Photosynthesis-associated Genes Research Articles

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 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- and plastid-encoded genes (PhANGs and PhAPGs). However, the mechanism for coordinative regulation between galactolipid biosynthesis in plastids and 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 deetiolation 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 GENOMES UNCOUPLED1 (GUN1)-mediated plastid-to-nucleus signaling pathway for 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 at the initial phase of deetiolation and optimizes the 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.

Overexpression of SLIM1 transcription factor accelerates vegetative development in Arabidopsis thaliana.

The transcription factor Sulfur Limitation 1 (SLIM1) belongs to the plant-specific Ethylene Insenstive3-Like transcription factor family and is known to coordinate gene expression in response to sulfur deficiency. However, the roles of SLIM1 in nutrient-sufficient conditions have not been characterized. Employing constitutive SLIM1 overexpression (35S::SLIM1) and CRISPR/Cas9 mutant plants (slim1-cr), we identified several distinct phenotypes in nutrient-sufficient conditions in Arabidopsis thaliana. Overexpression of SLIM1 results in plants with approximately twofold greater rosette area throughout vegetative development. 35S::SLIM1 plants also bolt earlier and exhibit earlier downregulation of photosynthesis-associated genes and earlier upregulation of senescence-associated genes than Col-0 and slim1-cr plants. This suggests that overexpression of SLIM1 accelerates development in A. thaliana. Genome-wide differential gene expression analysis relative to Col-0 at three time points with slim1-cr and two 35S::SLIM1 lines allowed us to identify 1,731 genes regulated directly or indirectly by SLIM1 in vivo.

Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species.

Codon usage bias (CUB) refers to different codons exhibiting varying frequencies of usage in the genome. Studying CUB is crucial for understanding genome structure, function, and evolutionary processes. Herein, we investigated the codon usage patterns and influencing factors of protein-coding genes in the chloroplast genomes of four sister genera (monophyletic Roscoea and Cautleya, and monophyletic Pommereschea and Rhynchanthus) from the Zingiberaceae family with contrasting habitats in southwestern China. These genera exhibit distinct habitats, providing a unique opportunity to explore the adaptive evolution of codon usage. We conducted a comprehensive analysis of nucleotide composition and codon usage on protein-coding genes in the chloroplast genomes. The study focused on understanding the relationship between codon usage and environmental adaptation, with a particular emphasis on genes associated with photosynthesis. Nucleotide composition analysis revealed that the overall G/C content of the coding genes was ˂ 48%, indicating an enrichment of A/T bases. Additionally, synonymous and optimal codons were biased toward ending with A/U bases. Natural selection is the primary factor influencing CUB characteristics, particularly photosynthesis-associated genes. We observed differential gene expressions related to light adaptation among sister genera inhabiting different environments. Certain codons were favored under specific conditions, possibly contributing to gene expression regulation in particular environments. This study provides insights into the adaptive evolution of these sister genera by analyzing CUB and offers theoretical assistance for understanding gene expression and regulation. In addition, the data support the relationship between RNA editing and CUB, and the findings shed light on potential research directions for investigating adaptive evolution.

Integrated global analysis in spider flowers illuminates features underlying the evolution and maintenance of C4 photosynthesis.

The carbon concentrating mechanism-C4 photosynthesis-represents a classic example of convergent evolution, but how this important trait originated and evolved remains largely enigmatic. The spider flower Gynandropsis gynandra is a valuable leafy vegetable crop and medicinal plant that has also been recognized as a C4 model species. Here we present a high-quality chromosome-scale annotated genome assembly of G. gynandra through a combination of Oxford Nanopore Technology (ONT), HiFi and Hi-C technology. The 17 super-scaffolds cover 98.66% of the estimated genome (997.61Mb), with a contig N50 of 11.43Mb and a scaffold N50 of 51.02Mb. Repetitive elements occupy up to 71.91% of its genome, and over half are long terminal repeat retrotransposons (LTR-RTs) derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Integrated multiomics analyses of G. gynandra and the ornamental horticulture C3 relative Tarenaya hassleriana reveal that species-specific whole-genome duplication, gene family expansion, recent LTR-RT amplification, and more recent tandem duplication events have all facilitated the evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in the Cleome genus. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. The mode of C3-to-C4 transition found here yields new insights into evolutionary convergence of a complex plant trait. The availability of this reference-grade genomic resource makes G. gynandra an ideal model system facilitating efforts toward C4-aimed crop engineering.

Assessing the biogeography of marine giant viruses in four oceanic transects

Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 m), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation genes that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.

SCL, Encoding a Chloroplast Signal Recognition Particle Receptor, Affects Chlorophyll Synthesis and Chloroplast Development in Rice

Crop yield is largely determined by the solar energy utilization efficiency of photosynthesis; plants with long stay-green periods have greater total photosynthetic production levels and crop yields. Here, a novel seedling chlorosis and lethality (scl) mutant exhibiting a yellow leaf and seedling-lethal phenotype was identified in rice (Oryza sativa L.). The mutant had deformed chloroplasts and almost no protein complexes in thylakoid membranes. The expression levels of photosynthesis-associated genes were significantly down-regulated in scl compared with the wild-type (WT). Positive transgenic lines generated by Agrobacterium tumefaciens-mediated transformation of the scl mutant with a complementation vector harboring SCL cDNA exhibited the normal green leaf phenotype, whereas the scl seedling harboring the empty vector displayed the yellow leaf phenotype, indicating that SCL is LOC_Os01g72800. A fusion protein expressing SCL with green fluorescent protein revealed the fluorescence signal localized to chloroplasts. The expression patterns of chloroplast development and chlorophyll biosynthesis and degradation-related genes were disordered in scl mutant, possibly resulting in the yellow leaf phenotype. These results indicated that the SCL loss of function impaired chloroplast development, chlorophyll biosynthesis, and light-harvesting chlorophyll-binding protein transportation in rice.

TCP15 interacts with GOLDEN2-LIKE 1 to control cotyledon opening in Arabidopsis.

After germination, exposure to light promotes the opening and expansion of the cotyledons and the development of the photosynthetic apparatus in a process called de-etiolation. This process is crucial for seedling establishment and photoautotrophic growth. TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors are important developmental regulators of plant responses to internal and external signals that are grouped into two main classes. In this study, we identified GOLDEN2-LIKE 1 (GLK1), a key transcriptional regulator of photomorphogenesis, as a protein partner of class I TCPs during light-induced cotyledon opening and expansion in Arabidopsis. The class I TCP TCP15 and GLK1 are mutually required for cotyledon opening and the induction of SAUR and EXPANSIN genes, involved in cell expansion. TCP15 also participates in the expression of photosynthesis-associated genes regulated by GLK1, like LHCB1.4 and LHCB2.2. Furthermore, GLK1 and TCP15 bind to the same promoter regions of different target genes containing either GLK or TCP binding motifs and binding of TCP15 is affected in a GLK1-deficient background, suggesting that a complex between TCP15 and GLK1 participates in the induction of these genes. We postulate that GLK1 helps to recruit TCP15 for the modulation of cell expansion genes in cotyledons and that the functional interaction between these transcription factors may serve to coordinate the expression of cell expansion genes with that of genes involved in the development of the photosynthetic apparatus.

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.

Gerbera POE1 (GhPOE1) is involved in leaf senescence in Arabidopsis

Senescence, the final stage of plant development, is a complex and highly controlled physiological process. Senescence occurs in various tissues and organs, and is especially apparent in leaves. Pollen Ole e 1 (POE1) proteins are known to initiate pollen germination, participate in the response to various stresses, and be involved in root development and seed germination. However, their role in plant senescence is not well defined. Using transcriptome data, we isolated a novel protein from Gerbera hybrida (gerbera) which is an ortholog of AT2G34700 (which encodes a Pollen Ole e 1 domain protein in Arabidopsis thaliana) and named GhPOE1. This protein is localized in the cytoplasm and expresses mainly in disk florets, old leaves, and old roots. We transformed GhPOE1 into wild-type Arabidopsis (Col-0) and obtained homozygous transgenic lines OE2, OE3 and OE5. Overexpression of GhPOE1 in these lines led to yellowing rosette leaves with decreased chlorophyll content and photochemical efficiency. Moreover, senescence-associated genes such as SAG12, SAG13, WRKY53, and SIRK (senescence-induced receptor-like kinase) were significantly up-regulated, and the photosynthesis-associated genes CAB2 (chlorophyll a/b-binding 2) and RBCS (ribulose bisphosphate carboxylase small chain) were down-regulated in the transgenic plants. Our results showed that GhPOE1 is a positive regulator of senescence that can promote leaf senescence in Arabidopsis. GhPOE1 is a new candidate gene for genetic engineering to prolong the vase life of cut gerbera flowers.

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.

Time-series transcriptomics reveals a BBX32-directed control of acclimation to high light in mature Arabidopsis leaves.

The photosynthetic capacity of mature leaves increases after several days' exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. How this chloroplast-level acclimation to HL is initiated and controlled is unknown. From expanded Arabidopsis leaves, we determined HL-dependent changes in transcript abundance of 3844 genes in a 0-6h time-series transcriptomics experiment. It was hypothesized that among such genes were those that contribute to the initiation of HL acclimation. By focusing on differentially expressed transcription (co-)factor genes and applying dynamic statistical modelling to the temporal transcriptomics data, a regulatory network of 47 predominantly photoreceptor-regulated transcription (co-)factor genes was inferred. The most connected gene in this network was B-BOX DOMAIN CONTAINING PROTEIN32 (BBX32). Plants overexpressing BBX32 were strongly impaired in acclimation to HL and displayed perturbed expression of photosynthesis-associated genes under LL and after exposure to HL. These observations led to demonstrating that as well as regulation of chloroplast-level acclimation by BBX32, CRYPTOCHROME1, LONG HYPOCOTYL5, CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA-105 are important. In addition, the BBX32-centric gene regulatory network provides a view of the transcriptional control of acclimation in mature leaves distinct from other photoreceptor-regulated processes, such as seedling photomorphogenesis.

Long-term abscisic acid promotes golden2-like1 degradation through constitutive photomorphogenic 1 in a light intensity-dependent manner to suppress chloroplast development.

Abiotic stress, a serious threat to plants, occurs for extended periods in nature. Abscisic acid (ABA) plays a critical role in abiotic stress responses in plants. Therefore, stress responses mediated by ABA have been studied extensively, especially in short-term responses. However, long-term stress responses mediated by ABA remain largely unknown. To elucidate the mechanism by which plants respond to prolonged abiotic stress, we used long-term ABA treatment that activates the signalling against abiotic stress such as dehydration and investigated mechanisms underlying the responses. Long-term ABA treatment activates constitutive photomorphogenic 1 (COP1). Active COP1 mediates the ubiquitination of golden2-like1 (GLK1) for degradation, contributing to lowering expression of photosynthesis-associated genes such as glutamyl-tRNA reductase (HEMA1) and protochlorophyllide oxidoreductase A (PORA), resulting in the suppression of chloroplast development. Moreover, COP1 activation and GLK1 degradation upon long-term ABA treatment depend on light intensity. Additionally, plants with COP1 mutation or exposed to higher light intensity were more sensitive to salt stress. Collectively, our results demonstrate that long-term treatment of ABA leads to activation of COP1 in a light intensity-dependent manner for GLK1 degradation to suppress chloroplast development, which we propose to constitute a mechanism of balancing normal growth and stress responses upon the long-term abiotic stress.

Induction of TOC and TIC genes during photomorphogenesis is mediated primarily by cryptochrome 1 in Arabidopsis

The majority of genes encoding photosynthesis-associated proteins in the nucleus are induced by light during photomorphogenesis, allowing plants to establish photoautotrophic growth. Therefore, optimizing the protein import apparatus of plastids, designated as the translocon at the outer and inner envelope membranes of chloroplast (TOC–TIC) complex, upon light exposure is a prerequisite to the import of abundant nuclear-encoded photosynthesis-associated proteins. However, the mechanism that coordinates the optimization of the TOC–TIC complex with the expression of nuclear-encoded photosynthesis-associated genes remains to be characterized in detail. To address this question, we investigated the mechanism by which plastid protein import is regulated by light during photomorphogenesis in Arabidopsis. We found that the albino plastid protein import2 (ppi2) mutant lacking Toc159 protein import receptors have active photoreceptors, even though the mutant fails to induce the expression of photosynthesis-associated nuclear genes upon light illumination. In contrast, many TOC and TIC genes are rapidly induced by blue light in both WT and the ppi2 mutant. We uncovered that this regulation is mediated primarily by cryptochrome 1 (CRY1). Furthermore, deficiency of CRY1 resulted in the decrease of some TOC proteins in vivo. Our results suggest that CRY1 plays key roles in optimizing the content of the TOC–TIC apparatus to accommodate the import of abundant photosynthesis-associated proteins during photomorphogenesis.

Identification and gene mapping of the starch accumulation and premature leaf senescence mutant ossac4 in rice

The rice mutant ossac4 (starch accumulating 4) was raised from seeds of the rice (Oryza sativa L.) indica maintainer line Xinong 1B treated with ethyl methanesulfonate. The distal and medial portions of the second leaf displayed premature senescence in the ossac4 mutant at the four-leaf stage. Physiological and biochemical analysis, and cytological examination revealed that the ossac4 mutant exhibited the premature leaf senescence phenotype. At the four-leaf stage, the leaves of the ossac4 mutant exhibited significantly increased contents of starch compared with those of the wild type (WT). Quantitative real-time PCR analysis showed that the expression levels of photosynthesis-associated genes were down-regulated and the expression levels of glucose metabolism-associated genes were abnormal. Genetic analysis indicated that the ossac4 mutation was controlled by a single recessive nuclear gene. The OsSAC4 gene was localized to a 322.7-kb interval between the simple-sequence repeat marker XYH11-90 and the single-nucleotide polymorphism marker SNP5300 on chromosome 11. The target interval contained 20 annotated genes. The present results demonstrated that ossac4 represents a novel starch accumulation and premature leaf senescence mutant, and lays the foundation for cloning and functional analysis of OsSAC4.

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

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

Comparative analysis of proso millet (Panicum miliaceum L.) leaf transcriptomes for insight into drought tolerance mechanisms

BackgroundDrought stress is a major abiotic stress that causes huge losses in agricultural production. Proso millet (Panicum miliaceum L.) can efficiently adapt to drought stress and provides important information and gene resources to improve drought tolerance. However, its complex drought-responsive mechanisms remain unclear.ResultsAmong 37 core Chinese proso millet cultivars, Jinshu 6 (JS6) was selected as the drought-sensitive test material, whereas Neimi 5 (NM5) was selected as the drought-tolerant test material under PEG-induced water stress. After sequencing, 1695 differentially expressed genes (DEGs) were observed in JS6 and NM5 without PEG-induced water stress (JS6CK and NM5CK). A total of 833 and 2166 DEGs were found in the two cultivars under simulated drought by using 20% PEG-6000 for 6 (JS6T6 and NM5T6) and 24 h (JS6T24 and NM5T24), respectively. The DEGs in JS6T6 and JS6T24 treatments were approximately 0.298- and 0.754-fold higher than those in NM5T6 and NM5T24, respectively. Compared with the respective controls, more DEGs were found in T6 treatments than in T24 treatments. A delay in the transcriptional responses of the ROS scavenging system to simulated drought treatment and relatively easy recovery of the expression of photosynthesis-associated genes were observed in NM5. Compared with JS6, different regulation strategies were observed in the jasmonic acid (JA) signal transduction pathway of NM5.ConclusionUnder PEG-induced water stress, NM5 maintained highly stable gene expression levels. Compared with drought-sensitive cultivars, the different regulation strategies in the JA signal transduction pathway in drought-tolerant cultivars may be one of the driving forces underlying drought stress tolerance.

A role for GLABRA1 in dark-induced senescence.

The GLABRA (GL1) gene, belonging to the transcription factor-encoding myb gene family, is responsible for trichome formation in Arabidopsis thaliana (L.) Heynh. The leaves and stems of glabra1 mutant plants are devoid of trichomes. Having an easily observable phenotype, the gl1 mutation was one of the first markers established for genetic mapping of Arabidopsis thaliana. Since then, the GL1 gene has been assigned roles in other processes, also related to leaf structure. In this study we present some previously undescribed effects of the gl1 mutation on dark-induced senescence. This process was induced by covering selected mature leaves of Columbia wild-type and gl1 Arabidopsis with black paper for 4 days, while the plants remained growing in a normal photoperiod. While no visible differences in the external symptoms of senescence could be observed in the darkened leaves, the expression of senescence-associated genes was significantly lower in gl1 plants as compared to the wild type. The darkening of leaves led to a decrease in photosynthetic activity and the expression of photosynthesis-associated genes, in comparison to the control leaves. This effect was much less pronounced in gl1 than in the wild type plants. Therefore, gl1 plants seem to be less susceptible to dark-induced aging, suggesting a possible role for the GL1 gene in controlling the onset and progress of senescence. This result is also of practical importance, since gl1 is the genetic background of many other mutants. It may therefore be advisable to revise some of the results obtained with such mutants in light of findings presented here.

Phytochrome activates the plastid-encoded RNA polymerase for chloroplast biogenesis via nucleus-to-plastid signaling

Light initiates chloroplast biogenesis by activating photosynthesis-associated genes encoded by not only the nuclear but also the plastidial genome, but how photoreceptors control plastidial gene expression remains enigmatic. Here we show that the photoactivation of phytochromes triggers the expression of photosynthesis-associated plastid-encoded genes (PhAPGs) by stimulating the assembly of the bacterial-type plastidial RNA polymerase (PEP) into a 1000-kDa complex. Using forward genetic approaches, we identified REGULATOR OF CHLOROPLAST BIOGENESIS (RCB) as a dual-targeted nuclear/plastidial phytochrome signaling component required for PEP assembly. Surprisingly, RCB controls PhAPG expression primarily from the nucleus by interacting with phytochromes and promoting their localization to photobodies for the degradation of the transcriptional regulators PIF1 and PIF3. RCB-dependent PIF degradation in the nucleus signals the plastids for PEP assembly and PhAPG expression. Thus, our findings reveal the framework of a nucleus-to-plastid anterograde signaling pathway by which phytochrome signaling in the nucleus controls plastidial transcription.

Uncoupled Expression of Nuclear and Plastid Photosynthesis-Associated Genes Contributes to Cell Death in a Lesion Mimic Mutant.

Chloroplast-to-nucleus retrograde signaling is essential for the coupled expression of photosynthesis-associated nuclear genes (PhANGs) and plastid genes (PhAPGs) to ensure the functional status of chloroplasts (Cp) in plants. Although various signaling components involved in the process have been identified in Arabidopsis (Arabidopsis thaliana), the biological relevance of such coordination remains an enigma. Here, we show that the uncoupled expression of PhANGs and PhAPGs contributes to the cell death in the lesion simulating disease1 (lsd1) mutant of Arabidopsis. A daylength-dependent increase of salicylic acid (SA) appears to rapidly up-regulate a gene encoding SIGMA FACTOR BINDING PROTEIN1 (SIB1), a transcriptional coregulator, in lsd1 before the onset of cell death. The dual targeting of SIB1 to the nucleus and the Cps leads to a simultaneous up-regulation of PhANGs and down-regulation of PhAPGs. Consequently, this disrupts the stoichiometry of photosynthetic proteins, especially in PSII, resulting in the generation of the highly reactive species singlet oxygen (1O2) in Cps. Accordingly, inactivation of the nuclear-encoded Cp protein EXECUTER1, a putative 1O2 sensor, significantly attenuates the lsd1-conferred cell death. Together, these results provide a pathway from the SA- to the 1O2-signaling pathway, which are intertwined via the uncoupled expression of PhANGs and PhAPGs, contributing to the lesion-mimicking cell death in lsd1.

Proteomic and functional analysis of soybean chlorophyll-deficient mutant cd1 and the underlying gene encoding the CHLI subunit of Mg-chelatase

Sufficient chlorophyll biosynthesis is vital for the growth of photoautotrophic plants. Mg-chelatase, consisting of three subunits (CHLI, CHLD, and CHLH), catalyzes the insertion of Mg2+ into protoporphyrin IX, which is the rate-limiting step of chlorophyll biosynthesis. A chlorophyll-deficient mutant (cd1) was previously identified by phenotype. This mutant shows a chlorina phenotype, abnormal chloroplasts, and lower chlorophyll content, plant height, and seed yield than the WT (Nannong 86-4). In this study, map-based cloning of cd1 revealed that a missense mutation (G1709A) was present in GmCHLI1b, leading to an amino acid substitution (D278N) in the Arg-finger domain. Yeast two-hybrid assays indicated that this substitution weakened the interaction between Gmcd1 and GmCHLI1a/b. In addition, GmCHLI1b was not a target protein of GmTrxF1/2 or GmNTRC1/2 in the Y2H system but could interact with them in a bimolecular fluorescence complementation (BiFC) assay. A proteomic analysis of leaf soluble proteins identified 31 differentially accumulated proteins, mainly involved in photosynthesis, carbon fixation in photosynthetic organisms, and carbohydrate/energy and amino acid/protein metabolism. These results indicated that cd1 possesses weaker photosynthesis, respiration and protein metabolism and that its leaf redox homeostasis is disrupted. Global transcriptome analysis of chlorophyll biosynthesis and RT-PCR demonstrated a transcriptional downregulation of photosynthesis-associated genes in cd1 during the diurnal rhythm. This study provides insights into the mechanisms of molecular regulation in the cd1 mutant and adds to the knowledge of the biological and biochemical functions of GmCHLIs in soybean.