lipids, predominantly triacylglycerols (TAGs), one of the most energy-dense molecules, and sterol esters. Such organelles are present in the whole plant kingdom, from microalgae to perennial trees, and can probably be found in all plant tissues. Several studies over the past decade have revealed that LDs are not merely simple energy storage compartments, but also dynamic structures involved in diverse cellular processes like membrane remodeling, regulation of energy homeostasis and stress responses. In this review, we aim to highlight the functions of LDs in plant development and response to environmental changes. In particular, we tackle the fate and roles of LDs during the plant post-stress recovery phase.

CRISPR/Cas9-mediated knockout of a polyester synthase-like gene delays flowering time in alfalfa

KEY MESSAGE

T-DNA and CRISPR/Cas9-mediated knockout of polyester synthase-like genes delays flowering time in Arabidopsis thaliana and Medicago sativa (alfalfa). Thus, we here present the first report of edited alfalfa with delayed flowering.

Genome-wide identification of the fibrillin gene family in chickpea (Cicer arietinum L.) and its response to drought stress

Fibrillin family members play multiple roles in growth, development, and protection against abiotic stress. In this study, we identified 12 potential CaFBNs that are ranging from 25 kDa-42.92 kDa and are mostly basic. These proteins were hydrophilic in nature and generally resided in the chloroplast. The CaFBN genes were located on different chromosomes like 1, 4, 5, and 7. All FBNs shared conserved motifs and possessed a higher number of stress-responsive elements. For evolutionary analysis, a phylogenetic tree of CaFBNs with other plants' FBNs was constructed and clustered into 11 FBN subgroups. For expression analysis, 21 day old chickpea seedling was exposed to dehydration stress by withholding water. We also performed various physiological and biochemical analyses to check that plant changes at the physiological and cellular levels while undergoing stress conditions. The transcript expression of CaFBNs was higher in aerial parts, especially in stems and leaves. Dehydration-specific transcriptome and qPCR analysis showed that FBN-1, FBN-2, and FBN-6 were highly expressed. In addition, our study provides a comprehensive overview of the FBN protein family and their importance during the dehydration stress condition in Cicer arietinum.

Overexpression of plastid lipid-associated protein in marine diatom enhances the xanthophyll synthesis and storage

Plastoglobules, which are lipoprotein structures surrounded by a single hydrophobic phospholipid membrane, are subcellular organelles in plant chromoplasts and chloroplasts. They contain neutral lipids, tocopherols, quinones, chlorophyll metabolites, carotenoids and their derivatives. Proteomic studies indicated that plastoglobules are involved in carotenoid metabolism and storage. In this study, one of the plastid lipid-associated proteins (PAP), the major protein in plastoglobules, was selected and overexpressed in Phaeodactylum tricornutum. The diameter of the plastoglobules in mutants was decreased by a mean of 19.2% versus the wild-type, while the fucoxanthin level was increased by a mean of 51.2%. All mutants exhibited morphological differences from the wild-type, including a prominent increase in the transverse diameter. Moreover, the unsaturated fatty acid levels were increased in different mutants, including an 18.9-59.3% increase in eicosapentaenoic acid content. Transcriptomic analysis revealed that PAP expression and the morphological changes altered xanthophyll synthesis and storage, which affected the assembly of the fucoxanthin chlorophyll a/c-binding protein and expression of antenna proteins as well as reduced the non-photochemical quenching activity of diatom cells. Therefore, metabolic regulation at the suborganelle level can be achieved by modulating PAP expression. These findings provide a subcellular structural site and target for synthetic biology to modify pigment and lipid metabolism in microalgae chassis cells.

Chromoplast plastoglobules recruit the carotenoid biosynthetic pathway and contribute to carotenoid accumulation during tomato fruit maturation

Tomato (Solanum lycopersicum) fruit maturation is associated with a developmental transition from chloroplasts (in mature green fruit) to chromoplasts (in red fruit). The hallmark red color of ripe tomatoes is due to carotenogenesis and accumulation of the red carotenoid lycopene inside chromoplasts. Plastoglobules (PG) are lipid droplets in plastids that are involved in diverse lipid metabolic pathways. In tomato, information on the possible role of PG in carotogenesis and the PG proteome is largely lacking. Here, we outline the role of PG in carotenogenesis giving particular attention to tomato fruit PG proteomes and metabolomes. The proteome analysis revealed the presence of PG-typical FBNs, ABC1K-like kinases, and metabolic enzymes, and those were decreased in the PG of tomato chromoplasts compared to chloroplasts. Notably, the complete β-carotene biosynthesis pathway was recruited to chromoplast PG, and the enzymes PHYTOENE SYNTHASE 1 (PSY-1), PHYTOENE DESATURASE (PDS), ZETA-CAROTENE DESATURASE (ZDS), and CAROTENOID ISOMERASE (CRTISO) were enriched up to twelvefold compared to chloroplast PG. We profiled the carotenoid and prenyl lipid changes in PG during the chloroplast to chromoplast transition and demonstrated large increases of lycopene and β-carotene in chromoplast PG. The PG proteome and metabolome are subject to extensive remodeling resulting in high accumulation of lycopene during the chloroplast-to-chromoplast transition. Overall, the results indicate that PGs contribute to carotenoid accumulation during tomato fruit maturation and suggest that they do so by functioning as a biosynthetic platform for carotenogenesis.

Genome-wide identification of wheat ABC1K gene family and functional dissection of TaABC1K3 and TaABC1K6 involved in drought tolerance

Activity of BC1 complex kinase (ABC1K) serves as an atypical kinase family involved in plant stress resistance. This study identified 44 ABC1K genes in the wheat genome, which contained three clades (I-III). TaABC1K genes generally had similar structural features, but differences were present in motif and exon compositions from different clade members. More type II functional divergence sites were detected between clade I and clade III and no positive selection site were found in TaABC1K family. The three-dimensional structure prediction by Alphafold2 showed that TaABC1K proteins had more α-helixes with a relatively even distribution, and different clade members had differences in the content of secondary structures. The cis-acting element analysis showed that TaABC1K genes contained abundant cis-acting elements related to plant hormones and environmental stress response in the promoter region, and generally displayed a significantly upregulated expression under drought stress. In particular, both TaABC1K3 and TaABC1K6 genes from clade I was highly induced by drought stress, and their overexpression in yeast and Arabidopsis enhanced drought tolerance by suppressing active oxygen burst and reducing photosynthesis impairment. Meanwhile, TaABC1K3 and TaABC1K6 could, respectively, complement the function of Arabidopsis abc1k3 and abc1k6 mutants and reduce photosynthesis damage caused by drought stress.

Fibrillin2 in chloroplast plastoglobules participates in photoprotection and jasmonate-induced senescence

Fibrillins (FBNs) are the major structural proteins of plastoglobules (PGs) in chloroplasts. PGs are associated with defense against abiotic and biotic stresses, as well as lipid storage. Although FBN2 is abundant in PGs, its independent function under abiotic stress has not yet been identified. In this study, the targeting of FBN2 to PGs was clearly demonstrated using an FBN2-YFP fusion protein. FBN2 showed higher expression in green photosynthetic tissues and was upregulated at the transcriptional level under high-light stress. The photosynthetic capacity of fbn2 knockout mutants generated using CRISPR/Cas9 technology decreased rapidly compared with that of wild-type (WT) plants under high-light stress. In addition to the photoprotective function of FBN2, fbn2 mutants had lower levels of plastoquinone-9 and plastochromanol-8. The fbn2 mutants were highly sensitive to methyl jasmonate (MeJA) and exhibited root growth inhibition and a pale-green phenotype due to reduced chlorophyll content. Consistently, upon MeJA treatment, the fbn2 mutants showed faster leaf senescence and more rapid chlorophyll degradation with decreased photosynthetic ability compared with the WT plants. The results of this study suggest that FBN2 is involved in protection against high-light stress and acts as an inhibitor of jasmonate-induced senescence in Arabidopsis (Arabidopsis thaliana).

The mysterious role of fibrillin in plastid metabolism: current advances in understanding

Fibrillins (FBNs) are a family of genes in cyanobacteria, algae, and plants. The proteins they encode possess a lipid-binding motif, exist in various types of plastids, and are associated with lipid bodies called plastoglobules, implicating them in lipid metabolism. FBNs present in the thylakoid and stroma are involved in the storage, transport, and synthesis of lipid molecules for photoprotective functions against high-light stress. In this review, the diversity of subplastid locations in the evolution of FBNs, regulation of FBNs expression by various stresses, and the role of FBNs in plastid lipid metabolism are comprehensively summarized and directions for future research are discussed.

Function of Protein Kinases in Leaf Senescence of Plants

Leaf senescence is an evolutionarily acquired process and it is critical for plant fitness. During senescence, macromolecules and nutrients are disassembled and relocated to actively growing organs. Plant leaf senescence process can be triggered by developmental cues and environmental factors, proper regulation of this process is essential to improve crop yield. Protein kinases are enzymes that modify their substrates activities by changing the conformation, stability, and localization of those proteins, to play a crucial role in the leaf senescence process. Impressive progress has been made in understanding the role of different protein kinases in leaf senescence recently. This review focuses on the recent progresses in plant leaf senescence-related kinases. We summarize the current understanding of the function of kinases on senescence signal perception and transduction, to help us better understand how the orderly senescence degeneration process is regulated by kinases, and how the kinase functions in the intricate integration of environmental signals and leaf age information.

The plastoglobule-localized protein AtABC1K6 is a Mn2+-dependent kinase necessary for timely transition to reproductive growth

The Absence of bc₁ Complex (ABC1) is an ancient, atypical protein kinase family that emerged prior to the archaeal-eubacterial divergence. Loss-of-function mutants in ABC1 genes are linked to respiratory defects in microbes and humans and to compromised photosynthetic performance and stress tolerance in plants. However, demonstration of protein kinase activity remains elusive, hampering their study. Here, we investigate a homolog from Arabidopsis thaliana, AtABC1K6, and demonstrate in vitro autophosphorylation activity, which we replicate with a human ABC1 ortholog. We also show that AtABC1K6 protein kinase activity requires an atypical buffer composition, including Mn²⁺ as a divalent cation cofactor and a low salt concentration. AtABC1K6 associates with plastoglobule lipid droplets of A. thaliana chloroplasts, along with five paralogs. We show that the protein kinase activity associated with isolated A. thaliana plastoglobules was inhibited at higher salt concentrations, but could accommodate Mg²⁺ as well as Mn²⁺, indicating salt sensitivity, but not the requirement for Mn²⁺, may be a general characteristic of ABC1 proteins. Finally, loss of functional AtABC1K6 impairs the developmental transition from vegetative to reproductive growth. This phenotype was complemented by the wild-type sequence of AtABC1K6, but not by a kinase-dead point mutant in the unique Ala-triad of the ATP-binding pocket, demonstrating the physiological relevance of the protein's kinase activity. We suggest that ABC1s are bona fide protein kinases with a unique regulatory mechanism. Our results open the door to detailed functional and mechanistic studies of ABC1 proteins and plastoglobules.

Singlet Oxygen Leads to Structural Changes to Chloroplasts during their Degradation in the Arabidopsis thaliana plastid ferrochelatase two Mutant

During stress, chloroplasts produce large amounts of reactive oxygen species (ROS). Chloroplasts also contain many nutrients, including 80% of a leaf's nitrogen supply. Therefore, to protect cells from photo-oxidative damage and to redistribute nutrients to sink tissues, chloroplasts are prime targets for degradation. Multiple chloroplast degradation pathways are induced by photo-oxidative stress or nutrient starvation, but the mechanisms by which damaged or senescing chloroplasts are identified, transported to the central vacuole and degraded are poorly defined. Here, we investigated the structures involved with degrading chloroplasts induced by the ROS singlet oxygen (1O2) in the Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant. Under mild 1O2 stress, most fc2 chloroplasts appeared normal, but had reduced starch content. A subset of chloroplasts was degrading, and some protruded into the central vacuole via 'blebbing' structures. A 3D electron microscopy analysis demonstrated that up to 35% of degrading chloroplasts contained such structures. While the location of a chloroplast within a cell did not affect the likelihood of its degradation, chloroplasts in spongy mesophyll cells were degraded at a higher rate than those in palisade mesophyll cells. To determine if degrading chloroplasts have unique structural characteristics, allowing them to be distinguished from healthy chloroplasts, we analyzed fc2 seedlings grown under different levels of photo-oxidative stress. A correlation was observed among chloroplast swelling, 1O2 signaling and the state of degradation. Finally, plastoglobule (PG) enzymes involved in chloroplast disassembly were upregulated while PGs increased their association with the thylakoid grana, implicating an interaction between 1O2-induced chloroplast degradation and senescence pathways.

More than just lipid balls: quantitative analysis of plastoglobule attributes and their stress-related responses

Plastoglobules are ubiquitous under non-stress conditions and their morphology, closely related to their composition, changes differently depending on the specific stress that the plant undergoes. Plastoglobules are lipoprotein structures attached to thylakoid membranes, which participate in chloroplast metabolism and stress responses. Their structure contains a coating lipid monolayer and a hydrophobic core that differ in composition. Their function in chloroplasts has been studied focussing on their composition. However, we currently lack a comprehensive study that quantitatively evaluates the occurrence and morphology of plastoglobules. Following a literature search strategy, we quantified the main morphological attributes of plastoglobules from photosynthetic chloroplasts of more than 1000 TEM images published over the last 53 years, covering more than 100 taxa and 15 stress types. The analysis shows that plastoglobules under non-stress conditions are spherical, with an average diameter of 100-200 nm and cover less than 3% of the chloroplast cross-section area. This percentage rises under almost every type of stress, particularly in senescence. Interestingly, an apparent trade-off between increasing either the number or the diameter of plastoglobules governs this response. Our results show that plastoglobules are ubiquitous in chloroplasts of higher plants under non-stress conditions. Besides, provided the specific molecular composition of the core and coat of plastoglobules, we conclude that specific stress-related variation in plastoglobules attributes may allow inferring precise responses of the chloroplast metabolism.

Arabidopsis fibrillin 1-2 subfamily members exert their functions via specific protein-protein interactions

Fibrillins (FBNs) are plastidial proteins found in photosynthetic organisms from cyanobacteria to higher plants. The function of most FBNs remains unknown. Here, we focused on members of the FBN subgroup comprising FBN1a, FBN1b, and FBN2. We show that these three polypeptides interact between each other, potentially forming a network around the plastoglobule surface. Both FBN2 and FBN1s interact with allene oxide synthase, and the elimination of any of these FBNs results in a delay in jasmonate-mediated anthocyanin accumulation in response to a combination of moderate high light and low temperature. Mutations in the genes encoding FBN1s or FBN2 also affect the protection of PSII under the combination of these stresses. Fully developed leaves of these mutants have lower maximum quantum efficiency of PSII (Fv/Fm) and higher oxidative stress than wild-type plants. These effects are additive, and the fbn1a-1b-2 triple mutant shows a stronger decrease in Fv/Fm and a greater increase in oxidative stress than fbn1a-1b or fbn2 mutants. Co-immunoprecipitation analysis indicated that FBN2 also interacts with other proteins involved in different metabolic processes. We propose that these fibrillins facilitate accurate positioning of different proteins involved in distinct metabolic processes, and that their elimination leads to dysfunction of those proteins.

Association of jasmonic acid priming with multiple defense mechanisms in wheat plants under high salt stress

Salinity is a global conundrum that negatively affects various biometrics of agricultural crops. Jasmonic acid (JA) is a phytohormone that reinforces multilayered defense strategies against abiotic stress, including salinity. This study investigated the effect of JA (60 μM) on two wheat cultivars, namely ZM9 and YM25, exposed to NaCl (14.50 dSm^-1) during two consecutive growing seasons. Morphologically, plants primed with JA enhanced the vegetative growth and yield components. The improvement of growth by JA priming is associated with increased photosynthetic pigments, stomatal conductance, intercellular CO₂, maximal photosystem II efficiency, and transpiration rate of the stressed plants. Furthermore, wheat cultivars primed with JA showed a reduction in the swelling of the chloroplast, recovery of the disintegrated thylakoids grana, and increased plastoglobuli numbers compared to saline-treated plants. JA prevented dehydration of leaves by increasing relative water content and water use efficiency via reducing water and osmotic potential using proline as an osmoticum. There was a reduction in sodium (Na⁺) and increased potassium (K⁺) contents, indicating a significant role of JA priming in ionic homeostasis, which was associated with induction of the transporters, viz., SOS1, NHX2, and HVP1. Exogenously applied JA mitigated the inhibitory effect of salt stress in plants by increasing the endogenous levels of cytokinins and indole acetic acid, and reducing the abscisic acid (ABA) contents. In addition, the oxidative stress caused by increasing hydrogen peroxide in salt-stressed plants was restrained by JA, which was associated with increased α-tocopherol, phenolics, and flavonoids levels and triggered the activities of superoxide dismutase and ascorbate peroxidase activity. This increase in phenolics and flavonoids could be explained by the induction of phenylalanine ammonia-lyase activity. The results suggest that JA plays a key role at the morphological, biochemical, and genetic levels of stressed and non-stressed wheat plants which is reflected in yield attributes. Hierarchical cluster analysis and principal component analyses showed that salt sensitivity was associated with the increments of Na⁺, hydrogen peroxide, and ABA contents. The regulatory role of JA under salinity stress was interlinked with increased JA level which consequentially improved ion transporting, osmoregulation, and antioxidant defense.

Bean and Pea Plastoglobules Change in Response to Chilling Stress

Plastoglobules (PGs) might be characterised as microdomains of the thylakoid membrane that serve as a platform to recruit proteins and metabolites in their spatial proximity in order to facilitate metabolic channelling or signal transduction. This study provides new insight into changes in PGs isolated from two plant species with different responses to chilling stress, namely chilling-tolerant pea (Pisum sativum) and chilling-sensitive bean (Phaseolus coccineus). Using multiple analytical methods, such as high-performance liquid chromatography and visualisation techniques including transmission electron microscopy and atomic force microscopy, we determined changes in PGs' biochemical and biophysical characteristics as a function of chilling stress. Some of the observed alterations occurred in both studied plant species, such as increased particle size and plastoquinone-9 content, while others were more typical of a particular type of response to chilling stress. Additionally, PGs of first green leaves were examined to highlight differences at this stage of development. Observed changes appear to be a dynamic response to the demands of photosynthetic membranes under stress conditions.

Insights into topology and membrane interaction characteristics of plastoglobule-localized AtFBN1a and AtLOX2

Plant chloroplasts harbor ubiquitous lipid droplets called plastoglobules. While physically connected to the thylakoid membrane, they are characterized by a unique set of about 30 proteins specifically associated with the plastoglobule. How these proteins selectively target the plastoglobule remains unknown. Protease shaving assays with isolated Arabidopsis thaliana thylakoid and plastoglobule show that a ca. 25 kD portion of the abundant structural protein of plastoglobules, Fibrillin 1a, is protected from protease digestion. Mapping of protease cleavage sites and experimentally identified phosphorylation sites onto a homology model of Fibrillin 1a indicates that this protected sequence corresponds to the C-terminal lipocalin-like domain, implicated in specific lipid binding. In contrast, protease shaving and membrane washing assays with another plastoglobule-associated protein harboring a C-terminal PLAT domain, Lipoxygenase 2, is consistent with an exposed PLAT domain positioned parallel with, and upon, the surface of the plastoglobule. We propose a model where conserved lipid-binding domains associate with either the surface or neutral core of the lipid droplet. Our study provides insight into the topology and membrane interactions of two plastoglobule-localized proteins.

Chloroplast dismantling in leaf senescence

In photosynthetic plant cells, chloroplasts act as factories of metabolic intermediates that support plant growth. Chloroplast performance is highly influenced by environmental cues. Thus, these organelles have the additional function of sensing ever changing environmental conditions, thereby playing a key role in harmonizing the growth and development of different organs and in plant acclimation to the environment. Moreover, chloroplasts constitute an excellent source of metabolic intermediates that are remobilized to sink tissues during senescence so that chloroplast dismantling is a tightly regulated process that plays a key role in plant development. Stressful environmental conditions enhance the generation of reactive oxygen species (ROS) by chloroplasts, which may lead to oxidative stress causing damage to the organelle. These environmental conditions trigger mechanisms that allow the rapid dismantling of damaged chloroplasts, which is crucial to avoid deleterious effects of toxic by-products of the degradative process. In this review, we discuss the effect of redox homeostasis and ROS generation in the process of chloroplast dismantling. Furthermore, we summarize the structural and biochemical events, both intra- and extraplastid, that characterize the process of chloroplast dismantling in senescence and in response to environmental stresses.

Isolation of Plastoglobules for Lipid Analyses

Plastoglobules are plastid compartments designed for the storage of neutral lipids. They share physical and structural characteristics with cytosolic lipid droplets. Hence, special care must be taken to avoid contamination by cytosolic lipid droplets during plastoglobule purification. We describe the isolation of pure plastoglobules from Arabidopsis thaliana leaves, and the methods we use to determine their lipid composition. After preparation of a crude chloroplast fraction, plastoglobules are isolated from plastid membranes by two steps of ultracentrifugation on discontinuous sucrose gradients. For lipid analyses, total lipids are then extracted by a standard chloroform-methanol protocol, and polar lipids are separated from neutral lipids by liquid-liquid extraction. While polar lipid classes are subsequently separated by thin-layer chromatography (TLC) with the classical Vitiello solvent mix, a double TLC development has to be performed for neutral lipids, to separate phytyl and steryl esters. Lipids are quantified by gas chromatography after conversion of the fatty acids into methyl esters.

Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks, and plastoglobular functions

Plastoglobules are dynamic protein-lipid microcompartments in plastids enriched for isoprenoid-derived metabolites. Chloroplast plastoglobules support formation, remodeling, and controlled dismantling of thylakoids during developmental transitions and environmental responses. However, the specific molecular functions of most plastoglobule proteins are still poorly understood. This review harnesses recent co-mRNA expression data from combined microarray and RNA-seq information in ATTED-II on an updated inventory of 34 PG proteins, as well as proteomics data across 30 Arabidopsis tissue types from ATHENA. Hierarchical clustering based on relative abundance for the plastoglobule proteins across non-photosynthetic and photosynthetic tissue types showed their coordinated protein accumulation across Arabidopsis parts, tissue types, development, and senescence. Evaluation of mRNA-based forced networks at different coefficient thresholds identified a central hub with seven plastoglobule proteins and four peripheral modules. Enrichment of specific nuclear transcription factors (e.g. Golden2-like) and support for crosstalk between plastoglobules and the plastid gene expression was observed, and specific ABC1 kinases appear part of a light signaling network. Examples of other specific findings are that FBN7b is involved with upstream steps of tetrapyrrole biosynthesis and that ABC1K9 is involved in starch metabolism. This review provides new insights into the functions of plastoglobule proteins and an improved framework for experimental studies.

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.

Chloroplast Localized FIBRILLIN11 Is Involved in the Osmotic Stress Response during Arabidopsis Seed Germination

Simple Summary

The FIBRILLIN11 (FBN11) of Arabidopsis has a lipid-binding FBN domain and a kinase domain. FBN11 is present in chloroplasts and is involved in salt and osmotic stress responses during seed germination. In mannitol, the seed germination rate of the fbn11 mutants significantly reduced compared to that of the wild type. The ABA-dependent and -independent stress response regulating genes were differentially expressed in fbn11 mutants and wild-type when grown in mannitol supplemented medium. These results suggest that chloroplast localized FBN11 is involved in mediating osmotic stress tolerance through the signaling pathway that regulates the stress response in the nucleus.

Abstract

Plants live in ever-changing environments, facing adverse environmental conditions including pathogen infection, herbivore attack, drought, high temperature, low temperature, nutrient deficiency, toxic metal soil contamination, high salt, and osmotic imbalance that inhibit overall plant growth and development. Plants have evolved mechanisms to cope with these stresses. In this study, we found that the FIBRILLIN11 (FBN11) gene in Arabidopsis, which has a lipid-binding FBN domain and a kinase domain, is involved in the plant’s response to abiotic stressors, including salt and osmotic stresses. FBN11 protein localizes to the chloroplast. FBN11 gene expression significantly changed when plants were exposed to the abiotic stress response mediators such as abscisic acid (ABA), sodium chloride (NaCl), and mannitol. The seed germination rates of fbn11 homozygous mutants in different concentrations of mannitol and NaCl were significantly reduced compared to wild type. ABA-dependent and -independent stress response regulatory genes were differentially expressed in the fbn11 mutant compared with wild type when grown in mannitol medium. These results suggest a clear role for chloroplast-localized FBN11 in mediating osmotic stress tolerance via the stress response regulatory signaling pathway in the nucleus.

Autophagy is required for lipid homeostasis during dark-induced senescence

Autophagy is an evolutionarily conserved mechanism that mediates the degradation of cytoplasmic components in eukaryotic cells. In plants, autophagy has been extensively associated with the recycling of proteins during carbon-starvation conditions. Even though lipids constitute a significant energy reserve, our understanding of the function of autophagy in the management of cell lipid reserves and components remains fragmented. To further investigate the significance of autophagy in lipid metabolism, we performed an extensive lipidomic characterization of Arabidopsis (Arabidopsis thaliana) autophagy mutants (atg) subjected to dark-induced senescence conditions. Our results revealed an altered lipid profile in atg mutants, suggesting that autophagy affects the homeostasis of multiple lipid components under dark-induced senescence. The acute degradation of chloroplast lipids coupled with the differential accumulation of triacylglycerols (TAGs) and plastoglobuli indicates an alternative metabolic reprogramming toward lipid storage in atg mutants. The imbalance of lipid metabolism compromises the production of cytosolic lipid droplets and the regulation of peroxisomal lipid oxidation pathways in atg mutants.

Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes

This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.

Lipidomes of phylogenetically different symbiotic dinoflagellates of corals

The structural base of all membranes of symbiotic dinoflagellates (SD) is composed of glycolipids and betaine lipids, whereas triacylglycerols (TG) constitute an energy reserve and are involved in biosynthesis of glycolipids. Since data on the SD lipidome and the host's influence on symbionts' lipidome are scanty, we analyzed and compared the lipidomes of SD isolated from the zoantharian Palythoa tuberculosa and the alcyonarian Sinularia heterospiculata. A sequencing of nuclear gene regions showed that both cnidarians hosted the dinoflagellates Cladocopium sp. (subclades C1 and C3), but the zoantharian also contained the dinoflagellates Durusdinium trenchii (clade D). The presence of the thermotolerant D. trenchii resulted in a higher unsaturation of mono- and digalactosyldiacylglycerols (MGDG and DGDG), but a lower unsaturation of sulfoquinovosyldiacylglycerol (SQDG). The same features were earlier described for same SD from a reef-building coral. Hence, the profile of glycolipid molecules, which form SD thylakoid membranes, seems to be species-specific and does not depend on the host's taxonomic position. In contrast, the betaine lipid molecular species profile of diacylglyceryl-3-O-carboxyhydroxymethylcholine (DGCC), which forms SD cell membranes, can be influenced by the host. The profiles of the TG molecular species from freshly isolated SD have been determined for the first time. These molecular species can be divided on the basis of the acyl group in sn-2 position. The TG with 16:0 acyl group in sn-2 position may enrich total TG of a cnidarian colony and originate from SD cytoplasm. In contrast, TG 18:3/18:4/18:3 may be biosynthetically related with DGDG and concentrated in SD plastoglobules. Our data may be useful for further investigations of natural and technogenic variations in microalgal lipids and symbiont-host interactions in marine ecosystems.

Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fibrillins (FBNs) constitute a plastid-lipid-associated protein family that plays a role in chloroplast development, lipids metabolism and stress responses in plants. Until now, FBNs have been functionally characterized in stability of thylakoid and responses to the different stress stimuli. Consequently, phylogeny, domain composition and structural features of 121 FBNs family proteins from ten representative species have been identified. As results, phylogenetic analysis demonstrated that FBNs proteins were grouped into 24 clades and further subdivided into three groups, including terrestrial plant-specific, algae-specific, and intermediate group. These FBNs genes had different numbers of introns and exons but encoded the conserved N-terminal chloroplast transport peptide (CTP) domains and plastid lipid-associated protein (PAP) domains, which greatly contributed to the sub-functionalization and neo-functionalization. Meanwhile, the CTP domains of eleven OsFBN proteins except OsFBN8 could help them transport into chloroplasts. The PAP domains of OsFBN2 and OsFBN4 showed the in vitro specific binding activity to C12-C22 fatty acids that were affected by YxD motif. The qRT-PCR analysis showed that OsFBN genes were differentially induced by heat stress and cold stress in rice. Collectively, this study has provided the new insights into the evolution, structure, and functions of FBN gene family and will help to elucidate the molecular mechanisms of these proteins functioning in growth, development and adaptations in the global climate change.

Genome-wide identification and characterization of the fibrillin gene family in Triticum aestivum

Background

The fibrillin (FBN) gene family is highly conserved and widely distributed in the photosynthetic organs of plants. Members of this gene family are involved in the growth and development of plants and their response to biotic and abiotic stresses. Wheat (Triticum aestivum), an important food crop, has a complex genetic background and little progress has occurred in the understanding of its molecular mechanisms.

Methods

In this study, we identified 26 FBN genes in the whole genome of T. aestivum through bioinformatic tools and biotechnological means. These genes were divided into 11 subgroups and were distributed on 11 chromosomes of T. aestivum. Interestingly, most of the TaFBN genes were located on the chromosomes 2A, 2B and 2D. The gene structure of each subgroup of gene family members and the position and number of motifs were highly similar.

Results

The evolutionary analysis results indicated that the affinities of FBNs in monocots were closer together. The tissue-specific analysis revealed that TaFBN genes were expressed in different tissues and developmental stages. In addition, some TaFBNs were involved in one or more biotic and abiotic stress responses. These results provide a basis for further study of the biological function of FBNs.

ABC1K10a, an atypical kinase, functions in plant salt stress tolerance

BACKGROUND

ABC1K (Activity of BC1 complex Kinase) is an evolutionarily primitive atypical kinase family widely distributed among prokaryotes and eukaryotes. The ABC1K protein kinases in Arabidopsis are predicted to localize either to the mitochondria or chloroplasts, in which plastid-located ABC1K proteins are involved in the response against photo-oxidative stress and cadmium-induced oxidative stress.

RESULTS

Here, we report that the mitochondria-localized ABC1K10a functions in plant salt stress tolerance by regulating reactive oxygen species (ROS). Our results show that the ABC1K10a expression is induced by salt stress, and the mutations in this gene result in overaccumulation of ROS and hypersensitivity to salt stress. Exogenous application of the ROS-scavenger GSH significantly represses ROS accumulation and rescues the salt hypersensitive phenotype of abc1k10a. ROS overaccumulation in abc1k10a mutants under salt stress is likely due to the defect in mitochondria electron transport chain. Furthermore, defects of several other mitochondria-localized ABC1K genes also result in salt hypersensitivity.

CONCLUSIONS

Taken together, our results reveal that the mitochondria-located ABC1K10a regulates mitochondrial ROS production and is a positive regulator of salt tolerance in Arabidopsis.

Protein Profiles of Lipid Droplets during the Hypersensitive Defense Response of Arabidopsis against Pseudomonas Infection

Lipid droplets (LDs) have classically been viewed as seed storage particles, yet they are now emerging as dynamic organelles associated with developmental and stress responses. Nevertheless, their involvement in plant immunity has still been little studied. Here, we found LD accumulation in Arabidopsis thaliana leaves that induced a hypersensitive response (HR) after Pseudomonas infection. We established a protocol to reproducibly isolate LDs and to analyze their protein content. The expression of GFP fusion proteins in Nicotiana benthamiana and in transgenic Arabidopsis lines validated the LD localization of glycerol-3-phosphate acyltransferase 4 (GPAT4) and 8 (GPAT8), required for cutin biosynthesis. Similarly, we showed LD localization of α-dioxygenase1 (α-DOX1) and caleosin3 (CLO3), involved in the synthesis of fatty acid derivatives, and that of phytoalexin-deficient 3 (PAD3), which is involved in camalexin synthesis. We found evidence suggesting the existence of different populations of LDs, with varying protein contents and distributions. GPAT4 and GPAT8 were associated with LDs inside stomata and surrounding cells of untreated leaves, yet they were mainly confined to LDs in guard cells after bacterial inoculation. By contrast, α-DOX1 and PAD3 were associated with LDs in the epidermal cells of HR-responding leaves, with PAD3 mostly restricted to cells near dead tissue, while CLO3 had a more ubiquitous distribution. As such, the nature of the proteins identified, together with the phenotypic examination of selected mutants, suggests that LDs participate in lipid changes and in the production and transport of defense components affecting the interaction of plants with invading pathogens.

Lipid droplets throughout the evolutionary tree

Intracellular lipid droplets are utilized for lipid storage and metabolism in organisms as evolutionarily diverse as animals, fungi, plants, bacteria, and archaea. These lipid droplets demonstrate great diversity in biological functions and protein and lipid compositions, yet fundamentally share common molecular and ultrastructural characteristics. Lipid droplet research has been largely fragmented across the diversity of lipid droplet classes and sub-classes. However, we suggest that there is great potential benefit to the lipid community in better integrating the lipid droplet research fields. To facilitate such integration, we survey the protein and lipid compositions, functional roles, and mechanisms of biogenesis across the breadth of lipid droplets studied throughout the natural world. We depict the big picture of lipid droplet biology, emphasizing shared characteristics and unique differences seen between different classes. In presenting the known diversity of lipid droplets side-by-side it becomes necessary to offer for the first time a consistent system of categorization and nomenclature. We propose a division into three primary classes that reflect their sub-cellular location: i) cytoplasmic lipid droplets (CYTO-LDs), that are present in the eukaryotic cytoplasm, ii) prokaryotic lipid droplets (PRO-LDs), that exist in the prokaryotic cytoplasm, and iii) plastid lipid droplets (PL-LDs), that are found in plant plastids, organelles of photosynthetic eukaryotes. Within each class there is a remarkable array of sub-classes displaying various sizes, shapes and compositions. A more integrated lipid droplet research field will provide opportunities to better build on discoveries and accelerate the pace of research in ways that have not been possible.

Lack of FIBRILLIN6 in Arabidopsis thaliana affects light acclimation and sulfate metabolism

Arabidopsis thaliana contains 13 fibrillins (FBNs), which are all localized to chloroplasts. FBN1 and FBN2 are involved in photoprotection of photosystem II, and FBN4 and FBN5 are thought to be involved in plastoquinone transport and biosynthesis, respectively. The functions of the other FBNs remain largely unknown. To gain insight into the function of FBN6, we performed coexpression and Western analyses, conducted fluorescence and transmission electron microscopy, stained reactive oxygen species (ROS), measured photosynthetic parameters and glutathione levels, and applied transcriptomics and metabolomics. Using coexpression analyses, FBN6 was identified as a photosynthesis-associated gene. FBN6 is localized to thylakoid and envelope membranes, and its knockout results in stunted plants. The delayed-growth phenotype cannot be attributed to altered basic photosynthesis parameters or a reduced CO₂ assimilation rate. Under moderate light stress, primary leaves of fbn6 plants begin to bleach and contain enlarged plastoglobules. RNA sequencing and metabolomics analyses point to an alteration in sulfate reduction in fbn6. Indeed, glutathione content is higher in fbn6, which in turn confers cadmium tolerance of fbn6 seedlings. We conclude that loss of FBN6 leads to perturbation of ROS homeostasis. FBN6 enables plants to cope with moderate light stress and affects cadmium tolerance.

Characterization of a Plastoglobule-Localized SOUL4 Heme-Binding Protein in Arabidopsis thaliana

Heme plays an active role in primary plant metabolic pathways as well as in stress signaling. In this study, we characterized the predicted heme-binding protein SOUL4. Proteomics evidence suggests that SOUL4 is a component of Arabidopsis plastoglobules (PGs, chloroplast lipid droplets). SOUL4 contains heme-binding motifs and the recombinant protein is shown here to bind heme in vitro. Fluorescence-tagged SOUL4 colocalized with the specific PG marker Fibrillin1A (FBN1A) in transiently transformed Nicotiana benthamiana leaves. In addition, SOUL4 cofractionated with another PG marker Fibrillin2 (FBN2) in sucrose gradient ultracentrifugation experiments. In vitro kinase experiments revealed that SOUL4 is phosphorylated by a yet unknown chloroplast protein kinase. Our data demonstrate that SOUL4 is a bona fide PG protein and may function in heme-buffering in the chloroplast.

Mutation of the Atypical Kinase ABC1K3 Partially Rescues the PROTON GRADIENT REGULATION 6 Phenotype in Arabidopsis thaliana

Photosynthesis is an essential pathway providing the chemical energy and reducing equivalents that sustain higher plant metabolism. It relies on sunlight, which is an inconstant source of energy that fluctuates in both intensity and spectrum. The fine and rapid tuning of the photosynthetic apparatus is essential to cope with changing light conditions and increase plant fitness. Recently PROTON GRADIENT REGULATION 6 (PGR6-ABC1K1), an atypical plastoglobule-associated kinase, was shown to regulate a new mechanism of light response by controlling the homeostasis of photoactive plastoquinone (PQ). PQ is a crucial electron carrier existing as a free neutral lipid in the photosynthetic thylakoid membrane. Perturbed homeostasis of PQ impairs photosynthesis and plant acclimation to high light. Here we show that a homologous kinase, ABC1K3, which like PGR6-ABC1K1 is associated with plastoglobules, also contributes to the homeostasis of the photoactive PQ pool. Contrary to PGR6-ABC1K1, ABC1K3 disfavors PQ availability for photosynthetic electron transport. In fact, in the abc1k1/abc1k3 double mutant the pgr6(abc1k1) the photosynthetic defect seen in the abc1k1 mutant is mitigated. However, the PQ concentration in the photoactive pool of the double mutant is comparable to that of abc1k1 mutant. An increase of the PQ mobility, inferred from the kinetics of its oxidation in dark, contributes to the mitigation of the pgr6(abc1k1) photosynthetic defect. Our results also demonstrate that ABC1K3 contributes to the regulation of other mechanisms involved in the adaptation of the photosynthetic apparatus to changes in light quality and intensity such as the induction of thermal dissipation and state transitions. Overall, we suggests that, besides the absolute concentration of PQ, its mobility and exchange between storage and active pools are critical for light acclimation in plants.

Plastoglobular protein 18 is involved in chloroplast function and thylakoid formation

Plastoglobules are lipoprotein particles that are found in different types of plastids. They contain a very specific and specialized set of lipids and proteins. Plastoglobules are highly dynamic in size and shape, and are therefore thought to participate in adaptation processes during either abiotic or biotic stresses or transitions between developmental stages. They are suggested to function in thylakoid biogenesis, isoprenoid metabolism, and chlorophyll degradation. While several plastoglobular proteins contain identifiable domains, others provide no structural clues to their function. In this study, we investigate the role of plastoglobular protein 18 (PG18), which is conserved from cyanobacteria to higher plants. Analysis of a PG18 loss-of-function mutant in Arabidopsis thaliana demonstrated that PG18 plays an important role in thylakoid formation; the loss of PG18 results in impaired accumulation, assembly, and function of thylakoid membrane complexes. Interestingly, the mutant accumulated less chlorophyll and carotenoids, whereas xanthophyll cycle pigments were increased. Accumulation of photosynthetic complexes is similarly affected in both a Synechocystis and an Arabidopsis PG18 mutant. However, the ultrastructure of cyanobacterial thylakoids is not compromised by the lack of PG18, probably due to its less complex architecture.

Plastoquinone homoeostasis by Arabidopsis proton gradient regulation 6 is essential for photosynthetic efficiency

Photosynthesis produces organic carbon via a light-driven electron flow from H2O to CO2 that passes through a pool of plastoquinone molecules. These molecules are either present in the photosynthetic thylakoid membranes, participating in photochemistry (photoactive pool), or stored (non-photoactive pool) in thylakoid-attached lipid droplets, the plastoglobules. The photoactive pool acts also as a signal of photosynthetic activity allowing the adaptation to changes in light condition. Here we show that, in Arabidopsis thaliana, proton gradient regulation 6 (PGR6), a predicted atypical kinase located at plastoglobules, is required for plastoquinone homoeostasis, i.e. to maintain the photoactive plastoquinone pool. In a pgr6 mutant, the photoactive pool is depleted and becomes limiting under high light, affecting short-term acclimation and photosynthetic efficiency. In the long term, pgr6 seedlings fail to adapt to high light and develop a conditional variegated leaf phenotype. Therefore, PGR6 activity, by regulating plastoquinone homoeostasis, is required to cope with high light.

Chloroplast Protein Degradation in Senescing Leaves: Proteases and Lytic Compartments

Leaf senescence is characterized by massive degradation of chloroplast proteins, yet the protease(s) involved is(are) not completely known. Increased expression and/or activities of serine, cysteine, aspartic, and metalloproteases were detected in senescing leaves, but these studies have not provided information on the identities of the proteases responsible for chloroplast protein breakdown. Silencing some senescence-associated proteases has delayed progression of senescence symptoms, yet it is still unclear if these proteases are directly involved in chloroplast protein breakdown. At least four cellular pathways involved in the traffic of chloroplast proteins for degradation outside the chloroplast have been described (i.e., "Rubisco-containing bodies," "senescence-associated vacuoles," "ATI1-plastid associated bodies," and "CV-containing vesicles"), which differ in their dependence on the autophagic machinery, and the identity of the proteins transported and/or degraded. Finding out the proteases involved in, for example, the degradation of Rubisco, may require piling up mutations in several senescence-associated proteases. Alternatively, targeting a proteinaceous protein inhibitor to chloroplasts may allow the inhibitor to reach "Rubisco-containing bodies," "senescence-associated vacuoles," "ATI1-plastid associated bodies," and "CV-containing vesicles" in essentially the way as chloroplast-targeted fluorescent proteins re-localize to these vesicular structures. This might help to reduce proteolytic activity, thereby reducing or slowing down plastid protein degradation during senescence.

Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides

BACKGROUND

Clostridium cellulovorans is a mesophilic, cellulosome-producing bacterium containing 57 genomic cellulosomal enzyme-encoding genes. In addition to cellulosomal proteins, C. cellulovorans also secretes non-cellulosomal proteins to degrade plant cell wall polysaccharides. Unlike other cellulosome-producing Clostridium species, C. cellulovorans can metabolize all major plant cell wall polysaccharides (cellulose, hemicelluloses, and pectins). In this study, we performed a temporal proteome analysis of C. cellulovorans to reveal strategies underlying plant cell wall polysaccharide degradation.

RESULTS

We cultured C. cellulovorans with five different carbon sources (glucose, cellulose, xylan, galactomannan, and pectin) and performed proteome analysis on cellular and secreted proteins. In total, we identified 1895 cellular proteins and 875 secreted proteins. The identified unique carbohydrate-degrading enzymes corresponding to each carbon source were annotated to have specific activity against each carbon source. However, we identified pectate lyase as a unique enzyme in C. cellulovorans cultivated on xylan, which was not previously associated with xylan degradation. We performed k-means clustering analysis for elucidation of temporal changes of the cellular and secreted proteins in each carbon sources. We found that cellular proteins in most of the k-means clusters are involved in carbohydrate metabolism, amino acid metabolism, translation, or membrane transport. When xylan and pectin were used as the carbon sources, the most increasing k-means cluster contained proteins involved in the metabolism of cofactors and vitamins. In case of secreted proteins of C. cellulovorans cultured either on cellulose or xylan, galactomannan, and pectin, the clusters with the most increasing trend contained either 25 cellulosomal proteins and five non-cellulosomal proteins or 8-19 cellulosomal proteins and 9-16 non-cellulosomal proteins, respectively. These differences might reflect mechanisms for degrading cellulose of other carbon source. Co-abundance analysis of the secreted proteins revealed that proteases and protease inhibitors accumulated coordinately. This observation implies that the secreted protease inhibitors and proteases protect carbohydrate-degrading enzymes from an attack from the plant.

CONCLUSION

In this study, we clarified, for the first time, the temporal proteome dynamics of cellular and secreted proteins in C. cellulovorans. This data will be valuable in understanding strategies employed by C. cellulovorans for degrading major plant cell wall polysaccharides.