Regulation and evolution of chlorophyll metabolism

Identification and characterization of ClAPRR2, a key candidate gene controlling watermelon stripe color

The stripe color of watermelon is a vital commercial trait and is the focus of attention of consumers and researchers. However, the genetic determinants of watermelon stripe color are incompletely understood. Based on the results of preliminary localization studies, we constructed a large-capacity F2 generation population (710 plants) using light-green striped ZXG1555 and green-striped Cream of Saskatchewan (COS) watermelon strains as parental lines for fine mapping. Genes controlling stripe color were located in an 85.284 kb region on chromosome 9, which contained five candidate genes. Combined with parental phenotypes, chlorophyll contents of rinds and stripes were assayed. Gene sequence alignment and transcriptional level analysis of parental lines predicted Cla97C09G175170 (encoding a two-component response regulator-like protein, APRR2) as the best candidate gene for stripe color trait. Two SNPs in the ClAPRR2 coding region caused amino acid substitutions, but were not located in the conserved domain, while a 12 bp insertion caused premature translation termination and a 35 amino acid deletion in the conserved domain and may have affected ClAPRR2 function in ZXG1555. Subcellular localization analysis showed that ClAPRR2 was expressed in the ZXG1555 cell membrane but was located in the nucleus and cell membrane of COS. Nucleotide polymorphisms and deletions were also detected in the promoter region between parental lines and caused cis-acting element variations. Luciferase activity suggested that promoter variations may not be the main factor in the regulation of ClAPRR2 expression.

Light quality affects chlorophyll biosynthesis and photosynthetic performance in Antarctic Chlamydomonas

The perennially ice-covered Lake Bonney in Antarctica has been deemed a natural laboratory for studying life at the extreme. Photosynthetic algae dominate the lake food webs and are adapted to a multitude of extreme conditions including perpetual shading even at the height of the austral summer. Here we examine how the unique light environment in Lake Bonney influences the physiology of two Chlamydomonas species. Chlamydomonas priscui is found exclusively in the deep photic zone where it receives very low light levels biased in the blue part of the spectrum (400-500 nm). In contrast, Chlamydomonas sp. ICE-MDV is represented at various depths within the water column (including the bright surface waters), and it receives a broad range of light levels and spectral wavelengths. The psychrophilic character of both species makes them an ideal system to study the effects of light quality and quantity on chlorophyll biosynthesis and photosynthetic performance in extreme conditions. We show that the shade-adapted C. priscui exhibits a decreased ability to accumulate chlorophyll and severe photoinhibition when grown under red light compared to blue light. These effects are particularly pronounced under red light of higher intensity, suggesting a loss of capability to acclimate to varied light conditions. In contrast, ICE-MDV has retained the ability to synthesize chlorophyll and maintain photosynthetic efficiency under a broader range of light conditions. Our findings provide insights into the mechanisms of photosynthesis under extreme conditions and have implications on algal survival in changing conditions of Antarctic ice-covered lakes.

The BCM1-EGY1 module balances chlorophyll biosynthesis and breakdown to confer chlorophyll homeostasis in land plants

Chlorophyll metabolism has evolved during plant evolution. The strictly light-dependent nature of chlorophyll biosynthesis found in angiosperms requires tight coordination of chlorophyll biosynthesis and breakdown to achieve chlorophyll homeostasis. However, the specific control mechanisms remain largely unclear. Here, we demonstrate that the scaffold protein BALANCE OF CHLOROPHYLL METABOLISM1 (BCM1) has co-evolved with the carboxy-terminal domains of specific enzymes involved in chlorophyll biosynthesis and breakdown, including GENOMES UNCOUPLED 4 (GUN4) and Mg-dechelatase 1 (SGR1). We found that the land plant-specific interaction of BCM1 with the carboxy-terminal domains of GUN4 and SGR1 is indispensable for concurrent stimulation of chlorophyll biosynthesis and suppression of chlorophyll breakdown. The land plant-specific carboxy-terminal domain is essential for the membrane docking and turnover of GUN4, whereas it is key for proteolysis of SGR1. More importantly, we identified the metallopeptidase Gravitropism-deficient and Yellow-green 1 (EGY1) as the proteolytic machinery responsible for BCM1-mediated proteolysis of SGR1. In summary, this study reveals the BCM1-EGY1 module has evolved to maintain chlorophyll homeostasis by the post-translational control of the balance between chlorophyll biosynthesis and breakdown. This mechanism thus represents an evolutionary response to the metabolic demands imposed on plants in terrestrial environments.

Identification of Candidate Genes for Green Rind Color in Watermelon

The color of the rind is one of the most crucial agronomic characteristics of watermelon (Citrullus lanatus L.). Its genetic analysis was conducted to provide the identification of genes regulating rind color and improving the quality of watermelon appearance. In this study, a mapping population of 505 F2 plants, derived from a cross between green (CG058) and light-green (CG265) rinds, along with a high-density genetic linkage (average 0.9 cM distance between bin markers), was used to map and identify possible candidate genes. The green rind trait was determined to be regulated by a single Mendelian locus and was precisely located within a 110 kb genomic site on chromosome nine (Chr 9). In the respective region, two potential genes, Cla97C09G175170 and Cla97C09G175180, were substantially downregulated in the light-green rind in comparison to the green rind. Previous studies revealed that Cla97C09G175170, encoding a two-component response regulator-like protein (APRR2), is possibly involved in the green rind trait in watermelon. Virus-induced gene silencing (VIGS) assay confirmed that ClAPRR2 is a key gene responsible for green rind color. Moreover, qRT-PCR analysis revealed that the transcription levels of multiple key genes in the chlorophyll (Chl) biosynthesis pathway were downregulated in the light-green rind relative to the green rind. The current findings have the potential to clarify the regulatory mechanisms that underlie the color of the watermelon rind. These data would provide valuable insights for the targeted molecular design and development of watermelon rinds.

LcASR enhances tolerance to abiotic stress in Leymus chinensis and Arabidopsis thaliana by improving photosynthetic performance

As a crucial forage grass, Leymus chinensis plays significant roles in soil and water conservation owing to its robust stress resistance. However, the underlying molecular mechanisms of its stress tolerance remain unclear. In this study, a novel gene, designated as LcASR (Abiotic Stress Resistance in Leymus chinensis), imparting resilience to both high light and drought, was identified. Under normal growth conditions, heterologous overexpression of LcASR in Arabidopsis (HO lines) showed no significant difference in appearance compared to wild-type. Nevertheless, HO lines accumulate significantly higher chlorophyll content during the dark-to-light transition compared to the wild-type, indicating that the LcASR protein participates in chlorophyll synthesis during chloroplast development. Meanwhile, transgenic Arabidopsis and L. chinensis plants exhibited resistance to abiotic stresses such as high light and drought. Photosystem complexes analysis revealed that LHCII proteins remained stable within their respective complexes during high light stress. We hypothesize that LcASR may play a role in fine tuning of chlorophyll synthesis to enable plant adaptation to diverse stress conditions. Moreover, overexpression of LcASR in L. chinensis led to agronomically valuable traits such as deeper green color, higher biomass accumulation, prolonged withering period, and extended grazing durations. This study uncovers a novel gene in L. chinensis that enhances forage yield and provides valuable genetic resources for sheepgrass breeding.

Multi-omics analysis provides insights into the mechanism underlying fruit color formation in Capsicum

Fruit color is a crucial attribute of fruit quality in peppers (Capsicum spp.). However, few studies have focused on the mechanism of color formation in immature pepper fruits. In this study, the light-yellow color observed in immature CSJ009 fruits compared to CSJ010 could be attributed to decreased chlorophyll and carotenoid pigments. Through integrated analysis of the transcriptome and metabolome of CSJ009 and CSJ010, we identified 23,930 differentially expressed genes (DEGs) and 345 differentially accumulated metabolites (DAMs). Furthermore, integrated analysis revealed a strong correlation between the HCT-like gene and metabolite MWS0178 (chlorogenic acid). Paraffin section assay revealed that the epidermal cells of immature CSJ010 fruits exhibited a more compact arrangement with significantly greater length than those of CSJ009. Quantitative determination of carotenoids showed that lutein emerged as the predominant carotenoid in immature pepper fruits. Additionally, missense mutation of LCYB2 is likely to lead to a decrease in β-carotene content in immature CSJ009 fruits, whereas CCS may directly catalyze the conversion of lycopene to β-carotene in mature fruits. The null mutation in CCS promoted the biosynthesis of β,ϵ-branch carotenoids leading to lutein being the most abundant carotenoid found in orange CSJ010 fruits. These findings provide important insights into the mechanism underlying color formation in pepper fruits and establish a foundation for the further exploration of color-related genes.

CfSGR1 and CfSGR2 from Cryptomeria fortunei exhibit contrasting responses to hormones and abiotic stress in transgenic Arabidopsis

Stay-green (SGR) genes are pivotal regulatory genes in the context of plant chlorophyll metabolism, but few studies on SGR homologues in Cryptomeria fortunei have been previously reported. We cloned two CfSGR genes and overexpressed them in Arabidopsis to explore their functions. Full-length CfSGR1 and CfSGR2 are 1265 and 1197 bp, encompassing open reading frames (ORFs) encoding 274 and 276 amino acids, respectively. SGRs exhibited high conservation in higher plants, and phylogenetic analysis indicated that SGRs from monocots and gymnosperms cluster in a clade. The proteins localized to chloroplasts and showed no transcriptional activity in yeast cells. The CfSGR gene expressions were induced by abiotic stresses and hormones. Under conditions of darkness, abscisic acid (ABA), salt, drought, or freezing stress, CfSGR2-transgenic Arabidopsis exhibited a delay in leaf yellowing compared to the WT, which was attributed to increased chlorophyll content and enhanced photosynthetic capacity. These transgenic plants exhibited improved resistance to stress via upregulated expression of resistance-related genes, increased antioxidant enzyme activities, and reduced malondialdehyde content and electrolyte leakage rate. In contrast, CfSGR1-transgenic plants may accelerate leaf yellowing and exhibit reduced stress resistance. Our findings highlight potential divergence in the functions of CfSGR genes concerning plant growth and development and responses to abiotic stresses or hormones, providing a scientific foundation for future breeding of stress-resistant C. fortunei cultivars.

Proteomic and phosphoproteomic analysis of a Haematococcus pluvialis (Chlorophyceae) mutant with a higher heterotrophic cell division rate reveals altered pathways involved in cell proliferation and nutrient partitioning

Haematococcus pluvialis has been used to produce the ketocarotenoid antioxidant, astaxanthin. Currently, heterotrophic cultivation of H. pluvialis is limited by slow growth rates. This work aimed to address this challenge by exploring the mechanisms of acetate metabolism in Haematococcus. Chemical mutagenesis and screening identified H. pluvialis strain KREMS 23D-3 that achieved up to a 34.9% higher cell density than the wild type when grown heterotrophically on acetate. An integrative proteomics and phosphoproteomics approach was employed to quantify 4955 proteins and 5099 phosphorylation sites from 2505 phosphoproteins in the wild-type and mutant strains of H. pluvialis. Among them, 12 proteins were significantly upregulated and 22 significantly downregulated in the mutant while phosphoproteomic analysis identified 143 significantly upregulated phosphorylation sites on 106 proteins and 130 downregulated phosphorylation sites on 114 proteins. Upregulation of anaphase-promoting complex phosphoproteins and downregulation of a putative cell cycle division 20 phosphoprotein in the mutant suggests rapid mitotic progression, coinciding with higher cell division rates. Upregulated coproporphyrinogen oxidase and phosphorylated magnesium chelatase in the mutant demonstrated altered nitrogen partitioning toward chlorophyll biosynthesis. The large proportion of differentially expressed phosphoproteins suggests phosphorylation is a key regulator for protein expression and activity in Haematococcus. Taken together, this study reveals the regulation of interrelated acetate metabolic pathways in H. pluvialis and provides protein targets that may guide future strain engineering work.

Effects of LED polarized and vortex light on growth and photosynthetic characteristics of pepper (Capsicum annuum L.)

Most studies currently focus on traditional illuminant regulating plant growth, while less attention has been given to the LED internal luminescence. This study examined how polarized and vortex light affect the growth and photosynthetic traits of pepper plants, with LED light used as the control. The findings indicated that circular polarized light significantly increased the aboveground biomass of pepper. Additionally, both polarized and vortex light treatment significantly influenced the root development of pepper. In comparison to the control group, the chlorophyll content was highest under circular polarized light, while the Pn, Sc, Tr, and Ci values were highest under linear polarized light, and the enzyme activity of Rubisco was increased. Circular polarized light notably increased the activities of POD, CAT, and SOD, the activity of SOD reached its peak under the left vortex light. Moreover, the content of MDA was observed to be the lowest under linear and right vortex light treatments. The expressions of key genes for chlorophyll synthesis (CaHEMA1 and CaCAO) and antioxidant enzyme synthesis (CaPOD, CaSOD, and CaMDHAR) were significantly altered under varying polarized light conditions, The latter genes, which play crucial roles in antioxidant enzyme activity, also showed significant variations in response to different polarized light treatments. In conclusion, polarized light significantly impacts the growth of pepper and is anticipated to be utilized for plant growth, setting the stage for future research in this area.

Elucidating substrate binding in the light-dependent protochlorophyllide oxidoreductase

The Light-Dependent Protochlorophyllide Oxidoreductase (LPOR) catalyzes a crucial step in chlorophyll biosynthesis: the rare biological photocatalytic reduction of the double C[double bond, length as m-dash]C bond in the precursor, protochlorophyllide (Pchlide). Despite its fundamental significance, limited structural insights into the active complex have hindered understanding of its reaction mechanism. Recently, a high-resolution cryo-EM structure of LPOR in its active conformation challenged our view of pigment binding, residue interactions, and the catalytic process. Surprisingly, this structure contrasts markedly with previous assumptions, particularly regarding the orientation of the bound Pchlide. To gain insights into the substrate binding puzzle, we conducted molecular dynamics simulations, quantum-mechanics/molecular-mechanics (QM/MM) calculations, and site-directed mutagenesis. Two Pchlide binding modes were considered, one aligning with historical proposals (mode A) and another consistent with the recent experimental data (mode B). Binding energy calculations revealed that in contrast to the non-specific interactions found for mode A, mode B exhibits distinct stabilizing interactions that support more thermodynamically favorable binding. A comprehensive analysis incorporating QM/MM-based local energy decomposition unraveled a complex interaction network involving Y177, H319, and the C131 carboxy group, influencing the pigment's excited state energy and potentially contributing to substrate specificity. Importantly, our results uniformly favor mode B, challenging established interpretations and emphasizing the need for a comprehensive re-evaluation of the LPOR reaction mechanism in a way that incorporates accurate structural information on pigment interactions and substrate-cofactor positioning in the binding pocket. The results shed light on the intricacies of LPOR's catalytic mechanism and provide a solid foundation for further elucidating the secrets of chlorophyll biosynthesis.

The Structure, Functions and Potential Medicinal Effects of Chlorophylls Derived from Microalgae

Microalgae are considered to be natural producers of bioactive pigments, with the production of pigments from microalgae being a sustainable and economical strategy that promises to alleviate growing demand. Chlorophyll, as the main pigment of photosynthesis, has been widely studied, but its medicinal applications as an antioxidant, antibacterial, and antitumor reagent are still poorly understood. Chlorophyll is the most important pigment in plants and algae, which not only provides food for organisms throughout the biosphere, but also plays an important role in a variety of human and man-made applications. The biological activity of chlorophyll is closely related to its chemical structure; its specific structure offers the possibility for its medicinal applications. This paper reviews the structural and functional roles of microalgal chlorophylls, commonly used extraction methods, and recent advances in medicine, to provide a theoretical basis for the standardization and commercial production and application of chlorophylls.

YGL3 Encoding an IPP and DMAPP Synthase Interacts with OsPIL11 to Regulate Chloroplast Development in Rice

As the source of isoprenoid precursors, the plastidial methylerythritol phosphate (MEP) pathway plays an essential role in plant development. Here, we report a novel rice (Oryza sativa L.) mutant ygl3 (yellow-green leaf3) that exhibits yellow-green leaves and lower photosynthetic efficiency compared to the wild type due to abnormal chloroplast ultrastructure and reduced chlorophyll content. Map-based cloning showed that YGL3, one of the major genes involved in the MEP pathway, encodes 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, which is localized in the thylakoid membrane. A single base substitution in ygl3 plants resulted in lower 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity and lower contents of isopentenyl diphosphate (IPP) compared to the wild type. The transcript levels of genes involved in the syntheses of chlorophyll and thylakoid membrane proteins were significantly reduced in the ygl3 mutant compared to the wild type. The phytochrome interacting factor-like gene OsPIL11 regulated chlorophyll synthesis during the de-etiolation process by directly binding to the promoter of YGL3 to activate its expression. The findings provides a theoretical basis for understanding the molecular mechanisms by which the MEP pathway regulate chloroplast development in rice.

Identification of hub genes that variate the qCSS12-mediated cold tolerance between indica and japonica rice using WGCNA

KEY MESSAGE

Cold-tolerant QTL qCSS12-regulated 14 hub genes are involved in the chloroplastic biological processes and in the protein synthesis and degradation processes in japonica rice. Low temperature is a main constraint factor for rice growth and production. To better understand the regulatory mechanisms underlying the cold tolerance phenotype in rice, here, we selected a cold-sensitive nearly isogenic line (NIL) NIL(qcss12) as materials to identify hub genes that are mediated by the cold-tolerant locus qCSS12 through weighted gene co-expression network analysis (WGCNA). Fourteen cold-responsive genes were identified, of which, 6 are involved in regulating biological processes in chloroplasts, including the reported EF-Tu, Prk, and ChlD, and 8 are involved in the protein synthesis and degradation processes. Differential expression of these genes between NIL(qcss12) and its controls under cold stress may be responsible for qCSS12-mediated cold tolerance in japonica rice. Moreover, natural variations in 12 of these hub genes are highly correlated with the cold tolerance divergence in two rice subspecies. The results provide deep insights into a better understanding of the molecular basis of cold adaptation in rice and provide a theoretical basis for molecular breeding.

Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes

Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.

Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis

IMPORTANCE

Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.

Molecular and genetic perspectives of cold tolerance in wheat

Environmental variation is the most crucial problem as it is causing food insecurity and negatively impacts food availability, utilization, assessment, and stability. Wheat is the largest and extensively cultivated staple food crop for fulfilling global food requirements. Abiotic stresses including salinity, heavy metal toxicity, drought, extreme temperatures, and oxidative stresses being the primary cause of productivity loss are a serious threat to agronomy. Cold stress is a foremost ecological constraint that is extremely influencing plant development, and yield. It is extremely hampering the propagative development of plant life. The structure and function of plant cells depend on the cell's immune system. The stresses due to cold, affect fluid in the plasma membrane and change it into crystals or a solid gel phase. Plants being sessile in nature have evolved progressive systems that permit them to acclimatize the cold stress at the physiological as well as molecular levels. The phenomenon of acclimatisation of plants to cold stress has been investigated for the last 10 years. Studying cold tolerance is critical for extending the adaptability zones of perennial grasses. In the present review, we have elaborated the current improvement of cold tolerance in plants from molecular and physiological viewpoints, such as hormones, the role of the posttranscriptional gene, micro RNAs, ICE-CBF-COR signaling route in cold acclimatization and how they are stimulating the expression of underlying genes encoding osmoregulatory elements and strategies to improve cold tolerance in wheat.

A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice

Chlorophyll biosynthesis is a crucial biological process in plants, and chlorophyll content is one of the most important traits in rice breeding programs. In this study, we identified a lethal, chlorophyll-deficient, yellow seedling (YS) phenotype segregating in progeny of CR5055-21, an F2 plant derived from a backcross between Korean japonica variety 'Hwaseong' (Oryza sativa) and CR5029, which is mostly Hwaseong with a small amount of Oryza grandiglumis chromosome segments. The segregation of the mutant phenotype was consistent with a single gene recessive mutation. Light microscopy of YS leaf cross-sections revealed loosely arranged mesophyll cells and sparse parenchyma in contrast to wildtype. In addition, transmission electron microscopy showed that chloroplasts did not develop in the mesophyll cells of the YS mutant. Quantitative trait loci (QTL)-seq analysis did not detect any significant QTL, however, examination of the individual delta-SNP index identified a 2-bp deletion (AG) in the OsCHLI gene, a magnesium (Mg)-chelatase subunit. A dCAPs marker was designed and genotyping of a segregating population (n = 275) showed that the mutant phenotype co-segregated with the marker. The 2-bp deletion was predicted to result in a frameshift mutation generating a premature termination. The truncated protein likely affects formation and function of Mg-chelatase, which consists of three different subunits that together catalyze the first committed step of chlorophyll biosynthesis. Transcriptome analysis showed that photosynthesis and carbohydrate metabolism pathways were significantly altered although expression of OsCHLI was not. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS mutant. Our findings demonstrated that OsCHLI plays an important role in leaf pigment biosynthesis and leaf structure development in rice.

Physiological and proteomic analyses reveal the important role of arbuscular mycorrhizal fungi on enhancing photosynthesis in wheat under cadmium stress

Arbuscular mycorrhizal fungi (AMF) are important in the phytoremediation of cadmium (Cd). Improving photosynthesis under Cd stress helps to increase crop yields. However, the molecular regulatory mechanisms of AMF on photosynthetic processes in wheat (Triticum aestivum) under Cd stress remain unclear. This study utilized physiological and proteomic analyses to reveal the key processes and related genes of AMF that regulate photosynthesis under Cd stress. The results showed that AMF promoted the accumulation of Cd in the roots of wheat but significantly reduced the content of Cd in the shoots and grains. The photosynthetic rates, stomatal conductance, transpiration rates, chlorophyll content, and accumulation of carbohydrates under Cd stress were increased by AMF symbiosis. Proteomic analysis showed that AMF significantly induced the expression of two enzymes involved in the chlorophyll biosynthetic pathway (coproporphyrinogen oxidase and Mg-protoporphyrin IX chelatase), improved the expression of two proteins related to CO₂ assimilation (ribulose-1,5-bisphosphate carboxylase and malic enzyme), and increased the expression of S-adenosylmethionine synthase, which positively regulates abiotic stress. Therefore, AMF may regulate photosynthesis under Cd stress by promoting chlorophyll biosynthesis, carbon assimilation, and S-adenosylmethionine metabolism.

Analysis of morphological traits and regulatory mechanism of a semi-dwarf, albino, and blue grain wheat line

The plant height and leaf color are important traits in crops since they contribute to the production of grains and biomass. Progress has been made in mapping the genes that regulate plant height and leaf color in wheat (Triticum aestivum L.) and other crops. Wheat line DW-B (dwarfing, white leaves, and blue grains) with semi-dwarfing and albinism at the tillering stage and re-greening at the jointing stage was created using Lango and Indian Blue Grain. Transcriptomic analyses of the three wheat lines at the early jointing stages indicated that the genes of gibberellin (GA) signaling pathway and chlorophyll (Chl) biosynthesis were expressed differently in DW-B and its parents. Furthermore, the response to GA and Chl contents differed between DW-B and its parents. The dwarfing and albinism in DW-B were owing to defects in the GA signaling pathway and abnormal chloroplast development. This study can improve understanding of the regulation of plant height and leaf color.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01379-z.

Phytol recycling: essential, yet not limiting for tomato fruit tocopherol accumulation under normal growing conditions

Tocopherols are potent membrane-bound antioxidant molecules that are paramount for plant physiology and also important for human health. In the past years, chlorophyll catabolism was identified as the primary source of phytyl diphosphate for tocopherol synthesis by the action of two enzymes, PHYTOL KINASE (VTE5) and PHYTHYL PHOSPHATE KINASE (VTE6) that are able to recycle the chlorophyll-derived phytol. While VTE5 and VTE6 were proven essential for tocopherol metabolism in tomato fruits, it remains unknown whether they are rate-limiting steps in this pathway. To address this question, transgenic tomato plants expressing AtVTE5 and AtVTE6 in a fruit-specific manner were generated. Although ripe transgenic fruits exhibited higher amounts of tocopherol, phytol recycling revealed a more intimate association with chlorophyll than with tocopherol content. Interestingly, protein-protein interactions assays showed that VTE5 and VTE6 are complexed, channeling free phytol and phytyl-P, thus mitigating their cytotoxic nature. Moreover, the analysis of tocopherol accumulation dynamics in roots, a chlorophyll-devoid organ, revealed VTE5-dependent tocopherol accumulation, hinting at the occurrence of shoot-to-root phytol trafficking. Collectively, these results demonstrate that phytol recycling is essential for tocopherol biosynthesis, even in chlorophyll-devoid organs, yet it is not the rate-limiting step for this pathway under normal growth conditions.

Transcriptome profiling provides insights into leaf color changes in two Acer palmatum genotypes

BACKGROUND

Ornamental trees with seasonally-dependent leaf color, such as Acer palmatum, have gained worldwide popularity. Leaf color is a main determinant of the ornamental and economic value of A. palmatum. However, the molecular mechanisms responsible for leaf color changes remain unclear.

RESULTS

We chose A. palmatum cultivars with yellow ('Jinling Huangfeng') and red ('Jinling Danfeng') leaves as the ideal material for studying the complex metabolic networks responsible for variations in leaf coloration. The 24 libraries obtained from four different time points in the growth of 'Jinling Huangfeng' and 'Jinling Danfeng' was subjected to Illumina high-throughput sequencing. We observed that the difference in cyanidin and delphinidin content is the primary reason behind the varying coloration of the leaves. Transcriptomic analyses revealed 225,684 unigenes, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) confirmed that they were involved in 'anthocyanin biosynthesis.' Eighteen structural genes involved in anthocyanin biosynthesis were thought to be related to anthocyanin accumulation, whereas 46 MYBs, 33 basic helix-loop-helixs (bHLHs), and 29 WD40s were presumed to be involved in regulating anthocyanin biosynthesis. Based on weighted gene co-expression network analysis (WGCNA), three candidate genes (ApRHOMBOID, ApMAPK, and ApUNE10) were screened in the significant association module with a correlation coefficient (r²) of 0.86.

CONCLUSION

In this study, the leaf color changes of two A. palmatum genotypes were analyzed. These findings provide novel insights into variations in leaf coloration and suggest pathways for targeted genetic improvements in A. palmatum.

Physiological analysis and transcriptome sequencing of a delayed-green leaf mutant 'Duojiao' of ornamental crabapple (Malus sp.)

Malus spectabilis 'Duojiao' is a spontaneous delayed-green leaf color mutant of M. spectabilis 'Riversii' and has chloroplasts with irregularly arranged vesicles and indistinct stromal lamellae. The yellow leaves of mutant have less chlorophyll (Chl), carotenoids, and flavonoids. Measurement of photosynthetic gas exchange indicated that the mutant has lower photosynthetic activity than 'Riversii' plants. Transcriptome sequencing with the Illumina platform was used to characterize differences in gene expression between the leaves of plants with yellow and green colors and elucidate the molecular mechanisms responsible for variation in leaf color in ornamental crabapple. In the comparison group of mutant yellow leaves and the maternal green leaves, 1848 differentially significant expressed genes (DEGs) were annotated by transcriptomic analysis. Many DEGs and transcription factors were identified related to chloroplast development, Chl synthesis and degradation, photosynthesis, carotenoid biosynthesis, flavonoid biosynthesis and other pathways related to plant leaf color formation. Among these, the Chl biosynthesis-related coproporphyrinogen gene, oxidative decarboxylase gene, and Chl a oxygenase gene were down-regulated, indicating that Chl biosynthesis was blocked. GLK1, which regulates chloroplast development, was down-regulated in yellow leaves. Parallel experiments showed that the content of the Chl synthesis precursors, protoporphyrinogen IX, chlorophyllide a, and chlorophyllide b and the activity of chlorophyllogen III oxidase and chlorophyllide a oxygenase in the yellow leaves of 'Duojiao' were lower than those in the green leaves of 'Riversii'. Thus, leaf color formation is greatly affected by Chl metabolism and chloroplast development. The reliability of the RNA-sequencing data was confirmed by quantitative real-time PCR analysis with 12 selected DEGs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01248-7.

Bulk segregant analysis-sequencing and RNA-Seq analyses reveal candidate genes associated with albino phenotype in Brassica napus

Inheritable albino mutants are excellent models for exploring the mechanism of chloroplast biogenesis and development. However, only a few non-lethal albino mutations have been reported to date in Brassica species. Here, we describe a resynthesized Brassica napus mutant, whose leaf, stem, and silique tissues showed an inheritable albino phenotype under field conditions after the bud stage but green phenotype in the greenhouse during the whole growing season, indicating that the albino phenotype depends on environmental conditions. Compared with the green leaves of the field-grown wild-type (GL) and greenhouse-grown mutant (WGL) plants, white leaves of the field-grown mutant (WL) showed significantly lower chlorophyll contents and structural defects in chloroplasts. Genetic analysis revealed that the albino phenotype of WL is recessive and is controlled by multiple genes. Bulk segregant analysis-sequencing (BSA-Seq) indicated that the candidate regions responsible for the albino phenotype spanned a total physical distance of approximately 49.68 Mb on chromosomes A03, A07, A08, C03, C04, C06, and C07. To gain insights into the molecular mechanisms that control chloroplast development in B. napus, we performed transcriptome (RNA-Seq) analysis of GL, WGL, and WL samples. GO and KEGG enrichment analyses suggested that differentially expressed genes (DEGs) associated with leaf color were significantly enriched in photosynthesis, ribosome biogenesis and chlorophyll metabolism. Further analysis indicated that DEGs involved in chloroplast development and chlorophyll metabolism were likely the main factors responsible for the albino phenotype in B. napus. A total of 59 DEGs were screened in the candidate regions, and four DEGs (BnaC03G0522600NO, BnaC07G0481600NO, BnaC07G0497800NO, and BnaA08G0016300NO) were identified as the most likely candidates responsible for the albino phenotype. Altogether, this study provides clues for elucidating the molecular mechanisms underlying chloroplast development in B. napus.

Comparative Transcriptomic and Metabolic Analyses Reveal the Coordinated Mechanisms in Pinus koraiensis under Different Light Stress Conditions

Light is one of the most important environmental cues that affects plant development and regulates its behavior. Light stress directly inhibits physiological responses and plant tissue development and even induces mortality in plants. Korean pine (Pinus koraiensis) is an evergreen conifer species widely planted in northeast China that has important economic and ecological value. However, the effects of light stress on the growth and development of Korean pine are still unclear. In this study, the effects of different shading conditions on physiological indices, molecular mechanisms and metabolites of Korean pine were explored. The results showed that auxin, gibberellin and abscisic acid were significantly increased under all shading conditions compared with the control. The contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoid also increased as the shading degree increased. Moreover, a total of 8556, 3751 and 6990 differentially expressed genes (DEGs) were found between the control and HS (heavy shade), control and LS (light shade), LS vs. HS, respectively. Notably, most DEGs were assigned to pathways of phytohormone signaling, photosynthesis, carotenoid and flavonoid biosynthesis under light stress. The transcription factors MYB-related, AP2-ERF and bHLH specifically increased expression during light stress. A total of 911 metabolites were identified, and 243 differentially accumulated metabolites (DAMs) were detected, among which flavonoid biosynthesis (naringenin chalcone, dihydrokaempferol and kaempferol) metabolites were significantly different under light stress. These results will provide a theoretical basis for the response of P. koraiensis to different light stresses.

Phenylalanine suppresses cell death caused by loss of fumarylacetoacetate hydrolase in Arabidopsis

Fumarylacetoacetate hydrolase (FAH) catalyzes the final step of Tyrosine (Tyr) degradation pathway essential to animals and the deficiency of FAH causes an inborn lethal disease. In plants, a role of this pathway was unknown until we found that mutation of Short-day Sensitive Cell Death1 (SSCD1), encoding Arabidopsis FAH, results in cell death under short day. Phenylalanine (Phe) could be converted to Tyr and then degraded in both animals and plants. Phe ingestion in animals worsens the disease caused by FAH defect. However, in this study we found that Phe represses cell death caused by FAH defect in plants. Phe treatment promoted chlorophyll biosynthesis and suppressed the up-regulation of reactive oxygen species marker genes in the sscd1 mutant. Furthermore, the repression of sscd1 cell death by Phe could be reduced by α-aminooxi-β-phenylpropionic acid but increased by methyl jasmonate, which inhibits or activates Phe ammonia-lyase catalyzing the first step of phenylpropanoid pathway, respectively. In addition, we found that jasmonate signaling up-regulates Phe ammonia-lyase 1 and mediates the methyl jasmonate enhanced repression of sscd1 cell death by Phe. These results uncovered the relation between chlorophyll biosynthesis, phenylpropanoid pathway and jasmonate signaling in regulating the cell death resulting from loss of FAH in plants.

Genome-wide identification and characterization of the bHLH gene family and analysis of their potential relevance to chlorophyll metabolism in Raphanus sativus L

BACKGROUND

Green-fleshed radish (Raphanus sativus L.) is an economically important root vegetable of the Brassicaceae family, and chlorophyll accumulates in its root tissues. It was reported that the basic helix-loop-helix (bHLH) transcription factors play vital roles in the process of chlorophyll metabolism. Nevertheless, a comprehensive study on the bHLH gene family has not been performed in Raphanus sativus L.

RESULTS

In this study, a total of 213 Raphanus sativus L. bHLH (RsbHLH) genes were screened in the radish genome, which were grouped into 22 subfamilies. 204 RsbHLH genes were unevenly distributed on nine chromosomes, and nine RsbHLH genes were located on the scaffolds. Gene structure analysis showed that 25 RsbHLH genes were intron-less. Collineation analysis revealed the syntenic orthologous bHLH gene pairs between radish and Arabidopsis thaliana/Brassica rapa/Brassica oleracea. 162 RsbHLH genes were duplicated and retained from the whole genome duplication event, indicating that the whole genome duplication contributed to the expansion of the RsbHLH gene family. RNA-seq results revealed that RsbHLH genes had a variety of expression patterns at five development stages of green-fleshed radish and white-fleshed radish. In addition, the weighted gene co-expression network analysis confirmed four RsbHLH genes closely related to chlorophyll content.

CONCLUSIONS

A total of 213 RsbHLH genes were identified, and we systematically analyzed their gene structure, evolutionary and collineation relationships, conserved motifs, gene duplication, cis-regulatory elements and expression patterns. Finally, four bHLH genes closely involved in chlorophyll content were identified, which may be associated with the photosynthesis of the green-fleshed radish. The current study would provide valuable information for further functional exploration of RsbHLH genes, and facilitate clarifying the molecular mechanism underlying photosynthesis process in green-fleshed radish.

Mutation in Mg-Protoporphyrin IX Monomethyl Ester (Oxidative) Cyclase Gene ZmCRD1 Causes Chlorophyll-Deficiency in Maize

Chlorophyll molecules are non-covalently associated with chlorophyll-binding proteins to harvest light and perform charge separation vital for energy conservation during photosynthetic electron transfer in photosynthesis for photosynthetic organisms. The present study characterized a pale-green leaf (pgl) maize mutant controlled by a single recessive gene causing chlorophyll reduction throughout the whole life cycle. Through positional mapping and complementation allelic test, Zm00001d008230 (ZmCRD1) with two missense mutations (p.A44T and p.T326M) was identified as the causal gene encoding magnesium-protoporphyrin IX monomethyl ester cyclase (MgPEC). Phylogenetic analysis of ZmCRD1 within and among species revealed that the p.T326M mutation was more likely to be causal. Subcellular localization showed that ZmCRD1 was targeted to chloroplasts. The pgl mutant showed a malformed chloroplast morphology and reduced number of starch grains in bundle sheath cells. The ZmCRD1 gene was mainly expressed in WT and mutant leaves, but the expression was reduced in the mutant. Most of the genes involved in chlorophyll biosynthesis, chlorophyll degradation, chloroplast development and photosynthesis were down-regulated in pgl. The photosynthetic capacity was limited along with developmental retardation and production reduction in pgl. These results confirmed the crucial role of ZmCRD1 in chlorophyll biosynthesis, chloroplast development and photosynthesis in maize.

OsbHLHq11, the Basic Helix-Loop-Helix Transcription Factor, Involved in Regulation of Chlorophyll Content in Rice

Photosynthesis is an important factor in determining the yield of rice. In particular, the size and efficiency of the photosynthetic system after the heading has a great impact on the yield. Research related to high-efficiency photosynthesis is essential to meet the growing demands of crops for the growing population. Chlorophyll is a key molecule in photosynthesis, a pigment that acts as an antenna to absorb light energy. Improvement of chlorophyll content characteristics has been emphasized in rice breeding for several decades. It is expected that an increase in chlorophyll content may increase photosynthetic efficiency, and understanding the genetic basis involved is important. In this study, we measured leaf color (CIELAB), chlorophyll content (SPAD), and chlorophyll fluorescence, and quantitative trait loci (QTL) mapping was performed using 120 Cheongcheong/Nagdong double haploid (CNDH) line after the heading date. A major QTL related to chlorophyll content was detected in the RM26981-RM287 region of chromosome 11. OsbHLHq11 was finally selected through screening of genes related to chlorophyll content in the RM26981-RM287 region. The relative expression level of the gene of OsbHLHq11 was highly expressed in cultivars with low chlorophyll content, and is expected to have a similar function to BHLH62 of the Gramineae genus. OsbHLHq11 is expected to increase photosynthetic efficiency by being involved in the chlorophyll content, and is expected to be utilized as a new genetic resource for breeding high-yield rice.

An Alternative Proposal for the Reaction Mechanism of Light-Dependent Protochlorophyllide Oxidoreductase

Light-dependent protochlorophyllide oxidoreductase is one of the few known enzymes that require a quantum of light to start their catalytic cycle. Upon excitation, it uses NADPH to reduce the C₁₇-C₁₈ in its substrate (protochlorophyllide) through a complex mechanism that has heretofore eluded precise determination. Isotopic labeling experiments have shown that the hydride-transfer step is very fast, with a small barrier close to 9 kcal mol^-1, and is followed by a proton-transfer step, which has been postulated to be the protonation of the product by the strictly conserved Tyr189 residue. Since the structure of the enzyme-substrate complex has not yet been experimentally determined, we first used modeling techniques to discover the actual substrate binding mode. Two possible binding modes were found, both yielding stable binding (as ascertained through molecular dynamics simulations) but only one of which placed the critical C17=C18 bond consistently close to the NADPH pro-S hydrogen and to Tyr189. This binding pose was then used as a starting point for the testing of previous mechanistic proposals using time-dependent density functional theory. The quantum-chemical computations clearly showed that such mechanisms have prohibitively high activation energies. Instead, these computations showed the feasibility of an alternative mechanism initiated by excited-state electron transfer from the key Tyr189 to the substrate. This mechanism appears to agree with the extant experimental data and reinterprets the final protonation step as a proton transfer to the active site itself rather than to the product, aiming at regenerating it for another round of catalysis.

Effects of peripheral substituents on epimerization kinetics of formylated chlorophylls

C132-[Formula: see text]-epimers of chlorophyll (Chl) molecules are important cofactors in the photosystem I reaction centers in oxygenic photosynthetic organisms; however, their production mechanism is still unclear. The reaction properties of Chl epimerization are helpful for a better understanding of the molecular mechanism of the in vivo formation of Chl C132-[Formula: see text]-epimers. We report herein the kinetic properties of the epimerization of formylated Chl molecules, Chl [Formula: see text] and Chl [Formula: see text], by use of triethylamine. Both Chl [Formula: see text] and Chl [Formula: see text] performed faster epimerization kinetics than Chl [Formula: see text], indicating that the electron-withdrawing ability of the formyl groups directly linked to the chlorin macrocycle is responsible for acceleration of the epimerization. Comparing the rate constants of the two mono-formylated Chl molecules indicated that the epimerization of Chl [Formula: see text] was faster than that of Chl [Formula: see text]. This difference is rationalized by invoking a combination of the inductive effects of the C3- and C7-substituents in Chls; the sums of Hammett [Formula: see text] parameters of the C3- and C7-substituents exhibited high correlations with the epimerization rate constants of Chls [Formula: see text], [Formula: see text], and [Formula: see text].

Ploidy level enhances the photosynthetic capacity of a tetraploid variety of Acer buergerianum Miq

Background

Polyploidy plays an important role in plant breeding and has widespread effects on photosynthetic capacity. To determine the photosynthetic capacity of the tetraploid variety Acer buergerianum Miq. ‘Xingwang’, we compared the gas exchange parameters, chloroplast structure, chlorophyll contents, and chlorophyll fluorescence parameters between the tetraploid Acer buergerianum ‘Xingwang’ and the diploid ‘S4’. To evaluate the effects of genome duplication on the photosynthetic capacity of Acer buergerianum ‘Xingwang’, the transcriptomes of the autotetraploid ‘Xingwang’ and the diploid ‘S4’ of A. buergerianum were compared.

Methods

The ploidy of Acer buergerianum ‘Xingwang’ was identified by flow cytometry and the chromosome counting method. An LI-6800 portable photosynthesis system analyzer was used to assess the gas exchange parameters of the tetraploid variety ‘Xingwang’ and diploid variety ‘S4’ of A. buergerianum. We used a BioMate 3S ultraviolet-visible spectrophotometer and portable modulated fluorometer to measure the chlorophyll contents and chlorophyll fluorescence parameters, respectively, of ‘Xingwang’ and ‘S4’. Illumina high-throughput sequencing technology was used to identify the differences in the genes involved in the photosynthetic differences and determine their expression characteristics.

Results

The single-cell DNA content and chromosome number of the tetraploid ‘Xingwang’ were twice those found in the normal diploid ‘S4’. In terms of gas exchange parameters, the change in stomatal conductance, change in intercellular CO₂ concentration, transpiration rate and net photosynthetic rate of ‘Xingwang’ were higher than those of the diploid ‘S4’. The chlorophyll contents, the maximal photochemical efficiency of PSII and the potential photochemical efficiency of PSII in ‘Xingwang’ were higher than those of ‘S4’. The chloroplasts of ‘Xingwang’ contained thicker thylakoid lamellae. By the use of Illumina sequencing technology, a total of 51,807 unigenes were obtained; they had an average length of 1,487 nt, and the average N50 was 2,034 nt. The lengths of most of the unigenes obtained ranged from 200–300 bp, with an average value of 5,262, followed by those longer than 3,000 bp, with an average value of 4,791. The data revealed numerous differences in gene expression between the two transcriptomes. In total, 24,221 differentially expressed genes were screened, and the percentage of differentially expressed genes was as high as 46.75% (24,224/51,807), of which 10,474 genes were upregulated and 13,747 genes were downregulated. We analyzed the key genes in the photosynthesis pathway and the porphyrin and chlorophyll metabolism pathway; the upregulation of HemB may promote an increase in the chlorophyll contents of ‘Xingwang’, and the upregulation of related genes in PSII and PSI may enhance the light harvesting of ‘Xingwang’, increasing its light energy conversion efficiency.

MusaATAF2 like protein, a stress-related transcription factor, induces leaf senescence by regulating chlorophyll catabolism and H2 O2 accumulation

NAC transcription factors are known for their diverse role in plants. In this study, we have demonstrated the role of MusaATAF2, a banana NAC transcription factor, in leaf senescence. Its expression gets strongly up-regulated during the early stress responses of drought and high salinity exposure and down-regulated under ABA application, which suggests MusaATAF2 is a stress-related NAC transcription factor. To study the role of MusaATAF2 in banana, we have transformed the banana embryogenic cells with MusaATAF2 coding region and generated transgenic banana plants. Overexpression of MusaATAF2 in banana plants caused yellow leaf phenotype under control condition, suggesting its role as a senescence-associated transcription factor. Transgenic banana leaves exhibited low chlorophyll content and high H₂ O₂ accumulation. Hormone analysis of the leaves demonstrated a higher accumulation of ABA in the transgenic plants than the controls. Transgenic plants overexpressing MusaATAF2 have a higher transcript abundance of two chlorophyll catabolic pathway genes (PAO and HCAR) and lower transcript abundance of ROS scavenging enzymes (TDP, THIO, CAT, APX, and PRXDN) than control. Together, all these analyses indicate that MusaATAF2 induces senescence by inducing chlorophyll degradation and H₂ O₂ accumulation in banana plants and controls its own expression using an ABA-dependent feedback loop.

Homoploid F1 hybrids and segmental allotetraploids of japonica and indica rice subspecies show similar and enhanced tolerance to nitrogen deficiency than parental lines

It remains unclear whether the merger of two divergent genomes by hybridization at the homoploid level or coupled with whole-genome duplication (WGD; allopolyploidy) can result in plants having better tolerance to stress conditions. In this study, we compared phenotypic performance and gene expression in the two diploid subspecies of rice (Oryza sativa subsp. japonica and indica), their reciprocal F1 hybrids, and in segmental allotetraploids under normal and nitrogen (N)-deficient conditions. We found that F1 hybrids and tetraploids showed higher and similar levels of tolerance to N deficiency than either parent. In parallel, total expression levels of 18 relevant functional genes were less perturbed by N deficiency in the F1 hybrids and tetraploids than in the parents. This was consistent with stable intrinsic partitioning of allelic/homoeologous expression defined by parental legacy in the homoploid F1 hybrids/tetraploids between the two conditions. The results suggest that genetic additivity at both the homoploid and allopolyploidy level might lead to similar beneficial phenotypic responses to nitrogen stress compared with the parents. The lack of synergistic responses to N limitation concomitant with WGD, relative to that exhibited by F1 hybrids, adds new empirical evidence in support of the emerging hypothesis that hybridization by itself can play a significant role in plant adaptive evolution in times of stress.

Identification of a delayed leaf greening gene from a mutation of pummelo

Delayed greening of young leaves is an unusual phenomenon of plants in nature. Citrus are mostly evergreen tree species. Here, a natural mutant of "Guanxi" pummelo (Citrus maxima), which shows yellow leaves at the young stage, was characterized to identify the genes underlying the trait of delayed leaf greening in plants. A segregating population with this mutant as the seed parent and a normal genotype as the pollen parent was generated. Two DNA pools respectively from the leaves of segregating seedlings with extreme phenotypes of normal leaf greening and delayed leaf greening were collected for sequencing. Bulked segregant analysis (BSA) and InDel marker analysis demonstrated that the delayed leaf greening trait is governed by a 0.3 Mb candidate region on chromosome 6. Gene expression analysis further identified a key candidate gene (Citrus Delayed Greening gene 1, CDG1) in the 0.3 Mb region, which showed significantly differential expression between the genotypes with delayed and normal leaf greening phenotypes. There was a 67 bp InDel region difference in the CDG1 promoter and the InDel region contains a TATA-box element. Confocal laser-scanning microscopy revealed that the CDG1-GFP fusion protein signals were co-localized with the chloroplast signals in the protoplasts. Overexpression of CDG1 in tobacco and Arabidopsis led to the phenotype of delayed leaf greening. These results suggest that the CDG1 gene is involved in controlling the delayed leaf greening phenotype with important functions in chloroplast development.

Using Diatom and Apicomplexan Models to Study the Heme Pathway of Chromera velia

Heme biosynthesis is essential for almost all living organisms. Despite its conserved function, the pathway’s enzymes can be located in a remarkable diversity of cellular compartments in different organisms. This location does not always reflect their evolutionary origins, as might be expected from the history of their acquisition through endosymbiosis. Instead, the final subcellular localization of the enzyme reflects multiple factors, including evolutionary origin, demand for the product, availability of the substrate, and mechanism of pathway regulation. The biosynthesis of heme in the apicomonad Chromera velia follows a chimeric pathway combining heme elements from the ancient algal symbiont and the host. Computational analyses using different algorithms predict complex targeting patterns, placing enzymes in the mitochondrion, plastid, endoplasmic reticulum, or the cytoplasm. We employed heterologous reporter gene expression in the apicomplexan parasite Toxoplasma gondii and the diatom Phaeodactylum tricornutum to experimentally test these predictions. 5-aminolevulinate synthase was located in the mitochondria in both transfection systems. In T. gondii, the two 5-aminolevulinate dehydratases were located in the cytosol, uroporphyrinogen synthase in the mitochondrion, and the two ferrochelatases in the plastid. In P. tricornutum, all remaining enzymes, from ALA-dehydratase to ferrochelatase, were placed either in the endoplasmic reticulum or in the periplastidial space.

Molecular landscape of etioplast inner membranes in higher plants

Etioplasts are photosynthetically inactive plastids that accumulate when light levels are too low for chloroplast maturation. The etioplast inner membrane consists of a paracrystalline tubular lattice and peripheral, disk-shaped membranes, respectively known as the prolamellar body and prothylakoids. These distinct membrane regions are connected into one continuous compartment. To date, no structures of protein complexes in or at etioplast membranes have been reported. Here, we used electron cryo-tomography to explore the molecular membrane landscape of pea and maize etioplasts. Our tomographic reconstructions show that ATP synthase monomers are enriched in the prothylakoids, and plastid ribosomes in the tubular lattice. The entire tubular lattice is covered by regular helical arrays of a membrane-associated protein, which we identified as the 37-kDa enzyme, light-dependent protochlorophyllide oxidoreductase (LPOR). LPOR is the most abundant protein in the etioplast, where it is responsible for chlorophyll biosynthesis, photoprotection and defining the membrane geometry of the prolamellar body. Based on the 9-Å-resolution volume of the subtomogram average, we propose a structural model of membrane-associated LPOR.

Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses

Green chrysanthemums are difficult to breed but have high commercial value. The molecular basis for the green petal color in chrysanthemum is not fully understood. This was investigated in the present study by RNA sequencing analysis of white and green ray florets collected at three stages of flower development from the F₁ progeny of the cross between Chrysanthemum × morifolium “Lüdingdang” with green-petaled flowers and Chrysanthemum vistitum with white-petaled flowers. The chlorophyll content was higher and chloroplast degradation was slower in green pools than in white pools at each developmental stage. Transcriptome analysis revealed that genes that were differentially expressed between the two pools were enriched in pathways related to chlorophyll metabolism and photosynthesis. We identified the transcription factor genes CmCOLa, CmCOLb, CmERF, and CmbHLH as regulators of the green flower color in chrysanthemum by differential expression analysis and weighted gene co-expression network analysis. These findings can guide future efforts to improve the color palette of chrysanthemum flowers through genetic engineering.

Photocatalysis as the 'master switch' of photomorphogenesis in early plant development

Enzymatic photocatalysis is seldom used in biology. Photocatalysis by light-dependent protochlorophyllide oxidoreductase (LPOR)-one of only a few natural light-dependent enzymes-is an exception, and is responsible for the conversion of protochlorophyllide to chlorophyllide in chlorophyll biosynthesis. Photocatalysis by LPOR not only regulates the biosynthesis of the most abundant pigment on Earth but it is also a 'master switch' in photomorphogenesis in early plant development. Following illumination, LPOR promotes chlorophyll production, plastid membranes are transformed and the photosynthetic apparatus is established. Given these remarkable, light-induced pigment and morphological changes, the LPOR-catalysed reaction has been extensively studied from catalytic, physiological and plant development perspectives, highlighting vital, and multiple, cellular roles of this intriguing enzyme. Here, we offer a perspective in which the link between LPOR photocatalysis and plant photomorphogenesis is explored. Notable breakthroughs in LPOR structural biology have uncovered the structural-mechanistic basis of photocatalysis. These studies have clarified how photon absorption by the pigment protochlorophyllide-bound in a ternary LPOR-protochlorophyllide-NADPH complex-triggers photocatalysis and a cascade of complex molecular and cellular events that lead to plant morphological changes. Photocatalysis is therefore the master switch responsible for early-stage plant development and ultimately life on Earth.

Comparative Analysis of Morphology, Photosynthetic Physiology, and Transcriptome Between Diploid and Tetraploid Barley Derived From Microspore Culture

Polyploids play an important role in the breeding of plant for superior characteristics, and many reports have focused on the effects upon photosynthesis from polyploidization in some plant species recently, yet surprisingly little of this is known for barley. In this study, homozygous diploid and tetraploid plants, derived from microspore culturing of the barley cultivar "H30," were used to assess differences between them in their cellular, photosynthetic, and transcriptomic characteristics. Our results showed that tetraploid barley has the distinct characteristics of polyploids, namely thicker and heavier leaves, enlarged stomata size or stomatal guard cell size, and more photosynthetic pigments and improved photosynthesis (especially under high light intensity). This enhanced photosynthesis of tetraploid barley was confirmed by several photosynthetic parameters, including net photosynthetic rate (P_n), stomatal conductance (G_s), intercellular CO₂ concentration (C_i), transpiration rate (T_r), maximum net photosynthetic rate (P_max), light saturation point (LSP), maximum RuBP saturated rate carboxylation (V_cmax), and maximum rate of electron transport (J_max). Transcriptomic analyses revealed that just ~2.3% of all detected genes exhibited differential expression patterns [i.e., differentially expressed genes (DEGs)], and that most of these - 580 of 793 DEGs in total - were upregulated in the tetraploid barley. The follow-up KEGG analysis indicated that the most enriched pathway was related to photosynthesis-antenna proteins, while the downregulation of DEGs was related mainly to the light-harvesting cholorophyII a/b-binding protein (Lhcb1) component, both validated by quantitative PCR (qPCR). Taken together, our integrated analysis of morphology, photosynthetic physiology, and transcriptome provides evidences for understanding of how polyploidization enhances the photosynthetic capacity in tetraploids of barley.

Exogenous DA-6 Improves the Low Night Temperature Tolerance of Tomato Through Regulating Cytokinin

Low night temperature (LNT) causes environmental stress and has a severe and negative impact on plant growth and productivity. Synthetic elicitors can regulate plant growth and induce defense mechanisms from this type of stress. Here, we evaluated the effect of the exogenous growth regulator diethyl aminoethyl hexanoate (DA-6) in tomato leaf response to LNT stress. Our results showed that exogenous DA-6 activates the expression of chlorophyll synthesis and photosystem-related genes, and results in higher photosynthetic activity and chlorophyll production. Furthermore, DA-6 can regulate the synthesis of endogenous cytokinin (CTK) and the expression of decomposition genes to stabilize chloroplast structure, reduce oxidative damage, and maintain the photochemical activity of tomato leaves under LNT stress. DA-6 maintains a high level of ABA content and induces the expression of CBF genes, indicating that DA-6 may participate in the cold response signaling pathway and induce the expression of downstream low temperature response genes and accumulation of compatible osmolytes. This study unravels a mode of action by which plant growth regulators can improve low temperature tolerance and provides important considerations for their application to alleviate the harmful effects of cold stress.

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

Chloroplast biogenesis requires the coordinated expression of the chloroplast and nuclear genomes, which is achieved by communication between the developing chloroplasts and the nucleus. Signals emitted from the plastids, so-called retrograde signals, control nuclear gene expression depending on plastid development and functionality. Genetic analysis of this pathway identified a set of mutants defective in retrograde signaling and designated genomes uncoupled (gun) mutants. Subsequent research has pointed to a significant role of tetrapyrrole biosynthesis in retrograde signaling. Meanwhile, the molecular functions of GUN1, the proposed integrator of multiple retrograde signals, have not been identified yet. However, based on the interactions of GUN1, some working hypotheses have been proposed. Interestingly, GUN1 contributes to important biological processes, including plastid protein homeostasis, through transcription, translation, and protein import. Furthermore, the interactions of GUN1 with tetrapyrroles and their biosynthetic enzymes have been revealed. This review focuses on our current understanding of the function of tetrapyrrole retrograde signaling on chloroplast biogenesis.

Adaptability to High Temperature and Stay-Green Genotypes Associated With Variations in Antioxidant, Chlorophyll Metabolism, and γ-Aminobutyric Acid Accumulation in Creeping Bentgrass Species

High temperature limits the cultivation and utilization of cool-season plants in many regions worldwide. Recently, extreme hot waves swept across the globe in summer, leading to enormous economic loss. The evaluation and identification of genotypic variation in thermotolerance within species are critical to breeding for environmental adaptation and also provide potential materials to explore thermo-resistant mechanism in plants. Forty-two accessions of creeping bentgrass (Agrostis stolonifera), which is a cool-season perennial grass for turf and ecological remediation, were collected from 15 different countries. Physiological traits, namely, chlorophyll (Chl) content, electrolyte leakage, photochemical efficiency, performance index on absorption basis, leaf relative water content, and osmotic potential were used to evaluate the heat tolerance of these materials in controlled growth chambers and field during summer. Stay-green and early-aging genotypes were selected to further reveal the potential mechanism of tolerance to senescence and heat damage associated with alterations in Chl metabolism, antioxidant and photosynthetic capacity, and endogenous γ-aminobutyric acid (GABA). Findings showed that there were significant genetic variations in physiological traits among 41 materials in response to high temperature stress. The 13M, PROVIDENCE, and LOFTS L-93 were the top three accessions with superior tolerance to heat and summer stress than other materials in terms of laboratory and field tests. In response to heat stress, the stay-green genotype PROVIDENCE exhibited significantly higher photochemical efficiency, net photosynthetic rate, transpiration rate, and water use efficiency than the heat-susceptible W6 6570. Delayed leaf senescence in relation to less Chl loss was detected in the PROVIDENCE associated with maintenance of significantly higher expression levels of Chl-anabolic genes (AsCHLH, AsPBGD, and AsPOR) and lower Chl-catabolic gene AsPPH under heat stress. Genetic attributes, such as better capacity to scavenge reactive oxygen species and higher endogenous GABA content could play positive roles in alleviating heat-induced senescence, oxidative damage, and metabolic disturbance in the PROVIDENCE.

Challenges and Opportunities of Light-Emitting Diode (LED) as Key to Modulate Antioxidant Compounds in Plants. A Review

Plant antioxidants are important compounds involved in plant defense, signaling, growth, and development. The quantity and quality of such compounds is genetically driven; nonetheless, light is one of the factors that strongly influence their synthesis and accumulation in plant tissues. Indeed, light quality affects the fitness of the plant, modulating its antioxidative profile, a key element to counteract the biotic and abiotic stresses. With this regard, light-emitting diodes (LEDs) are emerging as a powerful technology which allows the selection of specific wavelengths and intensities, and therefore the targeted accumulation of plant antioxidant compounds. Despite the unique advantages of such technology, LED application in the horticultural field is still at its early days and several aspects still need to be investigated. This review focused on the most recent outcomes of LED application to modulate the antioxidant compounds of plants, with particular regard to vitamin C, phenols, chlorophyll, carotenoids, and glucosinolates. Additionally, future challenges and opportunities in the use of LED technology in the growth and postharvest storage of fruits and vegetables were also addressed to give a comprehensive overview of the future applications and trends of research.

Protochlorophyllide synthesis by recombinant cyclases from eukaryotic oxygenic phototrophs and the dependence on Ycf54

The unique isocyclic E ring of chlorophylls contributes to their role as light-absorbing pigments in photosynthesis. The formation of the E ring is catalyzed by the Mg-protoporphyrin IX monomethyl ester cyclase, and the O₂-dependent cyclase in prokaryotes consists of a diiron protein AcsF, augmented in cyanobacteria by an auxiliary subunit Ycf54. Here, we establish the composition of plant and algal cyclases, by demonstrating the in vivo heterologous activity of O₂-dependent cyclases from the green alga Chlamydomonas reinhardtii and the model plant Arabidopsis thaliana in the anoxygenic photosynthetic bacterium Rubrivivax gelatinosus and in the non-photosynthetic bacterium Escherichia coli. In each case, an AcsF homolog is the core catalytic subunit, but there is an absolute requirement for an algal/plant counterpart of Ycf54, so the necessity for an auxiliary subunit is ubiquitous among oxygenic phototrophs. A C-terminal ∼40 aa extension, which is present specifically in green algal and plant Ycf54 proteins, may play an important role in the normal function of the protein as a cyclase subunit.

HCAR Is a Limitation Factor for Chlorophyll Cycle and Chlorophyll b Degradation in Chlorophyll-b-Overproducing Plants

The chlorophyll (Chl) cycle is the metabolic pathway for Chl a and Chl b inter-conversion. In this pathway, Chl b is synthesized from Chl a by the catalyzing action of chlorophyllide a oxygenase (CAO). In contrast, Chl b is firstly reduced to produce 7-hydroxymethyl Chl (HMChl) a, which is catalyzed by two isozymes of Chl b reductase (CBR), non-yellow coloring 1 (NYC1) and NYC1-like (NOL). Subsequently, HMChl a is reduced to Chl a by HMChl a reductase (HCAR). CAO plays a pivotal role in Chl a/b ratio regulation and plants over-accumulate Chl b in CAO-overexpressing plants. NYC1 is more accumulated in Chl-b-overproducing plants, while HCAR is not changed. To investigate the role of HCAR in Chl cycle regulation, the Chl metabolites of Chl-b-overproducing plants were analyzed. The results showed that HMChl a accumulated in these plants, and it decreased and the Chl a/b ratio increased by overexpressing HCAR, implying HCAR is insufficient for Chl cycle in Chl-b-overproducing plants. Furthermore, during dark-induced senescence, the non-programmed cell death symptoms (leaves dehydrated with green color retained) of Chl-b-overproducing plants were obviously alleviated, and the content of HM pheophorbide (HMPheide) a and Pheide b were sharply decreased by overexpressing HCAR. These results imply that HCAR is also insufficient for Chl degradation in Chl-b-overproducing plants during senescence, thus causing the accumulation of Chl metabolites and non-programmed cell death of leaves. With these results taken together, we conclude that HCAR is not well regulated and it is a limiting factor for Chl cycle and Chl b degradation in Chl-b-overproducing plants.

In situ formation of photoactive B-ring reduced chlorophyll isomer in photosynthetic protein LH2

Natural chlorophylls have a D-ring reduced chlorin π-system; however, no naturally occurring photosynthetically active B-ring reduced chlorins have been reported. Here we report a B-ring reduced chlorin, 17,18-didehydro-bacteriochlorophyll (BChl) a, produced by in situ oxidation of B800 bacteriochlorophyll (BChl) a in a light-harvesting protein LH2 from a purple photosynthetic bacterium Phaeospirillum molischianum. The regioselective oxidation of the B-ring of B800 BChl a is rationalized by its molecular orientation in the protein matrix. The formation of 17,18-didehydro-BChl a produced no change in the local structures and circular arrangement of the LH2 protein. The B-ring reduced 17,18-didehydro-BChl a functions as an energy donor in the LH2 protein. The photoactive B-ring reduced Chl isomer in LH2 will be helpful for understanding the photofunction and evolution of photosynthetic cyclic tetrapyrrole pigments.

Ecotoxicological effects of the azole antifungal agent clotrimazole on the macrophyte species Lemna minor and Lemna gibba

Pharmaceuticals are a large and diverse group of compounds used to treat, prevent and diagnose disease. Among these, a group that has been recently detected in the aquatic environment is that of the azole compounds, commonly used as antifungals. Clotrimazole (CLO) is a nonbiodegradable persistent azole compound, with broad-spectrum antifungal activity for which virtually no toxicological data are available, especially towards aquatic plants. The few existent data point to a documented interference with cytochrome P450 system of exposed organisms. Therefore, the aim of this paper was to evaluate the ecotoxicological effects of the fungicide CLO on two aquatic macrophyte species, namely, Lemna minor and Lemna gibba. To attain this purpose, an acute assay (96 h) was performed with both species being exposed to CLO, in a concentration range of 0 to 5 μg L^-1. The analyzed endpoints were levels of chlorophyll a and b, total, carotenoids, catalase (CAT) and glutathione -s-transferases activities (GSTs). In general, CLO exposure caused some minor alterations in L. minor and L. gibba pigment contents. Antioxidant enzymes exhibited a different pattern in both species, since the highest concentrations of CLO caused an increase on CAT activity, and a decrease on GSTs activity in L. minor, and the opposite in L. gibba, reflected by a decrease on CAT activity and an increase on GSTs activity in all tested concentrations. These results demonstrate that CLO exposure resulted in potential deleterious effects on macrophytes, namely with the involvement of the antioxidant defense mechanisms that were likely deployed to cope with pro-oxidative conditions established by CLO.

Can salicylic acid modulate biochemical, physiological and population alterations in a macrophyte species under chemical stress by diclofenac?

Salicylic acid (SA) is a pharmaceutical drug that may exert toxic effects by its own; however, simultaneous exposure of plants to SA and to other substances, often results in the significant changes in the patterns of toxic response/resistance to these other sources of chemical stress. Thus, the aim of this work was to investigate the capacity of SA of modulating Lemna minor responses co-exposed to the pharmaceutical drug, diclofenac - DCF. To attain this objective, L. minor was exposed for 7 days, to DCF alone, and to combinations of DCF with SA. After exposure, biochemical, physiological and population endpoints were analyzed as follows: catalase (CAT) and glutathione S-transferases (GSTs) activities, pigments content (chlorophyll a (Chl a), b (Chl b) and total (TChl), carotenoids (Car) and [Chl a]/[Chl b] and [TChl]/[Car] ratios), and growth specific rate, fresh weight and root length. Single exposures to DCF were capable of causing effects in all analyzed endpoints. However, co-exposure of DCF with SA partially reverted these effects. Finally, we may suggest that SA is capable to prevent the toxicity of DCF in macrophytes, by modulating the toxic response of exposed plants.

Transcriptome Analysis Shows Activation of Stress and Defense Responses by Silencing of Chlorophyll Biosynthetic Enzyme CHLI in Transgenic Tobacco

In the present study, we have shown the transcriptional changes in a chlorosis model transgenic tobacco plant, i-amiCHLI, in which an artificial micro RNA is expressed in a chemically inducible manner to silence the expression of CHLI genes encoding a subunit of a chlorophyll biosynthetic enzyme. Comparison to the inducer-treated and untreated control non-transformants and untreated i-amiCHLI revealed that 3568 and 3582 genes were up- and down-regulated, respectively, in the inducer-treated i-amiCHLI plants. Gene Ontology enrichment analysis of these differentially expressed genes indicated the upregulation of the genes related to innate immune responses, and cell death pathways, and the downregulation of genes for photosynthesis, plastid organization, and primary and secondary metabolic pathways in the inducer-treated i-amiCHLI plants. The cell death in the chlorotic tissues with a preceding H2O2 production was observed in the inducer-treated i-amiCHLI plants, confirming the activation of the immune response. The involvement of activated innate immune response in the chlorosis development was supported by the comparative expression analysis between the two transgenic chlorosis model systems, i-amiCHLI and i-hpHSP90C, in which nuclear genes encoding different chloroplast proteins were similarly silenced.

A Thylakoid Membrane Protein Functions Synergistically with GUN5 in Chlorophyll Biosynthesis

Chlorophyll (Chl) is essential for photosynthetic reactions and chloroplast development. While the enzymatic pathway for Chl biosynthesis is well established, the regulatory mechanism underlying the homeostasis of Chl levels remains largely unknown. In this study, we identified CBD1 (Chlorophyll Biosynthetic Defect1), which functions in the regulation of chlorophyll biosynthesis. The CBD1 gene was expressed specifically in green tissues and its protein product was embedded in the thylakoid membrane. Furthermore, CBD1 was precisely co-expressed and functionally correlated with GUN5 (Genome Uncoupled 5). Analysis of chlorophyll metabolic intermediates indicated that cbd1 and cbd1gun5 mutants over-accumulated magnesium protoporphyrin IX (Mg-Proto IX). In addition, the cbd1 mutant thylakoid contained less Mg than the wild type not only as a result of lower Chl content, but also implicating CBD1 in Mg transport. This was supported by the finding that CBD1 complemented a Mg²⁺ uptake-deficient Salmonella strain under low Mg conditions. Taken together, these results indicate that CBD1 functions synergistically with CHLH/GUN5 in Mg-Proto IX processing, and may serve as a Mg-transport protein to maintain Mg homeostasis in the chloroplast.