PsbR, a missing link in the assembly of the oxygen-evolving complex of plant photosystem II

Protein phosphorylation and oxidative protein modification promote plant photosystem II disassembly for repair

The light-driven water-splitting reaction of photosystem II exposes its key reaction center core protein subunits to irreversible oxidative photodamage. A rapid repair cycle replaces the photodamaged core subunits in plants, but how the large antenna-core supercomplex structures of plant photosystem II disassemble for repair is not currently understood. Here, we report the specific involvement of phosphorylation in removal of the peripheral antenna from the core and monomerization of the dimeric cores. However, monomeric cores disassemble further into smaller subcomplexes, even in the absence of phosphorylation, suggesting that there are other unknown mechanisms of disassembly. In this regard, we show that oxidative modifications of amino acids in core protein subunits of photosystem II are active mediators of monomeric core disassembly. Oxidative modifications thus likely disassemble only the damaged monomeric cores, ensuring an economical photosystem disassembly process. Taken together, our results suggest that phosphorylation and oxidative modification play distinct roles in photosystem II disassembly and repair.

The Trx-Prx redox pathway and PGR5/PGRL1-dependent cyclic electron transfer play key regulatory roles in poplar drought stress

Understanding drought resistance mechanisms is crucial for breeding poplar species suited to arid and semiarid regions. This study explored the drought responses of three newly developed 'Zhongxiong' series poplars using integrated transcriptomic and physiological analyses. Under drought stress, poplar leaves showed significant changes in differentially expressed genes linked to photosynthesis-related pathways, including photosynthesis-antenna proteins and carbon fixation, indicating impaired photosynthetic function and carbon assimilation. Additionally, drought stress triggered oxidative damage through increased reactive oxygen species production, leading to malondialdehyde accumulation. Weighted gene co-expression network analysis revealed that differentially expressed genes closely associated with physiological responses were enriched in cell redox homeostasis pathways, specifically the thioredoxin-peroxiredoxin pathway. Key genes in this pathway and in cyclic electron flow, such as PGR5-L1A, were downregulated, suggesting compromised reactive oxygen species scavenging and photoprotection under drought stress. Notably, ZX4 poplar exhibited higher drought tolerance, maintaining stronger activity in cyclic electron flow and the thioredoxin-peroxiredoxin pathway compared with ZX3 and ZX5. Genes like PGR5-L1A, 2-Cys Prx BAS1, PrxQ and TPX are promising candidates for enhancing drought resistance in poplars through genetic improvement, with potential applications for developing resilient forestry varieties.

Architecture and functional regulation of a plant PSII-LHCII megacomplex

Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the C4S4M2-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR-deletion mutant plants are studied through electron microscopy (EM), structural mass spectrometry, and ultrafast fluorescence spectroscopy [time-resolved fluorescence (TRF)]. The cryo-EM structure of a type I C4S4M2 megacomplex demonstrates that the three domains of PsbR bind to the stromal side of D1, D2, and CP43; associate with the single transmembrane helix of the redox active Cyt b559; and stabilize the luminal extrinsic PsbP, respectively. This megacomplex, with PsbR and PsbY centered around the narrow interface between two dimeric PSII cores, provides the supramolecular structural basis that regulates the plastoquinone occupancy in QB site, excitation energy transfer, and oxygen evolution. PSII-LHCII megacomplexes (types I and II) and LHC aggregation levels in Arabidopsis psbR mutant were also interrogated and compared to wild-type plants through EM and picosecond TRF.

Comparative proteomics in tall fescue to reveal underlying mechanisms for improving Photosystem II thermotolerance during heat stress memory

BACKGROUND

The escalating impacts of global warming intensify the detrimental effects of heat stress on crop growth and yield. Among the earliest and most vulnerable sites of damage is Photosystem II (PSII). Plants exposed to recurring high temperatures develop heat stress memory, a phenomenon that enables them to retain information from previous stress events to better cope with subsequent one. Understanding the components and regulatory networks associated with heat stress memory is crucial for the development of heat-resistant crops.

RESULTS

Physiological assays revealed that heat priming (HP) enabled tall fescue to possess higher Photosystem II photochemical activity when subjected to trigger stress. To investigate the underlying mechanisms of heat stress memory, we performed comparative proteomic analyses on tall fescue leaves at S0 (control), R4 (primed), and S5 (triggering), using an integrated approach of Tandem Mass Tag (TMT) labeling and Liquid Chromatography-Mass Spectrometry. A total of 3,851 proteins were detected, with quantitative information available for 3,835 proteins. Among these, we identified 1,423 differentially abundant proteins (DAPs), including 526 proteins that were classified as Heat Stress Memory Proteins (HSMPs). GO and KEGG enrichment analyses revealed that the HSMPs were primarily associated with the "autophagy" in R4 and with "PSII repair", "HSP binding", and "peptidase activity" in S5. Notably, we identified 7 chloroplast-localized HSMPs (HSP21, DJC77, EGY3, LHCA4, LQY1, PSBR and DEGP8, R4/S0 > 1.2, S5/S0 > 1.2), which were considered to be effectors linked to PSII heat stress memory, predominantly in cluster 4. Protein-protein interaction (PPI) analysis indicated that the ubiquitin-proteasome system, with key nodes at UPL3, RAD23b, and UCH3, might play a role in the selective retention of memory effectors in the R4 stage. Furthermore, we conducted RT-qPCR validation on 12 genes, and the results showed that in comparison to the S5 stage, the R4 stage exhibited reduced consistency between transcript and protein levels, providing additional evidence for post-transcriptional regulation in R4.

CONCLUSIONS

These findings provide valuable insights into the establishment of heat stress memory under recurring high-temperature episodes and offer a conceptual framework for breeding thermotolerant crops with improved PSII functionality.

Changes in Phytohormones and Transcriptomic Reprogramming in Strawberry Leaves under Different Light Qualities

Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the phytohormones and transcriptomic reprogramming in strawberry leaves under different light qualities are still unclear. In this study, we treated strawberry plants with sunlight, sunlight covered with a 50% sunshade net, no light, blue light (460 nm), red light (660 nm), and a 50% red/50% blue LED light combination for 3 days and 7 days. Our results revealed that the light quality has an effect on the contents of Chl a and Chl b, the minimal fluorescence (F0), and the Pn of strawberry plants. The light quality also affected the contents of abscisic acid (ABA), auxin (IAA), trans-zeatin-riboside (tZ), jasmonic acid (JA), and salicylic acid (SA). RNA sequencing (RNA-seq) revealed that differentially expressed genes (DEGs) are significantly enriched in photosynthesis antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolisms, carotenoid biosynthesis, tryptophan metabolism, phenylalanine metabolism, zeatin biosynthesis, and linolenic acid metabolism. We then selected the key DEGs based on the results of a weighted gene co-expression network analysis (WGCNA) and drew nine metabolic heatmaps and protein-protein interaction networks to map light regulation.

Effects of drought stress on photosynthetic physiological characteristics, leaf microstructure, and related gene expression of yellow horn

Yellow horn grows in northern China and has a high tolerance to drought and poor soil. Improving photosynthetic efficiency and increasing plant growth and yield under drought conditions have become important research content for researchers worldwide. Our study goal is to provide comprehensive information on photosynthesis and some candidate genes breeding of yellow horn under drought stress. In this study, seedlings' stomatal conductance, chlorophyll content, and fluorescence parameters decreased under drought stress, but non-photochemical quenching increased. The leaf microstructure showed that stomata underwent a process from opening to closing, guard cells from complete to dry, and surrounding leaf cells from smooth to severe shrinkage. The chloroplast ultrastructure showed that the changes of starch granules were different under different drought stress, while plastoglobules increased and expanded continuously. In addition, we found some differentially expressed genes related to photosystem, electron transport component, oxidative phosphate ATPase, stomatal closure, and chloroplast ultrastructure. These results laid a foundation for further genetic improvement and deficit resistance breeding of yellow horn under drought stress.

Selenite affected photosynthesis of Oryza sativa L. exposed to antimonite: Electron transfer, carbon fixation, pigment synthesis via a combined analysis of physiology and transcriptome

Selenium (Se) is a microelement that can counteract (a)biotic stresses in plants. Excess antimony (Sb) will inhibit plant photosynthesis, which can be alleviated by appropriate doses of Se but the associated mechanisms at the molecular levels have not been fully explored. Here, a rice variety (Yongyou 9) was exposed to selenite [Se(IV), 0.2 and 0.8 mg L-1] alone or combined with antimonite [Sb(III), 5 and 10 mg L-1]. When compared to the 10 mg L-1 Sb treatment alone, addition of Se in a dose-dependent manner 1) reduced the heat dissipation efficiency resulting from the inhibited donors, Sb concentrations in shoots and roots, leaf concentrations of fructose, H2O2 and O2•-; 2) enhanced heat dissipation efficiency resulting from the inhibited accepters value, concentrations of Chl a, sucrose and starch, and the enzyme activity of adenosine diphosphate glucose pyrophosphorylase, sucrose phosphate synthase, and sucrose synthase; but 3) did not alter gas exchange parameters, concentrations of Chl b and total Chl, enzyme activity of soluble acid invertase, and values of maximum P700 signal, photochemical efficiency of PSI and electron transport rate of PSI. Se alleviated the damage caused by Sb to the oxygen-evolving complex and promoted the transfer of electrons from QA to QB. When compared to the 10 mg L-1 Sb treatment alone, addition of Se 1) up-regulated genes correlated to synthesis pathways of Chl, carotenoid, sucrose and glucose; 2) disturbed signal transduction pathway of abscisic acid; and 3) upregulated gene expression correlated to photosynthetic complexes (OsFd1, OsFER1 and OsFER2).

Overexpression of 2-Cys Peroxiredoxin alleviates the NaHCO3 stress-induced photoinhibition and reactive oxygen species damage of tobacco

Plant 2-cysteine peroxiredoxin (2-Cys Prx) is a mercaptan peroxidase localized in chloroplasts and has unique catalytic properties. To explore the salt stress tolerance mechanisms of 2-Cys Prx in plants, we analyzed the effects of overexpressing the 2-CysPrx gene on the physiological and biochemical metabolic processes of tobacco under NaHCO3 stress through joint physiological and transcriptomic analysis. These parameters included growth phenotype, chlorophyll, photosynthesis, and antioxidant system. After NaHCO3 stress treatment, a total of 5360 differentially expressed genes (DEGs) were identified in 2-Cysprx overexpressed (OE) plants, and the number of DEGs was significantly lower than 14558 in wild-type (WT) plants. KEGG enrichment analysis showed that DEGs were mainly enriched in photosynthetic pathways, photosynthetic antenna proteins, and porphyrin and chlorophyll metabolism. Overexpressing 2-CysPrx significantly reduced the growth inhibition of tobacco induced by NaHCO3 stress, alleviating the down-regulation of the DEGs related to chlorophyll synthesis, photosynthetic electron transport and the Calvin cycle and the up-regulation of those related to chlorophyll degradation. In addition, it also interacted with other redox systems such as thioredoxins (Trxs) and the NADPH-dependent Trx reductase C (NTRC), and mediated the positive regulation of the activities of antioxidant enzymes such as peroxidase (POD) and catalase (CAT) and the expression of related genes, thereby reducing the accumulation of superoxide anion (O2·-), hydrogen peroxide (H2O2) and malondialdehyde (MDA). In conclusion, 2-CysPrx overexpression could alleviate the NaHCO3 stress-induced photoinhibition and oxidative damage by regulating chlorophyll metabolism, promoting photosynthesis and participating in the regulation of antioxidant enzymes, and thus improve the ability of plants to resist salt stress damage.

Heterologous expression of Zygophyllum xanthoxylon zinc finger protein gene (ZxZF) enhances the tolerance of poplar photosynthetic function to drought stress

The ZxZF transcription factor (TF) of Zygophyllum xanthoxylon (Bunge) Maxim, an extremely drought-resistant woody plant, is a C₂H₂ zinc finger protein. Studies have shown that C₂H₂ zinc finger proteins play important roles in activating stress-related genes and enhancing plant resistance. However, their function in regulating plant photosynthesis under drought stress is not well understood. Since poplar is an important greening and afforestation tree species, it is particularly important to cultivate excellent drought-tolerant varieties. The ZxZF transcription factor (TF) was heterogeneously expressed in Euroamerican poplar (Populus × euroameracana cl.'Bofengl') by genetic transformation. Based on the mechanism and potential function of poplar photosynthesis regulated by ZxZF under drought stress, transcriptomic and physiological determinations were used to reveal the important role of this gene in improving the drought resistance of poplar. The results showed that the overexpression of ZxZF TF in transgenic poplars could improve the inhibition of Calvin cycle by regulating stomatal opening and increasing the concentration of intercellular CO₂. The chlorophyll content, photosynthetic performance index, and photochemical efficiency of transgenic lines under drought stress were significantly higher than those of the wild type (WT). The overexpression of ZxZF TFs could alleviate the degree of photoinhibition of photosystems II and I under drought stress and maintain the efficiency of light energy capture and the photosynthetic electron transport chain. The transcriptomic data also showed that differentially expressed genes between the transgenic poplar and WT under drought stress were primarily enriched in metabolic pathways related to photosynthesis, such as photosynthesis, photosynthesis-antenna protein, porphyrin and chlorophyll metabolism, and photosynthetic carbon fixation, and the downregulation of genes related to chlorophyll synthesis, photosynthetic electron transport and Calvin cycle were alleviated. In addition, the overexpression of ZxZF TF can alleviate the inhibition of NADH dehydrogenase-like (NDH) cyclic electron flow of the poplar NDH pathway under drought stress, which plays an important role in reducing the excess pressure of electrons on the photosynthetic electron transport chain and maintaining the normal photosynthetic electron transport. In summary, the overexpression of ZxZF TFs can effectively alleviate the inhibition of drought on the assimilation of carbon in poplar and have a positive impact on light energy capture, the orderly transport of photosynthetic electron transport chain and the integrity of the photosystem, which is highly significant to acheivean in-depth understanding of the function of ZxZF TFs. This also provides an important basis for the breeding of new transgenic poplar varieties.

An approach to nearest neighbor analysis of pigment-protein complexes using chemical cross-linking in combination with mass spectrometry

Protein cross-linking is the process of chemically joining two amino acids in a protein or protein complex by a covalent bond. When combined with mass spectrometry, it becomes one of the structural mass spectrometry techniques gaining in importance for deriving valuable three-dimensional structural information on proteins and protein complexes. This platform complements existing structural methods, such as NMR spectroscopy, X-ray crystallography, and cryo-EM. Photosynthetic pigment protein complexes serve as light-energy harvesting systems and perform photochemical conversion as part of the "early events" of photosynthesis. This chapter outlines how to prepare cross-linking pigment protein complex samples for LC-MS/MS analysis, including identification of the cross-linked species, network analysis in a protein complex, and structural modeling and justification.

Candidate Genes for Salt Tolerance in Forage Sorghum under Saline Conditions from Germination to Harvest Maturity

To address the plant adaptability of sorghum (Sorghum bicolor) in salinity, the research focus should shift from only selecting tolerant varieties to understanding the precise whole-plant genetic coping mechanisms with long-term influence on various phenotypes of interest to expanding salinity, improving water use, and ensuring nutrient use efficiency. In this review, we discovered that multiple genes may play pleiotropic regulatory roles in sorghum germination, growth, and development, salt stress response, forage value, and the web of signaling networks. The conserved domain and gene family analysis reveals a remarkable functional overlap among members of the bHLH (basic helix loop helix), WRKY (WRKY DNA-binding domain), and NAC (NAM, ATAF1/2, and CUC2) superfamilies. Shoot water and carbon partitioning, for example, are dominated by genes from the aquaporins and SWEET families, respectively. The gibberellin (GA) family of genes is prevalent during pre-saline exposure seed dormancy breaking and early embryo development at post-saline exposure. To improve the precision of the conventional method of determining silage harvest maturity time, we propose three phenotypes and their underlying genetic mechanisms: (i) the precise timing of transcriptional repression of cytokinin biosynthesis (IPT) and stay green (stg1 and stg2) genes; (ii) the transcriptional upregulation of the SbY1 gene and (iii) the transcriptional upregulation of the HSP90-6 gene responsible for grain filling with nutritive biochemicals. This work presents a potential resource for sorghum salt tolerance and genetic studies for forage and breeding.

Effects of abiotic stress on photosystem II proteins

Photosystem II (PSII) represents the most vulnerable component of the photosynthetic machinery and its response in plants subjected to abiotic stress has been widely studied over many years. PSII is a thylakoid membrane-located multiprotein pigment complex that catalyses the light-induced electron transfer from water to plastoquinone with the concomitant production of oxygen. PSII is rich in intrinsic (PsbA and PsbD, namely D1 and D2, CP47 or PsbB and CP43 or PsbC) but also extrinsic proteins. The first ones are more largely conserved from cyanobacteria to higher plants while the extrinsic proteins are different among species. It has been found that extrinsic proteins involved in oxygen evolution change dramatically the PSII efficiency and PSII repair systems. However, little information is available on the effects of abiotic stress on their function and structure.

Single-molecule real-time sequencing of the full-length transcriptome of Halophila beccarii

Ecologically, Halophila beccarii Asch. is considered as a colonizing or a pioneer seagrass species and a “tiny but mighty” seagrass species, since it may recover quickly from disturbance generally. The use of transcriptome technology can provide a better understanding of the physiological processes of seagrasses. To date, little is known about the genome and transcriptome information of H. beccarii. In this study, we used single molecule real-time (SMRT) sequencing to obtain full-length transcriptome data and characterize the transcriptome structure. A total of 11,773 of the 15,348 transcripts were successfully annotated in seven databases. In addition, 1573 long non-coding RNAs, 8402 simple sequence repeats and 2567 transcription factors were predicted in all the transcripts. A GO analysis showed that 5843 transcripts were divided into three categories, including biological process (BP), cellular component (CC) and molecular function (MF). In these three categories, metabolic process (1603 transcripts), protein-containing complex (515 transcripts) and binding (3233 transcripts) were the primary terms in BP, CC, and MF, respectively. The major types of transcription factors were involved in MYB-related and NF-YB families. To the best of our knowledge, this is the first report of the transcriptome of H. beccarii using SMRT sequencing technology.

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

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

Transcriptomic analysis of OsRUS1 overexpression rice lines with rapid and dynamic leaf rolling morphology

Moderate leaf rolling helps to form the ideotype of rice. In this study, six independent OsRUS1-GFP overexpression (OsRUS1-OX) transgenic rice lines with rapid and dynamic leaf rolling phenotype in response to sunlight were constructed. However, the mechanism is unknown. Here, RNA-Seq approach was utilized to identify differentially expressed genes between flag leaves of OsRUS1-OX and wildtype under sunlight. 2920 genes were differentially expressed between OsRUS1-OX and WT, of which 1660 upregulated and 1260 downregulated. Six of the 16 genes in GO: 0009415 (response to water stimulus) were significantly upregulated in OsRUS1-OX. The differentially expressed genes between WT and OsRUS1-OX were assigned to 110 KEGG pathways. 42 of the 222 genes in KEGG pathway dosa04075 (Plant hormone signal transduction) were differentially expressed between WT and OsRUS1-OX. The identified genes in GO:0009415 and KEGG pathway dosa04075 were good candidates to explain the leaf rolling phenotype of OsRUS1-OX. The expression patterns of the 15 genes identified by RNA-Seq were verified by qRT-PCR. Based on transcriptomic and qRT-PCR analysis, a mechanism for the leaf rolling phenotype of OsRUS1-OX was proposed. The differential expression profiles between WT and OsRUS1-OX established by this study provide important insights into the molecular mechanism behind the leaf rolling phenotype of OsRUS1-OX.

Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes

Kobresia plants are important forage resources on the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. Therefore, it is beneficial to obtain Kobresia genome resources and study the adaptive characteristics of Kobresia plants on the Qinghai-Tibetan Plateau. Previously, we have assembled the genome of Carex littledalei (Kobresia littledalei), which is a diploid with 29 chromosomes. In this study, we assembled genomes of Carex parvula (Kobresia pygmaea) and Carex kokanica (Kobresia royleana) via using Illumina and PacBio sequencing data, which were about 783.49 Mb and 673.40 Mb in size, respectively. And 45,002 or 36,709 protein-coding genes were further annotated in the genome of C. parvula or C. kokanica. Phylogenetic analysis indicated that Kobresia in Cyperaceae separated from Poaceae about 101.5 million years ago after separated from Ananas comosus in Bromeliaceae about 117.2 million years ago. C. littledalei and C. parvula separated about 5.0 million years ago, after separated from C. kokanica about 6.2 million years ago. In this study, transcriptome data of C. parvula at three different altitudes were also measured and analyzed. Kobresia plants genomes assembly and transcriptome analysis will assist research into mechanisms of plant adaptation to environments with high altitude and cold weather.

Review: the effect of light on the key pigment compounds of photosensitive etiolated tea plant

BACKGROUND

Light is the ultimate energy source of plant photosynthesis, which has an important impact on the growth, development, physiology and biochemistry of tea plant. Photosensitive etiolated tea plant belongs to a kind of colored leaf plant, which is a physiological response to light intensity. Compared with conventional green bud and leaf of tea plant, the accumulation of pigment compounds (chlorophyll and carotenoids, etc.) closely related to a series of reactions of photosynthesis in photosensitive etiolated tea plant is reduced, resulting in the difference of leaf color of tea. This specific tea resource has high application value, among which high amino acid is one of its advantages. It can be used to process high-quality green tea with delicious taste and attractive aroma, which has been widely attention. The mechanism of the color presentation of the etiolated mutant tea leaves has been given a high topic and attention, especially, what changes have taken place in the pigment compounds of tea leaves caused by light, which makes the leaves so yellow. At present, there have been a lot of research and reports.

PURPOSE OF THE REVIEW

We describe the metabolism and differential accumulation of key pigment compounds affecting the leaf color of photosensitive etiolated tea that are triggered by light, and discuss the different metabolism and key regulatory sites of these pigments in different light environments in order to understand the "discoloration" matrix and mechanism of etiolated tea resources, answer the scientific question between leaf color and light. It provides an important strategy for artificial intervention of discoloration of colored tea plant.

CONCLUSION

The differential accumulation of pigment compounds in tea plant can be induced phytochrome in response to the change of light signal. The synthesis of chlorophyll in photoetiolated tea plants is hindered by strong light, among which, the sites regulated by coproporphyrinogen III oxidase and chlorophyllide a oxidase is sensitive to light and can be inhibited by strong light, resulting in the aggravation of leaf etiolation. The phenomenon can be disappeared or weakened by shading or reducing light intensity, and the leaf color is greenish, but the increase of chlorophyll-b accumulation is more than that of chlorophyll-a. The synthesis of carotenoids is inhibited strong light, and high the accumulation of carotenoids is reduced by shading. Most of the genes regulating carotenoids are up-regulated by moderate shading and down-regulated by excessive shading. Therefore, the accumulation of these two types of pigments in photosensitive etiolated tea plants is closely related to the light environment, and the leaf color phenotype shape of photosensitive etiolated tea plants can be changed by different light conditions, which provides an important strategy for the production and management of tea plant.

Plant and Algal PSII-LHCII Supercomplexes: Structure, Evolution and Energy Transfer

Photosynthesis is the process conducted by plants and algae to capture photons and store their energy in chemical forms. The light-harvesting, excitation transfer, charge separation and electron transfer in photosystem II (PSII) are the critical initial reactions of photosynthesis and thereby largely determine its overall efficiency. In this review, we outline the rapidly accumulating knowledge about the architectures and assemblies of plant and green algal PSII-light harvesting complex II (LHCII) supercomplexes, with a particular focus on new insights provided by the recent high-resolution cryo-electron microscopy map of the supercomplexes from a green alga Chlamydomonas reinhardtii. We make pair-wise comparative analyses between the supercomplexes from plants and green algae to gain insights about the evolution of the PSII-LHCII supercomplexes involving the peripheral small PSII subunits that might have been acquired during the evolution and about the energy transfer pathways that define their light-harvesting and photoprotective properties.

Transcriptional profiling reveals changes in gene regulation and signaling transduction pathways during temperature stress in wucai (Brassica campestris L.)

Background

Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a cold-tolerant plant that is vulnerable to high temperature. This study explored the response mechanism of wucai to low temperature. In this study, wucai seedlings were treated with different temperatures, including low temperature (LT), high temperature (HT), and a control.

Results

According to transcriptomics analysis, the number of differentially expressed genes (DEGs) in HT and LT was 10,702 and 7267, respectively, compared with the control. The key genes associated with the physiological response of wucai to the treatments were analyzed. The Kyoto Encyclopedia of Genes and Genomes and Gene Ontology annotations indicated the importance of the photosynthesis and photosynthetic-antenna protein pathways. We found that a high-temperature environment greatly inhibited the expression of important genes in the photosynthetic pathway (BrLhc superfamily members, PsaD, PsaE, PsaD, PsaD, PsbO, PsbP, PsbQ, PsbR, PsbS, PsbW, PsbY, Psb27, and Psb28), whereas low temperature resulted in the expression of certain key genes (BrLhc superfamily members, Psa F, Psa H, Psb S, Psb H, Psb 28). In addition, the wucai seedlings exhibited better photosynthetic performance under low-temperature conditions than high-temperature conditions.

Conclusions

Based on the above results, we speculate that upon exposure to low temperature, the plants developed higher cold tolerance by upregulating the expression of genes related to photosynthesis. Conversely, high-temperature stress inhibited the expression of pivotal genes and weakened the self-regulating ability of the plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07981-9.

Color-Specific Recovery to Extreme High-Light Stress in Plants

Plants pigments, such as chlorophyll and carotenoids, absorb light within specific wavelength ranges, impacting their response to environmental light changes. Although the color-specific response of plants to natural levels of light is well described, extreme high-light stress is still being discussed as a general response, without considering the impact of wavelengths in particular response processes. In this study, we explored how the plant proteome coordinated the response and recovery to extreme light conditions (21,000 µmol m^-2 s^-1) under different wavelengths. Changes at the protein and mRNA levels were measured, together with the photosynthetic parameters of plants under extreme high-light conditions. The changes in abundance of four proteins involved in photoinhibition, and in the biosynthesis/assembly of PSII (PsbS, PsbH, PsbR, and Psb28) in both light treatments were measured. The blue-light treatment presented a three-fold higher non-photochemical quenching and did not change the level of the oxygen-evolving complex (OEC) or the photosystem II (PSII) complex components when compared to the control, but significantly increased psbS transcripts. The red-light treatment caused a higher abundance of PSII and OEC proteins but kept the level of psbS transcripts the same as the control. Interestingly, the blue light stimulated a more efficient energy dissipation mechanism when compared to the red light. In addition, extreme high-light stress mechanisms activated by blue light involve the role of OEC through increasing PsbS transcript levels. In the proteomics spatial analysis, we report disparate activation of multiple stress pathways under three differently damaged zones as the enriched function of light stress only found in the medium-damaged zone of the red LED treatment. The results indicate that the impact of extreme high-light stress on the proteomic level is wavelength-dependent.

High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction

In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn₄CaO₅-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.

Ascorbate inactivates the oxygen-evolving complex in prolonged darkness

Ascorbate (Asc, vitamin C) is an essential metabolite participating in multiple physiological processes of plants, including environmental stress management and development. In this study, we acquired knowledge on the role of Asc in dark-induced leaf senescence using Arabidopsis thaliana as a model organism. One of the earliest effects of prolonged darkness is the inactivation of oxygen-evolving complexes (OEC) as demonstrated here by fast chlorophyll a fluorescence and thermoluminescence measurements. We found that inactivation of OEC due to prolonged darkness was attenuated in the Asc-deficient vtc2-4 mutant. On the other hand, the severe photosynthetic phenotype of a psbo1 knockout mutant, lacking the major extrinsic OEC subunit PSBO1, was further aggravated upon a 24-h dark treatment. The psbr mutant, devoid of the PSBR subunit of OEC, performed only slightly disturbed photosynthetic activity under normal growth conditions, whereas it showed a strongly diminished B thermoluminescence band upon dark treatment. We have also generated a double psbo1 vtc2 mutant, and it showed a slightly milder photosynthetic phenotype than the single psbo1 mutant. Our results, therefore, suggest that Asc leads to the inactivation of OEC in prolonged darkness by over-reducing the Mn-complex that is probably enabled by a dark-induced dissociation of the extrinsic OEC subunits. Our study is an example that Asc may negatively affect certain cellular processes and thus its concentration and localization need to be highly controlled.

Neoxanthin affects the stability of the C2 S2 M2 -type photosystem II supercomplexes and the kinetics of state transition in Arabidopsis

Neoxanthin (Neo), which is only bound to the peripheral antenna proteins of photosystem (PS) II, is a conserved carotenoid in all green plants. It has been demonstrated that Neo plays an important role in photoprotection and its deficiency fails to impact LHCII stability in vitro and indoor plant growth in vivo. Whether Neo is involved in maintaining the PSII complex structure or adaptive mechanisms for the everchanging environment has not yet been elucidated. In this study, the role of Neo in maintaining the structure and function of the PSII-LHCII supercomplexes was studied using Neo deficient Arabidopsis mutants. Our results show that Neo deficiency had little effect on the electron transport capacity and the plant fitness, but the PSII-LHCII supercomplexes were significantly impacted by the lack of Neo. In the absence of Neo, the M-type LHCII trimer cannot effectively associate with the C₂ S₂ -type PSII-LHCII supercomplexes even in moderate light conditions. Interestingly, Neo deficiency also leads to decreased PSII protein phosphorylation but rapid transition from state 1 to state 2. We suggest that Neo might enforce the interactions between LHCII and the minor antennas and that the absence of Neo makes M-type LHCII disassociate from the PSII complex, leading to the disassembly of the PSII-LHCII C₂ S₂ M₂ supercomplexes, which results in alterations in the phosphorylation patterns of the thylakoid photosynthetic proteins and the kinetics of state transition.

The oxygen-evolving complex: a super catalyst for life on earth, in response to abiotic stresses

The oxygen-evolving complex is integrated into photosystem (PSII). An essential part of oxygenic photosynthetic apparatus, embedded in the thylakoid membrane of chloroplasts. The OEC is a super catalyst to split water into molecular oxygen in the presence of light. The OEC consist of four Mn atoms, one Ca atom and five oxygen atoms (CaMn₄O₅) and this cluster is maintained by its surrounding proteins viz., PsbQ, PsbP, PsbO, PsbR. The function of this super catalyst with a high turnover frequency of 500 s^-1 in standard condition. Chlorophyll a fluorescence (OJIP transients) are used to understand structural and functional cohesion of photosynthetic apparatus. A further K-peak in OJIP curve reflects damage at the OEC donor site in response to salinity, drought, and high temperature. The decline in performance indices (PI, SFI) also revealed structural damage of photosynthetic apparatus that leads to disruption of electron transport rate under abiotic conditions. This review discusses the structural and function cohesion of the OEC in plant against variable abiotic conditions.

Transcriptional and physiological analyses of reduced density in apple provide insight into the regulation involved in photosynthesis

Different densities have a great influence on the physiological process and growth of orchard plants. Exploring the molecular basis and revealing key candidate genes for different densities management of orchard has great significance for production capacity improvement. In this study, transcriptome sequencing of apple trees was carried out at three different sampling heights to determine gene expression patterns under high density(HD) and low density(LD) and the physiological indices were measured to determine the effect of density change on plants. As a result, physiological indexes showed that the content of Chlorophyll, ACC, RUBP and PEP in the LD was apparently higher than that in control group(high density, HD). While the content of PPO and AO in the LD was noticeably lower than that in the HD. There were 3808 differentially expressed genes (DEGs) were detected between HD and LD, of which 1935, 2390 and 1108 DEGs were found in the three comparisons(middle-upper, lower-outer and lower-inner), respectively. 274 common differentially expressed genes (co-DEGs) were contained in all three comparisons. Functional enrichment and KEGG pathway analysis found these genes were involved in Carbon fixation in photosynthetic organisms, Circadian rhythm, Photosynthesis - antenna proteins, Photosynthesis, chlorophyll metabolism, Porphyrin, sugar metabolism and so on. Among these genes, LHCB family participated in photosynthesis as parts of photosystem II. In addition, SPA1, rbcL, SNRK2, MYC2, BSK, SAUR and PP2C are involved in Circadian rhythm, the expression of genes related to glycometabolism and hormone signaling pathway is also changed. The results revealed that the decrease of plant density changed the photosynthetic efficiency of leaves and the expression of photosynthesis-related genes, which provide a theoretical basis for the actual production regulation of apples.

Plastid ribosomal protein LPE2 is involved in photosynthesis and the response to C/N balance in Arabidopsis thaliana

The balance between cellular carbon (C) and nitrogen (N) must be tightly coordinated to sustain optimal growth and development in plants. In chloroplasts, photosynthesis converts inorganic C to organic C, which is important for maintenance of C content in plant cells. However, little is known about the role of chloroplasts in C/N balance. Here, we identified a nuclear-encoded protein LOW PHOTOSYNTHETIC EFFICIENCY2 (LPE2) that it is required for photosynthesis and C/N balance in Arabidopsis. LPE2 is specifically localized in the chloroplast. Both loss-of-function mutants, lpe2-1 and lpe2-2, showed lower photosynthetic activity, characterized by slower electron transport and lower PSII quantum yield than the wild type. Notably, LPE2 is predicted to encode the plastid ribosomal protein S21 (RPS21). Deficiency of LPE2 significantly perturbed the thylakoid membrane composition and plastid protein accumulation, although the transcription of plastid genes is not affected obviously. More interestingly, transcriptome analysis indicated that the loss of LPE2 altered the expression of C and N response related genes in nucleus, which is confirmed by quantitative real-time-polymerase chain reaction. Moreover, deficiency of LPE2 suppressed the response of C/N balance in physiological level. Taken together, our findings suggest that LPE2 plays dual roles in photosynthesis and the response to C/N balance.

New Findings on the Resistance Mechanism of an Elite Diploid Wild Potato Species JAM1-4 in Response to a Super Race Strain of Phytophthora infestans

Late blight is a devastating potato disease worldwide, caused by Phytophthora infestans. The P. infestans strain 2013-18-306 from Yunnan is a "supervirulent race" that overcomes all 11 known late blight resistance genes (R1 to R11) from Solanum demissum. In a previous study, we identified a diploid wild-type potato JAM1-4 (S. jamesii) with high resistance to 2013-18-306. dRenSeq analysis indicated the presence of novel R genes in JAM1-4. RNA-Seq was used to analyze the late blight resistance response genes and defense regulatory mechanisms of JAM1-4 against 2013-18-306. Gene ontology enrichment and KEGG pathway analysis showed that many disease-resistant pathways were significantly enriched. Analysis of differentially expressed genes (DEGs) revealed an active disease resistance mechanism of JAM1-4, and the essential role of multiple signal transduction pathways and secondary metabolic pathways comprised of SA-JA-ET in plant immunity. We also found that photosynthesis in JAM1-4 was inhibited to promote the immune response. Our study reveals the pattern of resistance-related gene expression in response to a super race strain of potato late blight and provides a theoretical basis for further exploration of potato disease resistance mechanisms, discovery of new late blight resistance genes, and disease resistance breeding.

Close relationship between the state of the oxygen evolving complex and rice cold stress tolerance

The results of the present work suggested a relationship between the growth stability and functional/structural parameters associated to the primary photochemistry and oxygen evolving complex (OEC) in tolerant rice plants under suboptimal low temperatures (SLT) stress. This was concluded from the absence of changes in net photosynthetic rate and in fraction of reaction centers to reduce quinone A, and very small changes in P680 efficiency to trap and donate electrons to quinone A and in fraction of active OEC in tolerant plants under cold stress but not in sensitive plants. The SLT stress also induced OEC activity limitations in both genotypes, but in a greater extent in sensitive plants. However, an assay using an artificial electron donor to replace OEC indicated that the P680⁺ capacity to accept electrons was not altered in both genotypes under SLT stress from the beginning of the stress treatment, suggesting that the OEC structure stability is related to rice SLT tolerance to sustain the photosynthesis. This hypothesis was also supported by the fact that tolerant plants but not sensitive plants did not alter the gene expression and protein content of PsbP under SLT stress, an OEC subunit with a role in stabilizing of OEC structure.

Methyl Jasmonate Affects Photosynthesis Efficiency, Expression of HvTIP Genes and Nitrogen Homeostasis in Barley

Jasmonates modulate many growth and developmental processes and act as stress hormones that play an important role in plant tolerance to biotic and abiotic stresses. Therefore, there is a need to identify the genes that are regulated through the jasmonate signalling pathway. Aquaporins, and among them the Tonoplast Intrinsic Proteins (TIPs), form the channels in cell membranes that are responsible for the precise regulation of the movement of water and other substrates between cell compartments. We identified the cis-regulatory motifs for the methyl jasmonate (MeJA)-induced genes in the promoter regions of all the HvTIP genes, which are active in barley seedlings, and thus we hypothesised that the HvTIP expression could be a response to jasmonate signalling. In the presented study, we determined the effect of methyl jasmonate on the growth parameters and photosynthesis efficiency of barley seedlings that had been exposed to different doses of MeJA (15–1000 µM × 120 h) in a hydroponic solution. All of the applied MeJA concentrations caused a significant reduction of barley seedling growth, which was most evident in the length of the first leaf sheath and dry leaf weight. The observed decrease of the PSII parameters after the exposure to high doses of MeJA (500 µM or higher) was associated with the downregulation of HvPsbR gene encoding one of the extrinsic proteins of the Oxygen Evolving Complex. The reduced expression of HvPsbR might lead to the impairment of the OEC action, manifested by the occurrence of the K-band in an analysis of fluorescence kinetics after MeJA treatment as well as reduced photosynthesis efficiency. Furthermore, methyl jasmonate treatment caused a decrease in the nitrogen content in barley leaves, which was associated with an increased expression the four tonoplast aquaporin genes (HvTIP1;2, HvTIP2;2, HvTIP4;1 and HvTIP4;2) predicted to transport the nitrogen compounds from the vacuole to the cytosol. The upregulation of the nitrogen-transporting HvTIPs might suggest their involvement in the vacuolar unloading of ammonia and urea, which both could be remobilised when the nitrogen content in the leaves decreases. Our research provides tips on physiological role of the individual TIP subfamily members of aquaporins under methyl jasmonate action.

Arabidopsis PsbP-Like Protein 1 Facilitates the Assembly of the Photosystem II Supercomplexes and Optimizes Plant Fitness under Fluctuating Light

In green plants, photosystem II (PSII) forms multisubunit supercomplexes (SCs) containing a dimeric core and light-harvesting complexes (LHCs). In this study, we show that Arabidopsis thaliana PsbP-like protein 1 (PPL1) is involved in the assembly of the PSII SCs and is required for adaptation to changing light intensity. PPL1 is a homolog of PsbP protein that optimizes the water-oxidizing reaction of PSII in green plants and is required for the efficient repair of photodamaged PSII; however, its exact function has been unknown. PPL1 was enriched in stroma lamellae and grana margins and associated with PSII subcomplexes including PSII monomers and PSII dimers, and several LHCII assemblies, while PPL1 was not detected in PSII-LHCII SCs. In a PPL1 null mutant (ppl1-2), assembly of CP43, PsbR and PsbW was affected, resulting in a reduced accumulation of PSII SCs even under moderate light intensity. This caused the abnormal association of LHCII in ppl1-2, as indicated by lower maximal quantum efficiency of PSII (Fv/Fm) and accelerated State 1 to State 2 transitions. These differences would lower the capability of plants to adapt to changing light environments, thereby leading to reduced growth under natural fluctuating light environments. Phylogenetic and structural analyses suggest that PPL1 is closely related to its cyanobacterial homolog CyanoP, which functions as an assembly factor in the early stage of PSII biogenesis. Our results suggest that PPL1 has a similar function, but the data also indicate that it could aid the association of LHCII with PSII.

Structural insight into light harvesting for photosystem II in green algae

Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II (PSII) to form various supercomplexes, including the C₂S₂M₂L₂ type, which is the largest PSII-LHCII supercomplex in algae and plants that is presently known. Here, we report high-resolution cryo-electron microscopy (cryo-EM) maps and structural models of the C₂S₂M₂L₂ and C₂S₂ supercomplexes from C. reinhardtii. The C₂S₂ supercomplex contains an LhcbM1-LhcbM2/7-LhcbM3 heterotrimer in the strongly associated LHCII, and the LhcbM1 subunit assembles with CP43 through two interfacial galactolipid molecules. The loosely and moderately associated LHCII trimers interact closely with the minor antenna complex CP29 to form an intricate subcomplex bound to CP47 in the C₂S₂M₂L₂ supercomplex. A notable direct pathway is established for energy transfer from the loosely associated LHCII to the PSII reaction centre, as well as several indirect routes. Structure-based computational analysis on the excitation energy transfer within the two supercomplexes provides detailed mechanistic insights into the light-harvesting process in green algae.

On the interface of light-harvesting antenna complexes and reaction centers in oxygenic photosynthesis

Photosynthetic pigment-protein complexes (PPCs) accomplish light-energy capture and photochemistry in natural photosynthesis. In this review, we examine three pigment protein complexes in oxygenic photosynthesis: light-harvesting antenna complexes and two reaction centers: Photosystem II (PSII), and Photosystem I (PSI). Recent technological developments promise unprecedented insights into how these multi-component protein complexes are assembled into higher order structures and thereby execute their function. Furthermore, the interfacial domain between light-harvesting antenna complexes and PSII, especially the potential roles of the structural loops from CP29 and the PB-loop of ApcE in higher plant and cyanobacteria, respectively, are discussed. It is emphasized that the structural nuances are required for the structural dynamics and consequently for functional regulation in response to an ever-changing and challenging environment.

Integration of Cross Species RNA-seq Meta-Analysis and Machine-Learning Models Identifies the Most Important Salt Stress-Responsive Pathways in Microalga Dunaliella

Photosynthetic microalgae are potentially yielding sources of different high-value secondary metabolites. Salinity is a complex stress that influences various metabolite-related pathways in microalgae. To obtain a clear view of the underlying metabolic pathways and resolve contradictory information concerning the transcriptional regulation of Dunaliella species in salt stress conditions, RNA-seq meta-analysis along with systems levels analysis was conducted. A p-value combination technique with Fisher method was used for cross species meta-analysis on the transcriptomes of two Dunaliella salina and Dunaliellatertiolecta species. The potential functional impacts of core meta-genes were surveyed based on gene ontology and network analysis. In the current study, the integration of supervised machine-learning algorithms with RNA-seq meta-analysis was performed. The analysis shows that the lipid and nitrogen metabolism, structural proteins of photosynthesis apparatus, chaperone-mediated autophagy, and ROS-related genes are the keys and core elements of the Dunaliella salt stress response system. Cross-talk between Ca²⁺ signal transduction, lipid accumulation, and ROS signaling network in salt stress conditions are also proposed. Our novel approach opens new avenues for better understanding of microalgae stress response mechanisms and for selection of candidate gene targets for metabolite production in microalgae.

Identification of Sugarcane Host Factors Interacting with the 6K2 Protein of the Sugarcane Mosaic Virus

The 6K2 protein of potyviruses plays a key role in the viral infection in plants. In the present study, the coding sequence of 6K2 was cloned from Sugarcane mosaic virus (SCMV) strain FZ1 into pBT3-STE to generate the plasmid pBT3-STE-6K2, which was used as bait to screen a cDNA library prepared from sugarcane plants infected with SCMV based on the DUALmembrane system. One hundred and fifty-seven positive colonies were screened and sequenced, and the corresponding full-length genes were cloned from sugarcane cultivar ROC22. Then, 24 genes with annotations were obtained, and the deduced proteins were classified into three groups, in which eight proteins were involved in the stress response, 12 proteins were involved in transport, and four proteins were involved in photosynthesis based on their biological functions. Of the 24 proteins, 20 proteins were verified to interact with SCMV-6K2 by yeast two-hybrid assays. The possible roles of these proteins in SCMV infection on sugarcane are analyzed and discussed. This is the first report on the interaction of SCMV-6K2 with host factors from sugarcane, and will improve knowledge on the mechanism of SCMV infection in sugarcane.

Integrated physiologic, proteomic, and metabolomic analyses of Malus halliana adaptation to saline-alkali stress

Saline-alkali stress is a severely adverse abiotic stress limiting plant growth. Malus halliana Koehne is an apple rootstock that is tolerant to saline-alkali stress. To understand the molecular mechanisms underlying the tolerance of M. halliana to saline-alkali stress, an integrated metabolomic and proteomic approach was used to analyze the plant pathways involved in the stress response of the plant and its regulatory mechanisms. A total of 179 differentially expressed proteins (DEPs) and 140 differentially expressed metabolites (DEMs) were identified. We found that two metabolite-related enzymes (PPD and PAO) were associated with senescence and involved in porphyrin and chlorophyll metabolism; six photosynthesis proteins (PSAH2, PSAK, PSBO2, PSBP1, and PSBQ2) were significantly upregulated, especially PSBO2, and could act as regulators of photosystem II (PSII) repair. Sucrose, acting as a signaling molecule, directly mediated the accumulation of D-phenylalanine, tryptophan, and alkaloid (vindoline and ecgonine) and the expression of proteins related to aspartate and glutamate (ASP3, ASN1, NIT4, and GLN1-1). These responses play a central role in maintaining osmotic balance and removing reactive oxygen species (ROS). In addition, sucrose signaling induced flavonoid biosynthesis by activating the expression of CYP75B1 to regulate the homeostasis of ROS and promoted auxin signaling by activating the expression of T31B5_170 to enhance the resistance of M. halliana to saline-alkali stress. The decrease in peroxidase superfamily protein (PER) and ALDH2C4 during lignin synthesis further triggered a plant saline-alkali response. Overall, this study provides an important starting point for improving saline-alkali tolerance in M. halliana via genetic engineering.

Transcriptome analysis of Asparagus officinalis reveals genes involved in the biosynthesis of rutin and protodioscin

Garden asparagus (Asparagus officinalis L.) is a popular vegetable cultivated worldwide. The secondary metabolites in its shoot are helpful for human health. We analyzed A. officinalis transcriptomes and identified differentially expressed genes (DEGs) involved in the biosynthesis of rutin and protodioscin, which are health-promoting functional compounds, and determined their association with stem color. We sequenced the complete mRNA transcriptome using the Illumina high-throughput sequencing platform in one white, three green, and one purple asparagus cultivars. A gene set was generated by de novo assembly of the transcriptome sequences and annotated using a BLASTx search. To investigate the relationship between the contents of rutin and protodioscin and their gene expression levels, rutin and protodioscin were analyzed using high-performance liquid chromatography. A secondary metabolite analysis using high-performance liquid chromatography showed that the rutin content was higher in green asparagus, while the protodioscin content was higher in white asparagus. We studied the genes associated with the biosynthesis of the rutin and protodioscin. The transcriptomes of the five cultivars generated 336 599 498 high-quality clean reads, which were assembled into 239 873 contigs with an average length of 694 bp, using the Trinity v2.4.0 program. The green and white asparagus cultivars showed 58 932 DEGs. A comparison of rutin and protodioscin biosynthesis genes revealed that 12 of the 57 genes associated with rutin and two of the 50 genes associated with protodioscin showed more than four-fold differences in expression. These DEGs might have caused a variation in the contents of these two metabolites between green and white asparagus. The present study is possibly the first to report transcriptomic gene sets in asparagus. The DEGs putatively involved in rutin and protodioscin biosynthesis might be useful for molecular engineering in asparagus.

Nitrogen Dioxide at Ambient Concentrations Induces Nitration and Degradation of PYR/PYL/RCAR Receptors to Stimulate Plant Growth: A Hypothetical Model

Exposing Arabidopsis thaliana (Arabidopsis) seedlings fed with soil nitrogen to 10-50 ppb nitrogen dioxide (NO₂) for several weeks stimulated the uptake of major elements, photosynthesis, and cellular metabolisms to more than double the biomass of shoot, total leaf area and contents of N, C P, K, S, Ca and Mg per shoot relative to non-exposed control seedlings. The ¹⁵N/¹⁴N ratio analysis by mass spectrometry revealed that N derived from NO₂ (NO₂-N) comprised < 5% of the total plant N, showing that the contribution of NO₂-N as N source was minor. Moreover, histological analysis showed that leaf size and biomass were increased upon NO₂ treatment, and that these increases were attributable to leaf age-dependent enhancement of cell proliferation and enlargement. Thus, NO₂ may act as a plant growth signal rather than an N source. Exposure of Arabidopsis leaves to 40 ppm NO₂ induced virtually exclusive nitration of PsbO and PsbP proteins (a high concentration of NO₂ was used). The PMF analysis identified the ninth tyrosine residue of PsbO1 (⁹Tyr) as a nitration site. ⁹Tyr of PsbO1 was exclusively nitrated after incubation of the thylakoid membranes with a buffer containing NO₂ and NO₂^- or a buffer containing NO₂^- alone. Nitration was catalyzed by illumination and repressed by photosystem II (PSII) electron transport inhibitors, and decreased oxygen evolution. Thus, protein tyrosine nitration altered (downregulated) the physiological function of cellular proteins of Arabidopsis leaves. This indicates that NO₂-induced protein tyrosine nitration may stimulate plant growth. We hypothesized that atmospheric NO₂ at ambient concentrations may induce tyrosine nitration of PYR/PYL/RCAR receptors in Arabidopsis leaves, followed by degradation of PYR/PYL/RCAR, upregulation of target of rapamycin (TOR) regulatory complexes, and stimulation of plant growth.

Chlorophyll catabolism precedes changes in chloroplast structure and proteome during leaf senescence

The earliest visual changes of leaf senescence occur in the chloroplast as chlorophyll is degraded and photosynthesis declines. Yet, a comprehensive understanding of the sequence of catabolic events occurring in chloroplasts during natural leaf senescence is still missing. Here, we combined confocal and electron microscopy together with proteomics and biochemistry to follow structural and molecular changes during Arabidopsis leaf senescence. We observed that initiation of chlorophyll catabolism precedes other breakdown processes. Chloroplast size, stacking of thylakoids, and efficiency of PSII remain stable until late stages of senescence, whereas the number and size of plastoglobules increase. Unlike catabolic enzymes, whose level increase, the level of most proteins decreases during senescence, and chloroplast proteins are overrepresented among these. However, the rate of their disappearance is variable, mostly uncoordinated and independent of their inherent stability during earlier developmental stages. Unexpectedly, degradation of chlorophyll-binding proteins lags behind chlorophyll catabolism. Autophagy and vacuole proteins are retained at relatively high levels, highlighting the role of extra-plastidic degradation processes especially in late stages of senescence. The observation that chlorophyll catabolism precedes all other catabolic events may suggest that this process enables or signals further catabolic processes in chloroplasts.

Identification of genomic loci associated with 21chlorophyll fluorescence phenotypes by genome-wide association analysis in soybean

BACKGROUND

Photosynthesis is able to convert solar energy into chemical energy in the form of biomass, but the efficiency of photosynthetic solar energy conversion is low. Chlorophyll fluorescence measurements are rapid, non-destructive, and can provide a wealth of information about the efficiencies of the photosynthetic light reaction processes. Efforts aimed at assessing genetic variation and/or mapping of genetic loci associated with chlorophyll fluorescence phenotypes have been rather limited.

RESULTS

Evaluation of SoySNP50K iSelect SNP Beadchip data from the 189 genotypes phenotyped in this analysis identified 32,453 SNPs with a minor allele frequency (MAF) ≥ 5%. A total of 288 (non-unique) SNPs were significantly associated with one or more of the 21 chlorophyll fluorescence phenotypes. Of these, 155 were unique SNPs and 100 SNPs were only associated with a single fluorescence phenotype, while 28, 11, 2, and 14 SNPs, were associated with two, three, four and five or more fluorescence phenotypes, respectively. The 288 non-unique SNPs represent 155 unique SNPs that mark 53 loci. The 155 unique SNPs included 27 that were associated with three or more phenotypes, and thus were called multi-phenotype SNPs. These 27 multi-phenotype SNPs marked 13 multi-phenotype loci (MPL) identified by individual SNPs associated with multiple chlorophyll fluorescence phenotypes or by more than one SNP located within 0.5 MB of other multi-phenotype SNPs.

CONCLUSION

A search in the genomic regions highlighted by these 13 MPL identified genes with annotations indicating involvement in photosynthetic light dependent reactions. These, as well as loci associated with only one or two chlorophyll fluorescence traits, should be useful to develop a better understanding of the genetic basis of photosynthetic light dependent reactions as a whole as well as of specific components of the electron transport chain in soybean. Accordingly, additional genetic and physiological analyses are necessary to determine the relevance and effectiveness of the identified loci for crop improvement efforts.

Identification of genomic loci associated with 21chlorophyll fluorescence phenotypes by genome-wide association analysis in soybean

BACKGROUND

Photosynthesis is able to convert solar energy into chemical energy in the form of biomass, but the efficiency of photosynthetic solar energy conversion is low. Chlorophyll fluorescence measurements are rapid, non-destructive, and can provide a wealth of information about the efficiencies of the photosynthetic light reaction processes. Efforts aimed at assessing genetic variation and/or mapping of genetic loci associated with chlorophyll fluorescence phenotypes have been rather limited.

RESULTS

Evaluation of SoySNP50K iSelect SNP Beadchip data from the 189 genotypes phenotyped in this analysis identified 32,453 SNPs with a minor allele frequency (MAF) ≥ 5%. A total of 288 (non-unique) SNPs were significantly associated with one or more of the 21 chlorophyll fluorescence phenotypes. Of these, 155 were unique SNPs and 100 SNPs were only associated with a single fluorescence phenotype, while 28, 11, 2, and 14 SNPs, were associated with two, three, four and five or more fluorescence phenotypes, respectively. The 288 non-unique SNPs represent 155 unique SNPs that mark 53 loci. The 155 unique SNPs included 27 that were associated with three or more phenotypes, and thus were called multi-phenotype SNPs. These 27 multi-phenotype SNPs marked 13 multi-phenotype loci (MPL) identified by individual SNPs associated with multiple chlorophyll fluorescence phenotypes or by more than one SNP located within 0.5 MB of other multi-phenotype SNPs.

CONCLUSION

A search in the genomic regions highlighted by these 13 MPL identified genes with annotations indicating involvement in photosynthetic light dependent reactions. These, as well as loci associated with only one or two chlorophyll fluorescence traits, should be useful to develop a better understanding of the genetic basis of photosynthetic light dependent reactions as a whole as well as of specific components of the electron transport chain in soybean. Accordingly, additional genetic and physiological analyses are necessary to determine the relevance and effectiveness of the identified loci for crop improvement efforts.

Photosystem II Extrinsic Proteins and Their Putative Role in Abiotic Stress Tolerance in Higher Plants

Abiotic stress remains one of the major challenges in managing and preventing crop loss. Photosystem II (PSII), being the most susceptible component of the photosynthetic machinery, has been studied in great detail over many years. However, much of the emphasis has been placed on intrinsic proteins, particularly with respect to their involvement in the repair of PSII-associated damage. PSII extrinsic proteins include PsbO, PsbP, PsbQ, and PsbR in higher plants, and these are required for oxygen evolution under physiological conditions. Changes in extrinsic protein expression have been reported to either drastically change PSII efficiency or change the PSII repair system. This review discusses the functional role of these proteins in plants and indicates potential areas of further study concerning these proteins.

Isolation and characterization of a photosystem II preparation from thylakoid membranes of the extreme halophyte Salicornia veneta Pignatti et Lausi

Salicornia veneta (Pignatti et Lausi) is an extreme halophyte living in salt marsh where NaCl concentration may be as high as 1 M. Here we report on the isolation and characterization of a PSII preparation obtained by Triton X-100 solubilisation of the thylakoid membrane. By a combination of gel electrophoresis, immunoblotting and mass spectrometry, the depletion of a number of PSII proteins such as PsbQ, PsbM and PsbT was highlighted. Moreover, the requirement of Cl^- and Ca²⁺ for optimal oxygen evolution was determined, showing that in absence of PsbQ a higher level of these ions are required. At high Cl^- concentrations, oxygen evolution was inhibited in the same way in Salicornia veneta and spinach. Reconstitution of Salicornia veneta PSII preparation with partially purified spinach PsbP and PsbQ restored oxygen evolution activity at low Cl^- and Ca²⁺ concentrations. Adaptation to high salt makes several PSII proteins dispensable.

Rice tolerance to suboptimal low temperatures relies on the maintenance of the photosynthetic capacity

The purpose of this research was to identify differences between two contrasting rice cultivars in their response to suboptimal low temperatures stress. A transcriptomic analysis of the seedlings was performed and results were complemented with biochemical and physiological analyses. The microarray analysis showed downregulation of many genes related with PSII and particularly with the oxygen evolving complex in the sensitive cultivar IR50. Complementary studies indicated that the PSII performance, the degree of oxygen evolving complex coupling with the PSII core and net photosynthetic rate diminished in this cultivar in response to the stress. However, the tolerant cultivar Koshihikari was able to maintain its energy equilibrium by sustaining the photosynthetic capacity. The increase of oleic acid in Koshihikari could be related with membrane remodelling of the chloroplasts and hence contribute to tolerance. Overall, these results work as a ground for future analyses that look forward to characterize possible mechanisms to tolerate this stress.

miRNA and mRNA Expression Profiles Reveal Insight into Chitosan-Mediated Regulation of Plant Growth

Chitosan has been numerously studied as a plant growth regulator and stress tolerance inducer. To investigate the roles of chitosan as bioregulator on plant and unravel its possible metabolic responses mechanisms, we simultaneously investigated mRNAs and microRNAs (miRNAs) expression profiles of wheat seedlings in response to chitosan heptamer. We found 400 chitosan-responsive differentially expressed genes, including 268 up-regulated and 132 down-regulated mRNAs, many of which were related to photosynthesis, primary carbon and nitrogen metabolism, defense responses, and transcription factors. Moreover, miRNAs also participate in chitosan-mediated regulation on plant growth. We identified 87 known and 21 novel miRNAs, among which 56 miRNAs were induced or repressed by chitosan heptamer, such as miRNA156, miRNA159a, miRNA164, miRNA171a, miRNA319, and miRNA1127. The integrative analysis of miRNA and mRNA expression profiles in this case provides fundamental information for further investigation of regulation mechanisms of chitosan on plant growth and will facilitate its application in agriculture.

Transcriptomic analysis reveals the differentially expressed genes and pathways involved in drought tolerance in pearl millet [Pennisetum glaucum (L.) R. Br]

Pearl millet is a cereal crop known for its high tolerance to drought, heat and salinity stresses as well as for its nutritional quality. The molecular mechanism of drought tolerance in pearl millet is unknown. Here we attempted to unravel the molecular basis of drought tolerance in two pearl millet inbred lines, ICMB 843 and ICMB 863 using RNA sequencing. Under greenhouse condition, ICMB 843 was found to be more tolerant to drought than ICMB 863. We sequenced the root transcriptome from both lines under control and drought conditions using an Illumina Hi-Seq platform, generating 139.1 million reads. Mapping of sequenced reads against the foxtail millet genome, which has been relatively well-annotated, led to the identification of several differentially expressed genes under drought stress. Total of 6799 and 1253 differentially expressed genes were found in ICMB 843 and ICMB 863, respectively. Pathway and gene function analysis by KEGG online tool revealed that the drought response in pearl millet is mainly regulated by pathways related to photosynthesis, plant hormone signal transduction and mitogen-activated protein kinase signaling. The changes in expression of drought-responsive genes determined by RNA sequencing were confirmed by reverse-transcription PCR for 7 genes. These results are a first step to understanding the molecular mechanisms of drought tolerance in pearl millet and lay a foundation for its genetic improvement.

Subunit and chlorophyll organization of the plant photosystem II supercomplex

Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a dimeric core and up to four light-harvesting complexes (LHCs), which act as antenna proteins. Here we solved a three-dimensional (3D) structure of the C₂S₂M₂ supercomplex from Arabidopsis thaliana using cryo-transmission electron microscopy (cryo-EM) and single-particle analysis at an overall resolution of 5.3 Å. Using a combination of homology modelling and restrained refinement against the cryo-EM map, it was possible to model atomic structures for all antenna complexes and almost all core subunits. We located all 35 chlorophylls of the core region based on the cyanobacterial PSII structure, whose positioning is highly conserved, as well as all the chlorophylls of the LHCII S and M trimers. A total of 13 and 9 chlorophylls were identified in CP26 and CP24, respectively. Energy flow from LHC complexes to the PSII reaction centre is proposed to follow preferential pathways: CP26 and CP29 directly transfer to the core using several routes for efficient transfer; the S trimer is directly connected to CP43 and the M trimer can efficiently transfer energy to the core through CP29 and the S trimer.

Selective nitration of PsbO1 inhibits oxygen evolution from isolated Arabidopsis thylakoid membranes

Treatment of isolated Arabidopsis thaliana thylakoid membranes with nitrogen dioxide (NO₂) induces selective nitration of the tyrosine residue at the ninth amino acid (⁹Tyr) of PsbO1. This selective nitration is triggered by light and is inhibited by photosynthetic electron transport inhibitors. Therefore, we postulated that, similar to ¹⁶¹Tyr of D1 (Y_Z), ⁹Tyr of PsbO1 is redox active and is selectively oxidized by photosynthetic electron transport in response to illumination to a tyrosyl radical that is highly susceptible to nitration. This tyrosyl radical may combine rapidly at diffusion-controlled rates with NO₂ to form 3-nitrotyrosine. If this postulation is correct, the nitration of ⁹Tyr of PsbO1 should decrease oxygen evolution activity. We investigated the effects of PsbO1 nitration on oxygen evolution from isolated thylakoid membranes, and found that nitration decreased oxygen evolution to ≥ 0% of the control. Oxygen evolution and nitration were significantly negatively correlated. This finding is consistent with redox active properties of the ⁹Tyr gene of PsbO1, and suggests that PsbO1 ⁹Tyr acts as an electron relay, such as Y_Z in the photosystem II oxygenic electron transport chain.

Characterization and Complementation of a Chlorophyll-Less Dominant Mutant GL1 in Lagerstroemia indica

Crape myrtle (Lagerstroemia indica) is a woody ornamental plant popularly grown because of its long-lasting, midsummer blooms and beautiful colors. The GL1 dominant mutant is the first chlorophyll-less mutant identified in crape myrtle. It was obtained from a natural yellow leaf bud mutation. We previously revealed that leaf color of the GL1 mutant is affected by light intensity. However, the mechanism of the GL1 mutant on light response remained unclear. The acclimation response of mutant and wild-type (WT) plants was assessed in a time series after transferring from low light (LL) to high light (HL) by analyzing chlorophyll synthesis precursor content, photosynthetic performance, and gene expression. In LL conditions, coproporphyrinogen III (Coprogen III) content had the greatest amount of accumulation in the mutant compared with WT, increasing by 100%. This suggested that the yellow leaf phenotype of the GL1 dominant mutant might be caused by disruption of coproporphyrinogen III oxidase (CPO) biosynthesis. Furthermore, the candidate gene, oxygen-independent CPO (HEMN), might only affect expression of upstream genes involved in chlorophyll metabolism in the mutant. Moreover, two genes, photosystem II (PSII) 10 kDa protein (psbR) and chlorophyll a/b binding protein gene (CAB1), had decreased mRNA levels in the GL1 mutant within the first 96 h following LL/HL transfer compared with the WT. Hierarchical clustering revealed that these two genes shared a similar expression trend as the oxygen-dependent CPO (HEMF). These findings provide evidence that GL1 is highly coordinated with PSII stability and chloroplast biogenesis.

Light-triggered selective nitration of PsbO1 in isolated Arabidopsis thylakoid membranes is inhibited by photosynthetic electron transport inhibitors

PsbO1 is exclusively nitrated when isolated thylakoid membranes are incubated in a buffer bubbled with nitrogen dioxide (NO₂) containing NO₂ and nitrite. NO₂ is the primary intermediate for this selective nitration. Isolated thylakoid membranes were incubated in NO₂-bubbled buffer at 25°C in the light or dark. Protein analysis confirmed the selective nitration of PsbO1. Illumination was found to be essential in PsbO1 nitration. A nitration mechanism whereby nitratable tyrosine residues of PsbO1 are, prior to nitration, selectively photo-oxidized by photosynthetic electron transport to tyrosyl radicals to combine with NO₂ to form 3-nitrotyrosine was hypothesized. We tested the electron transport inhibitors 3-(3,4-dichlorophenyl)-1,1- dimethylurea, sodium azide, and 1,5-diphenylcarbazide and found distinct inhibition of nitration of PsbO1. We also propose a possible nitration mechanism.