Heat shock protein cognate 70-4 and an E3 ubiquitin ligase, CHIP, mediate plastid-destined precursor degradation through the ubiquitin-26S proteasome system in Arabidopsis

Chloroplast precursor protein preClpD overaccumulation triggers multilevel reprogramming of gene expression and a heat shock-like response

Thousands of nucleus-encoded chloroplast proteins are synthesized as precursors on cytosolic ribosomes and posttranslationally imported into chloroplasts. Cytosolic accumulation of unfolded chloroplast precursor proteins (e.g., under stress conditions) is hazardous to the cell. The global cellular responses and regulatory pathways involved in triggering appropriate responses are largely unknown. Here, by inducible and constitutive overexpression of ClpD-GFP to result in precursor protein overaccumulation, we present a comprehensive picture of multilevel reprogramming of gene expression in response to chloroplast precursor overaccumulation stress (cPOS), reveal a critical role of translational activation in the expression of cytosolic chaperones (heat-shock proteins, HSPs), and demonstrate that chloroplast-derived reactive oxygen species act as retrograde signal for the transcriptional activation of small HSPs. Furthermore, we reveal an important role of the chaperone ClpB1/HOT1 in maintaining cellular proteostasis upon cPOS. Together, our observations uncover a cytosolic heat shock-like response to cPOS and provide insights into the underlying molecular mechanisms.

Chloroplast protein translocation complexes and their regulation

Chloroplasts, refined through more than a billion years of evolution in plants and algae, act as highly efficient and resilient converters of solar energy. Additionally, these organelles function as complex anabolic factories, synthesizing a wide array of primary and secondary metabolites. The functionality of chloroplasts is dependent on the involvement of more than 3,000 proteins, the majority of which are encoded by the nuclear genome. These nucleus-encoded proteins must cross the chloroplast double lipid membrane to become functional. This translocation process is facilitated by the translocons at the outer and inner envelope membranes of chloroplasts (the outer chloroplast [TOC] and the inner chloroplast [TIC] complexes, respectively) and is driven by an energy-providing motor. Despite decades of research, the composition of these complexes remains highly controversial, especially regarding the TIC and motor components. However, recent studies have provided valuable insight into the TOC/TIC complexes, while also raising new questions about their mechanisms. In this review, we explore the latest advancements in understanding the structure and function of these complexes. Additionally, we briefly examine the processes of protein quality control, retrograde signaling, and discuss promising directions for future research in this field.

Wheat CHIP E3 ubiquitin ligase, TaCEU, forms a complex with TaCHSP70 to regulate targeted proteins, enhancing thermotolerance in transgenic Arabidopsis

Heat stress significantly impacts plant growth and productivity by causing protein misfolding, oxidative damage, and disruptions in cellular homeostasis. This stress is particularly critical during flowering and grain-filling stages, where even brief exposure to high temperatures can result in severe yield losses. Plants have evolved complex molecular mechanisms to mitigate heat stress, including the activation of heat shock proteins and the ubiquitin-proteasome system to maintain protein quality and cellular function. Understanding these processes is essential for breeding stress-resistant crops capable of adapting to climate change. In this study, we characterized TaCEU, a wheat carboxy-terminal Hsp70-interacting protein and E3 ubiquitin ligase, with a conserved structure across plant species. TaCEU is highly upregulated under heat and ABA stress and plays a pivotal role in maintaining protein homeostasis during heat stress. We confirmed TaCEU's role as an E3 ligase through in vitro ubiquitination assays, demonstrating its ability to form polyubiquitin chains. Subcellular localization studies confirmed TaCEU's presence in the nucleus and plasma membrane, suggesting functional versatility. Interaction studies identified TaAP and TaCHSP70 as key partners, with TaCEU and TaCHSP70 collaboratively targeting TaAP for degradation via the UPS proteasome system. Functional analysis of TaCEU-overexpressing Arabidopsis revealed enhanced thermotolerance, including increased root length, fresh weight, and antioxidant enzyme activity under heat stress. Transcript analysis further indicated the upregulation of heat stress-responsive genes, highlighting TaCEU's critical role in stress adaptation. These findings establish TaCEU as a key regulator of thermotolerance and protein homeostasis. TaCEU regulates protein stability and enhancing thermotolerance, making it a promising target for developing heat-resistant crops to address the challenges of climate change.

Transcriptomic and proteomic-based analysis of the mechanisms by which drought and salt stresses affect the quality of Isatidis Folium

Isatidis Folium, derived from the dried leaves of Isatis indigotica Fort., has been used for centuries as a traditional Chinese herb with antibacterial and antiviral properties. However, heterogeneity in cultivation conditions and climatic variations poses challenges to accurately and effectively evaluate its quality. Current quality control methods cannot provide a comprehensive and effective identification of herbal quality and preparation efficacy. This study aimed to investigate the impact of different environmental factors on the biosynthesis and accumulation of medicinal components and identify biomarker genes and functional proteins associated with abiotic stress responses of Isatis indigotica Fort. We proposed evaluating the quality of Isatidis Folium based on multi-component quantitative analysis and integrating transcriptomic, proteomic, and physiological indicators to elucidate the mechanisms of herbal quality variation. The results revealed that abiotic stress conditions significantly altered the levels of bioactive constituents, physiological indices, and specific genes and proteins. Notably, biological pathways such as porphyrin metabolism, photosynthesis, and carbon fixation by photosynthetic organisms were implicated in phototoxicity within the photosystem under abiotic stresses. Biological pathways related to indole metabolism, specifically phenylalanine, tyrosine, and tryptophan synthesis, tryptophan metabolism, and indole alkaloid synthesis, were recognized as critical regulatory networks modulating indole alkaloid content. Candidate biomarkers such as HemB, PsbB, RBS2, RIBA2, TRPA, and TRPB were identified as potential factors of quality deterioration under adverse conditions. Based on the integration of chemical analysis and multi-omics techniques, a new hierarchical quality control scenario for Isatidis Folium was finally proposed, providing a research foundation for the innovation-driven development of traditional Chinese medicine.

Genome-Wide Identification of the ClpB Gene Family in Tomato and Expression Analysis Under Heat Stress

Tomato is a widely grown horticultural crop, and its growth process is often affected by high temperatures. Caseinolytic Protease B (ClpB), a homologous protein to heat shock protein 101 (HSP101), plays a vital role in plant heat adaptation and development. In this study, we identified six SlClpB genes in tomatoes, distributed across four chromosomes. Collinearity analysis revealed that the gene pairs SlClpB-2 and SlClpB-3A, as well as SlClpB-3C and SlClpB-12, resulted from segmental duplication events. Phylogenetic and motif analyses showed that ClpB proteins possess highly conserved domains across different species. We used RNA-seq data to analyze the expression patterns of the ClpB family. Among them, SlClpB-3A and SlClpB-12 exhibited increased expression in multiple tissues under heat stress. Specifically, SlClpB-2, SlClpB-3A, and SlClpB-3C were highly expressed in the fruit orange stage and in flower buds under heat treatment, while in seedlings, SlClpB-2 and SlClpB-3A exhibited heat-induced expression. Real-time quantitative fluorescent PCR (qRT-PCR) results showed that the expression of SlClpB-2 and SlClpB-3A was significantly increased under heat stress in the leaves and buds of Ailsa Craig, Micro-Tom, and M82. Overall, our findings provide valuable insights into the regulatory mechanisms of SlClpB genes in response to heat stress.

The lowdown on breakdown: Open questions in plant proteolysis

Proteolysis, including post-translational proteolytic processing as well as protein degradation and amino acid recycling, is an essential component of the growth and development of living organisms. In this article, experts in plant proteolysis pose and discuss compelling open questions in their areas of research. Topics covered include the role of proteolysis in the cell cycle, DNA damage response, mitochondrial function, the generation of N-terminal signals (degrons) that mark many proteins for degradation (N-terminal acetylation, the Arg/N-degron pathway, and the chloroplast N-degron pathway), developmental and metabolic signaling (photomorphogenesis, abscisic acid and strigolactone signaling, sugar metabolism, and postharvest regulation), plant responses to environmental signals (endoplasmic-reticulum-associated degradation, chloroplast-associated degradation, drought tolerance, and the growth-defense trade-off), and the functional diversification of peptidases. We hope these thought-provoking discussions help to stimulate further research.

Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants

Proteome composition is dynamic and influenced by many internal and external cues, including developmental signals, light availability, or environmental stresses. Protein degradation, in synergy with protein biosynthesis, allows cells to respond to various stimuli and adapt by reshaping the proteome. Protein degradation mediates the final and irreversible disassembly of proteins, which is important for protein quality control and to eliminate misfolded or damaged proteins, as well as entire organelles. Consequently, it contributes to cell resilience by buffering against protein or organellar damage caused by stresses. Moreover, protein degradation plays important roles in cell signaling, as well as transcriptional and translational events. The intricate task of recognizing specific proteins for degradation is achieved by specialized systems that are tailored to the substrate's physicochemical properties and subcellular localization. These systems recognize diverse substrate cues collectively referred to as "degrons," which can assume a range of configurations. They are molecular surfaces recognized by E3 ligases of the ubiquitin-proteasome system but can also be considered as general features recognized by other degradation systems, including autophagy or even organellar proteases. Here we provide an overview of the newest developments in the field, delving into the intricate processes of protein recognition and elucidating the pathways through which they are recruited for degradation.

Chloroplast protein StFC-II was manipulated by a Phytophthora effector to enhance host susceptibility

Oomycete secretes a range of RxLR effectors into host cells to manipulate plant immunity by targeting proteins from several organelles. In this study, we report that chloroplast protein StFC-II is hijacked by a pathogen effector to enhance susceptibility. Phytophthora infestans RxLR effector Pi22922 is activated during the early stages of P. infestans colonization. Stable overexpression of Pi22922 in plants suppresses flg22-triggered reactive oxygen species (ROS) burst and enhances leaf colonization by P. infestans. A potato ferrochelatase 2 (FC-II, a nuclear-encoded chloroplast-targeted protein), a key enzyme for heme biosynthesis in chloroplast, was identified as a target of Pi22922 in the cytoplasm. The pathogenicity of Pi22922 in plants is partially dependent on FC-II. Overexpression of StFC-II decreases resistance of potato and Nicotiana benthamiana against P. infestans, and silencing of NbFC-II in N. benthamiana reduces P. infestans colonization. Overexpression of StFC-II increases heme content and reduces chlorophyll content and photosynthetic efficiency in potato leaves. Moreover, ROS accumulation both in chloroplast and cytoplasm is attenuated and defense-related genes are down-regulated in StFC-II overexpression transgenic potato and N. benthamiana leaves. Pi22922 inhibits E3 ubiquitin ligase StCHIP-mediated StFC-II degradation in the cytoplasm and promotes its accumulation in chloroplasts. In summary, this study characterizes a new mechanism that an oomycete RxLR effector suppresses host defenses by promoting StFC-II accumulation in chloroplasts, thereby compromising the host immunity and promoting susceptibility.

Elongation factor MdEF-Tu coordinates with heat shock protein MdHsp70 to enhance apple thermotolerance

High-temperature stress results in protein misfolding/unfolding and subsequently promotes the accumulation of cytotoxic protein aggregates that can compromise cell survival. Heat shock proteins (HSPs) function as molecular chaperones that coordinate the refolding and degradation of aggregated proteins to mitigate the detrimental effects of high temperatures. However, the relationship between HSPs and protein aggregates in apples under high temperatures remains unclear. Here, we show that an apple (Malus domestica) chloroplast-localized, heat-sensitive elongation factor Tu (MdEF-Tu), positively regulates apple thermotolerance when it is overexpressed. Transgenic apple plants exhibited higher photosynthetic capacity and better integrity of chloroplasts during heat stress. Under high temperatures, MdEF-Tu formed insoluble aggregates accompanied by ubiquitination modifications. Furthermore, we identified a chaperone heat shock protein (MdHsp70), as an interacting protein of MdEF-Tu. Moreover, we observed obviously elevated MdHsp70 levels in 35S: MdEF-Tu apple plants that prevented the accumulation of ubiquitinated MdEF-Tu aggregates, which positively contributes to the thermotolerance of the transgenic plants. Overall, our results provide new insights into the molecular chaperone function of MdHsp70, which mediates the homeostasis of thermosensitive proteins under high temperatures.

Long noncoding RNA TRABA suppresses β-glucosidase-encoding BGLU24 to promote salt tolerance in cotton

Salt stress severely damages the growth and yield of crops. Recently, long noncoding RNAs (lncRNAs) were demonstrated to regulate various biological processes and responses to environmental stresses. However, the regulatory mechanisms of lncRNAs in cotton (Gossypium hirsutum) response to salt stress are still poorly understood. Here, we observed that a lncRNA, trans acting of BGLU24 by lncRNA (TRABA), was highly expressed while GhBGLU24-A was weakly expressed in a salt-tolerant cotton accession (DM37) compared to a salt-sensitive accession (TM-1). Using TRABA as an effector and proGhBGLU24-A-driven GUS as a reporter, we showed that TRABA suppressed GhBGLU24-A promoter activity in double transgenic Arabidopsis (Arabidopsis thaliana), which explained why GhBGLU24-A was weakly expressed in the salt-tolerant accession compared to the salt-sensitive accession. GhBGLU24-A encodes an endoplasmic reticulum (ER)-localized β-glucosidase that responds to salt stress. Further investigation revealed that GhBGLU24-A interacted with RING-type E3 ubiquitin ligase (GhRUBL). Virus-induced gene silencing (VIGS) and transgenic Arabidopsis studies revealed that both GhBGLU24-A and GhRUBL diminish plant tolerance to salt stress and ER stress. Based on its substantial effect on ER-related degradation (ERAD)-associated gene expression, GhBGLU24-A mediates ER stress likely through the ERAD pathway. These findings provide insights into the regulatory role of the lncRNA TRABA in modulating salt and ER stresses in cotton and have potential implications for developing more resilient crops.

Overexpression of the Small Ubiquitin-Like Modifier protease OTS1 gene enhances drought tolerance in sugarcane (Saccharum spp. hybrid)

Sugarcane is an economically important crop plant across the globe as it is the primary source of sugar and biofuel. Its growth and development are greatly influenced by water availability; therefore, in periods of water scarcity, yields are severely compromised. Small Ubiquitin-Like Modifier (SUMO) proteases play an important role in stress responses by regulating the SUMO-related post-translational modification of proteins. In an attempt to enhance drought tolerance in sugarcane, this crop was genetically transformed with a cysteine protease (OVERLY TOLERANT TO SALT-1; OTS1) from Arabidopsis thaliana using particle bombardment. Transgenic plants were analysed in terms of photosynthetic capacity, oxidative damage, antioxidant accumulation and the SUMO-enrich protein profile was assessed. Sugarcane transformed with the AtOTS1 gene displayed enhanced drought tolerance and delayed leaf senescence under water deficit compared to the untransformed wild type (WT). The AtOTS1 transgenic plants maintained a high relative moisture content and higher photosynthesis rate when compared to the WT. In addition, when the transgene was expressed at high levels, the transformed plants were able to maintain higher stomatal conductance and chlorophyl content under moderate stress compared to the WT. Under severe water deficit stress, the transgenic plants accumulated less malondialdehyde and maintained membrane integrity. SUMOylation of total protein and protease activity was lower in the AtOTS1 transformed plants compared to the WT, with several SUMO-enriched proteins exclusively expressed in the transgenics when exposed to water deficit stress. SUMOylation of proteins likely influenced various mechanisms contributing to enhanced drought tolerance in sugarcane.

Chloroplast protein translocation pathways and ubiquitin-dependent regulation at a glance

Chloroplasts conduct photosynthesis and numerous metabolic and signalling processes that enable plant growth and development. Most of the ∼3000 proteins in chloroplasts are nucleus encoded and must be imported from the cytosol. Thus, the protein import machinery of the organelle (the TOC-TIC apparatus) is of fundamental importance for chloroplast biogenesis and operation. Cytosolic factors target chloroplast precursor proteins to the TOC-TIC apparatus, which drives protein import across the envelope membranes into the organelle, before various internal systems mediate downstream routing to different suborganellar compartments. The protein import system is proteolytically regulated by the ubiquitin-proteasome system (UPS), enabling centralized control over the organellar proteome. In addition, the UPS targets a range of chloroplast proteins directly. In this Cell Science at a Glance article and the accompanying poster, we present mechanistic details of these different chloroplast protein targeting and translocation events, and of the UPS systems that regulate chloroplast proteins.

The molecular chaperone mtHSC70-1 interacts with DjA30 to regulate female gametophyte development and fertility in Arabidopsis

Arabidopsis mitochondria-targeted heat shock protein 70 (mtHSC70-1) plays important roles in the establishment of cytochrome c oxidase-dependent respiration and redox homeostasis during the vegetative growth of plants. Here, we report that knocking out the mtHSC70-1 gene led to a decrease in plant fertility; the fertility defect of the mutant was completely rescued by introducing the mtHSC70-1 gene. mtHSC70-1 mutants also showed defects in female gametophyte (FG) development, including delayed mitosis, abnormal nuclear position, and ectopic gene expression in the embryo sacs. In addition, we found that an Arabidopsis mitochondrial J-protein gene (DjA30) mutant, j30+/- , had defects in FG development and fertility similar to those of mtHSC70-1 mutant. mtHSC70-1 and DjA30 had similar expression patterns in FGs and interacted in vivo, suggesting that these two proteins might cooperate during female gametogenesis. Further, respiratory chain complex IV activity in mtHSC70-1 and DjA30 mutant embryo sacs was markedly downregulated; this led to the accumulation of mitochondrial reactive oxygen species (ROS). Scavenging excess ROS by introducing Mn-superoxide dismutase 1 or catalase 1 gene into the mtHSC70-1 mutant rescued FG development and fertility. Altogether, our results suggest that mtHSC70-1 and DjA30 are essential for the maintenance of ROS homeostasis in the embryo sacs and provide direct evidence for the roles of ROS homeostasis in embryo sac maturation and nuclear patterning, which might determine the fate of gametic and accessory cells.

Selective autophagy regulates chloroplast protein import and promotes plant stress tolerance

Chloroplasts are plant organelles responsible for photosynthesis and environmental sensing. Most chloroplast proteins are imported from the cytosol through the translocon at the outer envelope membrane of chloroplasts (TOC). Previous work has shown that TOC components are regulated by the ubiquitin-proteasome system (UPS) to control the chloroplast proteome, which is crucial for the organelle's function and plant development. Here, we demonstrate that the TOC apparatus is also subject to K63-linked polyubiquitination and regulation by selective autophagy, potentially promoting plant stress tolerance. We identify NBR1 as a selective autophagy adaptor targeting TOC components, and mediating their relocation into vacuoles for autophagic degradation. Such selective autophagy is shown to control TOC protein levels and chloroplast protein import and to influence photosynthetic activity as well as tolerance to UV-B irradiation and heat stress in Arabidopsis plants. These findings uncover the vital role of selective autophagy in the proteolytic regulation of specific chloroplast proteins, and how dynamic control of chloroplast protein import is critically important for plants to cope with challenging environments.

Regulation of chloroplast protein degradation

Chloroplasts are unique organelles that not only provide sites for photosynthesis and many metabolic processes, but also are sensitive to various environmental stresses. Chloroplast proteins are encoded by genes from both nuclear and chloroplast genomes. During chloroplast development and responses to stresses, the robust protein quality control systems are essential for regulation of protein homeostasis and the integrity of chloroplast proteome. In this review, we summarize the regulatory mechanisms of chloroplast protein degradation refer to protease system, ubiquitin-proteasome system, and the chloroplast autophagy. These mechanisms symbiotically play a vital role in chloroplast development and photosynthesis under both normal or stress conditions.

Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system

Proteolysis is an essential process to maintain cellular homeostasis. One pathway that mediates selective protein degradation and which is in principle conserved throughout the kingdoms of life is the N-degron pathway, formerly called the ‘N-end rule’. In the cytosol of eukaryotes and prokaryotes, N-terminal residues can be major determinants of protein stability. While the eukaryotic N-degron pathway depends on the ubiquitin proteasome system, the prokaryotic counterpart is driven by the Clp protease system. Plant chloroplasts also contain such a protease network, which suggests that they might harbor an organelle specific N-degron pathway similar to the prokaryotic one. Recent discoveries indicate that the N-terminal region of proteins affects their stability in chloroplasts and provides support for a Clp-mediated entry point in an N-degron pathway in plastids. This review discusses structure, function and specificity of the chloroplast Clp system, outlines experimental approaches to test for an N-degron pathway in chloroplasts, relates these aspects into general plastid proteostasis and highlights the importance of an understanding of plastid protein turnover.

UPL5 modulates WHY2 protein distribution in a Kub-site dependent ubiquitination in response to [Ca2+]cyt-induced leaf senescence

The translocation of proteins between various compartments of cells is the simplest and most direct way of an/retrograde communication. However, the mechanism of protein trafficking is far understood. In this study, we showed that the alteration of WHY2 protein abundance in various compartments of cells was dependent on a HECT-type ubiquitin E3 ligase UPL5 interacting with WHY2 in the cytoplasm, plastid, and nucleus, as well as mitochondrion to selectively ubiquitinate various Kub-sites (Kub 45 and Kub 227) of WHY2. Plastid genome stability can be maintained by the UPL5-WHY2 module, accompany by the alteration of photosystem activity and senescence-associated gene expression. In addition, the specificity of UPL5 ubiquitinating various Kub-sites of WHY2 was responded to cold or CaCl₂ stress, in a dose [Ca²⁺]_cyt-dependent manner. This demonstrates the integration of the UPL5 ubiquitination with the regulation of WHY2 distribution and retrograde communication between organelle and nuclear events of leaf senescence.

Research progress on maintaining chloroplast homeostasis under stress conditions: a review

On a global scale, drought, salinity, extreme temperature, and other abiotic stressors severely limit the quality and yield of crops. Therefore, it is crucial to clarify the adaptation strategies of plants to harsh environments. Chloroplasts are important environmental sensors in plant cells. For plants to thrive in different habitats, chloroplast homeostasis must be strictly regulated, which is necessary to maintain efficient plant photosynthesis and other metabolic reactions under stressful environments. To maintain normal chloroplast physiology, two important biological processes are needed: the import and degradation of chloroplast proteins. The orderly import of chloroplast proteins and the timely degradation of damaged chloroplast components play a key role in adapting plants to their environment. In this review, we briefly described the mechanism of chloroplast TOC-TIC protein transport. The importance and recent progress of chloroplast protein turnover, retrograde signaling, and chloroplast protein degradation under stress are summarized. Furthermore, the potential of targeted regulation of chloroplast homeostasis is emphasized to improve plant adaptation to environmental stresses.

Comparative transcriptomic and proteomic analysis reveals common molecular factors responsive to heat and drought stresses in sweetpotaoto (Ipomoea batatas)

Introduction

Crops are affected by various abiotic stresses, among which heat (HT) and drought (DR) stresses are the most common in summer. Many studies have been conducted on HT and DR, but relatively little is known about how drought and heat combination (DH) affects plants at molecular level.

Methods

Here, we investigated the responses of sweetpotato to HT, DR, and DH stresses by RNA-seq and data-independent acquisition (DIA) technologies, using controlled experiments and the quantification of both gene and protein levels in paired samples.

Results

Twelve cDNA libraries were created under HT, DR, and DH conditions and controls. We identified 536, 389, and 907 DEGs in response to HT, DR, and DH stresses, respectively. Of these, 147 genes were common and 447 were specifically associated with DH stress. Proteomic analysis identified 1609, 1168, and 1535 DEPs under HT, DR, and DH treatments, respectively, compared with the control, of which 656 were common and 358 were exclusive to DH stress. Further analysis revealed the DEGs/DEPs were associated with heat shock proteins, carbon metabolism, phenylalanine metabolism, starch and cellulose metabolism, and plant defense, amongst others. Correlation analysis identified 6465, 6607, and 6435 co-expressed genes and proteins under HT, DR, and DH stresses respectively. In addition, a combined analysis of the transcriptomic and proteomic data identified 59, 35, and 86 significantly co-expressed DEGs and DEPs under HT, DR, and DH stresses, respectively. Especially, top 5 up-regulated co-expressed DEGs and DEPs (At5g58770, C24B11.05, Os04g0679100, BACOVA_02659 and HSP70-5) and down-regulated co-expressed DEGs and DEPs (AN3, PMT2, TUBB5, FL and CYP98A3) were identified under DH stress.

Discussion

This is the first study of differential genes and proteins in sweetpotato under DH stress, and it is hoped that the findings will assist in clarifying the molecular mechanisms involved in sweetpotato resistance to heat and drought stress.

Chloroplast proteostasis: A story of birth, life, and death

Protein homeostasis (proteostasis) is a dynamic balance of protein synthesis and degradation. Because of the endosymbiotic origin of chloroplasts and the massive transfer of their genetic information to the nucleus of the host cell, many protein complexes in the chloroplasts are constituted from subunits encoded by both genomes. Hence, the proper function of chloroplasts relies on the coordinated expression of chloroplast- and nucleus-encoded genes. The biogenesis and maintenance of chloroplast proteostasis are dependent on synthesis of chloroplast-encoded proteins, import of nucleus-encoded chloroplast proteins from the cytosol, and clearance of damaged or otherwise undesired "old" proteins. This review focuses on the regulation of chloroplast proteostasis, its interaction with proteostasis of the cytosol, and its retrograde control over nuclear gene expression. We also discuss significant issues and perspectives for future studies and potential applications for improving the photosynthetic performance and stress tolerance of crops.

Biogenic signals from plastids and their role in chloroplast development

Plant seeds do not contain differentiated chloroplasts. Upon germination, the seedlings thus need to gain photoautotrophy before storage energies are depleted. This requires the coordinated expression of photosynthesis genes encoded in nuclear and plastid genomes. Chloroplast biogenesis needs to be additionally coordinated with the light regulation network that controls seedling development. This coordination is achieved by nucleus to plastid signals called anterograde and plastid to nucleus signals termed retrograde. Retrograde signals sent from plastids during initial chloroplast biogenesis are also called biogenic signals. They have been recognized as highly important for proper chloroplast biogenesis and for seedling development. The molecular nature, transport, targets, and signalling function of biogenic signals are, however, under debate. Several studies disproved the involvement of a number of key components that were at the base of initial models of retrograde signalling. New models now propose major roles for a functional feedback between plastid and cytosolic protein homeostasis in signalling plastid dysfunction as well as the action of dually localized nucleo-plastidic proteins that coordinate chloroplast biogenesis with light-dependent control of seedling development. This review provides a survey of the developments in this research field, summarizes the unsolved questions, highlights several recent advances, and discusses potential new working modes.

Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis

Photosynthesis is the energetic basis for most life on Earth, and in plants it operates inside double membrane-bound organelles called chloroplasts. The photosynthetic apparatus comprises numerous proteins encoded by the nuclear and organellar genomes. Maintenance of this apparatus requires the action of internal chloroplast proteases, but a role for the nucleocytosolic ubiquitin-proteasome system (UPS) was not expected, owing to the barrier presented by the double-membrane envelope. Here, we show that photosynthesis proteins (including those encoded internally by chloroplast genes) are ubiquitinated and processed via the CHLORAD pathway: They are degraded by the 26S proteasome following CDC48-dependent retrotranslocation to the cytosol. This demonstrates that the reach of the UPS extends to the interior of endosymbiotically derived chloroplasts, where it acts to regulate photosynthesis, arguably the most fundamental process of life.

Chloroplast protein import machinery and quality control

Most chloroplast proteins are nucleus-encoded, translated on cytoplasmic ribosomes as precursor proteins, and imported into chloroplasts through TOC and TIC, the translocons of the outer and inner chloroplast envelope membranes. While the composition of the TOC complex is well established, there is still some controversy about the importance of a recently identified TIC complex consisting of Tic20, Tic214, Tic100, and Tic56. TOC and TIC form a supercomplex with a protein channel at the junction of the outer and inner envelope membranes through which preproteins are pulled into the stroma by the ATP-powered Ycf2 complex consisting of several FtsH-like ATPases and/or by chloroplast Hsp proteins. Several components of the TOC/TIC system are moonlighting proteins with additional roles in chloroplast gene expression and metabolism. Chaperones and co-chaperones, associated with TOC and TIC on the cytoplasmic and stromal side of the chloroplast envelope, participate in the unfolding and folding of the precursor proteins and act together with the ubiquitin-proteasome system in protein quality control. Chloroplast protein import is also intimately linked with retrograde signaling, revealing altogether an unsuspected complexity in the regulation of this process.

Chaperone-assisted E3 ligase CHIP: A double agent in cancer

The carboxy-terminus of Hsp70-interacting protein (CHIP) is a ubiquitin ligase and co-chaperone belonging to Ubox family that plays a crucial role in the maintenance of cellular homeostasis by switching the equilibrium of the folding-refolding mechanism towards the proteasomal or lysosomal degradation pathway. It links molecular chaperones viz. HSC70, HSP70 and HSP90 with ubiquitin proteasome system (UPS), acting as a quality control system. CHIP contains charged domain in between N-terminal tetratricopeptide repeat (TPR) and C-terminal Ubox domain. TPR domain interacts with the aberrant client proteins via chaperones while Ubox domain facilitates the ubiquitin transfer to the client proteins for ubiquitination. Thus, CHIP is a classic molecule that executes ubiquitination for degradation of client proteins. Further, CHIP has been found to be indulged in cellular differentiation, proliferation, metastasis and tumorigenesis. Additionally, CHIP can play its dual role as a tumor suppressor as well as an oncogene in numerous malignancies, thus acting as a double agent. Here, in this review, we have reported almost all substrates of CHIP established till date and classified them according to the hallmarks of cancer. In addition, we discussed about its architectural alignment, tissue specific expression, sub-cellular localization, folding-refolding mechanisms of client proteins, E4 ligase activity, normal physiological roles, as well as involvement in various diseases and tumor biology. Further, we aim to discuss its importance in HSP90 inhibitors mediated cancer therapy. Thus, this report concludes that CHIP may be a promising and worthy drug target towards pharmaceutical industry for drug development.

Mitochondrial HSC70-1 Regulates Polar Auxin Transport through ROS Homeostasis in Arabidopsis Roots

Arabidopsis mitochondrial-localized heat shock protein 70-1 (mtHSC70-1) modulates vegetative growth by assisting mitochondrial complex IV assembly and maintaining reactive oxygen species (ROS) homeostasis. In addition, mtHSC70-1 affects embryo development, and this effect is mediated by auxin. However, whether mtHSC70-1 regulates vegetative growth through auxin and knowledge of the link between ROS homeostasis and auxin distribution remain unclear. Here, we found that mtHSC70-1 knockout seedlings (mthsc70-1a) displayed shortened roots, decreased fresh root weight and lateral root number, increased root width and abnormal root morphology. The introduction of the mtHSC70-1 gene into mthsc70-1a restored the growth and development of roots to the level of the wild type. However, sugar and auxin supplementation could not help the mutant roots restore to normal. Moreover, mthsc70-1a seedlings showed a decrease in meristem length and activity, auxin transport carrier (PINs and AUX1) and auxin abundances in root tips. The application of exogenous reducing agents upregulated the levels of PINs in the mutant roots. The introduction of antioxidant enzyme genes (MSD1 or CAT1) into the mthsc70-1a mutant rescued the PIN and local auxin abundances and root growth and development. Taken together, our data suggest that mtHSC70-1 regulates polar auxin transport through ROS homeostasis in Arabidopsis roots.

Molecular mechanisms of resistance to Myzus persicae conferred by the peach Rm2 gene: A multi-omics view

The transcriptomic and metabolomic responses of peach to Myzus persicae infestation were studied in Rubira, an accession carrying the major resistance gene Rm2 causing antixenosis, and GF305, a susceptible accession. Transcriptome and metabolome showed both a massive reconfiguration in Rubira 48 hours after infestation while GF305 displayed very limited changes. The Rubira immune system was massively stimulated, with simultaneous activation of genes encoding cell surface receptors involved in pattern-triggered immunity and cytoplasmic NLRs (nucleotide-binding domain, leucine-rich repeat containing proteins) involved in effector-triggered immunity. Hypersensitive reaction featured by necrotic lesions surrounding stylet punctures was supported by the induction of cell death stimulating NLRs/helpers couples, as well as the activation of H2O2-generating metabolic pathways: photorespiratory glyoxylate synthesis and activation of the futile P5C/proline cycle. The triggering of systemic acquired resistance was suggested by the activation of pipecolate pathway and accumulation of this defense hormone together with salicylate. Important reduction in carbon, nitrogen and sulphur metabolic pools and the repression of many genes related to cell division and growth, consistent with reduced apices elongation, suggested a decline in the nutritional value of apices. Finally, the accumulation of caffeic acid conjugates pointed toward their contribution as deterrent and/or toxic compounds in the mechanisms of resistance.

Variations in Circadian Clock Organization & Function: A Journey from Ancient to Recent

Circadian clock components exhibit structural variations in different plant systems, and functional variations during various abiotic stresses. These variations bear relevance for plant fitness and could be important evolutionarily. All organisms on earth have the innate ability to measure time as diurnal rhythms that occur due to the earth's rotations in a 24-h cycle. Circadian oscillations arising from the circadian clock abide by its fundamental properties of periodicity, entrainment, temperature compensation, and oscillator mechanism, which is central to its function. Despite the fact that a myriad of research in Arabidopsis thaliana illuminated many detailed aspects of the circadian clock, many more variations in clock components' organizations and functions remain to get deciphered. These variations are crucial for sustainability and adaptation in different plant systems in the varied environmental conditions in which they grow. Together with these variations, circadian clock functions differ drastically even during various abiotic and biotic stress conditions. The present review discusses variations in the organization of clock components and their role in different plant systems and abiotic stresses. We briefly introduce the clock components, entrainment, and rhythmicity, followed by the variants of the circadian clock in different plant types, starting from lower non-flowering plants, marine plants, dicots to the monocot crop plants. Furthermore, we discuss the interaction of the circadian clock with components of various abiotic stress pathways, such as temperature, light, water stress, salinity, and nutrient deficiency with implications for the reprogramming during these stresses. We also update on recent advances in clock regulations due to post-transcriptional, post-translation, non-coding, and micro-RNAs. Finally, we end this review by summarizing the points of applicability, a remark on the future perspectives, and the experiments that could clear major enigmas in this area of research.

Chloroplast envelope ATPase PGA1/AtFtsH12 is required for chloroplast protein accumulation and cytosol-chloroplast protein homeostasis in Arabidopsis

The establishment of photosynthetic protein complexes during chloroplast development requires the influx of a large number of chloroplast proteins that are encoded by the nuclear genome, which is critical for cytosol and chloroplast protein homeostasis and chloroplast development. However, the mechanisms regulating this process are still not well understood in higher plants. Here, we report the isolation and characterization of the pale green Arabidopsis pga1-1 mutant, which is defective in chloroplast development and chloroplast protein accumulation. Using genetic and biochemical evidence, we reveal that PGA1 encodes AtFtsH12, a chloroplast envelope-localized protein of the FtsH family proteins. We determined a G703R mutation in the GAD motif of the conserved ATPase domain renders the pga1-1 a viable hypomorphic allele of the essential gene AtFtsH12. In de-etiolation assays, we showed that the accumulation of photosynthetic proteins and the expression of photosynthetic genes were impaired in pga1-1. Using the FNR_ctp-GFP and pTAC2-GFP reporters, we demonstrated that AtFtsH12 was required for the accumulation of chloroplast proteins in vivo. Interestingly, we identified an increase in expression of the mutant AtFtsH12 gene in pga1-1, suggesting a feedback regulation. Moreover, we found that cytosolic and chloroplast proteostasis responses were triggered in pga1-1. Together, taking advantage of the novel pga1-1 mutant, we demonstrate the function of AtFtsH12 in chloroplast protein homeostasis and chloroplast development.

GREEN FLUORESCENT PROTEIN variants with enhanced folding are more efficiently imported into chloroplasts

Chloroplasts and mitochondria are subcellular organelles that evolved from cyanobacteria and α-proteobacteria, respectively. Although they have their own genomes, the majority of their proteins are encoded by nuclear genes, translated by cytosolic ribosomes, and imported via outer and inner membrane translocon complexes. The unfolding of mature regions of proteins is thought to be a prerequisite for the import of the proteins into these organelles. However, it is not fully understood how protein folding properties affect their import into these organelles. In this study, we examined the import behavior of chloroplast and mitochondrial reporters with normal green fluorescent protein (GFP) and two GFP variants with enhanced folding propensity, superfolder GFP (sfGFP) and extra-superfolder GFP (esGFP), which is folded better than sfGFP. sfGFP and esGFP were less dependent on the sequence motifs of the transit peptide (TP) and import machinery during protein import into Arabidopsis (Arabidopsis thaliana) chloroplasts, compared with normal GFP. sfGFP and esGFP were efficiently imported into chloroplasts by a mutant TP with an alanine substitution in the N-terminal MLM motif, whereas the same mutant TP showed a defect in importing normal GFP into chloroplasts. Moreover, sfGFP and esGFP were efficiently imported into plastid protein import 2 (ppi2) and heat shock protein 93-V (hsp93-V) plants, which have mutations in atToc159 and Hsp93-V, respectively. In contrast, the presequence-mediated mitochondrial import of sfGFP and esGFP was severely impaired. Based on these results, we propose that the chloroplast import machinery is more tolerant to different folding states of preproteins, whereas the mitochondrial machinery is more specialized in the translocation of unfolded preproteins.

The Role of E3 Ubiquitin Ligases in Chloroplast Function

Chloroplasts are ancient organelles responsible for photosynthesis and various biosynthetic functions essential to most life on Earth. Many of these functions require tightly controlled regulatory processes to maintain homeostasis at the protein level. One such regulatory mechanism is the ubiquitin-proteasome system whose fundamental role is increasingly emerging in chloroplasts. In particular, the role of E3 ubiquitin ligases as determinants in the ubiquitination and degradation of specific intra-chloroplast proteins. Here, we highlight recent advances in understanding the roles of plant E3 ubiquitin ligases SP1, COP1, PUB4, CHIP, and TT3.1 as well as the ubiquitin-dependent segregase CDC48 in chloroplast function.

The plastid-encoded protein Orf2971 is required for protein translocation and chloroplast quality control

Photosynthesis and the biosynthesis of many important metabolites occur in chloroplasts. In these semi-autonomous organelles, the chloroplast genome encodes approximately 100 proteins. The remaining chloroplast proteins, close to 3,000, are encoded by nuclear genes whose products are translated in the cytosol and imported into chloroplasts. However, there is still no consensus on the composition of the protein import machinery including its motor proteins and on how newly imported chloroplast proteins are refolded. In this study, we have examined the function of orf2971, the largest chloroplast gene of Chlamydomonas reinhardtii. The depletion of Orf2971 causes the accumulation of protein precursors, partial proteolysis and aggregation of proteins, increased expression of chaperones and proteases, and autophagy. Orf2971 interacts with the TIC (translocon at the inner chloroplast envelope) complex, catalyzes ATP (adenosine triphosphate) hydrolysis, and associates with chaperones and chaperonins. We propose that Orf2971 is intimately connected to the protein import machinery and plays an important role in chloroplast protein quality control.

Genome-wide identification and expression analysis of the Hsp20, Hsp70 and Hsp90 gene family in Dendrobium officinale

Dendrobium officinale, an important orchid plant with great horticultural and medicinal values, frequently suffers from abiotic or biotic stresses in the wild, which may influence its well-growth. Heat shock proteins (Hsps) play essential roles in the abiotic stress response of plants. However, they have not been systematically investigated in D. officinale. Here, we identified 37 Hsp20 genes (DenHsp20s), 43 Hsp70 genes (DenHsp70s) and 4 Hsp90 genes (DenHsp90s) in D. officinale genome. These genes were classified into 8, 4 and 2 subfamilies based on phylogenetic analysis and subcellular predication, respectively. Sequence analysis showed that the same subfamily members have relatively conserved gene structures and similar protein motifs. Moreover, we identified 33 pairs of paralogs containing 30 pairs of tandem duplicates and 3 pairs of segmental duplicates among these genes. There were 7 pairs in DenHsp70s under positive selection, which may have important functions in helping cells withstand extreme stress. Numerous gene promoter sequences contained stress and hormone response cis-elements, especially light and MeJA response elements. Under MeJA stress, DenHsp20s, DenHsp70s and DenHsp90s responded to varying degrees, among which DenHsp20-5,6,7,16 extremely up-regulated, which may have a strong stress resistance. Therefore, these findings could provide useful information for evolutional and functional investigations of Hsp20, Hsp70 and Hsp90 genes in D. officinale.

Chloroplasts Protein Quality Control and Turnover: A Multitude of Mechanisms

As the organelle of photosynthesis and other important metabolic pathways, chloroplasts contain up to 70% of leaf proteins with uniquely complex processes in synthesis, import, assembly, and turnover. Maintaining functional protein homeostasis in chloroplasts is vitally important for the fitness and survival of plants. Research over the past several decades has revealed a multitude of mechanisms that play important roles in chloroplast protein quality control and turnover under normal and stress conditions. These mechanisms include: (i) endosymbiotically-derived proteases and associated proteins that play a vital role in maintaining protein homeostasis inside the chloroplasts, (ii) the ubiquitin-dependent turnover of unimported chloroplast precursor proteins to prevent their accumulation in the cytosol, (iii) chloroplast-associated degradation of the chloroplast outer-membrane translocon proteins for the regulation of chloroplast protein import, (iv) chloroplast unfolded protein response triggered by accumulated unfolded and misfolded proteins inside the chloroplasts, and (v) vesicle-mediated degradation of chloroplast components in the vacuole. Here, we provide a comprehensive review of these diverse mechanisms of chloroplast protein quality control and turnover and discuss important questions that remain to be addressed in order to better understand and improve important chloroplast functions.

Importation of chloroplast proteins under heat stress is facilitated by their SUMO conjugations

Chloroplasts are hypersensitive to heat stress (HS). SUMOylation, a critical post-translational modification, is conservatively involved in HS responses. However, the functional connection between SUMOylation and chloroplasts under HS remains to be studied. The bioinformatics, biochemistry, and cell biology analyses were used to detect the SUMOylation statuses of Arabidopsis nuclear-encoded chloroplast proteins and the effect of SUMOylation on subcellular localization of these proteins under HS. PSBR, a subunit of photosystem II, was used as an example for a detailed investigation of functional mechanisms. After a global SUMOylation site prediction of nuclear-encoded chloroplast proteins, biochemical data showed that most of the selected candidates are modified by SUMO3 in the cytoplasm. The chloroplast localization of these SUMOylation targets under long-term HS is partially maintained by the SUMO ligase AtSIZ1. The HS-induced SUMOylation on PSBR contributes to the maintenance of its chloroplast localization, which is dependent on its chloroplast importation efficiency correlated to phosphorylation. The complementation analysis provided evidence that SUMOylation is essential for the physiological function of PSBR under HS. Our study illustrated a general regulatory mechanism of SUMOylation in maintaining the chloroplast protein importation during HS and provided hints for further investigation on protein modifications associated with plant organelles under stress conditions.

A proteostasis network safeguards the chloroplast proteome

Several protein homeostasis (proteostasis) pathways safeguard the integrity of thousands of proteins that localize in plant chloroplasts, the indispensable organelles that perform photosynthesis, produce metabolites, and sense environmental stimuli. In this review, we discuss the latest efforts directed to define the molecular process by which proteins are imported and sorted into the chloroplast. Moreover, we describe the recently elucidated protein folding and degradation pathways that modulate the levels and activities of chloroplast proteins. We also discuss the links between the accumulation of misfolded proteins and the activation of signalling pathways that cope with folding stress within the organelle. Finally, we propose new research directions that would help to elucidate novel molecular mechanisms to maintain chloroplast proteostasis.

Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling

Posttranslational modifications add complexity and diversity to cellular proteomes. One of the most prevalent modifications across eukaryotes is ubiquitination, which is orchestrated by E3 ubiquitin ligases. U-box-containing E3 ligases have massively expanded in the plant kingdom and have diversified into plant U-box proteins (PUBs). PUBs likely originated from two or three ancestral forms, fusing with diverse functional subdomains that resulted in neofunctionalization. Their emergence and diversification may reflect adaptations to stress during plant evolution, reflecting changes in the needs of plant proteomes to maintain cellular homeostasis. Through their close association with protein kinases, they are physically linked to cell signaling hubs and activate feedback loops by dynamically pairing with E2-ubiquitin-conjugating enzymes to generate distinct ubiquitin polymers that themselves act as signals. Here, we complement current knowledgewith comparative genomics to gain a deeper understanding of PUB function, focusing on their evolution and structural adaptations of key U-box residues, as well as their various roles in plant cells.

Ubiquitination and Ubiquitin-Like Modifications as Mediators of Alternative Pre-mRNA Splicing in Arabidopsis thaliana

Alternative splicing (AS) is a common post-transcriptional regulatory process in eukaryotes. AS has an irreplaceable role during plant development and in response to environmental stress as it evokes differential expression of downstream genes or splicing factors (e.g., serine/arginine-rich proteins). Numerous studies have reported that loss of AS capacity leads to defects in plant growth and development, and induction of stress-sensitive phenotypes. A role for post-translational modification (PTM) of AS components has emerged in recent years. These modifications are capable of regulating the activity, stability, localization, interaction, and folding of spliceosomal proteins in human cells and yeast, indicating that PTMs represent another layer of AS regulation. In this review, we summarize the recent reports concerning ubiquitin and ubiquitin-like modification of spliceosome components and analyze the relationship between spliceosome and the ubiquitin/26S proteasome pathway in plants. Based on the totality of the evidence presented, we further speculate on the roles of protein ubiquitination mediated AS in plant development and environmental response.

Prokaryotic and eukaryotic traits support the biological role of the chloroplast outer envelope

The plastid outer envelope (OE) is a mixture of components inherited from their prokaryotic ancestor like galactolipids, carotenoids and porin type ion channels supplemented with eukaryotic inventions to make the endosymbiotic process successful as well as to control plastid biogenesis and differentiation. In this review we wanted to highlight the importance of the OE proteins and its evolutionary origin. For a long time, the OE was thought to be a diffusion barrier only, but with the recent discoveries of all kinds of different proteins in the OE it has been shown that the OE can modulate various functions within the cell. The phenotypic changes show that channels like the outer envelope proteins OEP40, OEP16 or JASSY have a pronounced ion selectivity that cannot be replaced by other ion channels present in the OE. Eukaryotic additions, like the GTPase receptors Toc33 and Toc159 or the ubiquitin proteasome system for chloroplast protein quality control, round up the profile of the OE.

The CDC48 complex mediates ubiquitin-dependent degradation of intra-chloroplast proteins in plants

Chloroplasts are the site of numerous biochemical reactions including photosynthesis, but they also produce reactive oxygen species (ROS) that negatively affect chloroplast integrity. The chaperone-like CDC48 complex plays critical roles in ubiquitin-dependent protein degradation in yeast and mammals, but its function in plants is largely unknown. Here, we show that defects in CDC48A and its cofactors UFD1 and NPL4 lead to the accumulation of ubiquitinated chloroplast proteins in Arabidopsis thaliana. We reveal that two plastid genome-encoded proteins, RbcL and AtpB, associate with the CDC48 complex. Strikingly, RbcL and AtpB are ubiquitinated and degraded by the 26S proteasome pathway upon ROS stress, and these processes are impaired by defects of the CDC48 complex. Functional analysis demonstrates that the CDC48 complex is required for plant tolerance to ROS. This study reveals a role for the plant CDC48 complex in modulating ubiquitin-dependent degradation of intra-chloroplast proteins in response to oxidative stress.

Regulation of heat shock proteins 70 and their role in plant immunity

Heat shock proteins 70 (HSP70s) are steadily gaining more attention in the field of plant biotic interactions. Though their regulation and activity in plants are much less well characterized than are those of their counterparts in mammals, accumulating evidence indicates that the role of HSP70-mediated defense mechanisms in plant cells is indispensable. In this review, we summarize current knowledge of HSP70 post-translational control in plants. We comment on the phytohormonal regulation of HSP70 expression and protein abundance, and identify a prominent role for cytokinin in HSP70 control. We outline HSP70s' subcellular localizations, chaperone activity, and chaperone-mediated protein degradation. We focus on the role of HSP70s in plant pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity, and discuss the contribution of different HSP70 subfamilies to plant defense against pathogens.

Coordination of Chloroplast Activity with Plant Growth: Clues Point to TOR

Photosynthesis is the defining function of most autotrophic organisms. In the plantae kingdom, chloroplasts host this function and ensure growth. However, these organelles are very sensitive to stressful conditions and the photosynthetic process can cause photooxidative damage if not perfectly regulated. In addition, their function is energivorous in terms of both chemical energy and nutrients. To coordinate chloroplast activity with the cell’s need, continuous signaling is required: from chloroplasts to cytoplasm and from nucleus to chloroplasts. In this opinion article, several mechanisms that ensure this communication are reported and the many clues that point to an important role of the Target of Rapamycin (TOR) kinase in the coordination between the eukaryotic and prokaryotic sides of plants are highlighted.

Sex-linked deubiquitinase establishes uniparental transmission of chloroplast DNA

Most sexual organisms inherit organelles from one parent, commonly by excluding organelles from the smaller gametes. However, post-mating elimination of organelles derived from one gamete ensures uniparental inheritance, where the underlying mechanisms to distinguish organelles by their origin remain obscure. Mating in Chlamydomonas reinhardtii combines isomorphic plus and minus gametes, but chloroplast DNA from minus gametes is selectively degraded in zygotes. Here, we identify OTU2p (otubain protein 2), encoded in the plus mating-type locus MT+, as the protector of plus chloroplast. Otu2p is an otubain-like deubiquitinase, which prevents proteasome-mediated degradation of the preprotein translocase of the outer chloroplast membrane (TOC) during gametogenesis. Using OTU2p-knockouts and proteasome inhibitor treatment, we successfully redirect selective DNA degradation in chloroplasts with reduced TOC levels regardless of mating type, demonstrating that plus-specific Otu2p establishes uniparental chloroplast DNA inheritance. Our work documents that a sex-linked organelle quality control mechanism drives the uniparental organelle inheritance without dimorphic gametes.

Most sexual organisms ensure that organelles are inherited from a single parent. Here, the authors describe OTU2p, a Chlamydomonas deubiquitinase that drives uniparental organelle inheritance without gametic dimorphism by preventing proteasome-mediated degradation exclusively in gametes of the plus mating type.

Ubiquitylomes and proteomes analyses provide a new interpretation of the molecular mechanisms of rice leaf senescence

We identified a typical rice premature senescence leaf mutant 86 (psl86) and exhibited the first global ubiquitination data during rice leaf senescence. Premature leaf senescence affects the yield and quality of rice, causing irreparable agricultural economic losses. In this study, we reported a rice premature senescence leaf mutant 86 (psl86) in the population lines of rice (Oryza sativa) japonica cultivar 'Yunyin' (YY) mutagenized using ethyl methane sulfonate (EMS) treatment. Immunoblotting analysis revealed that a higher ubiquitination level in the psl86 mutant compared with YY. Thus, we performed the proteome and ubiquitylome analyses to identify the differential abundance proteins and ubiquitinated proteins (sites) related to leaf senescence. Among 885 quantified lysine ubiquitination (Kub) sites in 492 proteins, 116 sites in 94 proteins were classified as up-regulated targets and seven sites in six proteins were classified as down-regulated targets at a threshold of 1.5. Proteins with up-regulated Kub sites were mainly enriched in the carbon fixation in photosynthetic organisms, glycolysis/gluconeogenesis and the pentose phosphate pathway. Notably, 14 up-regulated Kub sites in 11 proteins were enriched in the carbon fixation in photosynthetic organism pathway, and seven proteins (rbcL, PGK, GAPA, FBA5, ALDP, CFBP1 and GGAT) were down-regulated, indicating this pathway is tightly regulated by ubiquitination during leaf senescence. To our knowledge, we present the first global data on ubiquitination during rice leaf senescence.

Salicylic Acid Acts Antagonistically to Plastid Retrograde Signaling by Promoting the Accumulation of Photosynthesis-associated Proteins in Arabidopsis

Plastids are involved in phytohormone metabolism as well as photosynthesis. However, the mechanism by which plastid retrograde signals and phytohormones cooperatively regulate plastid biogenesis remains elusive. Here, we investigated the effects of an inhibitor and a mutation that generate biogenic plastid signals on phytohormones and vice versa. Inhibition of plastid biogenesis by norflurazon (NF) treatment and the plastid protein import2 (ppi2) mutation caused a decrease in salicylic acid (SA) and jasmonic acid (JA). This effect can be attributed in part to the altered expression of genes involved in the biosynthesis and the metabolism of SA and JA. However, SA-dependent induction of the PATHOGENESIS-RELATED1 gene was virtually unaffected in NF-treated plants and the ppi2 mutant. Instead, the level of chlorophyll in these plants was partially restored by the exogenous application of SA. Consistent with this observation, the levels of some photosynthesis-associated proteins increased in the ppi2 and NF-treated plants in response to SA treatment. This regulation in true leaves seems to occur at the posttranscriptional level since SA treatment did not induce the expression of photosynthesis-associated genes. In salicylic acid induction deficient 2 and lesions simulating disease resistance 1 mutants, endogenous SA regulates the accumulation of photosynthesis-associated proteins through transcriptional and posttranscriptional mechanisms. These data indicate that SA acts antagonistically to the inhibition of plastid biogenesis by promoting the accumulation of photosynthesis-associated proteins in Arabidopsis, suggesting a possible link between SA and biogenic plastid signaling.

Nanopore-Based Comparative Transcriptome Analysis Reveals the Potential Mechanism of High-Temperature Tolerance in Cotton (Gossypium hirsutum L.)

Extreme high temperatures are threatening cotton production around the world due to the intensification of global warming. To cope with high-temperature stress, heat-tolerant cotton cultivars have been bred, but the heat-tolerant mechanism remains unclear. This study selected heat-tolerant (‘Xinluzao36′) and heat-sensitive (‘Che61-72′) cultivars of cotton treated with high-temperature stress as plant materials and performed comparative nanopore sequencing transcriptome analysis to reveal the potential heat-tolerant mechanism of cotton. Results showed that 120,605 nonredundant sequences were generated from the raw reads, and 78,601 genes were annotated. Differentially expressed gene (DEG) analysis showed that a total of 19,600 DEGs were screened; the DEGs involved in the ribosome, heat shock proteins, auxin and ethylene signaling transduction, and photosynthesis pathways may be attributed to the heat tolerance of the heat-tolerant cotton cultivar. This study also predicted a total of 5118 long non-coding RNAs (lncRNAs)and 24,462 corresponding target genes. Analysis of the target genes revealed that the expression of some ribosomal, heat shock, auxin and ethylene signaling transduction-related and photosynthetic proteins may be regulated by lncRNAs and further participate in the heat tolerance of cotton. This study deepens our understandings of the heat tolerance of cotton.

Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles

The gametophyte of ferns reproduces either by sexual or asexual means. In the latter, apogamy represents a peculiar case of apomixis, in which an embryo is formed from somatic cells. A proteomic and physiological approach was applied to the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative D. oreades. The proteomic analysis compared apogamous vs. female gametophytes, whereas the phytohormone study included, in addition to females, three apogamous stages (filamentous, spatulate, and cordate). The proteomic profiles revealed a total of 879 proteins and, after annotation, different regulation was found in 206 proteins of D. affinis and 166 of its sexual counterpart. The proteins upregulated in D. affinis are mostly associated to protein metabolism (including folding, transport, and proteolysis), ribosome biogenesis, gene expression and translation, while in the sexual counterpart, they account largely for starch and sucrose metabolism, generation of energy and photosynthesis. Likewise, ultra-performance liquid chromatography-tandem spectrometry (UHPLC-MS/MS) was used to assess the levels of indol-3-acetic acid (IAA); the cytokinins: 6-benzylaminopurine (BA), trans-Zeatine (Z), trans-Zeatin riboside (ZR), dyhidrozeatine (DHZ), dyhidrozeatin riboside (DHZR), isopentenyl adenine (iP), isopentenyl adenosine (iPR), abscisic acid (ABA), the gibberellins GA₃ and GA₄, salicylic acid (SA), and the brassinosteroids: brassinolide (BL) and castasterone (CS). IAA, the cytokinins Z, ZR, iPR, the gibberellin GA₄, the brassinosteoids castasterone, and ABA accumulated more in the sexual gametophyte than in the apogamous one. When comparing the three apogamous stages, BA and SA peaked in filamentous, GA₃ and BL in spatulate and DHRZ in cordate gametophytes. The results point to the existence of large metabolic differences between apogamous and sexual gametophytes, and invite to consider the fern gametophyte as a good experimental system to deepen our understanding of plant reproduction.

Spider mite egg extract modifies Arabidopsis response to future infestations

Transcriptional plant responses are an important aspect of herbivore oviposition studies. However, most of our current knowledge is derived from studies using Lepidopteran models, where egg-laying and feeding are separate events in time. Little is known regarding plant response to pests where females feed and oviposit simultaneously. The present study characterized oviposition-induced transcriptomic response of Arabidopsis to Tetranychus urticae egg extracts. Transcriptional evidence indicates that early events in plant response to the egg extract involve responses typical to biotic stresses, which include the alteration in the levels of Ca²⁺ and ROS, the modification of pathways regulated by the phytohormones jasmonic acid and ethylene, and the production of volatiles and glucosinolates as defence mechanisms. These molecular changes affect female fertility, which was significantly reduced when mites fed on plants pre-exposed to the egg extract. However, longer periods of plant exposure to egg extract cause changes in the transcriptional response of the plant reveal a trend to a decrease in the activation of the defensive response. This alteration correlated with a shift at 72 h of exposition in the effect of the mite feeding. At that point, plants become more susceptible and suffer higher damage when challenged by the mite.

A chloroplast redox relay adapts plastid metabolism to light and affects cytosolic protein quality control

In chloroplasts, thiol-dependent redox regulation is linked to light since the disulfide reductase activity of thioredoxins (Trxs) relies on photo-reduced ferredoxin (Fdx). Furthermore, chloroplasts harbor an NADPH-dependent Trx reductase (NTR) with a joint Trx domain, termed NTRC. The activity of these two redox systems is integrated by the redox balance of 2-Cys peroxiredoxin (Prx), which is controlled by NTRC. However, NTRC was proposed to participate in redox regulation of additional targets, prompting inquiry into whether the function of NTRC depends on its capacity to maintain the redox balance of 2-Cys Prxs or by direct redox interaction with chloroplast enzymes. To answer this, we studied the functional relationship of NTRC and 2-Cys Prxs by a comparative analysis of the triple Arabidopsis (Arabidopsis thaliana) mutant, ntrc-2cpab, which lacks NTRC and 2-Cys Prxs, and the double mutant 2cpab, which lacks 2-Cys Prxs. These mutants exhibit almost indistinguishable phenotypes: in growth rate, photosynthesis performance, and redox regulation of chloroplast enzymes in response to light and darkness. These results suggest that the most relevant function of NTRC is in controlling the redox balance of 2-Cys Prxs. A comparative transcriptomics analysis confirmed the phenotypic similarity of the two mutants and suggested that the NTRC-2-Cys Prxs system participates in cytosolic protein quality control. We propose that NTRC and 2-Cys Prxs constitute a redox relay, exclusive to photosynthetic organisms that fine-tunes the redox state of chloroplast enzymes in response to light and affects transduction pathways towards the cytosol.

Crosstalk between the chloroplast protein import and SUMO systems revealed through genetic and molecular investigation in Arabidopsis

The chloroplast proteome contains thousands of different proteins that are encoded by the nuclear genome. These proteins are imported into the chloroplast via the action of the TOC translocase and associated downstream systems. Our recent work has revealed that the stability of the TOC complex is dynamically regulated by the ubiquitin-dependent chloroplast-associated protein degradation pathway. Here, we demonstrate that the TOC complex is also regulated by the small ubiquitin-like modifier (SUMO) system. Arabidopsis mutants representing almost the entire SUMO conjugation pathway can partially suppress the phenotype of ppi1, a pale-yellow mutant lacking the Toc33 protein. This suppression is linked to increased abundance of TOC proteins and improvements in chloroplast development. Moreover, data from molecular and biochemical experiments support a model in which the SUMO system directly regulates TOC protein stability. Thus, we have identified a regulatory link between the SUMO system and the chloroplast protein import machinery.

All green plants grow by converting light energy into chemical energy. They do this using a process called photosynthesis, which happens inside compartments in plant cells called chloroplasts. Chloroplasts use thousands of different proteins to make chemical energy. Some of these proteins allow the chloroplasts to absorb light energy using chlorophyll, the pigment that makes leaves green. The vast majority of these proteins are transported into the chloroplasts through a protein machine called the TOC complex. When plants lack parts of the TOC complex, their chloroplasts develop abnormally, and their leaves turn yellow.

Photosynthesis can make toxic by-products, so cells need a way to turn it off when they are under stress; for example, by lowering the number of TOC complexes on the chloroplasts. This is achieved by tagging TOC complexes with a molecule called ubiquitin, which will lead to their removal from chloroplasts, slowing photosynthesis down. It is unknown whether another, similar, molecular tag called SUMO aids in this destruction process.

To find out, Watson et al. examined a mutant of the plant Arabidopsis thaliana. This mutant had low levels of the TOC complex, turning its leaves pale yellow. A combination of genetic, molecular, and biochemical experiments showed that SUMO molecular tags control the levels of TOC complex on chloroplasts. Increasing the amount of SUMO in the mutant plants made their leaves turn yellower, while interfering with the genes responsible for depositing SUMO tags turned the leaves green. This implies that in plants with less SUMO tags, cells stopped destroying their TOC complexes, allowing the chloroplasts to develop better, and changing the colour of the leaves. The SUMO tagging of TOC complexes shares a lot of genetic similarities with the ubiquitin tag system.

It is possible that SUMO tags may help to control the CHLORAD pathway, which destroys TOC complexes marked with ubiquitin. Understanding this relationship, and how to influence it, could help to improve the performance of crops. The next step is to understand exactly how SUMO tags promote the destruction of the TOC complex.