The Role of Tetrapyrrole- and GUN1-Dependent Signaling on Chloroplast Biogenesis

Recent advance on the physiological functions of proteases in chloroplast

Chloroplast proteases play an essential role in orchestrating chloroplast biogenesis and maintaining the homeostasis of diverse metabolic pathways within these organelles, including photosynthesis, amino acid biosynthesis, and stress response regulation. Recent advances in chloroplast proteostasis research have systematically elucidated the physiological functions of key protease families (e.g., FtsH, Deg, and CLP complexes) within chloroplast. This review systematically integrates cutting-edge advances in the physiological functions of chloroplast proteolytic systems, including protein maturation, protein quantity control, protein quality control, and amino acid recovery, and provide a fresh perspective to understand proteases in chloroplasts. According to the latest research progress, the key remaining problems and future research directions in this field are highlighted.

Regulatory and retrograde signaling networks in the chlorophyll biosynthetic pathway

Plants, algae and photosynthetic bacteria convert light into chemical energy by means of photosynthesis, thus providing food and energy for most organisms on Earth. Photosynthetic pigments, including chlorophylls (Chls) and carotenoids, are essential components that absorb the light energy necessary to drive electron transport in photosynthesis. The biosynthesis of Chl shares several steps in common with the biosynthesis of other tetrapyrroles, including siroheme, heme and phycobilins. Given that many tetrapyrrole precursors possess photo-oxidative properties that are deleterious to macromolecules and can lead to cell death, tetrapyrrole biosynthesis (TBS) requires stringent regulation under various developmental and environmental conditions. Thanks to decades of research on model plants and algae, we now have a deeper understanding of the regulatory mechanisms that underlie Chl synthesis, including (i) the many factors that control the activity and stability of TBS enzymes, (ii) the transcriptional and post-translational regulation of the TBS pathway, and (iii) the complex roles of tetrapyrrole-mediated retrograde signaling from chloroplasts to the cytoplasm and the nucleus. Based on these new findings, Chls and their derivatives will find broad applications in synthetic biology and agriculture in the future.

A comprehensive review on the recent advances for 5-aminolevulinic acid production by the engineered bacteria

5-Aminolevulinic acid (5-ALA) is a non-proteinogenic amino acid essential for synthesizing tetrapyrrole compounds, including heme, chlorophyll, cytochrome, and vitamin B12. As a plant growth regulator, 5-ALA is extensively used in agriculture to enhance crop yield and quality. The complexity and low yield of chemical synthesis methods have led to significant interest in the microbial synthesis of 5-ALA. Advanced strategies, including the: enhancement of precursor and cofactor supply, compartmentalization of key enzymes, product transporters engineering, by-product formation reduction, and biosensor-based dynamic regulation, have been implemented in bacteria for 5-ALA production, significantly advancing its industrialization. This article offers a comprehensive review of recent developments in 5-ALA production using engineered bacteria and presents new insights to propel the field forward.

The interplay of singlet oxygen and ABI4 in plant growth regulation

Abscisic acid (ABA) and the AP2/ERF (APETALA 2/ETHYLENE-RESPONSIVE FACTOR)-type transcription factor ABA INSENSITIVE 4 (ABI4) control plant growth and development. We review how singlet oxygen, which is produced in chloroplasts of the fluorescent mutant of Arabidopsis thaliana (arabidopsis), and ABI4 may cooperate in transcriptional and translational reprogramming to cause plants to halt growth or demise. Key elements of singlet oxygen- and ABI4-dependent chloroplast-to-nucleus retrograde signaling involve the chloroplast EXECUTER (EX) 1 and EX2 proteins as well as nuclear WRKY transcription factors. Mutants designed to study singlet oxygen signaling, that lack either ABI4 or the EX1 and EX2 proteins, do not show most of the growth effects of singlet oxygen. We propose a model that positions ABI4 downstream of WRKY transcription factors and EX1 and EX2.

The chloroplast protease system degrades stromal DUF760-1 and DUF760-2 domain-containing proteins at different rates

The chloroplast chaperone CLPC1 aids to select, unfold, and deliver hundreds of proteins to the CLP protease for degradation. Through in vivo CLPC1, trapping we previously identified dozens of proteins that are (potential) substrate adaptors or substrates for the CLP chaperone-protease system. In this study, we show that two of these highly trapped proteins, DUF760-1 and DUF760-2, are substrates for the CLP protease in Arabidopsis (Arabidopsis thaliana). Loss-of-function mutants and transgenic plants were created for phenotyping, protein expression, and localization using immunoblotting and confocal microscopy. In planta BiFC, cycloheximide chase assays, and yeast 2-hybrid analyses were conducted to determine protein interactions and protein half-life. Both DUF760 proteins directly interacted with the N-domain of CLPC1 and both were highly enriched in clpc1-1 and clpr2-1 mutants. Accordingly, in vivo cycloheximide chase assays demonstrated that both DUF760 proteins are degraded by the CLP protease. The half-life of DUF760-1 was 4 to 6 h, whereas DUF760-2 was highly unstable and difficult to detect unless CLP proteolysis was inhibited. Null mutants for DUF760-1 and DUF760-2 showed weak but differential pigment phenotypes and differential sensitivity to protein translation inhibitors. This study demonstrates that DUF760-1 and DUF760-2 are substrates of the CLP chaperone-protease system and excellent candidates for the determination of CLP substrate degrons.

Plastid retrograde signaling: A developmental perspective

Chloroplast activities influence nuclear gene expression, a phenomenon referred to as retrograde signaling. Biogenic retrograde signals have been revealed by changes in nuclear gene expression when chloroplast development is disrupted. Research on biogenic signaling has focused on repression of Photosynthesis-Associated Nuclear Genes (PhANGs), but this is just one component of a syndrome involving altered expression of thousands of genes involved in diverse processes, many of which are upregulated. We discuss evidence for a framework that accounts for most of this syndrome. Disruption of chloroplast biogenesis prevents the production of signals required to progress through discrete steps in the program of photosynthetic differentiation, causing retention of juvenile states. As a result, expression of PhANGs and other genes that act late during photosynthetic differentiation is not initiated, while expression of genes that act early is retained. The extent of juvenility, and thus the transcriptome, reflects the disrupted process: lack of plastid translation blocks development very early, whereas disruption of photosynthesis without compromising plastid translation blocks development at a later stage. We discuss implications of these and other recent observations for the nature of the plastid-derived signals that regulate photosynthetic differentiation and the role of GUN1, an enigmatic protein involved in biogenic signaling.

The pentatricopeptide repeat protein DG1 promotes the transition to bilateral symmetry during Arabidopsis embryogenesis through GUN1-mediated plastid signals

During Arabidopsis embryogenesis, the transition of the embryo's symmetry from radial to bilateral between the globular and heart stage is a crucial event, involving the formation of cotyledon primordia and concurrently the establishment of a shoot apical meristem (SAM). However, a coherent framework of how this transition is achieved remains to be elucidated. In this study, we investigated the function of DELAYED GREENING 1 (DG1) in Arabidopsis embryogenesis using a newly identified dg1-3 mutant. The absence of chloroplast-localized DG1 in the mutants led to embryos being arrested at the globular or heart stage, accompanied by an expansion of WUSCHEL (WUS) and SHOOT MERISTEMLESS (STM) expression. This finding pinpoints the essential role of DG1 in regulating the transition to bilateral symmetry. Furthermore, we showed that this regulation of DG1 may not depend on its role in plastid RNA editing. Nevertheless, we demonstrated that the DG1 function in establishing bilateral symmetry is genetically mediated by GENOMES UNCOUPLED 1 (GUN1), which represses the transition process in dg1-3 embryos. Collectively, our results reveal that DG1 functionally antagonizes GUN1 to promote the transition of the Arabidopsis embryo's symmetry from radial to bilateral and highlight the role of plastid signals in regulating pattern formation during plant embryogenesis.

Intra-chloroplast proteases: A holistic network view of chloroplast proteolysis

Different proteases and peptidases are present within chloroplasts and nonphotosynthetic plastids to process precursor proteins and to degrade cleaved chloroplast transit peptides and damaged, misfolded, or otherwise unwanted proteins. Collectively, these proteases and peptidases form a proteolysis network, with complementary activities and hierarchies, and build-in redundancies. Furthermore, this network is distributed across the different intra-chloroplast compartments (lumen, thylakoid, stroma, envelope). The challenge is to determine the contributions of each peptidase (system) to this network in chloroplasts and nonphotosynthetic plastids. This will require an understanding of substrate recognition mechanisms, degrons, substrate, and product size limitations, as well as the capacity and degradation kinetics of each protease. Multiple extra-plastidial degradation pathways complement these intra-chloroplast proteases. This review summarizes our current understanding of these intra-chloroplast proteases in Arabidopsis and crop plants with an emphasis on considerations for building a qualitative and quantitative network view.

Orchestration of Photosynthesis-Associated Gene Expression and Galactolipid Biosynthesis during Chloroplast Differentiation in Plants

The chloroplast thylakoid membrane is composed of membrane lipids and photosynthetic protein complexes, and the orchestration of thylakoid lipid biosynthesis and photosynthesis-associated protein accumulation is considered important for thylakoid development. Galactolipids consist of ∼80% of the thylakoid lipids, and their biosynthesis is fundamental for chloroplast development. We previously reported that the suppression of galactolipid biosynthesis decreased the expression of photosynthesis-associated nuclear-encoded genes (PhAPGs) and photosynthesis-associated plastid-encoded genes (PhAPGs). However, the mechanism for coordinative regulation between galactolipid biosynthesis in plastids and the expression of PhANGs and PhAPGs remains largely unknown. To elucidate this mechanism, we investigated the gene expression patterns in galactolipid-deficient Arabidopsis seedlings during the de-etiolation process. We found that galactolipids are crucial for inducing both the transcript accumulation of PhANGs and PhAPGs and the accumulation of plastid-encoded photosynthesis-associated proteins in developing chloroplasts. Genetic analysis indicates the contribution of the GENOMES UNCOUPLED1 (GUN1)-mediated plastid-to-nucleus signaling pathway to PhANG regulation in response to galactolipid levels. Previous studies suggested that the accumulation of GUN1 reflects the state of protein homeostasis in plastids and alters the PhANG expression level. Thus, we propose a model that galactolipid biosynthesis determines the protein homeostasis in plastids in the initial phase of de-etiolation and optimizes GUN1-dependent signaling to regulate the PhANG expression. This mechanism might contribute to orchestrating the biosynthesis of lipids and proteins for the biogenesis of functional chloroplasts in plants.

Transcriptome analysis reveals molecular mechanisms underlying chloroplast biogenesis in albino Agave angustifolia plantlets

Albino plants display partial or complete loss of photosynthetic pigments and defective thylakoid membrane development, consequently impairing plastid function and development. These distinctive attributes render albino plants excellent models for investigating chloroplast biogenesis. Despite their potential, limited exploration has been conducted regarding the molecular alterations underlying these phenotypes, extending beyond photosynthetic metabolism. In this study, we present a novel de novo transcriptome assembly of an albino somaclonal variant of Agave angustifolia Haw., which spontaneously emerged during the micropropagation of green plantlets. Additionally, RT-qPCR analysis was employed to validate the expression of genes associated with chloroplast biogenesis, and plastome copy numbers were quantified. This research aims to gain insight into the molecular disruptions affecting chloroplast development and ascertain whether the expression of critical genes involved in plastid development and differentiation is compromised in albino tissues of A. angustifolia. Our transcriptomic findings suggest that albino Agave plastids exhibit high proliferation, activation of the protein import machinery, altered transcription directed by PEP and NEP, dysregulation of plastome expression genes, reduced expression of photosynthesis-associated nuclear genes, disruption in the tetrapyrrole and carotenoid biosynthesis pathway, alterations in the plastid ribosome, and an increased number of plastome copies, among other alterations.

Transcriptional profile reveals the physiological responses to prey availability in the mixotrophic chrysophyte Poterioochromonas malhamensis

Mixotrophic flagellates, which have diverse nutritional modes and play important roles in connecting the microbial loop with the classical food chain, are ideal models to study the mechanisms of adaptation between different nutritional modes in protists. In their natural ecosystems, mixotrophic flagellates may encounter microalgal prey of different digestibility, which may affect the carbon flow. To date, a molecular biological view of the metabolic processes in the mixotrophic flagellate Poterioochromonas malhamensis during nutritional adaptation and feeding on microalgal prey of different digestibility is still lacking. Accordingly, this study focused on the gene expression differences in P. malhamensis under autotrophy, being fed by the digestible microalga Chlorella sorokiniana GT-1, and being fed by the indigestible microalga C. sorokiniana CMBB-146. Results showed that the growth rate of P. malhamensis under autotrophy was much lower than that when fed by digestible microalgae. Addition of C. sorokiniana CMBB-146 could only increase the growth rate of P. malhamensis in the first 3 days, but the cell concentration of P. malhamensis started to decrease gradually after 4 days. Compared to autotrophic P. malhamensis, total 6,583 and 3,510 genes were significantly and differentially expressed in P. malhamensis fed by digestible microalgae and indigestible microalgae, respectively. Compared to autotrophic cells, genes related to the ribosome, lysosome, glycolysis, gluconeogenesis, TCA cycle, β-oxidation, duplication, and β-1,3-glucan in P. malhamensis grazing on digestible prey were up-regulated, while genes related to light harvesting and key enzymes referring to chlorophyll were down-regulated. Genes related to apoptosis and necrosis in P. malhamensis were up-regulated after grazing on indigestible microalgae compared to the autotrophic group, which we suggest is associated with the up-regulation of genes related to lysosome enzymes. This study provides abundant information on the potential intracellular physiological responses of P. malhamensis during the process of nutritional adaptation.

Chloroplast-localized GUN1 contributes to the acquisition of basal thermotolerance in Arabidopsis thaliana

Heat stress (HS) severely affects different cellular compartments operating in metabolic processes and represents a critical threat to plant growth and yield. Chloroplasts are crucial for heat stress response (HSR), signaling to the nucleus the environmental challenge and adjusting metabolic and biosynthetic functions accordingly. GENOMES UNCOUPLED 1 (GUN1), a chloroplast-localized protein, has been recognized as one of the main players of chloroplast retrograde signaling. Here, we investigate HSR in Arabidopsis wild-type and gun1 plantlets subjected to 2 hours of HS at 45°C. In wild-type plants, Reactive Oxygen Species (ROS) accumulate promptly after HS, contributing to transiently oxidize the cellular environment and acting as signaling molecules. After 3 hours of physiological recovery at growth temperature (22°C), the induction of enzymatic and non-enzymatic antioxidants prevents oxidative damage. On the other hand, gun1 mutants fail to induce the oxidative burst immediately after HS and accumulate ROS and oxidative damage after 3 hours of recovery at 22°C, thus resulting in enhanced sensitivity to HS. These data suggest that GUN1 is required to oxidize the cellular environment, participating in the acquisition of basal thermotolerance through the redox-dependent plastid-to-nucleus communication.

Retrograde and anterograde signaling in the crosstalk between chloroplast and nucleus

The chloroplast is a complex cellular organelle that not only performs photosynthesis but also synthesizes amino acids, lipids, and phytohormones. Nuclear and chloroplast genetic activity are closely coordinated through signaling chains from the nucleus to chloroplast, referred to as anterograde signaling, and from chloroplast to the nucleus, named retrograde signaling. The chloroplast can act as an environmental sensor and communicates with other cell compartments during its biogenesis and in response to stress, notably with the nucleus through retrograde signaling to regulate nuclear gene expression in response to developmental cues and stresses that affect photosynthesis and growth. Although several components involved in the generation and transmission of plastid-derived retrograde signals and in the regulation of the responsive nuclear genes have been identified, the plastid retrograde signaling network is still poorly understood. Here, we review the current knowledge on multiple plastid retrograde signaling pathways, and on potential plastid signaling molecules. We also discuss the retrograde signaling-dependent regulation of nuclear gene expression within the frame of a multilayered network of transcription factors.

β-Cyclocitral Does Not Contribute to Singlet Oxygen-Signalling in Algae, but May Down-Regulate Chlorophyll Synthesis

Light stress signalling in algae and plants is partially orchestrated by singlet oxygen (¹O₂), a reactive oxygen species (ROS) that causes significant damage within the chloroplast, such as lipid peroxidation. In the vicinity of the photosystem II reaction centre, a major source of ¹O₂, are two β-carotene molecules that quench ¹O₂ to ground-state oxygen. ¹O₂ can oxidise β-carotene to release β-cyclocitral, which has emerged as a ¹O₂-mediated stress signal in the plant Arabidopsis thaliana. We investigated if β-cyclocitral can have similar retrograde signalling properties in the unicellular alga Chlamydomonas reinhardtii. Using RNA-Seq, we show that genes up-regulated in response to exogenous β-cyclocitral included CAROTENOID CLEAVAGE DIOXYGENASE 8 (CCD8), while down-regulated genes included those associated with porphyrin and chlorophyll anabolism, such as tetrapyrrole-binding protein (GUN4), magnesium chelatases (CHLI1, CHLI2, CHLD, CHLH1), light-dependent protochlorophyllide reductase (POR1), copper target 1 protein (CTH1), and coproporphyrinogen III oxidase (CPX1). Down-regulation of this pathway has also been shown in β-cyclocitral-treated A. thaliana, indicating conservation of this signalling mechanism in plants. However, in contrast to A. thaliana, a very limited overlap in differential gene expression was found in β-cyclocitral-treated and ¹O₂-treated C. reinhardtii. Furthermore, exogenous treatment with β-cyclocitral did not induce tolerance to ¹O₂. We conclude that while β-cyclocitral may down-regulate chlorophyll synthesis, it does not seem to contribute to ¹O₂-mediated high light stress signalling in algae.

Post-translational regulation of metabolic checkpoints in plant tetrapyrrole biosynthesis

Tetrapyrrole biosynthesis produces metabolites that are essential for critical reactions in photosynthetic organisms, including chlorophylls, heme, siroheme, phytochromobilins, and their derivatives. Due to the paramount importance of tetrapyrroles, a better understanding of the complex regulation of tetrapyrrole biosynthesis promises to improve plant productivity in the context of global climate change. Tetrapyrrole biosynthesis is known to be controlled at multiple levels-transcriptional, translational and post-translational. This review addresses recent advances in our knowledge of the post-translational regulation of tetrapyrrole biosynthesis and summarizes the regulatory functions of the various auxiliary factors involved. Intriguingly, the post-translational network features three prominent metabolic checkpoints, located at the steps of (i) 5-aminolevulinic acid synthesis (the rate-limiting step in the pathway), (ii) the branchpoint between chlorophyll and heme synthesis, and (iii) the light-dependent enzyme protochlorophyllide oxidoreductase. The regulation of protein stability, enzymatic activity, and the spatial organization of the committed enzymes in these three steps ensures the appropriate flow of metabolites through the tetrapyrrole biosynthesis pathway during photoperiodic growth. In addition, we offer perspectives on currently open questions for future research on tetrapyrrole biosynthesis.

Chloroplastic pentatricopeptide repeat proteins (PPR) in albino plantlets of Agave angustifolia Haw. reveal unexpected behavior

BACKGROUND

Pentatricopeptide repeat (PPR) proteins play an essential role in the post-transcriptional regulation of genes in plastid genomes. Although important advances have been made in understanding the functions of these genes, there is little information available on chloroplastic PPR genes in non-model plants and less in plants without chloroplasts. In the present study, a comprehensive and multifactorial bioinformatic strategy was applied to search for putative PPR genes in the foliar and meristematic tissues of green and albino plantlets of the non-model plant Agave angustifolia Haw.

RESULTS

A total of 1581 PPR transcripts were identified, of which 282 were chloroplastic. Leaf tissue in the albino plantlets showed the highest levels of expression of chloroplastic PPRs. The search for hypothetical targets of 12 PPR sequences in the chloroplast genes of A. angustifolia revealed their action on transcripts related to ribosomes and translation, photosystems, ATP synthase, plastid-encoded RNA polymerase and RuBisCO.

CONCLUSIONS

Our results suggest that the expression of PPR genes depends on the state of cell differentiation and plastid development. In the case of the albino leaf tissue, which lacks functional chloroplasts, it is possible that anterograde and retrograde signaling networks are severely compromised, leading to a compensatory anterograde response characterized by an increase in the expression of PPR genes.

GUN1 involvement in the redox changes occurring during biogenic retrograde signaling

Chloroplast biogenesis requires a tight communication between nucleus and plastids. By retrograde signals, plastids transmit information about their functional and developmental state to adjust nuclear gene expression, accordingly. GENOMES UNCOUPLED 1 (GUN1), a chloroplast-localized protein integrating several developmental and stress-related signals, is one of the main players of retrograde signaling. Here, we focused on the interplay between GUN1 and redox regulation during biogenic retrograde signaling, by investigating redox parameters in Arabidopsis wild type and gun1 seedlings. Our data highlight that during biogenic retrograde signaling superoxide anion (O₂^-) and hydrogen peroxide (H₂O₂) play a different role in response to GUN1. Under physiological conditions, even in the absence of a visible phenotype, gun1 mutants show low activity of superoxide dismutase (SOD) and ascorbate peroxidase (APX), with an increase in O₂^- accumulation and lipid peroxidation, suggesting that GUN1 indirectly protects chloroplasts from oxidative damage. In wild type seedlings, perturbation of chloroplast development with lincomycin causes H₂O₂ accumulation, in parallel with the decrease of ROS-removal metabolites and enzymes. These redox changes do not take place in gun1 mutants which, in contrast, enhance SOD, APX and catalase activities. Our results indicate that in response to lincomycin, GUN1 is necessary for the H₂O₂-dependent oxidation of cellular environment, which might contribute to the redox-dependent plastid-to nucleus communication.

Impacts of phosphatidylglycerol on plastid gene expression and light induction of nuclear photosynthetic genes

Phosphatidylglycerol (PG) is the only major phospholipid in the thylakoid membrane of chloroplasts. PG is essential for photosynthesis, and loss of PG in Arabidopsis thaliana results in severe defects of growth and chloroplast development, with decreased chlorophyll accumulation, impaired thylakoid formation, and down-regulation of photosynthesis-associated genes encoded in nuclear and plastid genomes. However, how the absence of PG affects gene expression and plant growth remains unclear. To elucidate this mechanism, we investigated transcriptional profiles of a PG-deficient Arabidopsis mutant pgp1-2 under various light conditions. Microarray analysis demonstrated that reactive oxygen species (ROS)-responsive genes were up-regulated in pgp1-2. However, ROS production was not enhanced in the mutant even under strong light, indicating limited impacts of photooxidative stress on the defects of pgp1-2. Illumination to dark-adapted pgp1-2 triggered down-regulation of photosynthesis-associated nuclear-encoded genes (PhANGs), while plastid-encoded genes were constantly suppressed. Overexpression of GOLDEN2-LIKE1 (GLK1), a transcription factor gene regulating chloroplast development, in pgp1-2 up-regulated PhANGs but not plastid-encoded genes along with chlorophyll accumulation. Our data suggest a broad impact of PG biosynthesis on nuclear-encoded genes partially via GLK1 and a specific involvement of this lipid in plastid gene expression and plant development.

An Argon-Ion-Induced Pale Green Mutant of Arabidopsis Exhibiting Rapid Disassembly of Mesophyll Chloroplast Grana

Argon-ion beam is an effective mutagen capable of inducing a variety of mutation types. In this study, an argon ion-induced pale green mutant of Arabidopsis thaliana was isolated and characterized. The mutant, designated Ar50-33-pg1, exhibited moderate defects of growth and greening and exhibited rapid chlorosis in photosynthetic tissues. Fluorescence microscopy confirmed that mesophyll chloroplasts underwent substantial shrinkage during the chlorotic process. Genetic and whole-genome resequencing analyses revealed that Ar50-33-pg1 contained a large 940 kb deletion in chromosome V that encompassed more than 100 annotated genes, including 41 protein-coding genes such as TYRAAt1/TyrA1, EGY1, and MBD12. One of the deleted genes, EGY1, for a thylakoid membrane-localized metalloprotease, was the major contributory gene responsible for the pale mutant phenotype. Both an egy1 mutant and F1 progeny of an Ar50-33-pg1 × egy1 cross-exhibited chlorotic phenotypes similar to those of Ar50-33-pg1. Furthermore, ultrastructural analysis of mesophyll cells revealed that Ar50-33-pg1 and egy1 initially developed wild type-like chloroplasts, but these were rapidly disassembled, resulting in thylakoid disorganization and fragmentation, as well as plastoglobule accumulation, as terminal phenotypes. Together, these data support the utility of heavy-ion mutagenesis for plant genetic analysis and highlight the importance of EGY1 in the structural maintenance of grana in mesophyll chloroplasts.